This version of BIP! Finder aims to ease the exploration of COVID-19-related literature by enabling ranking articles based on various impact metrics.
Last Update: 18 - 01 - 2023 (628506 entries)
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| Title | Venue | Year | Impact | Source | |
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| 5651 | Natural SARS-CoV-2 infection in two cats in Spain Purpose SARS-CoV-2 is a zoonotic pathogen able to infect humans, pets and other animal species, mustelids and felids being highly susceptible. Experimentally, it has been shown that SARS-CoV-2 replicates efficiently in cats, inducing humoral immunity and causing a variable clinical presentation. Here we report the case of two cats (G1 and G2) naturally infected with SARS-CoV-2 after contact with their COVID-19 positive owner diagnosed in September 2020. Methods & Materials Oral swabs soaked in PBS were collected daily from 1 to 16 days after the owner tested positive for SARS-CoV-2. Urine and feces were taken several times during this period. Samples were analyzed by in-house real-time RT-PCR (based on CDC 2019-nCoV_N1). Serum samples, collected at day 30, were tested by IDVet multi-species ELISA. Vero E6 cells was used for virus isolation. Partial spike gene was sequenced by Sanger and compared with the owner sequence and the reference Wuhan 2019 (NC_045512.2). Results G1 showed apathy, anorexia, lack of grooming and mild respiratory symptoms (tearing and sneezing) for 5 days and then recovered gradually. G2 remained clinically asymptomatic. Viral RNA peak in oral swabs was detected in both cats at day 2 showing similar Ct value (25). SARS-CoV-2 was consistently shedding in G1 for 9 days, after sporadically detected until day 16. Viral shedding in G2 decreased quickly during the first 6 days. Faeces were positive to SARS-CoV-2 until 9 (G1) or 12 (G2) days post-viral detection. Viral RNA in urine was sporadically detected in G2 with high Ct values. Specific antibodies were detected in both cats one month after infection. Virus isolation was not successful. Cats and owner sequences of the spike protein were homologous with two mutations (A222V and D614G) that classify the virus within the 20A.EU1 clade. Conclusion SARS-CoV-2 natural infection of two cats occurred after close contact with their infected owner. Both cats developed humoral immune response but they showed different clinical presentation and viral shedding pattern. Oral swabs and feces are proper samples for SARS-CoV-2 detection in cats. Variant 20A.EU1 detected in this study emerged in early summer 2020, presumably in Spain, and subsequently spread throughout Europe. | Int J Infect Dis | 2022 | CORD-19 | |
| 5652 | Serosurvey of SARS-CoV-2 in dogs and cats from Portugal Purpose Severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) causes COVID-19, which was first reported in humans in 2019, in Wuhan, China. This RNA virus has highly efficient transmission. Sporadic cases of infection in pets have been described. Human to animal transmission seems to occur, however, the epidemiologic role of pets remains unclear. This study aimed to screen dogs and cats from the North and Centre regions of Portugal for the exposure to SARS-CoV-2, during the peak of SARS-CoV-2 human infection in Portugal, which occurred between October 2020 and March 2021. Methods & Materials A cross-sectional study was conducted in dogs and cats presented to veterinary medical centres from Portugal between October 2020 and March 2021, that required blood sampling as part of their diagnostic plan. Only surplus sera or plasma samples were used in this research. Sera or plasma were tested for the presence of specific antibodies anti-SARS-CoV-2 using a commercial ELISA adapted for multi-species detection (ID Screen SARS-CoV-2Double Antigen Multispecies®, IDVet). Laboratory results were expressed in S/P values and samples with an S/P% ≥ 60% were classified as positive. Results A total of 107 animals were sampled (dogs n=60; cats n=47). The canine population was composed by 25 purebred and 35 crossbreed dogs, with ages ranging from 5 months to 15 years of age. Cats were mainly of the domestic short-hair breed (n=45), with ages ranging between 6 months and 9 years old. The estimated rate of exposure was of 5.0% (95% CI: 1.71-13.7%) in dogs (n=3) and 2.13% (95% CI: 1.18-14.26%) in cats (n=1). A doubtful result (50≥S/P%<60%) was obtained in 6.7% (95% CI: 2.6-15.9%) of dogs (n=4) and in 4.26% (95% CI: 2.6-15.9%) of cats (n=3). Conclusion To our best knowledge, this is the first serosurvey conducted in pets in Portugal. An exposure to the agent has been evidenced in dogs and in cats. Further studies must clarify the impact of the exposure in animal health and the role of the pets in spreading the virus. | Int J Infect Dis | 2022 | CORD-19 | |
| 5653 | Harmonized Scenario-Based Laboratory Coding System to Guide Real-Time Public Health Actions in Quebec Province, Canada Purpose Effective public health (PH) response to emerging pathogens requires effective information systems integrating surveillance data from multiple sources. For laboratories, data entry of multiple variables both at pre-analytical steps and again in laboratory information systems (LIS) is time-consuming and difficult to implement in a resource-limited setting and negatively affects the timeliness of the surveillance system. We set up a simple harmonized laboratory query that summarized 22 public-health relevant scenarios and variables, reduced to a two-digit code. Methods & Materials Information data specialists were mobilized to integrate data from the 108 different LIS using the harmonized query, which provided timely access to COVID-19 testing indications, volumes, and positivity rates stratified by age, health region, clinical settings, outbreak context or Health-Care worker status. The information system allowed to develop multiple indicators for a better understanding of the pandemic and the COVID-19 transmission in population subgroups. Results Dashboards were available for public health and infection prevention and control officers in their location. Multiple stakeholders were able to interpret real-time data for more than 40 000 different qPCR tests every day. The data allowed to adjust prescription practice and promote optimal usage and plan contingencies within Quebec's qPCR lab capacities. It also served as the basis to monitor community transmission through test positivity rate in various settings. The coding system also allowed labs to easily implement sample triage, which reduced turnaround time to less than 24h for most samples. Starting May 2021, public health authorities add monitoring of the positive predictive value of rapid antigen test used at the community level to support evidence-based public health decisions about the best possible use of those assays. Conclusion This simple scenario-based coding system allowed timely PH and management of both sampling and processing priorities which proved most useful during surge periods. Quebec Public Health Authorities were better able to target preventive actions and to plan outreach screening activities in subpopulations, neighbourhoods, and communities, while modulating clinical criteria to get access to testing and allowing laboratories to better triage samples. | Int J Infect Dis | 2022 | CORD-19 | |
| 5654 | Feasibility and accuracy of variant PCR assays for low- and middle-income countries in SARS-CoV-2 surveillance Purpose Surveillance of different SARS-CoV-2 variants of concern (VOCs) is a crucial aspect in control of the pandemic. Although sequencing is the gold-standard to detect VOCs, it is labor intensive and is costly. We compared a cost-effective real-time PCR assay that detects single nucleotide polymorphisms (SNPs) of VOCs, with next generation sequencing (NGS) in surveillance of VOCs. Methods & Materials A total of 782 SARS CoV-2 PCR positive samples From May – August 2021 were screened using two variant RT-qPCR assays (Seegene Allplex™ SARS-CoV-2 Variant Assay I and II), which detects 7 SNPs in the spike protein assigning them to one of the VOCs. We compared the results of the variant RT-qPCR with Illumina (n=97) and Oxford Nanopore (n=53) platforms in a subset of samples (n=150). Sequences with > 25x coverage were used and assigned to a Pangolin lineage. Results 516 samples amplified for N501Y and HV69/70 deletion of the spike protein were assigned as alpha (B.1.1.7). Two samples with spike K417N mutation along with N501Y and E484K were considered to be beta (B.1.351) and 175 samples which are only positive for spike L452R mutation were considered to be delta (B.1.617). 120/156 samples designated as alpha, 22/175 designated as delta and 2 samples designated as beta by RT-qPCR were sequenced either by Illumina or Oxford nanopore platforms. The sequencing results showed a 100% accuracy with the variant RT-qPCR for identification of VOCs. Conclusion RT-qPCR that detected SNPs specific for VOCs, appear to be highly sensitive and specific in detection of VOCs and had a similar specificity of genomic sequencing. Therefore, this could be a rapid and less expensive method for surveillance of VOCs, in lower income countries. However, as it only detects specific SNPs, any emerging mutations of concern in these VOCs or newly emerging variants, will not be detected. | Int J Infect Dis | 2022 | CORD-19 | |
| 5655 | Successful Reversal of the 2020 Covid-19 Response Induced Collateral Damage on Malaria Control in Saudi Arabia Purpose Saudi Arabia is committed to malaria elimination by 2025 and its National Malaria Program (NMP) has made enormous progress so far. However, in 2020, the COVID-19 pandemic response induced a collateral damage on the NMP: an unprecedented outbreak in Jazan, where malaria importation/transmission remains a challenge. Can a multisectoral, multidisciplinary response to this outbreak rapidly reverse the damage? Methods & Materials This observational study, nested within the NMP surveillance system, analyzed indicators recorded in Jazan (Indoor Residual Spraying [IRS] coverage; confirmed patients and larval source management [LSM]) temporally for the period between 2019 to 2021. Results By September 2021, only January to June 2021 data was available. In 2020, the COVID-19 movement restrictions and reassignment of NMP staff to pandemic response precipitated an unprecedented epidemic in Jazan with 3022 confirmed cases: comparing with 2019 figures (818), this represented a 27-fold increase. Limiting comparison to between January and June for the 3 years, patients treated were 543, 2212 and 1261, respectively. The obvious effect of the lockdown and reassigned officers is also reflected in the IRS coverage for 2019, 2020 and 2021 (till June), being 90%, 77% and 89%, respectively. The low 2020 IRS coverage (WHO minimum recommended level: 80%) supports the observed increased transmission. The 1261 cases in 2021, a 43% reduction from 2020, correlated with the 89% IRS coverage indicative of post intervention reversal. All patients were treated according to WHO protocol. Additionally, the poor indices of Anopheles arabiensis LSM (7040 for 2020, more than 2-fold increase from the 2019 figure of 3257) indicated pandemic disruption of larviciding activities. The 2021 midyear figure of 8471 suggests intensified LSM is needed to achieve further reductions in transmission. The Ministries of Health and Environment, Water and Agriculture coordinated IRS and LSM interventions. Conclusion The pandemic response engendered an unprecedented malaria epidemic and threatened years of malaria control progress. However, the improved, post-intervention and post-lockdown data provided suggests that positive rebounds can be achieved when responses are coordinated using a multi-sectoral, One Health platform. | Int J Infect Dis | 2022 | CORD-19 | |
| 5656 | Does the Hygiene Hypothesis Explain COVID-19 Cases and Death? A Global Analysis Purpose At the start of the COVID-19 pandemic there was widespread speculation on the role of the hygiene hypothesis in the incidence and mortality of COVID-19. This study sought to determine if such a correlation exists via a global analysis using many surrogate factors representing the hygiene hypothesis. Methods & Materials Publicly available data from 190 countries were gathered. These data included COVID-19 total case numbers and deaths through December 28, 2020; water, sanitation, and hygiene (WaSH) metrics; data on mortality due to various types of air pollution; and other factors such as control of solid waste, emission growth rate of methane and carbon dioxide, and daily adjusted life years lost to unsafe drinking water and sanitation. Using IBM SPSS 27.0, these factors were analyzed using multiple regression analyses to determine the combination of factors most predictive of COVID-19 total cases and deaths. Separate regressions were conducted for the two criterion variables. Results The analysis revealed positive correlations between two predictor variables: a nation's mortality due to air pollution (MDAP) and control of solid waste (CSW), with COVID-19 total number of cases. The combination of predictors accounted for approximately 28% of the variance in total number of cases. Concerning the number of COVID-19 deaths, 9.6% of the variance was accounted for by MDAP. Findings support previous studies pointing to the likelihood of air pollution as a potential catalyst for COVID-19 spread. Conclusion Decreasing air pollution is an important mitigating strategy for dealing with respiratory viruses, as it correlates with decreased damage to the respiratory system and decreased time for the virus to circulate in denser particles of polluted air. Thus, MDAP is an effective predictor of COVID-19 cases, and to a lesser extent, deaths. The positive correlation with cases and CSW indicates a likelihood that lockdowns throughout the world wreaked havoc on solid waste disposal systems, particularly in nations with prior effective CSW mechanisms. Although the hygiene hypothesis is not supported, findings should encourage societies to implement policies which focus on minimizing air pollution and strengthen systems to CSW and attenuate a descent into another global pandemic. | Int J Infect Dis | 2022 | CORD-19 | |
