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This paper argues for the regular testing of people in groups that are more likely to be exposed to SARS-CoV-2, to reduce the spread of COVID-19 and resume economic activity. We call this 'stratified periodic testing'. It is 'stratified' as it is based on at-risk groups, and 'periodic' as everyone in the group is tested at regular intervals. We argue that this is a better use of scarce testing resources than 'universal random testing', as has been recently discussed globally. We find that, under reasonable assumptions and allowing for false negative results 30 per cent of the time, 17 per cent of a subgroup would need to be tested each day to lower the effective reproduction number R from 2.5 to 0.75, under stratified periodic testing. Using the same assumptions the universal random testing rate would need to be 27 per cent (as opposed to 7 per cent as argued by Romer (2020b)). We obtain this rate of testing using a corrected method for calculating the impact of an infectious person on others, and allowing for asymptomatic cases. We also find that the effect of one day's delay between testing positive and self-isolating is similar to having a test that is 30 per cent less accurate. [ABSTRACT FROM AUTHOR]

Massive-scale SARS-CoV-2 testing using the SwabSeq diagnostic platform came with quality assurance challenges due to the novelty and scale of sequencing-based testing. The SwabSeq platform relies on accurate mapping between specimen identifiers and molecular barcodes to match a result back to a patient specimen. To identify and mitigate mapping errors, we instituted quality control using placement of negative controls within a rack of patient samples. We designed 2-dimensional paper templates to fit over a 96-position rack of specimens with holes to show the control tube placements. We designed and 3-dimensionally printed plastic templates that fit onto 4 racks of patient specimens and provide accurate indications of the correct control tube placements. The final plastic templates dramatically reduced plate mapping errors from 22.55% in January 2021 to less than 1% after implementation and training in January 2021. We show how 3D printing can be a cost-effective quality assurance tool to mitigate human error in the clinical laboratory. [ABSTRACT FROM AUTHOR]

Background We aimed to review the evidence from studies relating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) culture with the results of reverse-transcription polymerase chain reaction (RT-PCR) and other variables that may influence the interpretation of the test, such as time from symptom onset. Methods We searched LitCovid, medRxiv, Google Scholar, and the World Health Organization coronavirus disease 2019 (COVID-19) database for COVID-19 up to 10 September 2020. We included studies attempting to culture or observe SARS-CoV-2 in specimens with RT-PCR positivity. Studies were dual-extracted and the data summarized narratively by specimen type. Where necessary, we contacted corresponding authors of included papers for additional information. We assessed quality using a modified Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2) risk-of-bias tool. Results We included 29 studies reporting attempts at culturing, or observing tissue infection by, SARS-CoV-2 in sputum, nasopharyngeal or oropharyngeal, urine, stool, blood, and environmental specimens. The quality of the studies was moderate with lack of standardized reporting. The data suggest a relationship between the time from onset of symptom to the timing of the specimen test, cycle threshold (Ct), and symptom severity. Twelve studies reported that Ct values were significantly lower and log copies higher in specimens producing live virus culture. Two studies reported that the odds of live virus culture were reduced by approximately 33% for every 1-unit increase in Ct. Six of 8 studies reported detectable RNA for >14 days, but infectious potential declined after day 8 even among cases with ongoing high viral loads. Four studies reported viral culture from stool specimens. Conclusions Complete live viruses are necessary for transmission, not the fragments identified by PCR. Prospective routine testing of reference and culture specimens and their relationship to symptoms, signs, and patient co-factors should be used to define the reliability of PCR for assessing infectious potential. Those with high Ct are unlikely to have infectious potential. [ABSTRACT FROM AUTHOR]