| 5657 | Using Electron Microscopy to Detect SARS-CoV-2 in Human and Animal Tissues Purpose Global efforts to combat the COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have placed renewed focus on the use of transmission electron microscopy (EM) for infectious disease diagnosis and detection. Recently, attempts to identify SARS-CoV-2 directly in human autopsy and animal necropsy tissues have inaccurately identified normal subcellular structures, including coated vesicles, multivesicular bodies, and rough endoplasmic reticulum, as coronavirus particles. Working with SARS-CoV-2 positive autopsy and necropsy tissues, the Infectious Diseases Pathology Branch at CDC sought to use EM to accurately detect coronavirus particles. Methods & Materials Two sample types were used, formalin-fixed wet tissue and formalin-fixed paraffin embedded (FFPE) tissue blocks. Wet tissue samples provide the best preservation of ultrastructure but require a time-intensive search for viral particles. FFPE tissues enable a targeted approach to finding viral particles but with deteriorated ultrastructure. Areas of formalin-fixed wet tissue showing evident disease pathology were selected for EM, while areas of interest from FFPE blocks were selected based on results from SARS-CoV-2 immunohistochemistry and in situ hybridization results. All samples were post-fixed with 1% osmium tetroxide, en-bloc stained with uranyl acetate, dehydrated, and embedded in Epon-Araldite resin. Results A multifaceted approach for SARS-CoV-2 detection in autopsy and necropsy tissues allowed for swift and accurate determination of the localization of coronavirus and correlation of histopathological and ultrastructural features of SARS-CoV-2 infection. Coronavirus particles were found associated with degenerating cells in the alveolar space, in pneumocytes, and near collagen of the heart in fetal tissue as well as in the syncytiotrophoblast of the placenta. In animal tissues, virus was found in the bronchiolar epithelium and type 1 pneumocytes. Conclusion Comprehensive studies of SARS-CoV-2 infection, and all emerging pathogens, are crucial to improving the understanding of pathogenesis and for the formulation of clinical treatments and transmission prevention measures. An important part of this process is providing robust EM evidence of SARS-CoV-2 localization within tissues to ensure that misinterpretations of subcellular structures as virus are reduced, enabling more accurate conclusions concerning COVID-19 pathology and disease. | Int J Infect Dis | 2022 | CORD-19 | |
| 5658 | Identification of Major SARS CoV-2 Variants in India using in silico PCR-RFLP analysis Purpose As of June 30, 2021, WHO reported 181,344,224 confirmed cases worldwide and 3,934,252 deaths due to SARS CoV-2. India accounts almost 10% of the total mortality. The mutated Variants of Concern (VoC) and Variants of Interest (VoI) has acquired non-synonymous amino acid substitutions in Spike (S), ORF1a, ORF1b, Nucleocapsid (N), Membrane (M), Envelope (E), ORF6, ORF7a, ORF3a and ORF8 regions exhibiting more virulence and higher transmission rate. The S gene displaying nucleotide polymorphisms are studied for identification of major SARS CoV-2 variants circulating in India using in silico PCR-RFLP analysis. Methods & Materials DNA sequences of major SARS CoV-2 variants [alpha (B.1.1.7), beta (B.1.351), delta (B.1.617.2), epsilon (B.1.429+B.1.427), eta (B.1.525) and zeta (P.2)] prevailing in India retrieved from GISAID database were annotated using VIPR-VIGOR4 genome annotator tool. The S gene of variants were aligned using CLUSTALW algorithm in MEGA-X with default parameters and analyzed for sequence identity using Geneious Prime v2019.2.1. Primers were designed using Primer-BLAST tool, proof-read using FastPCR v6.7.46 and PCR-amplified using Snapgene v.3.2.1. Unique restriction sites in S amplicons of each variant were subjected to online Restriction Analyzer tool. The S amplicons were digested with restriction endonucleases and the band profile of each variant were visualized in the gel simulation tool using Snapgene v.3.2.1. Results The percentage of identical sites present in S region among SARS CoV-2 variants was found to be 98.6%. The amplified products were in the length of 3,689 and 3,698 bp. Out of 400 restriction endonucleases identified, 14 buffer-compatible enzymes were selected for single-step restriction digestion to generate unique RFLP profiles for each variant. The BsaXI-XcmI-AcuI triple digest showed unique banding pattern identifiers on 2% agarose gel for individual variants including alpha, eta, delta and zeta. The ApaLI-BsaI double digest produced distinct band profiles for beta and epsilon variants. Conclusion Our study strongly suggests PCR-RFLP analysis of Spike region can differentiate major SARS CoV-2 variants that are circulating in India. Further, quadruple digestion based wet lab experiments are underway to explore the possibility of surveillance of the major variants using a single-tube reaction followed by agarose gel-based profiling. | Int J Infect Dis | 2022 | CORD-19 | |
| 5659 | Implementing a SARS-CoV-2 Early Warning System in Valencia (Spain) and its Correlation with Epidemiological Indicators Purpose To implement a SARS-CoV-2 wastewater surveillance system in Valencia and study the correlation between SARS-CoV-2 concentration levels and epidemiological indicators. Methods & Materials The working strategy developed in the municipality of Valencia consisted of monitoring wastewater effluents collected by 790,000 people. The city was divided into 24 different hydraulic sectors. 3,023 samples of untreated wastewater were collected and analysed between May 2020 and May 2021. RNA extraction from sewage material was carried out using the NucleoSpin RNA virus Kit. SARS-CoV-2 RNA detection was performed by RT-qPCR using One-Step PrimeScript™ RT-PCR Kit (Perfect Real Time), targeting the nucleoprotein (N), N1 and N2 fragments, and envelope protein (E) gene. Mengovirus RNA recovery rates were used as quality assurance parameters according to ISO 15216-1:2017. Results A total of 2,169 samples were positive for SARS-CoV-2 RNA material. SARS-CoV-2 variations were detected throughout the entire study evidencing trends during the first, second and third wave. As the National State of Emergency ended (June 2020), SARS-CoV-2 values began to increase reaching the first and most significant concentration spike of the study (20th-26th of July 2020), with a weekly average aggregate concentration of 34,5M GC/L (an increase of 2 units in the log scale). This translated in the worsening of epidemiological indicators (number of cases, hospitalizations, deaths and cumulative incidence (CI)), which maintained a stable increase until a second spike was detected during an important bank holiday in October (9th-12th), where the concentration changed from 28M GC/L to 345M GC/L in a 3-day period while the city was registering 1,100 new weekly cases and a CI of 200 cases/100,000 residents. Finally, a third wave placed Valencia with the worst historical epidemiological data (6,545 new cases; 1,000 new hospitalizations; CI= 1,318,04 cases/100,000 inhabitants) with a weekly SARS-CoV-2 average aggregate concentration of 967M GC/L, leading health officials to implement new restrictive measures. Conclusion Wastewater surveillance could be used as a complimentary tool to estimate the presence and prevalence of COVID-19 in communities and can be used for preventive purposes, as an increasing SARS-CoV-2 trend in wastewater could be a signal of the possible re-emergence of the pandemic. | Int J Infect Dis | 2022 | CORD-19 | |
| 5660 | Predicted Global Spread of SARS-CoV-2 Alpha Variant of Concern via Air Travel Purpose To predict the global spread of SARS-CoV-2 Alpha Variant of Concern (VoC) from England via air travel and compare against observed importation. Methods & Materials Risk models were used to estimate a country's likelihood of importing at least one traveller infected with the Alpha VoC from England by January 19, 2021. First, the prior 60-day incidence of Alpha VoC associated with each English airport was estimated using cumulative Alpha VoC cases reported by Public Health England between September 20, 2020 – January 4, 2021 proportionately allocated to each airport. Each airport's catchment population was derived from a probabilistic Huff model. Next, the prevalence of the Alpha VoC for each airport was derived from the estimated incidence to represent the probability that at least one departing traveller was infected with the Alpha VoC for each English airport. The prevalence and forecasted flight volumes were used to estimate the likelihood of each destination airport receiving at least one infected traveller from England. Forecasted flight volumes were based on historical passenger volumes data from the International Air Transport Association and prospective flight schedules from CIRIUM. All airport-level likelihoods were aggregated to the country-level. Each country's predicted likelihood was compared against observed cases of Alpha VoC by January 25, 2021, collected by cov-lineages.org and a manual search of online sources. Results Among 211 countries, the median likelihood was 1.6% (interquartile range: 17.5%) and the mean was 13.9% (SD: 23.5%). In total, 28.9% (n=55) of countries had observed importation of the Alpha VoC by January 25th. Fifteen of 16 countries with a predicted likelihood of importation greater than 50% had reported at least one case (kappa = 0.88), while 31 of 39 countries with a predicted likelihood lower than 1% did not detect a case (kappa = 0.92). Conclusion Risk models based on air travel to inform public health preparedness accurately identified most potential destinations at highest risk of importing the SARS-CoV-2 Alpha VoC. | Int J Infect Dis | 2022 | CORD-19 | |
| 5661 | Mathematical modelling of COVID-19: a systematic review and quality assessment in the early epidemic response phase Purpose Epidemiological models have played a key role in informing national response strategies for the current COVID-19 pandemic. We aimed to identify how mathematical models were employed in the early phase of the pandemic, at a time of great epidemiological uncertainty, as well as to formally assess the quality of models used. Hence we aimed to identify areas for improvement in model-based decision-making for future unknown disease threats. Methods & Materials A systematic review of mathematical modelling studies estimating the epidemiological impact of COVID-19 (risk of importation/spread) and non-pharmaceutical interventions (NPI) was conducted. We systematically searched PubMed, Embase, and preprints in ARxiv, MedRxiv and bioRxiv. We adopted two published quality assessment frameworks to formally assess the extent in which modelling studies met minimal requirements for incorporation of uncertainty and good modelling practice. Results In total, 166 articles met our eligibility criteria. The vast majority (129 studies, 78%) of models evaluated the effectiveness NPIs. NPI effectiveness was predominantly modelled in China and Italy, but varied by global region. Asian studies largely evaluated the impact of quarantine and isolation (64 studies), whereas European modelling studies modelled the impact of containment (15 studies), quarantine of travellers, and the isolation of cases. Early models primarily concerned compartmental, deterministic frameworks using SEIR or variants of SEIR compartments (93 studies, 56%) assuming homogenous, symptomatic transmission. Incorporation of parameter uncertainty through model calibration (inference of unknown parameters by fitting models to data) and sensitivity analyses were relatively common (66% and 56% of studies respectively), the former mainly using Chinese data. In contrast, inclusion of structural uncertainty (uncertainty in disease characteristics) was relatively uncommon, as was validation of model output to external data. Conclusion This work allows for the identification of existing challenges in the mathematical modelling of emerging diseases, and emphasises minimal criteria for enhancing reliable model estimation and reporting. Limited availability of epidemiological data in the early phase of a new disease treat challenges model calibration to local, and validation to external data, emphasising the critical importance of enforcing standardised protocols for early epi-data collection, and raising awareness among modellers and decision-makers alike in handling uncertainty. | Int J Infect Dis | 2022 | CORD-19 | |
| 5662 | A four-month follow-up study of Cardiac performance in patients hospitalized with COVID-19 in a Tertiary Care Government Medical Hospital Purpose Myocardial injury is one of the most frequently observed injury in patients hospitalized with coronavirus disease 2019 (COVID-19) pneumonia. Cardiac abnormalities ranging from elevations of cardiac necrosis biomarkers to cardiac dysfunction associated with myocarditis has been reported during the acute COVID-19 phase. Not much information is available on late cardiac manifestations in patients who have recovered from the cute COVID-19 illness. Our purpose is to present and quantify the extent of alterations in cardiac function in patients hospitalized 4 months earlier for COVID-19 infection. Methods & Materials A prospective echocardiographic evaluation was conducted of 39 patients hospitalized 4±1 month earlier for a laboratory-confirmed and symptomatic COVID-19. Thorough analysis of risk-factors was noted using a pre-prepared questionnaire. Echocardiographic measurements and respective cardiac investigations were analyzed using inferential and sensitivity analysis. Results Of the 39 patients (mean age 54 ± 11 years, 73% male), twenty-seven (69%) had pre-existing cardiovascular risks factors (systemic hypertension, diabetes, or dyslipidemia), and four patients (10.3%) had a known prior myocardial infarction (MI). Seventeen patients (43.6%) experienced myocardial injury during the index COVID-19 hospitalization as identified by a rise in cardiac troponin levels. Four months later, 71.8% of patients still reported clinical symptoms including exertional dyspnea for 69%. Under resting condition, echocardiographic measurements were indifferent between patients with versus without myocardial injury during the acute phase of COVID-19 infection. On the contrary, low-level exercise (25W for 3 min) showed a significant increase in the average E/e' ratio (P < 0.01) and the systolic pulmonary artery pressure (P < 0.05) in patients with myocardial injury during the acute COVID-19 phase. Sensitivity analyses showed that these left ventricular diastolic markers changes were observed irrespective of pre-existing cardiovascular risk factors or established cardiac diseases further cementing that the SARS-CoV-2 infection was the primary cause. Conclusion Four months after the acute COVID-19 phase, statistically significant cardiac diastolic abnormalities were observed in patients who experienced myocardial injury but not in patients without cardiac involvement. | Int J Infect Dis | 2022 | CORD-19 | |
| 5663 | Contact patterns during the COVID-19 pandemic: findings from British Columbia, Canada Purpose Interpersonal interaction between infectious and uninfected individuals facilitates the spread of COVID-19. Physical distancing measures could prevent COVID-19 transmission by reducing the contacts among individuals in the population. In this study, we describe contact rates of residents of British Columbia, Canada to assess the impact of COVID-19 related physical distancing measures in the province. Methods & Materials We used data from the BC COVID-19 Population Mixing Patterns survey (BC-Mix) to investigate the contact patterns of residents of British Columbia from September 2020 to July 12, 2021. The BC-Mix is an ongoing repeated online survey with approximately 60,000 participants. Survey respondents provided the number of close contacts made in a single day in response to the question How many people did you have in-person contact with between 5 am yesterday and 5am today?” In-person contact was defined as “face-to-face two-way conversation with three or more words, or physical skin-to-skin contact such as a handshakes, hugs, kisses and contact sports”. Survey weights were applied in the estimation of overall contact rates and contact rates stratified by age, sex and health region. Results A total of 31, 696 respondents were eligible for analysis. Overall average daily contacts decreased by about 28% in response to the physical distancing measures that went into effect on November 19, 2020 (from an average of 6.42 contacts per person prior to this date to 4.62 contacts per person after this date). From September 2020 to February 2021, the average number of daily contacts were higher among female respondents compared to male respondents. However, no notable difference in the average number of daily contact rates was observed between male and female respondents in subsequent weeks. Over the study period, younger age groups (< 55 years) reported higher daily contact overall than older age groups (≥ 55years years). There was also a marked difference in contact rates by health regions over the study period. Conclusion Contact patterns in British Columbia varied between September 2020 and July 2021, with a marked decline in average daily contacts noted immediately following the introduction of stricter physical distancing measures in November 2020. | Int J Infect Dis | 2022 | CORD-19 | |
| 5664 | Improved contact tracing using network analysis and spatial-temporal proximity Purpose Contact tracing is a crucial tool in infection prevention and control (IPC), which aims to identify outbreaks and prevent onward transmission. What constitutes a contact is typically based on strict binary criteria (i.e., being at a location at the same time). Missing data, indirect contacts and background sources can however substantially alter contact-tracing investigations. Here, we present StEP, a Spatial-temporal Epidemiological Proximity model that accounts for imperfect data by introducing a network-based notion of contact based on spatial-temporal proximity derived from background flows of patient movement. Methods & Materials We showcase StEP by analysing outbreaks of multidrug-resistant bacteria and COVID-19 within a large hospital Trust in London (UK).StEP utilises spatial-temporal patient trajectories and the background hospital movement flows to recover enhanced contact networks. Firstly, we study a well-characterised outbreak of carbapenemase-producing Enterobacteriaceae (CPE) involving 116 hospitalised patients where genetic sequencing is used to learn model parameters. Secondly, our trained model is deployed in an unsupervised manner on three unseen outbreaks involving 867 patients of related CPE-types. Thirdly, we test application to an altogether novel pathogen by analysing a hospital outbreak of COVID-19 among 90 hospital patients, and demonstrate the power of StEP when characterising newly emerging diseases, even when there is a lack of sequencing data. Results In addition to recovering core contact structures, StEP identifies missing contacts that link seemingly unconnected infection clusters, revealing a larger extent of transmission than conventional methods. Via genomic analyses we confirm that the additional contacts detected through StEP lead to improved alignment to the plasmid phylogeny (the major outbreak driving force). Hence the StEP contact network is most aligned to the transmission structure. Conclusion By considering spatial-temporal information in a continuous manner, StEP tackles several challenges associated with traditional contact-tracing. StEP allows both direct and indirect contacts as possible routes of disease transmission and is tuneable to a pathogen's epidemiological characteristics. Such flexible use of heterogeneous data in uncertain situations can significantly enhance IPC. | Int J Infect Dis | 2022 | CORD-19 | |
| 5665 | Factors influencing on hospitalization of COVID-19 patients with comorbidity Purpose During COVID-19 pandemic, the total number of patients is periodically growing, including the number of those requiring hospitalization. The factors that increase the risk of hospitalization with COVID-19 remain poorly understood. Aim identification of factors influencing on the likelihood of hospitalization in COVID-19 patients with comorbidity. Methods & Materials A retrospective cohort study of 74314 COVID-19 patients with a comorbidity within March-November 2020 in Russia. Using multivariate logistic regression, significant factors influencing hospitalization were identified. Results As a result, a logistic function was obtained that included 16 factors out of 21, which was statistically significant. In accordance with R2 Nigelkirk coefficient of determination, composition of the factors are 46.6%. Based on the regression coefficient values, the age of the patients, the sex of the patients, the severity of the disease, cardiovascular diseases, respiratory diseases, endocrine pathology, oncology and other diseases, fever, dyspnea and late address for medical care (after 5 day of disease) are factors that increase the likelihood of hospitalization. Rhinitis, loss of taste, belonging to contact with contact with COVID-19 patient, early seeking for medical care had an inverse relationship with the risk of hospitalization. The chances of hospitalization of patients with oncology is increased 1.496 times (95% CI:1.159-1.932), with endocrine diseases - by 1.573 times (95% CI:1.238 -1.999), in patients with cardiovascular pathology - by 1.502 times (95% CI:1.185-1.903),), in patients with bronchopulmonary pathology - by 1.439 times (95% CI:1.133-1.828), with other comobidities - by 1.501 times (95% CI:1.184-1.904), in patients with moderate the course of the disease - by 8.353 times in comparison with patients with a mild course (95% CI:8,000-8.721), in patients with a severe course of the disease risk is increased by 68.291 times (95% CI:59.279-78.673), risk of hospitalization in men compared with women is increased 1.393 times (95% CI: 1.348-1.438), in patients with fever - 1.14 times (95% CI: 1.09-1.20), with dispnoea - 1.526 (95% CI: 1.495- 1.596). The chances of hospitalization with an increase in age by 1 year increased 1.012 times (95% CI: 1.010-1.013). Conclusion These factors will help healthcare workers with the decisions regarding hospitalization of patients. | Int J Infect Dis | 2022 | CORD-19 | |
| 5666 | Extensively Drug-Resistant Salmonella enterica serovar Typhi in Pediatric population during CoVID-19 Pandemic Purpose The Extensively Drug-resistant (XDR) Salmonella isolates exhibiting resistance to the first line and the second-line antibiotic options are presently a grave public health concern in Pakistan. Here, we report the first large-scale emergence and spread of an XDR S. Typhi in Peshawar, Pakistan during Coronavirus disease (CoVID-19) pandemic. Initially XDR typhoid cases were reported during post rainy season but now the disease has become endemic during winter months. Methods & Materials From December 2020 till January 2021, we reported the high level of emerging resistance to different groups of antibiotics among Salmonella isolates from paediatric age group with enteric fever. A total of 548 blood cultures from symptomatic patients were submitted to Microbiology section of Pathology Laboratory, Rehman Medical Institute, Peshawar. All samples were incubated in BACTEC 9240 and processed according to standard guidelines (sub-cultured on Blood and MacConkey's agar and non-lactose fermenting colonies were biochemically tested for Salmonella typhi and confirmed by Salmonella specific anti-sera. Demographic data including age, gender, address and clinical features were also recorded. Results Salmonella Typhi was isolated in 71 and 548 blood samples during December 2020 and January 2021, out of which 66 (92.9%) and 5% (7%) were MDR, respectively. All isolates revealed high level of resistance to co-trimaxazole (93%) and complete resistance to chloramphenicol (100%), ampicillin (100%), ciprofloxacin (100%), ceftriaxone (100%), cefixime (100%). All XDR typhoid isolates were sensitive to azithromycin and carbapenems. The children under 15 years’ age (88%) has a significantly high prevalence among children as compared to adults (p=0.0016), males (76%) were affected more than females (24%). Conclusion The emergence of XDR S. typhi with high level of resistance is quite alarming. With inadequate treatments options, the present situation calls for immediate effective preventive measures including food and water safety, improved sanitation, public awareness sessions and typhoid vaccination campaigns. | Int J Infect Dis | 2022 | CORD-19 | |
| 5667 | Prevalence of Covishield COVID-19 Vaccine (ChAdOx1 nCoV-19) Adverse Effects among Healthcare Workers in Sri Lanka Purpose A Community vaccination programme is the best approach to combat COVID-19 pandemic. The first priority was given to the health care workers (HCWs) with the introduction of Indian Covishield (ChAdOx1 nCoV-19) vaccine to Sri Lanka since February 2021. An independent post-vaccine surveillance is important to identify the occurrence of adverse effects(A/E) in the population. Methods & Materials A multicentered cross-sectional survey was conducted in four provinces of Sri Lanka to estimate the prevalence of A/E after covishield vaccination A/E among HCWs after the first dose. A self-administered questionnaire was used to gather demographic data and A/E. Data was analysed using descriptive statistics. Results Of 4834 participants, 3500(72.4%) were females. The median age was 42.23(SD±9.64) years. Only 0.8%(n=31) persons has had Covid infection in the past. 2.2% were breastfeeding mothers and 0.2% were pregnant ladies. 87.4% of persons had at least one A/E and 53.1% had local A/E. Body aches(68.2%), headaches(63.8%), fever(58%), chills 51.4%), fatigue(41.2%), arthralgia(38.1%) and rigors (32%) were the most commonly reported systemic A/E. Most of the systemic A/E were more prevalent among the ≤42-year-old group, and females. Their duration was mainly 24 hours. Mean duration of onset of fever is 9.76 hours. Pain and redness at the site were the most commonly reported local A/E. All of the local A/E were more prevalent among the ≤42-year-old group and females. Mean duration of pain at the site is 4.47 hours. 1.7%(n=61) had reactions within first 20 minutes. 0.08%(n=4) developed anaphylaxis, 0.8%(n=31) had urticaria. 15.4% had at least one comorbidities but there were no significant association between having a comorbidity and developing systemic or local. 1.3% had history of drug or food allergies, they did not show significant relation to current vaccine induced allergies or anaphylaxis. 69.2% attended the routine work despite having minor A/E. 0.13%(n=7) were hospitalised and treated. 22.4% were stayed at home and rested for 24-48 hours due to A/E. Conclusion Eventhough more than 60% reported minor A/E, there were only a few serious A/E. A/E were more prevalent in younger age and females. Overall, the first dose of the Covishield vaccine was well-tolerated by HCWs. | Int J Infect Dis | 2022 | CORD-19 | |
| 5668 | Development of Duplex and Multiplex Reverse Transcription Loop Mediated Isothermal Amplification (RT-LAMP) Assays for Clinical Diagnosis of SARS-COV-2 in Sri Lanka Purpose Despite the rollout of several vaccines targeting SARS-CoV-2, attainment of near-universal vaccination is a challenging task, particularly for low- and middle-income nations such as Sri Lanka. Rapid, reliable diagnostics for the detection of the virus is of vital importance for the predominantly export- and tourism-based economy of the country. Herein, we report the development of a RT-LAMP assay as an alternative to the gold-standard RT-qPCR method for diagnostic laboratories in Sri Lanka in a cost-effective and highly reliable manner. Methods & Materials About 313 nasopharyngeal and oropharyngeal samples from the community were collected and subjected to RNA purification and subjected to simultaneous RT-qPCR and RT-LAMP experiments by using previously published primers in a thermocycler. Duplex (containing N and E gene primers) and multiplex (containing N, E and ORF1ab gene primers) RT-LAMP assay results were compared with standard RT-qPCR results using an agreement attribute statistical test. The effect of guanidine hydrochloride was also analyzed. Results The limit of detection for the duplex assay was found to be 10 copies µL-1 at a constant temperature of 63°C, and 5 copies µL-1 for multiplex assays at 66.4°C. Both types of RT-LAMP assay were specific only for the SARS-COV-2 virus, successfully distinguishing it from multiple other human viruses. Attribute agreement analysis between duplex- and multiplex RT-LAMP vs RT-qPCR yielded 93% and 96.5% scores, respectively. Moreover, both RT-LAMP assays showed 100% agreement with RT-qPCR when Ct was <25 in positive samples and showed 100% (duplex) or 97.22% (multiplex) at 35≥ Ct ≥25. The discrepancy between agreements at higher Ct values was attributed to the higher sensitivity of the multiplex RT-LAMP assay. The addition of guanidine hydrochloride increased the sensitivity and decreased detection time significantly for both the duplex and multiplex assays. Conclusion Overall, we have demonstrated a potentially rapidly deployable diagnostic test kit not only for widespread community use but particularly for high-risk locations such as ports of entry or manufacturing facilities to mitigate the effects of the SARS-CoV-2 virus in Sri Lanka. | Int J Infect Dis | 2022 | CORD-19 | |