Background Although much of the public health effort to combat coronavirus disease 2019 (COVID-19) has focused on disease control strategies in public settings, transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within households remains an important problem. The nature and determinants of household transmission are poorly understood. Methods To address this gap, we gathered and analyzed data from 22 published and prepublished studies from 10 countries (20 291 household contacts) that were available through 2 September 2020. Our goal was to combine estimates of the SARS-CoV-2 household secondary attack rate (SAR) and to explore variation in estimates of the household SAR. Results The overall pooled random-effects estimate of the household SAR was 17.1% (95% confidence interval [CI], 13.7–21.2%). In study-level, random-effects meta-regressions stratified by testing frequency (1 test, 2 tests, >2 tests), SAR estimates were 9.2% (95% CI, 6.7–12.3%), 17.5% (95% CI, 13.9–21.8%), and 21.3% (95% CI, 13.8–31.3%), respectively. Household SARs tended to be higher among older adult contacts and among contacts of symptomatic cases. Conclusions These findings suggest that SARs reported using a single follow-up test may be underestimated, and that testing household contacts of COVID-19 cases on multiple occasions may increase the yield for identifying secondary cases. [ABSTRACT FROM AUTHOR]

: Biological, Clinical, and Technical Considerations These considerations are important when performing serology studies, with anti-S1/S2 serology tests preferably used to assess true seroprevalence; anti-RBD-specific serology immunoassays may be better suited to reflecting the presence of neutralizing antibodies. We read with interest the report by Geisler et al[1] and commend the authors for their efforts to address the important need to evaluate the clinical performance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic assays in pediatric populations, especially with respect to serology, given the noted differences in immune responses between children and adults.[2] We do feel, however, that the title of this paper may be misleading. This behavior would make it challenging to define whether anti-RBD antibodies are false negatives or if anti-S1 antibodies are false positives. [Extracted from the article]

Coronavirus disease 2019 (COVID-19) vaccines are highly efficacious at preventing symptomatic infection, severe disease, and death. Most of the evidence that COVID-19 vaccines also reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is based on retrospective, observational studies. Specifically, an increasing number of studies are evaluating vaccine effectiveness against the secondary attack rate of SARS-CoV-2 using data available in existing health-care databases or contact-tracing databases. Since these types of databases were designed for clinical diagnosis or management of COVID-19, they are limited in their ability to provide accurate information on infection, infection timing, and transmission events. We highlight challenges with using existing databases to identify transmission units and confirm potential SARS-CoV-2 transmission events. We discuss the impact of common diagnostic testing strategies, including event-prompted and infrequent testing, and illustrate their potential biases in estimating vaccine effectiveness against the secondary attack rate of SARS-CoV-2. We articulate the need for prospective observational studies of vaccine effectiveness against the SARS-CoV-2 secondary attack rate, and we provide design and reporting considerations for studies using retrospective databases. [ABSTRACT FROM AUTHOR]

Background Twice weekly lateral flow tests (LFTs) for secondary school children was UK Government policy from 8 March 2021. We evaluate use of LFTs (both supervised at test centres, and home test kits) in school-aged children in Cheshire and Merseyside. Methods We report (i) number of LFT positives (ii) proportion of LFT positive with confirmatory reverse transcription polymerase chain reaction (PCR) test within 2 days, and (iii) agreement between LFT-positive and confirmatory PCR, and dependence of (i–iii) on COVID-19 prevalence. Findings 1 248 468 LFTs were taken by 211 255 12–18 years old, and 163 914 by 52 116 5–11 years old between 6 November 2020 and 31 July 2021. Five thousand three hundred and fourteen (2.5%) 12–18 years old and 1996 (3.8%) 5–11 years old returned LFT positives, with 3829 (72.1%) and 1535 (76.9%) confirmatory PCRs, and 3357 (87.7%) and 1383 (90.1%) confirmatory PCR-positives, respectively. Monthly proportions of LFT positive with PCR negative varied between 4.7% and 35.3% in 12–18 years old (corresponding proportion of all tests positive: 9.7% and 0.3%). Deprivation and non-White ethnicity were associated with reduced uptake of confirmatory PCR. Interpretation Substantial inequalities in confirmatory testing need more attention to avoid further disadvantage through education loss. When prevalence is low additional measures, including confirmatory testing, are needed. Local Directors of Public Health taking more control over schools testing may be needed. Funding DHSC, MRC, NIHR, EPSRC. [ABSTRACT FROM AUTHOR]