| 5669 | High SARS-CoV-2 attack rates among asymptomatic hospital workers from Ecuador Purpose To determine the SARS-CoV-2 risk of infection in Ecuadorian hospital. This study aims to describe the SARS-CoV-2 attacks rate and viral loads among patient care workers and other staff from Ecuadorian hospitals during the first wave of COVID-19 pandemic. Methods & Materials : Study design and setting. We carried out a cross-sectional study to describe the attack rate of SARS-CoV-2 infection among patient care workers (physicians, nurses and nursing assistants) and other healthcare personnel (administrative and services staff) from 9 hospitals of the Andean and Costal Regions of Ecuador from May to October 2020. Sample collection, RNA Extraction and RT-qPCR for SARS-CoV-2 diagnosis using the CDC protocol. The samples were processed in the BSL2 certified molecular biology laboratory at Universidad de Las Americas. Nasopharyngeal swabs were collected on 0.5mL TE pH 8 buffer for SARS-CoV-2 diagnosis by RT-qPCR following an adapted version of the CDC protocol. Statistical analysis. Chi cuadrado with the statistic program SPSS Results A total of 1243 patient care workers and 428 of other healthcare staff were tested for SARS-CoV-2 infection. The SARS-CoV-2 attack rate was 12% (145/1243) for patient care workers and 19% (80/428) for other healthcare personnel, being this difference statistically significant (p<0.05). For each hospital, the following SARS-CoV-2 attack rates were obtained for patient care workers and other staff: 35% and 50% in “Hogar ABEI”, 21% and 26% in “Clínica Nuestra Señora de Guadalupe”, 15% and 18% in “Hospital de Atención Integral al Adulto Mayor”, 5% and 11% in “Hospital de Especialidades Eugenio Espejo”, 12% and 22% in “Hospital Geriátrico Dr. Bolívar Arguello”, 13% and 22% in “Hospital Dr. Gustavo Domínguez”, 22% and 12% in “Hospital General Dr. Napoleón Dávila”, 9% and 14% in “Hospital Pablo Arturo” and 5% and 13% in “Hospital San Francisco de Quito”. Moreover, we found 47 individuals (19 among patient care workers and 28 among other staff) with viral loads larger than 108 copies/mL that may be considered super spreaders. Conclusion Ecuadorian hospital workers at a high-risk group for SARS-CoV-2 infection. Regular SARS-CoV-2 testing should be mandatory for this group as even asymptomatic SARS-CoV-2 super spreaders can be detected. | Int J Infect Dis | 2022 | CORD-19 | |
| 5670 | COVID-19 Surveillance Enhanced by an Integrated Electronic Infectious Diseases Information System in Albania Purpose The objective of this paper is to showcase how COVID -19 control has been enhanced by interrelating syndromic surveillance, case based surveillance and laboratory surveillance and outbreak investigation into an integrated electronic Infectious Diseases Information System (IDIS). Methods & Materials Development of IDIS began in December 2016 with the goal to modernize the Albanian surveillance system by developing a user-friendly, comprehensive database for case investigation, contact tracing, and laboratory data focusing on the improvement of the timeliness indicators of disease detection and response. The platform is based on open-source software solutions featuring (1) integration of data from different surveillance systems such as indicator, syndromic and event base; (2) better investigation and management of outbreaks and reduced data-entry time and errors (3) generation of line listing and contact-tracing and workflows to appropriately follow-up of cases and contacts; (4) integration with the national vaccination registry for retrieving vaccination history and prospectively apply ring vaccinations during outbreak control; (5) integration with laboratory information system public and private to retrieve diagnostic information; and (6) repository with qualitative and quantitative cache of epidemiological information and data; Results The IDIS system has assisted public health surveillance to document COVID-19 cases and to take disease control actions such as case isolation, contact tracing and contact isolation, and more recently vaccination. To date 400.000 potential cases of COVID -19 have been notified in the system has been notified 273.000 have been individually investigated. About 487.000 laboratory results have been linked with case based information and respective contacts. The system has proved useful for data analysis as a series of epidemiological indicators have been calculated to inform evidence based decision making in controlling COVID-19 epidemic in Albania. Conclusion IDIS implementation has improved the consistency, communication, and effective use of public health data. In particular integration of different surveillance systems and workflows which are developed within IDIS provide an array of instruments to epidemiologists to detect cases faster, make better decisions based on multiple data sources and more effectively plan response measures. | Int J Infect Dis | 2022 | CORD-19 | |
| 5671 | Tracking SARS-CoV-2 in urban wastewater samples during the first wave of COVID-19 epidemic in Lombardy (Italy) Purpose The value of SARS-CoV-2 monitoring in urban wastewater samples (WWS) for surveillance of virus spread at a population-wide level has been largely demonstrated. Aim of this study was to optimize an analytical workflow to detect SARS-CoV-2 RNA in WWS and to monitor SARS-CoV-2 spread during the first wave of COVID-19 epidemic (March–June 2020) in Lombardy, northern Italy. Methods & Materials The workflow consisted in WWS concentration by using PEG-8000 precipitation, a modified RNA extraction (QIAamp MinElute Virus Spin Kit; QIAGEN) and a one-step real-time RT-PCR detecting two portions of the N gene of SARS-CoV-2. Composite 24-hour WWS were collected once a week at the inlet of 8 wastewater treatment plants (WWTPs) with an overall catchment of 2,276,000 inhabitants, located in representative COVID-19 hotspots in Lombardy, from the end of March to mid-June 2020. 107 WWS were obtained and analysed. SARS-CoV-2 RNA copies/L/WWS were multiplied by the flow rate of each WWTP (m3/day) and the obtained load (copies/day/1,000 people) was normalized to the number of inhabitants served by WWTPs. Results The optimized workflow allowed to identify 1E+3 copies/mL of SARS-CoV-2 in concentrated WWS with a turnaround time of 8 hours. Overall, the presence of SARS-CoV-2 RNA was identified in 65/107 WWS (61%). The highest rate of positive WWS (78.7%; 26/33) was identified in the Bergamo province, that was the epicentre during the first wave of COVID-19 epidemic (March-June 2020) in Lombardy. The highest amount of SARS-CoV-2 RNA was identified in late March/early April, when the overall viral load reflecting the number of individuals shedding the virus ranged from 9.3E+10 copies/day/1,000 people to 8.2E+8 copies/day/1,000 people. Since the end of May, WWS tested negative to SARS-CoV-2 detection. Conclusion According to the epidemiological features of the first wave of SARS-CoV-2 epidemic in Lombardy, the highest amount of SARS-CoV-2 RNA was detected in WWS collected in the areas most affected by COVID-19 (i.e. Bergamo province). This optimized workflow of WWS surveillance can help assessing the real number of individuals – both symptomatic and asymptomatic – able to spread the virus and appraising the effect of preventive measures. | Int J Infect Dis | 2022 | CORD-19 | |
| 5672 | Comparison of Cytokines Levels Among Covid-19 Patients Living at Sea Level and High Altitude Purpose The inflammatory response in COVID-19 among people living at different altitudes has not been studied. Given that chronic hypoxia promotes cytokines production in the absence of disease, the inflammatory response against SARS-CoV-2 may also be different in these populations. The aim of this study was to compare pro-inflammatory cytokine levels among healthy and COVID-19 patients living at different altitudes above sea level. Methods & Materials A descriptive cross-sectional study was performed in two Peruvian cities at different altitudes for comparison: Lima (sea level) and Huaraz (3052 meters above sea level). Patients with COVID-19 diagnosis confirmed by reverse-transcriptase polymerase chain reaction (RT-PCR) were compared to healthy subjects, according to their residing location. Five important proinflammatory cytokines were measured including: IL-6, IL-2, IL-10, IFN-γ and TNF-α using ELISA-based assays. Cytokines levels were calculated and their mean, maximum and minimum levels were reported according to each study group. The difference between means was compared using the ANOVA and post-hoc Turkey Test, a signifiant value of p<0.05 was considered significant. Results A total of 35 COVID-19 patients and 10 healthy subjects were recruited from each study site. The mean levels of IL-6 (p<0.03) and TNF-α (p<0.01) were significantly different among the study groups. In the case of IL-6, patients from Lima had a mean level of 16.2 pg/ml (healthy) and 48.3 pg/ml (COVID-19), meanwhile, patients from Huaraz had levels of 67.3 pg/ml (healthy) and 97.9 pg/ml (COVID-19). Regarding TNF-α, patients from Lima had a mean level of 25.9 pg/ml (healthy) and 61.6 pg/ml (COVID-19), meanwhile, patients from Huaraz had levels of 89.0 pg/ml (healthy) and 120.6 pg/ml (COVID-19). The levels of IL-2, IL-10 and IFN-γ were not significantly different in the study groups. Conclusion Patients with COVID-19 residing in high-altitude tend to have higher levels of inflammatory cytokines, particularly IL-6 and TNF-α. Altogether, this findings demonstrates the need to perform more studies in populations residing at high altitude, given that inflammatory response may be significantly different in these populations. | Int J Infect Dis | 2022 | CORD-19 | |
| 5673 | Methods for Counting COVID-19 Deaths in US States and Territories Purpose The US Centers for Disease Control and Prevention (CDC) never issued guidelines on how states should publicly report COVID-19 deaths, and as a result, states ended up settling on different methods. Critics have claimed that some methods, such as counting “deaths with COVID-19” rather than “deaths from COVID-19”, resulted in overcounts of COVID-19 deaths. While it is clear from alternate measures like excess mortality that all states undercounted COVID-19 deaths, we investigated whether different methods had any effect on state death reporting. Methods & Materials We identified the methods states use to report COVID-19 deaths on their dashboards, then compared state-reported data collected by CDC in its COVID Data Tracker against data from the CDC's National Center for Health Statistics (NCHS)’s national review of death certificates measuring deaths from COVID-19. Comparing state data against this standardized national dataset allowed us to see if state definitions affected their reporting. Results Contrary to critics’ claims, few states have definitions that could systematically include individuals who died of causes unrelated to COVID-19. State death definitions instead vary along two lines: whether positive PCR tests were required to count COVID-19 deaths—with states requiring tests having cumulative totals 9.03% lower than NCHS data, while states not requiring them had totals 10.21% higher (p=.06)—and whether states exclusively used death certificates to measure COVID-19 deaths, with these states’ totals coming in 27.63% higher than NCHS data, compared to 3.26% higher for states using additional information (p=.11). Conclusion Rather than certain methods leading to systematic overcounts of COVID-19 deaths, it appears some methods could be especially prone to undercounts. Only states using death certificate reviews had counts substantially higher than NCHS data, and since NCHS also uses death certificates, the difference appears to be a matter of the faster speed of state review. Meanwhile, many states using different methods have discovered they missed large quantities of COVID-19 deaths in their counts. The CDC should have provided leadership to states on how they should report COVID-19 deaths to avoid any preventable undercounts, and public communication to quell misinformation about overcounts. | Int J Infect Dis | 2022 | CORD-19 | |
| 5674 | Identification of coinfections by Viral and Bacterial Pathogens in Covid-19 Hospitalized Patients in Peru: Molecular Diagnosis and Clinical Characteristics Purpose The impact of respiratory coinfections in COVID-19 is still not well understood. This study sought to identify the respiratory pathogens causing coinfections in patients with moderate/severe SARS-CoV-2 pneumonia from a hospital in Peru. Also, to describe the clinical characteristics and outcomes of coinfected and non-coinfected patients. Methods & Materials A descriptive study was conducted on hospitalized patients with a confirmed diagnosis of moderate/severe pneumonia due to SARS-CoV-2 infection. The selection criteria included patients older than 18 years of age who were admitted to the Guillermo Almenara Irigoyen Hospital in Lima, Peru during the period July-November 2020. Pregnant women were excluded from the study. A nasopharyngeal swab sample was obtained from the patients included in the study. Diagnosis of SARS-CoV-2 infection was performed by reverse-transcriptase polymerase chain reaction (RT-PCR). The detection of the following respiratory viruses was performed by RT-PCR: Influenza A and B, Respiratory syncitial virus (RSV) A and B; and Adenovirus. The detection of atypical bacteria, Mycoplasma pneumoniae and Chlamydia pneumoniae was carried out using conventional polymerase chain reaction. Results A total of 295 patients with confirmed SARS-CoV-2 infection were enrolled during the study period. A coinfection with one or more respiratory pathogen was detected in 154 (52.20%) patients at hospital admission. The most common coinfections were Mycoplasma pneumoniae (28.12%), Chlamydia pneumoniae (8.81%) and with both bacteria (11.53%); followed by Adenovirus (1.70%), Mycoplasma pneumoniae/Adenovirus (0.71%), Chlamydia pneumoniae/Adenovirus (0.71%), RSV-B/Chlamydia pneumoniae (0.32%), Mycoplasma pneumoniae/Chlamydia pneumoniae/Adenovirus (0.32%). Sepsis was more frequent among coinfected patients than non coinfected (33.12% vs 20.57%, p = 0.018). Expectoration was less frequent in coinfected individuals compared to non coinfected (5.84% vs 12.77%, p = 0.045). We could highlight that the majority of patients were administered an antibiotic (69.50%). The correlation between the empirical use of macrolides in patients with Mycoplasma pneumoniae and Chlamydia pneumoniae was observed in 41% of the cases. Conclusion Mycoplasma pneumoniae and Chlamydia pneumoniae were the main microorganisms associated with SARS-CoV-2 coinfection at hospital admission. The presence of multiple coinfections was described in some patients. Antibiotics should be carefully prescribed, as high rates of antibiotic use was found, particularly with macrolides. | Int J Infect Dis | 2022 | CORD-19 | |