Pooled testing has been successfully used to expand SARS-CoV-2 testing, especially in settings requiring high volumes of screening of lower-risk individuals, but efficiency of pooling declines as prevalence rises. We propose a differentiated pooling strategy that independently optimizes pool sizes for distinct groups with different probabilities of infection to further improve the efficiency of pooled testing. We compared the efficiency (results obtained per test kit used) of the differentiated strategy with a traditional pooling strategy in which all samples are processed using uniform pool sizes under a range of scenarios. For most scenarios, differentiated pooling is more efficient than traditional pooling. In scenarios examined here, an improvement in efficiency of up to 3.94 results per test kit could be obtained through differentiated versus traditional pooling, with more likely scenarios resulting in 0.12 to 0.61 additional results per kit. Under circumstances similar to those observed in a university setting, implementation of our strategy could result in an improvement in efficiency between 0.03 to 3.21 results per test kit. Our results can help identify settings, such as universities and workplaces, where differentiated pooling can conserve critical testing resources. [ABSTRACT FROM AUTHOR]

Background Identifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections during peripartum hospitalizations is important to guide care, implement prevention measures, and understand infection burden. Methods This cross-sectional analysis used electronic health record data from hospitalizations during which pregnancies ended (peripartum hospitalizations) among a cohort of pregnant persons at 3 US integrated healthcare networks (sites 1–3). Maternal demographic, medical encounter, SARS-CoV-2 testing, and pregnancy and neonatal outcome information was extracted for persons with estimated delivery and pregnancy end dates during March 2020–February 2021 and ≥1 antenatal care record. Site-stratified multivariable logistic regression was used to identify factors associated with testing and compare pregnancy and neonatal outcomes among persons tested. Results Among 17 858 pregnant persons, 10 863 (60.8%) had peripartum SARS-CoV-2 testing; 222/10 683 (2.0%) had positive results. Testing prevalence varied by site and was lower during March–May 2020. Factors associated with higher peripartum SARS-CoV-2 testing odds were Asian race (adjusted odds ratio [aOR]: 1.36; 95% confidence interval [CI]: 1.03–1.79; referent: White) (site 1), Hispanic or Latino ethnicity (aOR: 1.33; 95% CI: 1.08–1.64) (site 2), peripartum Medicaid coverage (aOR: 1.33; 95% CI: 1.06–1.66) (site 1), and preterm hospitalization (aOR: 1.69; 95% CI: 1.19–2.39 [site 1]; aOR: 1.39; 95% CI: 1.03–1.88 [site 2]). Conclusions Findings highlight potential disparities in SARS-CoV-2 peripartum testing by demographic and pregnancy characteristics. Testing practice variations should be considered when interpreting studies relying on convenience samples of pregnant persons testing positive for SARS-CoV-2. Efforts to address testing differences between groups could improve equitable testing practices and care for pregnant persons with SARS-CoV-2 infections. [ABSTRACT FROM AUTHOR]

Background The efficacy of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) convalescent plasma (CCP) for preventing infection in exposed, uninfected individuals is unknown. CCP might prevent infection when administered before symptoms or laboratory evidence of infection. Methods This double-blinded, phase 2 randomized, controlled trial (RCT) compared the efficacy and safety of prophylactic high titer (≥1:320 by Euroimmun ELISA) CCP with standard plasma. Asymptomatic participants aged ≥18 years with close contact exposure to a person with confirmed coronavirus disease 2019 (COVID-19) in the previous 120 hours and negative SARS-CoV-2 test within 24 hours before transfusion were eligible. The primary outcome was new SARS-CoV-2 infection. Results In total, 180 participants were enrolled; 87 were assigned to CCP and 93 to control plasma, and 170 transfused at 19 sites across the United States from June 2020 to March 2021. Two were excluded for screening SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) positivity. Of the remaining 168 participants, 12/81 (14.8%) CCP and 13/87 (14.9%) control recipients developed SARS-CoV-2 infection; 6 (7.4%) CCP and 7 (8%) control recipients developed COVID-19 (infection with symptoms). There were no COVID-19-related hospitalizations in CCP and 2 in control recipients. Efficacy by restricted mean infection free time (RMIFT) by 28 days for all SARS-CoV-2 infections (25.3 vs 25.2 days; P =.49) and COVID-19 (26.3 vs 25.9 days; P =.35) was similar for both groups. Conclusions Administration of high-titer CCP as post-exposure prophylaxis, although appearing safe, did not prevent SARS-CoV-2 infection. Clinical Trials Registration NCT04323800. [ABSTRACT FROM AUTHOR]