| 5675 | Colorimetric reverse transcriptional loop-mediated isothermal amplification for rapid detection of SARS-CoV-2 Purpose With the increasing incidence of a novel coronavirus SARS-CoV-2 causing COVID-19 cases, accurate and early detection infection is need of the hour for effective prevention and management. Therefore, the aim of this study was to develop a colorimetric reverse transcriptional loop-mediated isothermal amplification for rapid detection of SARS-CoV-2. Methods & Materials Inactivated SARS-CoV-2 virus samples were procured from the National Institute of Virology, Pune, India. Various genes were targeted for primer design, such as nucleocapsid, spike, RNA dependent RNA polymerase, and envelop genes region of SARS-CoV-2. In-vitro synthesised viral RNA was used for the standardisation of the RT-LAMP. RT-LAMP products were visualised by the naked eye using hydroxy naphthol blue dye. The sensitivity of RT-LAMP assay was performed by diluting in-vitro synthesised viral RNA at a different concentration such as 5 ng/µl, 25 ng/µl, 50 ng/µl, 200 ng/µl. Additionally, the RNA copy number was estimated and tested with RT-LAMP. In-silico analysis was carried to calculating the percentage of mismatch using various viral sequences, including SARS-CoV-2, other coronaviruses, and other related RNA virus sequences available at GenBank. Results RT-LAMP assay was standardised using in-vitro synthesised viral RNA. Temperature and time standardisation revealed, all the targets i.e., E, S, N, and RdRp gene regions had an optimum temperature of 63°C and time, 60 min. The sensitivity of all the target genes were ten copies of viral RNA. RT-LAMP amplified products were visualised by the naked eye using hydroxy naphthol blue dye and verified by agarose gel electrophoresis. All the primers used for the RT-LAMP assay showed a zero percent mismatch with SARS-CoV-2 sequences available at GenBank. Conclusion Colorimetric reverse transcriptional loop-mediated isothermal amplification assay developed in this study could provide a visual and faster alternative to the RT-qPCR assays. | Int J Infect Dis | 2022 | CORD-19 | |
| 5676 | Antimicrobial Resistance and One Health in the post-COVID-19 Era: What should Health Students Learn? Purpose Antimicrobial resistance (AMR) is a critical worldwide health issue that jeopardizes our ability to fight illnesses. The COVID-19 pandemic exacerbated the problem, which was largely caused by irrational off-label use of antivirals, anthelmintics, antimalarials, and, most notably, macrolide antibiotics. The One Health Approach is progressively becoming the most widely utilized in the fight against AMR. Our aim is to address the lack of teachings in AMR and the One Health Approach in health student curricula, as well as to provide recommendations that can be implemented as we progress beyond the COVID-19 era. Methods & Materials We conducted a literature review to identify the status of AMR and One Health education in health curriculum over the world while analysing the relevance and urgency of the topic within the COVID-19 era. Results We identified multiple gaps and discrepancies in AMR and One Health education that could be attributed to multiple reasons including the absence of a formal curriculum on the topics, and lack of interprofessional educational practices. The development and implementation of AMR and One Health topics in the school curriculum is important in equipping future health professionals to fully combat AMR in their respective fields. It can also therefore be encouraged that institutions synergize to share knowledge on useful ways of training healthcare students in addition to meaningful ways to communicate AMR concerns with patients and the public. Various teaching modalities could influence the outcome of antimicrobial prescribing practices. These could be improved by a re-evaluation of problem-based learning strategies, enhancing content and conduction of virtual learning platforms and development of a standardized curriculum on antimicrobial resistance. Interprofessional education and team-based learning can also be a facilitator to familiarize students with the One Health concept. Conclusion Today's health professionals need to provide mentorship and teaching for students on AMR and One Health. This will aid to develop today's young professionals and future health professionals with the necessary skills to prevent and tackle the spread of AMR with appreciation and knowledge of the One Health Approach. | Int J Infect Dis | 2022 | CORD-19 | |
| 5677 | Multidrug resistant Gram-negative bacilli infection in critically ill patients with COVID-19 Purpose Rapid spread of multidrug resistant Gram-negative bacilli (MDR-GNB) infection in Coronavirus disease (COVID-19) critically ill patients was observed even in those without underlying diseases and in all age groups. We conducted a prospective cohort study to assess the risk factors for acquisition of MDR-GNB infection in COVID-19 patients and its impact on patients´ outcome. Methods & Materials We included 43 consecutive patients with COVID-19 from a total of 8874 patients with COVID-19 admitted into the ICU of Aleman Hospital, Argentina, from May 1st 2020 to June 30th 2021. Followed up until death or 30 days after hospital discharge. We divided them into 4 groups: colonized with MDR-GNB (G1), colonized with MDR-GNB and infected with non-carbapenem resistant bacteria (G2), colonized and infected with MDR-GNB (G3), and infected with MDR-GNB without previous colonization (G4). Microbiological sampling was performed according to patient's conditions or epidemiological surveillance. Outcomes considered were length of hospital stay (LOS), mortality and readmission rate. Results Seven, five, six and twenty five patients were distributed respectively in G1, G2, G3 and G4. Male/female ratio was 2:1 with a median age of 68 years (IQR 62–75). Chronic pulmonary disease (18.6%) was the main comorbidity. Mean LOS was 40.16 days (P=0.79). Prolonged biomedical devices used were observed in 93% of patients (P=0.33). Ventilator associated pneumonia (n:15/36) and catheter-related bloodstream infection (n:16/36) were the most frequent infections (P=0.29, P=0.69). The most common carbapenem-resistant pathogens were Klebsiella pneumoniae (n: 38/60) and Pseudomonas aeruginosa (n:8/60). All patients were exposed to antibiotics before MDR-GNB was diagnosed. The first isolation of MDR-GNB was on average 14 days after hospital admission (P=0,84). Time between MDR-GNB colonization and infection was twice as much between G2 and G3 (8.4 Vs. 4 days, P=0.83). We observed no difference in all-cause mortality rate and readmission rate between the groups (P=0.75, P=0.97). Conclusion Prolonged ICU hospitalizations in addition to use of invasive devices and antibiotics exposure correlate with a higher risk of developing MDR-GNB colonization and infection in COVID-19 critically ill patients. | Int J Infect Dis | 2022 | CORD-19 | |
| 5678 | Tracking Changes in SARS-CoV-2 Transmission with a Novel Outpatient Sentinel Surveillance System in Chicago, Illinois, USA Purpose Public health indicators typically used for monitoring the COVID-19 epidemic can be biased or lag behind changing community transmission patterns. Hospital admissions lag infection by 10 – 17 days, and test positivity rate is sensitive to changing availability of, access to, and demand for diagnostic testing. The U.S. city of Chicago investigated whether sentinel surveillance of recently symptomatic individuals receiving an outpatient diagnostic test for SARS-CoV-2 could provide early warning of increasing transmission. Methods & Materials From May 2020 to June 2021, the Chicago Department of Public Health (CDPH) and Illinois Department of Public Health (IDPH) established community-based SARS-CoV-2 diagnostic testing sites throughout Chicago. From November 2020, these sites collected and reported patient data on symptom status and symptom onset date to CDPH and IDPH. Symptomatic individuals residing in Chicago who reported symptom onset within four days of diagnostic test were included in the sentinel population. COVID-19 case counts among the sentinel population were used to calculate the instantaneous reproductive number R(t) over time, which was compared to R(t) curves calculated from COVID-like illness (CLI) hospital admissions, CLI emergency department visits, and COVID-19-diagnosed emergency department visits. Pearson correlation between time-shifted sentinel case counts and each of these indicators was used to estimate the potential lead time provided by outpatient sentinel surveillance. Results From November 1, 2020, to June 13, 2021, IDPH and CDPH collected a total of 15,023 sentinel samples at community-based testing sites, an average of ∼470 samples per week. Trends in sentinel COVID-19 cases preceded CLI hospital admissions by 10 to 14 days. R(t) calculated from sentinel cases tracked well with R(t) calculated from CLI hospital admissions, CLI emergency department visits, and COVID-19-diagnosed emergency department visits. Adjusting case counts to account for changing testing volume over time improved correlation with other indicators. Conclusion Outpatient sentinel surveillance of recently symptomatic individuals accurately captures trends in SARS-CoV-2 community transmission and provides early warning of increases in transmission rate. The reliability of outpatient sentinel surveillance can be limited by low testing volume, slow test turnaround time, and delays in reporting. | Int J Infect Dis | 2022 | CORD-19 | |
| 5679 | Sensitive and visual detection of SARS-CoV-2 using polymerase spiral reaction assay Purpose Testing of SARS-CoV-2 for large populations is crucial for diagnosis, epidemiology, and surveillance of COVID-19. Currently, reverse transcription (RT) qPCR (RT-qPCR) is being performed worldwide and considered as a gold standard. As an alternative nucleic acid amplification test (NAAT)-based method, RT- polymerase spiral reaction (RT-PSR) assay can be a rapid, robust, and cost-effective point-of-care detection of SARS-CoV-2. Methods & Materials Inactivated SARS-CoV-2 virus samples were provided by the National Institute of Virology, India for this study. Specific primers targeting Nucleocapsid (N) gene, and RNA-dependent RNA polymerase (RdRp) genes of SARS-CoV-2 were designed for RT-PSR assay. Purified RNA was used for the standardisation of the RT-PSR using in vitro synthesised viral RNA. A simple visual detection of SARS-CoV-2 by the naked eye was optimised using hydroxy naphthol blue dye. The sensitivity of the assay was performed by diluting viral RNA at various concentrations. The limit of detection was estimated and tested with RT-PSR. Computational analysis was performed to determine the specificity of the primers by calculating the percentage of mismatch using various novel coronavirus sequences, other coronaviruses, and other related RNA virus sequences. Results Temperature and time for RT-PSR assay were found to be optimum at 63°C and 60 min, respectively, for both the gene targets. RT-PSR assay amplified even at a concentration of 5 ng/µl and could detect ten copies and one copy of RNA targeting RdRp and N gene, respectively. RT-PSR amplified products were visually detected by the naked eye and further verified by agarose gel electrophoresis. Primers used for the RT-PSR assay showed zero percent mismatch with SARS-CoV-2 sequences and mismatch with other viruses. Conclusion The RT-PSR assay developed in this study could be considered a good alternative to the RT-qPCR assays. | Int J Infect Dis | 2022 | CORD-19 | |
| 5680 | Public Search Interests Related to COVID-19: Insights from Google Search Trends in Bangladesh Purpose Public response monitoring is critical to reducing COVID-19 infections and developing effective public health strategies. This study explored Google search trends to understand public responses to COVID-19 concerns in Bangladesh. Methods & Materials We used country-level Google search trends data to examine the association between Google search terms related to COVID-19 deaths, face masks, and COVID-19 vaccines and the actual and one-week lagged actual COVID-19 death counts from February 2, 2020, to December 19, 2020, in Bangladesh. Results Search terms related to COVID-19 deaths, face masks, and COVID-19 vaccines increased and peaked during March and April, but then began declining gradually after June 2020. The mean relative search volume for face masks (35 points) was higher than for death information (8 points) and vaccines (16 points) throughout the study period, and searching for masks peaked (100 points) during the third week of March. Search interests for death information and face masks were negatively correlated with the actual and one-week lagged actual COVID-19 death counts. Conclusion In response to declining trends in COVID-19-related google search terms, policymakers should strengthen ongoing risk communication and preventive information dissemination programs to control and prevent COVID-19 cases and deaths. | Int J Infect Dis | 2022 | CORD-19 | |
| 5681 | Access to Information, Concerns, Myths and Truths on Food Safety During COVID-19: An Overview of Portuguese Population Purpose The COVID-19 pandemic raised questions and concerns about the possibility of transmission of SARS-CoV-2 via foods. While cases of COVID were rapidly rising, information related to the virus and ways of prevention was also increasing, with much of this information being provided by the media and the general population. In this context, this study had two main objectives: 1) To understand the doubts and concerns of the Portuguese population related to food safety during the first wave of COVID-19 and how they clarified these issues and 2) to analyze the population's opinion on myths and truths related to the transmission of the infection. Methods & Materials A survey including questions about a) concerns and information on food safety during the first wave of COVID-19 pandemic; b) myths and truths about COVID-1 and c) respondents’ profile. The survey was released online between June and October of 2020. Results The main doubt of the respondents was related to the manipulation of food (40,7%) followed by the possibility of transmission of COVID-19 through food (12,6%) and which foods should be avoided due to the pandemic (12,6%). 33,3% of the participants stated that television was the main mean of information accessed to clarify these doubts, followed by a Guideline launched by the Directorate-General of Health (31,8%). However, 50,3% said that they had only found answers to some of their questions. 50% of the respondents with higher level of education and 30% of the respondents with lower level of education had doubts about the possibility of the transmission of COVID-19 through food. Also, most of the survey participants disagreed with the affirmations regarding popular ways of disinfecting food to prevent infection. Conclusion COVID-19 pandemic raised several doubts, however when related to food safety, the main doubt was about the manipulation of food due to the concern of SARS-CoV-2 transmission. Most respondents do not believe myths about COVID-19 and food safety, but this was dependent on the level of education. | Int J Infect Dis | 2022 | CORD-19 | |
| 5682 | The discovery of novel coronaviruses in bat guano, Sarawak, Malaysian Borneo Purpose Virological surveillance was conducted in to determine the presence of bat CoVs in the bat population in Wind Cave Nature Reserve, Sarawak, Malaysian Borneo. Methods & Materials Partial RNA dependent RNA polymerase (RdRp) gene sequences of 11 bat-CoV positive guano collected in Wind Cave Nature Reserve was analysed. Five pellets of fresh guano from insectivorous bats were collected on plastic tarp and pooled in 500uL of ice-cold viral transport medium. The 440-bp gene was amplified using family-wide hemi-nested RT-PCR for phylogenetic analysis. Amplicon sequences were analysed using Basic Local Alignment Search Tool software (BLAST) to determine their corresponding species. Sequence alignment was carried out without primer sequence and phylogenetic tree with Maximum Likelihood bootstrap-Bayesian inference value (MLb/PPv) support. Results The positive rate was 47.6% (10/21) with the distribution of 60% (n=6/10) and 40% (n=4/10) Alpha and Beta-coronaviruses respectively. BatCoVs identified in this study formed four novel monophyletic clades referred to as Borneo Alpha-1 and -2, and Borneo Beta-1 and -2. Borneo Alpha-1 and -2 viruses diverged to form a monophyletic clade with Decacovirus-1 and Decacovirus-2 respectively (83.0-85.1% and 80.7-81.0% nucleotide identity) with batCoV found in Sabah (NCBI Accession# KX284940). Borneo Beta-1 viruses are also closely related to BatCoV found in Sabah (KX284939) (86.5-87.5% nt identity), forming a monophyletic group with Sarbecovirus. Meanwhile, Borneo Beta-2 are closer to BatCoVs in Loas (MN312609) (89.7-90.4% nt identity), forming a monophyletic clade with Hibecovirus. It is worthy to note that viruses found in the Sarbecovirus subgenus such as SARS-CoV-1 and SARS-CoV-2 attributed to two zooneses with Public Health Emergency of International Concern (PHEIC) over the past two decades. However, Borneo Beta-1 viruses are distant to the RaTG13 (MN996532) (69.1-697% nt identity), the proposed progenitor of the pandemic SARS-CoV-2. Conclusion The study has discovered both novel alpha and beta bat-coronaviruses in 40% of the guano sampled in Wind Cave Nature Reserve, Sarawak, East Malaysia based on the phylogeny of the partial RdRp gene sequence. The batCoVs are phylogenetically grouped into four clades via phylogeny confirms the presence of Borneo Beta-1 clade being monophyletic to the epidemic Sarbecoviruses. | Int J Infect Dis | 2022 | CORD-19 | |
| 5683 | Hesitancy to COVID-19 Vaccines among University Students in Lebanon Purpose The aim of the study is to assess the readiness and behavioral intentions of students enrolled at the American University of Beirut (AUB), Lebanon to obtain the COVID-19 vaccine. To our knowledge, this is the first study to assess vaccine hesitancy among university students in Lebanon. Methods & Materials We conducted an online survey between May 11 and June 18, 2021 administered to a total of 3805 undergraduate and graduate students. We used three models as the theoretical framework of the study. These include the Integrated Behavioral Model (IBM) (to assess attitude, perception and behavioral intentions), Precaution Adoption Process Model (PAPM) (to assess readiness to adopt a preventive health behavior), and the Extended Parallel Processing Model (EPPM) (to assess cognition and emotional reactions). Chi square and logistic regression were performed using STATA. Results The study included 800 participants (21.02%) from all faculties (n=7) at AUB. The mean age was 21 years with the majority being undergraduate students (75%). The vaccine acceptance group represented 87.01% of the study participants while the hesitant and refusal groups accounted for 10.21%, and 2.77%, respectively. Our results showed that hesitancy was significantly associated with nationality, residency status and university rank (p value< 0.05). Moreover, there was a significant association between hesitancy and agreement/disagreement to the conspiracy type of thinking questions. Interestingly, the majority of the hesitant group agreed that the mainstream media is creating unnecessary fear towards COVID-19 (54.43%) and that millions more people per year die from flu than from COVID-19 (40.51%). Students reporting that pharmaceutical companies adequately tested the safety of the vaccine (OR=0.52; 95% CI=0.19-1.43; p value=0.21) and those who consider the vaccine in agreement with their personal views (OR= 0.11, 95% CI= 0.02-0.51, p value= 0.004) were less likely to be hesitant. Interestingly, history of COVID-19 infection didn't affect the participants’ willingness to get vaccinated. Conclusion Our results showed a low hesitancy rate among students enrolled at AUB. The factors associated with hesitancy can be used as a core content to organize social campaigns for spreading awareness and increasing the acceptance rate of COVID-19 vaccination. | Int J Infect Dis | 2022 | CORD-19 | |
| 5684 | Severe Acute Respiratory Infection Collaborative surveillance and monitoring outbreak, Viet Nam Purpose Lack of understanding of the circulation, emergence of avian influenza new strain viruses, and risk of transmission from animal to human were big challenges causing heavy losses in human life and socio-economic. SARI collaborative surveillance has been set up and operated to fill the gaps in the border province of Vietnam - Cambodia. Methods & Materials Clinical, epidemiological data and outcomes of SARI patients were collected in provincial hospital. Samples were performed by PCR technique for influenza and non-influenza viruses included Coronaviruses, Paramyxoviruses, Filoviruses, and Flaviviruses. Positive influenza samples were isolated and characterized. Information sharing and risk analysis were conducted between animal health and public health sectors Results SARI patient per year was 14.4% (3016/20956) among hospitalized and incident rate was 534.4/100000 population. Annual death caused by SARI ranged from 6.6 - 12.5%. Most SARI patients were neonatal (55.4% - 529/95)). Among 20.1% (955/4741) represented SARI patients were tested, respiratory and influenza virus-positive samples were 70.4% (673/955) and 24.9% (238/955) respectively. Influenza A/H1N1pdm09 virus was dominant (50.9%) and RSV accounted for 16.6% (159/955) and mostly in children <5. Coronaviruses and paramyxoviruses were detected. Coinfected respiratory viruses was 25.6% (245/955). H5N1, H9, and H5N6 viruses have been detected in domestic poultry and pig. Conclusion Collaborative surveillance fundamentally contributed to monitoring the evolution, showed risk of transmission of avian influenza viruses to human exists considerably high, and strengthened the pandemic preparedness capacity of public health and animal health sectors. Intensive studies and wider expansion to multi-sector coordination and across-national borders are needed. | Int J Infect Dis | 2022 | CORD-19 | |
| 5685 | Longitudinal surveillance of Post-Acute Sequelae of SARS-CoV-2 among Long Beach City residents, April-December, 2020 Purpose There have been limited studies on the post-acute sequelae of SARS-CoV-2 (PASC) throughout the course of the disease and recovery. The purpose of this study was to identify the prevalence and associated factors of PASC in a diverse population to inform patients’ expectations and public health policy. Methods & Materials Confirmed Coronavirus Disease 2019 (COVID-19) surveillance data was obtained from the California Reportable Disease Information Exchange (CalREDIE) surveillance system between April 1, 2020 and December 10, 2020. Simple random sampling without replacement was used to select participants for the study. Interview questions, guided by the CalREDIE COVID-19 case investigation questionnaire, focused on tracking self-reported symptoms prior to diagnosis, at time of positive test result, one-month post-testing, two months post-testing, and on the date of the final interview. Results One third of participants reported PASC two months post-testing, most commonly reporting fatigue, anosmia, and dyspnea. Individuals forty years and older, female, Black/African American, and with asthma or obesity had the highest odds of developing PASC in our study population. Conclusion Age, gender, pre-existing conditions, and ethnicity/race were associated with developing PASC in a diverse sample of hospitalized and non-hospitalized participants. As the number of recovered COVID-19 patients increases, it is critical to understand the impacts of PASC and differential access to care and recovery among diverse populations in order to guide patient expectations and equitable public health policies. | Int J Infect Dis | 2022 | CORD-19 | |
| 5686 | Hesitancy of COVID-19 vaccine in a working-age population in a town in Central Maharashtra in Western India: A survey based on vaccine characteristics Purpose Assessments of public sentiments and opinion polls on vaccinations recommend that COVID-19 vaccine hesitancy is globally expanding; nonetheless, the usefulness of opinion polls to plan mass vaccination campaigns for vaccines and to gauge acknowledgment in a country's populace is restricted. Hence, we aimed to evaluate the impacts of vaccine characteristics, information on herd immunity, and general medical practitioner (GP) recommendation on vaccine hesitancy in a working-age population in Kolhapur, a town in Central Maharashtra in Western India. Methods & Materials In this survey, adults aged 18-64 years residing in Kolhapur, with no history of SARS-CoV-2 infection, were randomly selected in April-2021. Participants completed a questionnaire on their background and vaccination behavior-related variables, and were then randomly assigned according to a full factorial design to one of three groups to receive differing information on herd immunity and to one of two groups regarding GP recommendation of vaccination. Participants then completed a series of eight discrete choice tasks designed to assess vaccine acceptance or refusal based on hypothetical vaccine characteristics, risk of serious side-effects, location of manufacture, and place of administration. Responses were statistically analyzed. Results Responses were collected from 843 working-age adults, of whom 163 (19.33%) opted for no vaccination (outright vaccine refusal) and 680 (80.66%) did not. Here, outright vaccine refusal was associated with a lower perceived severity of COVID-19, whereas vaccine hesitancy was lower when herd immunity benefits were communicated and in working versus non-working individuals, and those with experience of COVID-19. For a mass vaccination campaign involving mass vaccination centers and communication of herd immunity benefits, our results predicted outright vaccine refusal in 23.6% (95% CI 19•7-28•4) of the Kolhapur working-age population. Predicted hesitancy was highest for vaccines manufactured in China with 50% efficacy and a 1 in 10,000 risk of serious side-effects (vaccine acceptance 27•4% [26•8-28•0]), and lowest for a vaccine manufactured in the USA with >90% efficacy and a 1 in 1,00,000 risk of serious side-effects (vaccine acceptance 73•6% [69.6-78•1]). Conclusion COVID-19 vaccine acceptance depends on the characteristics of vaccines and the national vaccination strategy, amongst various other factors, in the working-age population in Kolhapur. | Int J Infect Dis | 2022 | CORD-19 | |
| 5687 | Circulation of coronavirus in bats from northern and central Argentina: preliminary study Purpose Bats have proven throughout history to be the reservoir and disseminator of a wide variety of viruses in nature, where they have sometimes been linked to important infections in public health, such is the case of coronaviruses causing SARS-CoV, MERS-CoV and SARS-CoV-2. Considering the importance of these previous events and due to the lack of information on the coronavirus present in the bat population in Argentina, we decided to monitor their circulation in two provinces in which there is continuous contact of these animals with others (domestic and wild) and human beings. Methods & Materials Samples of pharyngeal swabs and fecal matter were collected from different species of bats from the provinces of Jujuy (northern Argentina) and La Pampa (central Argentina), and from other wild and domestic animals that cohabitated with bats. The samples were stored in RNA Shield® 1X until processing. The viral RNA extraction was performed with Quick-RNA Viral Kit (ZYMO RESEARCH®) and the cDNA with EasyScript First-Strand cDNA Synthesis SuperMix (TRANS®). Each sample was analyzed individually by nested PCR directed to a conserved 440 bp fragment located within the viral polymerase gene (Chu et al., 2006). Results Preliminary results from 43 stool samples and 53 pharyngeal swabs from insectivorous and hematophagous bats demonstrated the presence of alfacoronavirus sequences in four fecal samples (3 insectivorous bats and 1 hematophagous bat) and in one pharyngeal swab sample from an insectivorous bat. Through comparison with GenBank sequences, the closest relatives identified were alphacoronaviruses of the species Myotis riparius/ nigricans, Molossus rufus and Desmodus rotundus. Interestingly, we found alphacoronavirus sequences of one species present in another bat species since the colonies were in close contact. Samples from other animal species are in the process of being analyzed. Conclusion The identification of new coronaviruses that naturally inhabit bat populations and in animal species that share the biological niche, contributes to the knowledge of viral evolution and the biology behind the jump between animal species. | Int J Infect Dis | 2022 | CORD-19 | |
| 5688 | Structural-Equation-Modelling (SEM) to analyze climatic factor's role on COVID-19 spreading Purpose Climate seems to influence the COVID-19 spreading, but the results of the published studies are conflicting. Aim of this study was to perform a world-wide investigation to analyze the role of all the main climatic factors (CF), trying to identify the causes that led to the discrepancy of the results. Methods & Materials 134,871 data (from 209 countries) were used for the analysis. These were extrapolated from an initial data-set of 1.200.000 data. To avoid biases present in most of the previously studies, a set of specific requirements was adopted: long observation period (16 weeks), • the use of a relative time scale to synchronize the beginning of the outbreak among the countries, • multiple data collection points (up to 4 cities/per country) to overcome the problem of climate variability within a country, • the use of an appropriate technique to test the relationships among interdependent variables, • the use of a lag-period to compensate the shift between the infection exposure and the diagnosis’ confirmation. Data's analysis was performed with SEM, a flexible statistical technique for modeling causal chain of effects simultaneously. Using hypothesis-testing, this technique examines the relationships between observed variables and latent variables, in turn linked to observed variables, their indicators. With this statistical model it was possible to consider the integrated effects of all the CF on COVID-19 and, at the same time, to investigate the effects of population density (PD) too. Results The results of the analysis showed that both climate and population density significantly influence the spread of COVID-19 (p<0.001; p<0.01, respectively). Overall, climate outweighs population density (path coefficients: climate vs incidence=0.18, climate vs prevalence=0.11, PD vs incidence=0.04, PD vs prevalence=0.05). Among the climatic factors, irradiation plays the most relevant role, with a factor-loading of -0.77, followed by temperature (-0.56), humidity (0.52), precipitation (0.44), and pressure (0.073); for all p<0.001. Fit indices demonstrated a good fit of the model (determination-coefficient=0.826, Root-Mean-Square-Error-of-Approximation=0.088, Standardized-Root-Mean-Square-Residual=0.078). Conclusion This study demonstrates that CF significantly influence the spread of SARS-CoV-2. However, demographic factors, together with other determinants, can affect the transmission, overcoming the protective effect of climate, where favourable. | Int J Infect Dis | 2022 | CORD-19 | |