There is an ongoing debate on airborne transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a risk factor for infection. In this study, the level of SARS-CoV-2 in air and on surfaces of SARS-CoV-2 infected nursing home residents was assessed to gain insight in potential transmission routes. During outbreaks, air samples were collected using three different active and one passive air sampling technique in rooms of infected patients. Oropharyngeal swabs (OPS) of the residents and dry surface swabs were collected. Additionally, longitudinal passive air samples were collected during a period of 4 months in common areas of the wards. Presence of SARS-CoV-2 RNA was determined using RT-qPCR, targeting the RdRp- and E-genes. OPS, samples of two active air samplers and surface swabs with Ct-value ≤35 were tested for the presence of infectious virus by cell culture. In total, 360 air and 319 surface samples from patient rooms and common areas were collected. In rooms of 10 residents with detected SARS-CoV-2 RNA in OPS, SARS-CoV-2 RNA was detected in 93 of 184 collected environmental samples (50.5%) (lowest Ct 29.5), substantially more than in the rooms of residents with negative OPS on the day of environmental sampling (n = 2) (3.6%). SARS-CoV-2 RNA was most frequently present in the larger particle size fractions [>4 μm 60% (6/10); 1–4 μm 50% (5/10); <1 μm 20% (2/10)] (Fischer exact test P = 0.076). The highest proportion of RNA-positive air samples on room level was found with a filtration-based sampler 80% (8/10) and the cyclone-based sampler 70% (7/10), and impingement-based sampler 50% (5/10). SARS-CoV-2 RNA was detected in 10 out of 12 (83%) passive air samples in patient rooms. Both high-touch and low-touch surfaces contained SARS-CoV-2 genome in rooms of residents with positive OPS [high 38% (21/55); low 50% (22/44)]. In one active air sample, infectious virus in vitro was detected. In conclusion, SARS-CoV-2 is frequently detected in air and on surfaces in the immediate surroundings of room-isolated COVID-19 patients, providing evidence of environmental contamination. The environmental contamination of SARS-CoV-2 and infectious aerosols confirm the potential for transmission via air up to several meters. [ABSTRACT FROM AUTHOR]

The article explores rapid identification of infected individuals in the early stages of an outbreak in order to isolate and prevent further transmission is of utmost importance. Public health responses utilized to accomplish this goal include identification and isolation of infected individuals based on symptom presentation then monitoring of contacts for symptoms before proceeding with further isolation.

Background: COVID-19 is a highly contagious respiratory disease that can be transmitted through human exhaled breath. It has caused immense loss and has challenged the healthcare sector. It has affected the economy of countries and thereby affected numerous sectors. Analysis of human breath samples is an attractive strategy for rapid diagnosis of COVID-19 by monitoring breath biomarkers. Content: Breath collection is a noninvasive process. Various technologies are employed for detection of breath biomarkers like mass spectrometry, biosensors, artificial learning, and machine learning. These tools have low turnaround time, robustness, and provide onsite results. Also, MS-based approaches are promising tools with high speed, specificity, sensitivity, reproducibility, and broader coverage, as well as its coupling with various chromatographic separation techniques providing better clinical and biochemical understanding of COVID-19 using breath samples. Summary: Herein, we have tried to review the MS-based approaches as well as other techniques used for the analysis of breath samples for COVID-19 diagnosis. We have also highlighted the different breath analyzers being developed for COVID-19 detection. [ABSTRACT FROM AUTHOR]