| 5689 | Comparison of Cycle Threshold and Clinical Status Among Different Age Groups of COVID-19 Cases Purpose Aim of the study was to compare the viral load and clinical status among different age groups with COVID-19 infection Methods & Materials A retrospective cross-sectional study was carried out to analyse the Ct values of positive samples reported during April 2020 till May 2021. Result of 13,820 number of RT-PCR positive samples were included for analysis of Ct values. Ct values of confirmatory genes were taken into consideration and Ct values below 25, >25 to 30 and >30 was categorized as high, moderate and low viral load respectively. Age group was stratified into ≤18 years, 18-60 and >60 years as young, adult and elderly respectively. The data was analysed using SPSS windows version 25.0. Results The Mean Ct value was 27.9, 26, and 26.2 in young, adult and elderly age group respectively. Mean Ct value of young patients were significantly higher as compared to adult and elderly patients (p<0.05). The percentage of high viral load (Ct<25) was found to be significantly higher in adults and elderly (44.6% & 43.7%) as compared to young (32.2%) (p<0.001). Majority of the covid 19 positive cases belonging to <18 years age (75.9%) were asymptomatic as compared to 64.5% and 59.7% in adult and elderly age groups respectively. Conclusion Present study observed a significantly high proportion of viral load in the adult and elderly population which plays a substantial contribution to SARS CoV-2 transmission, whereas the majority of the young population being asymptomatic play major role as silent transmitters. The study reemphasizes the need for strict adherence to COVID appropriate behaviours. | Int J Infect Dis | 2022 | CORD-19 | |
| 5690 | Detection and Contact Tracing of COVID-19 in Indonesia through a Red Cross Community Based Surveillance System Purpose Epidemics and pandemics begin and end in communities. Communities play a critical role in prevention, detection, and response to infectious disease threats when meaningfully engaged. Surveillance and contact tracing are core components of effective public health preparedness and response efforts. But, surveillance systems that rely on case detection via healthcare facilities may fail or be slow to detect and trace many cases. Communities are often the first to identify unusual disease patterns in humans and animals. Community-Based Surveillance (CBS) gives a voice to communities, enables them to communicate unusual health events to authorities, and complements facility-based surveillance systems. Methods & Materials Since 2019, Indonesia Red Cross (PMI) has piloted CBS in 8 villages within four provinces. Initiated for passive surveillance, the volunteers trained to report ‘alerts’ of epidemic-prone diseases to health authorities. The concept was then adapted to an active approach focussing on COVID-19 and scaled to 74 villages across eight provinces. Partnering with local authorities, volunteers supported COVID-19 screening, detection, tracing, and local response, all while implementing volunteer safety standards. The reporting system was created and coordinated by a structure within PMI. Results From August 2020-June 2021, community volunteers made 1,079 alerts: 99% of the alerts were reported to health authorities, with 71.1% followed up within 24 hours. After alert detection, volunteers sensitized family members on preventive measures while individuals awaited follow-up visits for diagnosis and management by health authorities. 64% of alerts were PCR positive for COVID-19, 12% were negative, 14% did not undergo testing, and test results for 10% of the alerts were unavailable. Of 979 contacts traced by volunteers, authorities followed up 99%, confirming 29% positive and 34% negative for COVID-19; the remaining 37% included those recommended to isolate without testing and those for whom test results were unavailable. Conclusion CBS has supported early detection and contact tracing of COVID-19 in Indonesia. The community case definition used to identify potential alerts was sensitive and easily understood by non-health workers. The system proved readily scalable and adaptable, enabling a shift from passive to active surveillance and making it feasible to be implemented anywhere in the community. | Int J Infect Dis | 2022 | CORD-19 | |
| 5691 | SARS-CoV-2 Surveillance in Peri-Domestic and Wildlife Species in Ontario, Canada Purpose The rapid emergence and spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has sparked concerns of spillover to naïve wildlife populations and it is unclear if wildlife could ultimately serve as a reservoir for the virus. Evidence of SARS-CoV-2 has been detected in captive and wild animals (e.g., mink, tiger, lion). Moreover, the SARS-CoV-2 variants of concern (VOCs) likely have a broader host range, suggested by the susceptibility of laboratory mice (Mus musculus) to the Beta and Gamma variants but not wild-type SARS-CoV-2. Peri-domestic animals (i.e., wild and feral animals living near humans) represent highly relevant species to assess spillover since they likely have a greater chance of exposure to the virus from humans. Thus, monitoring wildlife at the human-animal interface is critical in understanding the epidemiology of SARS-CoV-2. We therefore are investigating the presence of SARS-CoV-2 in key peri-domestic and wild animals across southern Ontario, Canada through a One Health framework. Methods & Materials In collaboration with the Ministry of Natural Resources and Forestry, oral and rectal swabs are opportunistically collected from two peri-domestic species, raccoons (Procyon lotor) and skunks (Mephitis mephitis), across southern Ontario where high population densities and incidence of SARS-CoV-2 in humans likely provide spillover opportunity. Additionally, oral and rectal swab, and respiratory and intestinal tissues from trapped wild mink (Neovison vison) are collected in collaboration with the Ontario Fur Managers Federation. Samples are analyzed at the Sunnybrook Research Institute via a RT-qPCR for two SARS-CoV-2 gene targets: the 5’ untranslated region (UTR) and the envelope gene (E). Results From September 2020 to January 2021, 264 oral and 264 rectal swabs were collected from 207 raccoons and 57 skunks. All samples were negative for SARS-CoV-2 RNA. The study is presently ongoing. Conclusion Based on these preliminary data, there is little evidence to suggest spillover of SARS-CoV-2 to the sampled animals during this period. Notably, these animals were sampled prior to the emergence of SARS-CoV-2 VOCs, and our results do not preclude the possibility of future spillover to wildlife at the human-animal interface. Results from ongoing surveillance efforts post-VOC emergence will also be discussed. | Int J Infect Dis | 2022 | CORD-19 | |
| 5692 | Indications for and Findings on Transthoracic Echocardiography in COVID-19 patients admitted to a Tertiary Care Government Medical Hospital Purpose We aimed to document the performance of transthoracic echocardiography (TTE) and the spectrum of echocardiographic findings as complications associated with coronavirus disease 2019 (COVID-19). Methods & Materials A retrospective analysis was performed among adult patients admitted to a tertiary care government hospital in Maharashtra between January 01, 2021 and May 31, 2021. Patients were included if they underwent TTE during the hospitalization after a known positive diagnosis for COVID-19. Demographic and clinical data were obtained using chart abstraction from the medical record system. Results Of 1539 patients, 187 (12.15%) underwent TTE following positive results on severe acute respiratory syndrome coronavirus-2 polymerase chain reaction testing. The most common clinical indications for TTE were concern for a major acute cardiovascular event (52.95%) and hemodynamic instability (32.29%). Although most patients had preserved biventricular function, 41.30% were found to have left ventricular ejection fractions ≤ 50%, and 13.9% had at least moderately reduced right ventricular function. Eleven patients had wall motion abnormalities suggestive of stress-induced cardiomyopathy. Using Spearman rank correlation, there was an inverse relationship between high-sensitivity troponin T and left ventricular ejection fraction (ρ = -0.41, P < 0.01). Amongst 37 patients with prior echocardiograms, only seven (18.91%) had new reductions in LVEF of >10%. Clinical management was changed in seventeen individuals (26.98%) in whom TTE was ordered for concern for acute major cardiovascular events and seven (14.58%) in whom TTE was ordered for hemodynamic evaluation. Conclusion Our study describes the clinical indications for use and diagnostic performance of TTE, as well as findings seen on TTE, in hospitalized patients with COVID-19. In appropriately selected patients, TTE can be an invaluable tool for guiding COVID-19 clinical management. | Int J Infect Dis | 2022 | CORD-19 | |
| 5693 | Reactivation of CMV and HSV-1 Among Severe COVID-19 Patients May be Triggered by Increased Level of Pulmonary Dioxin Purpose Reactivation of cytomegalovirus (CMV) infection was recently found to influence worse clinical outcome following SARS-CoV-2 infection (doi: 10.1186/s12979-020-00185-x). Other findings showed that CMV and herpes simplex virus 1 (HSV-1) reactivations are observed in patients with COVID-19 acute respiratory distress syndrome (ARDS) (HYPERLINK https://doi.org/10.1186/s13054-020-03252-3 doi.org/10.1186/s13054-020-03252-3). Addressing occurrence of Herpesviridae reactivation in immunocompetent patients and still unspecified triggers of reactivation, we tested potent xenobiotic 2,3,7,8-tetrachrolodibenzo-p-dioxin (TCDD), which current body burden (DBB) ranges from 20 pg/g (TEQ in fat) in general population to 100 pg/g in older people. Methods & Materials In silico quantitation of active dioxin response enhancers (DRE) in promoters of viral genes. Plaque assay of viral titer. Virus DNA hybridization assay. Clinico-epidemiological analysis. Results In silico analysis revealed in regulatory region of CMV IE genes from 5 to 10 DRE, and from 6 to 8 DRE in regulatory region of HSV-1 IE genes. We established that a picomolar TCDD can trigger up-regulation of CMV and HSV-1 genes via AhR:Arnt transcription factor in macrophage (doi.org/10.1016/j.ijid.2012.05.265) and glial human cell lines (doi.org/10.1016/j.jalz.2016.06.1268), respectively. In fact, viral reactivation may be triggered in COVID-19 ARDS patients by higher pulmonary TCDD concentrations, as lipid storm within lungs of severe COVID-19 patients has been recently reported (doi.org/10.1101/2020.12.04.20242115). Due to hydrophobic character (Log PO/W: 7.05), TCDD partitions into inflammatory lipids in lung tissue thus augmenting its local concentration. Population-based epidemiological data on SARS-CoV-2 first wave of pandemic showed that picomolar TCDD can reactivate CMV (measured by high CMV seropositivity), as cumulative mortality rate 4.5 times was revealed in Lombardi region of Italy where after Seveso industrial accident TCDD plasma level in pre-exposed subjects still is 15 times the level in rest of Italy (doi.org/10.3389/fpubh.2020.620416). Also, Arctic Native (AN) peoples have TCDD body burden 7 times that in general population, as they consume dioxin-contaminated fat in seafood, and their COVID-19 mortality is 2.2 times of that among non-AN Alaskans (doi: 10.15585/mmwr.mm6949a3). Conclusion TCDD in picomolar range may trigger CMV expression in lung cells and commit virus to the lytic cycle, which can be applied to reactivation of Herpesviridae infection in immunocompetent patients with COVID-19 ARDS syndrome. | Int J Infect Dis | 2022 | CORD-19 | |
| 5694 | Determination of SARS-CoV-2 Contamination in a Neonatal Intensive Care Unit (NICU) Environment Using Droplet Digital PCR (ddPCR) Purpose Neonatal infections with SARS-CoV-2 are thought to be less contagious than in older children and adults. The transmission of SARS-CoV-2 from neonates and their environment has not been well studied. Droplet Digital PCR (ddPCR) is an emerging and sensitive technology that can aid infection control investigations. We sought to document surface contamination within the immediate environment of a preterm neonate with congenital COVID-19 using ddPCR. Methods & Materials On day 5 of life, a total of 23 environmental samples were collected in Eswabs (Amies media) based on proximity to the neonate, from the inside (7) and outside (16) of the neonate's incubator for ddPCR analysis. Samples were extracted, using an in-house method and each extract was run for reverse-transcription ddPCR measurement using the Bio-Rad SARS-CoV-2 ddPCR Kit. The 96-well RT-ddPCR ready plate was loaded into the QX200 Droplet Reader (Bio-Rad, Pleasanton, CA). The fluorescence intensity of each droplet was measured, and droplets were determined to be positive or negative for gene targets (N1, N2). Results All samples collected from outside of the incubator were negative.These included: a stethoscope hanging outside of the incubator, nearby keyboard/mouse, wireless phone receiver, barcode scanner, blood culture bottles, pens/pencils, light switches, weigh scale, countertop/shelf, cart with drawers and incubator port release clips. Samples collected from inside the incubator were positive for SARS-CoV-2. These results reported in copies per microlitre (cp/µL) extract included: the swaddle cloth (0.4 N2), sheets behind the neonate's head (11.4 N1, 16.9 N2), cardiorespiratory and saturation monitor leads and cables near the neonate's head (2.8 N1,4.5 N2), near the neonate's feet (2.1 N1, 3.7 N2), and nametags hanging on a panel (1.0 N1,1.2 N2). The highest levels were noted from the neonate's drool (25.2 N1, 35.2 N2). Conclusion The presence of SARS-CoV-2 was confirmed by ddPCR in environmental samples inside the incubator confirming the ability of the neonate to spread the virus in close quarters. No virus was identified outside of the incubator which suggests appropriate hand hygiene and disinfection of environmental surfaces. ddPCR appears to be a useful tool for investigating the potential role of fomites in COVID-19 transmission | Int J Infect Dis | 2022 | CORD-19 | |
| 5695 | Detection of SARS-CoV-2 IgM Antibodies in Febrile Patients From an Endemic Region of Dengue and Chikungunya Purpose The rapid expansion of the novel SARS-CoV-2 virus has raised serious public health concerns due to the possibility of misdiagnosis in regions where arboviral diseases are endemic. We performed the first study in northern Peru to describe the detection SARS-CoV-2 IgM antibodies in febrile patients from an endemic zone for dengue virus (DENV) and chikungunya virus (CHIKV). Methods & Materials A cross-sectional study was performed in febrile patients attending primary healthcare centers from April 2020 through March 2021. This study was carried out jointly with the national surveillance system for the etiological identification of acute febrile illness (AFI). Patients are included if they attended outpatient clinics with AFI (axillary temperature greater than or equal to 38°C in the previous 7 days) along with one or more of the following symptoms: headache, myalgias, arthralgias, retro-ocular pain, lumbar pain, arthritis, nausea, rash, among others. Serum samples were collected from each patient, for the molecular and serological detection of DENV and CHIKV by RT-PCR and IgM ELISA-based assay, respectively. Also, the detection of IgM antibodies against SARS-CoV-2 with an ELISA-based assay was performed. Results 464 patients were included during the study period, of which 188 (40.51%) were positive for one pathogen, meanwhile 32 (6.90%) presented co-infections between 2 or more pathogens. The majority of patients with monoinfections were positive for SARS-CoV-2 IgM with 73.40%, followed by DENV 18.09% and CHIKV 8.51%. The most frequent co-infection was DENV + SARS-CoV-2 with 65.63%, followed by DENV + CHIKV and DENV + CHIKV + SARS-CoV-2, both with 12.50%. The presence of polyarthralgias in hands (p<0.01) and feet (p=0.05) were more frequently reported in patients with CHIKV monoinfection. Also conjunctivitis was more common in patients positive for SARS-CoV-2 IgM (p<0.01). The rest of the symptoms were similar among all the study groups. Conclusion In conclusion, a high prevalence of SARS-CoV-2 IgM antibodies were frequently detected in acute sera from febrile patients with a clinical suspicion of arboviral disease. These results highlight the need to consider SARS-CoV-2 infection as a differential diagnosis of AFI in endemic areas for arbovirosis, as well as consider co-infections between these pathogens. | Int J Infect Dis | 2022 | CORD-19 | |
| 5696 | Characteristics and Early Predictors of Intensive Care Unit Admission among COVID-19 Patients in Qatar Purpose This study aimed to explore the early predictors of intensive care unit (ICU) admission and in-hospital mortality among patients diagnosed with Coronavirus disease (COVID-19). Methods & Materials This was a case-control study of adult patients with confirmed COVID-19. Cases were defined as patients admitted to ICU during the period February 29 - May 29, 2020. For each case enrolled, one control was matched by age and gender. Univariate and multivariate logistic regression models were used to identify the predictors for ICU admission and in-hospital mortality among the COVID‐19 patients. Results A total of 1560 patients with confirmed COVID-19 were included. Each group included 780 patients with a predominant male gender (89.7%) and a median age of 49 years (interquartile range, IQR=18). Predictors independently associated with ICU admission included having cardiovascular disease (CVD) (adjusted odds ratio (aOR)=1.64, 95% confidence interval (CI): 1.16 - 2.32, p= 0.005), diabetes (aOR=1.52, 95% CI: 1.08 - 2.13, p= 0.016), body mass index ≥30 kg/m2 (aOR=1.46, 95% CI: 1.03-2.08, p= 0.034), lymphocytes ≤0.8 × 103/μL (aOR=2.69, 95% CI: 1.80-4.02, p<0.001), aspartate aminotransferase (AST) >120 U/L (aOR= 2.59, 95% CI: 1.53-4.36, p<0.001), ferritin >600 μg/L (aOR=1.96, 95% CI: 1.40-2.74, p<0.001), C-reactive protein (CRP) >100 mg/L (aOR=4.09, 95% CI: 2.81-5.96, p<0.001), and dyspnea (aOR=2.50, 95% CI: 1.77-3.54, p <0.001). Similarly, significant predictors of mortality included CVD (aOR=2.16, 95% CI: 1.32- 3.53, p=0.002), diabetes (aOR=1.77, 95% CI: 1.07-2.90, p=0.025), cancer (aOR=4.65, 95% CI: 1.50-14.42, p= 0.008), lymphocytes ≤0.8 x,103/μL (aOR=2.34, 95% CI: 1.45-3.78, p= 0.001), and AST >120 U/L (aOR= 1.89, 95% CI: 1.04-3.43, p=0.036). Conclusion Having CVD, diabetes, lymphopenia, and increased AST were independent predictors for both ICU admission and in-hospital mortality in patients with COVID-19. In addition, obesity, high ferritin, and CRP levels were also associated with increased risk of ICU admission, while cancer was strongly associated with in-hospital mortality. Early identification and monitoring of patients at risk is essential in planning the level of care needed to prevent delay in medical intervention. | Int J Infect Dis | 2022 | CORD-19 | |
| 5697 | Global Study: Participation in One Health Networks and Involvement in COVID-19 Response Activities Purpose This global study examined whether being part of a One Health Network (OHN) was associated with being involved in COVID-19 response activities at the early stages of the pandemic. Barriers to workforce involvement in the pandemic response and the perceived value of OHN activities were studied to inform future targeted evidence-based strategies for workforce capacity-building. Methods & Materials We conducted a cross-sectional descriptive study, using an online questionnaire that was globally distributed in July-August 2020. With a snowball sampling approach via OHN listservs, social media, and further sharing, we aimed to reach individuals in the global health workforce across locations, organizations, and sectors to survey their participation in OHN activities and involvement in COVID-19 response. Results The sample included 1050 respondents from various types of organizations and work sectors, from 94 countries across all WHO regions. Being part of an OHN was positively associated with involvement in the COVID-19 response (odds ratio: 1.8, 95% confidence interval: 1.3 - 2.4). The OHN activities most indicated as useful during COVID-19 pandemic by the survey respondents included 'increased public awareness of One Health' and 'networking with professionals across sectors with common interests'. Overall, 44% of survey respondents who were part of an OHN found OHN activities very or extremely helpful to their COVID-19 response. Lack of opportunities was a commonly reported barrier to involvement in COVID-19 response globally, and lack of funding was a barrier particularly in the WHO Africa region. Conclusion This study provides a snapshot of the multisectoral response to COVID-19 and an assessment of the contribution of OHNs. The lessons learned during this pandemic can be used to identify measures to improve global health capacity, including OHN activities to build and strengthen workforce response to future global health challenges. | Int J Infect Dis | 2022 | CORD-19 | |
| 5698 | Medical Students and Youth-Led Efforts against Infodemic Purpose The IFMSA, voicing the opinion of 1.3 million medical students from 131 countries, acknowledges the importance of health literacy in driving social change. Today, the Pandemic is accompanied by a global epidemic of misinformation, spreading rapidly through social media platforms and other outlets, posing a critical threat to public health due to the COVID-19 outbreak. As this problem continues to mount, it becomes even more evident that a unified approach is required to secure high levels of compliance with public health measures and combat the infodemic. Methods & Materials A global study was conducted by IFMSA, in collaboration with the WHO, composed of a survey to get data about all the organizations, institutions, NGOs, and other entities that focus on fact-checking and correcting misinformation about COVID-19. The survey was filled by medical students from the end of April to the end of May who reported name, type, the scope of work, languages, primary funding source, type, and source of information shared by the organization. Results We discovered 182 initiatives from 62 countries worldwide that verified information in 48 languages. Social media, the internet, radio, SMS, printed media, and hearsay were identified as the main sources of misinformation. Video podcasts with experts, regular social media updates and newsletters, were described as best practices, in addition to debunking myths on a regular basis and verifying statements by public figures. Also, the quality of fact-checking differed between initiatives. Conclusion Data showed that myths and false information are spreading through different means from public figures to daily social media outlets. Fighting misinformation should use innovative and accessible approaches, There is an urgent need for national initiatives and political engagement for myth-busting. IFMSA and WHO is following up by designing a platform to share fact-checking initiatives and recommendations openly, and by creating an AI system with Amazon to analyze articles in social media. Our surveys identified the need for fact-checking quality and quantity improvement and help provide an open-access source for worldwide and national fact-checking initiatives. | Int J Infect Dis | 2022 | CORD-19 | |
| 5699 | Investigating SARS-CoV-2 Test Positivity Calculations Across US Jurisdictions Purpose Throughout the COVID-19 pandemic, many US epidemiologists and policymakers turned to an indicator called test positivity, or the percent of tests coming back positive for SARS-CoV-2, to contextualize COVID-19 case counts with testing volume. But the nation's patchworked health data infrastructure, composed of 56 systems managed by each state and territory, complicated efforts to calculate the metric in a comparable way across US jurisdictions. We set out to map jurisdictional reporting differences in test positivity and investigate whether they interfered with its effectiveness and comparability as an indicator. Understanding these differences is important because jurisdictional test positivity informed consequential policy and individuals’ understanding of risk in their communities. Methods & Materials We surveyed the health department websites of all US states and territories to examine how these jurisdictions were presenting test positivity on COVID-19 dashboards. When details about definitions were unavailable on jurisdictional websites, we reached out to jurisdictional public health officials for clarification. We also scored jurisdictions' presentations against best practices we identified for calculating the metric. Results Among the 48 states and territories posting test positivity values, we observed no consensus on how to calculate the metric—jurisdictions used different units, test types, averaging techniques, and dating schemes. By looking at data for jurisdictions that posted multiple test positivity metrics, we observed that these definitional differences could result in variations from 31% to 300%. Only four states were following all ten of the best practices for reporting test positivity. Conclusion The sheer number of ways states and territories define test positivity is alarming, given how much the indicator influenced US COVID-19 policy. Based on our survey, we believe the confidence of regulators in the precision and national comparability of test positivity is misplaced: The metric's value reflects state and territorial reporting decisions as much as actual viral prevalence. These findings underscore the need to invest in centralized public health infrastructure and create national reporting standards to improve unity of state reporting. | Int J Infect Dis | 2022 | CORD-19 | |
| 5700 | SARS-CoV-2, Lung Protective Ventilation, Low Middle Income Countries and Pediatric Intensivists as Cross Disciplinary Knowledge Translation and Implementation Science Specialists Purpose We hypothesized that despite the low incidence of severe SARS-CoV-2 infections in children in Guyana, due to their specific skillset in lung protective ventilation, our Pediatric Intensivists were uniquely positioned to address significant training and readiness gaps in our colleagues attending a surging critically ill Adult COVID-19 patient population. Methods & Materials In Guyana, there are few clinicians trained in Critical-Care Medicine (CCM). The high incidence of ventilator dependence in seriously ill SARS-CoV2 patients, combined with a dearth of CCM practitioners competent in complex mechanical ventilation management left Guyana ill prepared to manage these patients. This knowledge deficit was further exacerbated in that many clinicians at our National Infectious Diseases Hospital were co-opted into CCM roles from other specialties with little to no CCM training. We have a very small core of Pediatric Surgical Critical Care Medicine staff that was formally trained in PCCM outside of Guyana. This core was instrumental in establishing a unique and formal Pediatric Critical-Care Medicine Micro-Modular Fellowship (PCCM-MMF) program that allowed the creation of Guyana's only Pediatric ICU. A significant number of that core are also involved in Guyana‘s National COVID Task Force. Given that all graduates of our PCCM-MMF program are extensively trained in Lung Protective Ventilation, it was very appropriate to utilize them to augment Adult critical care capacity. Thirty physicians with primarily adult practices and little to no previous knowledge of ventilator management were enrolled in a multi-modal triphasic mechanical ventilation short course facilitated by PCCM staff. Results We were able to rapidly enable two cohorts of 15 Adult clinicians to competently address critical knowledge deficits and staffing shortfalls. We improved morbidity and mortality amongst our mechanically ventilated adult COVID-19 patients, as well as relieved significant multifactorial caregiver strain. Conclusion Our successful utilization of PCCM staff as Mechanical Ventilation didactic and clinical educators for an Adult patient population carries implications for cross disciplinary Knowledge Translation and Implementation Science in a wide variety of practice milieus. We are actively pursuing research opportunities to further experiment with other skill sets incorporated in our PCCM Micro-Modular Fellowship and welcome potential collaborators. | Int J Infect Dis | 2022 | CORD-19 |
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