Background: The epidemiology and clinical manifestation of coronavirus disease 2019 (COVID-19) in the pediatric population is different from the adult population. The purpose of this study is to identify effects of the COVID-19 pandemic on laboratory test utilization in a pediatric hospital. Methods: We performed retrospective analysis on test utilization data from Ann & Robert H. Lurie Children's Hospital of Chicago, an academic pediatric medical center. Data between two 100-day periods prior to (prepandemic) and during the pandemic (mid-pandemic) were analyzed to evaluate changes in test volume, lab utilization, and test positivity rate. We also evaluated these metrics based on in- vs outpatient testing and performed modeling to determine what variables significantly impact the test positivity rate. Results: During the pandemic period, there was an expected surge in COVID-19 testing, while over 84% of lab tests studied decreased in ordering volume. The average number of tests ordered per patient was not significantly different during the pandemic for any of the laboratories (adjusted P value > 0.05). Thirty-three studied tests showed significant change in positivity rate during the pandemic. Linear modeling revealed test volume and inpatient status as the key variables associated with change in test positivity rate. Conclusions: Excluding severe acute respiratory syndrome coronavirus 2 tests, the COVID-19 pandemic has generally led to decreased test ordering volume and laboratory utilization. However, at this pediatric hospital, the average number of tests performed per patient and test positivity rates were comparable between pre- and mid-pandemic periods. These results suggest that, overall, clinical test utilization at this site remained consistent during the pandemic. [ABSTRACT FROM AUTHOR]

Background: Currently, the rapid antigen test (RAT) and reverse transcriptase–polymerase chain reaction (RT–PCR) are considered the main stakeholders in COVID-19 diagnosis. In RT–PCR, any of at least 2 evolutionary conserved genes (RdRP, E-, N-, ORF1ab gene) and S-gene of SARS-CoV-2 are endorsed, and in RAT, the nucleocapsid antigen (N-Ag) of SARS-CoV-2 is considered due to its stability and fewer chances of mutation effects. In the present work, we evaluated the performance of the AG-Q COVID-19 N-Ag self-test kit and conducted a validation study in comparison with the RT–PCR. Methods: AG-Q COVID-19 N-Ag rapid test kit is an Indian Council of Medical Research (ICMR) approved product developed and marketed by Agappe Diagnostics Limited. The RT–PCR assay was performed with a COVIPATH COVID-19 RT–PCR kit from Thermo Fisher Scientific. Results: We observed 19 false-negative results in antigen self-tests, including samples of threshold cycle (Ct) values 22/22 (N-gene/ORF1ab-gene) in RT–PCR, indicating inadequate sampling by the patients in self-tests, leading to false-negative results and increased chances of the disease spreading. Based on the RT–PCR Ct value vs antigen self-test comparison, it is evident that proper sampling is crucial in performing antigen self-tests. Also, there were weak positive results in antigen self-tests with a Ct value of 18/19 in RT–PCR. Conclusions: Although the sensitivity and diagnostic accuracy offered by the AG-Q COVID-19 N-Antigen self-test in comparison with RT–PCR fulfills the ICMR tenets for RAT, this study recommends the laboratory/hospital-based RAT execution would be appropriate, rather than the self-test. [ABSTRACT FROM AUTHOR]

Background: Point-of-care SARS-CoV-2 antigen tests have great potential to help combat the COVID-19 pandemic. In the performance of a rapid, antigen-based SARS-CoV-2 test (RAT), our study had 3 main objectives: to determine the accuracy of nasal swabs, the accuracy of using nasopharyngeal swabs for nasal collection (nasalNP), and the effectiveness of using residual extraction buffer for real-time reverse-transcriptase PCR (RT–PCR) confirmation of positive RAT (rPan). Methods: Symptomatic adults recently diagnosed with COVID-19 in the community were recruited into the study. Nasal samples were collected using either a nasalNP or nasal swab and tested immediately with the RAT in the individual's home by a health care provider. 500 µL of universal transport media was added to the residual extraction buffer after testing and sent to the laboratory for SARS-CoV-2 testing using RT–PCR. Parallel throat swabs tested with RT–PCR were used as the reference comparators. Results: One hundred and fifty-five individuals were included in the study (99 nasal swabs, 56 nasalNP). Sensitivities of nasal samples tested on the RAT using either nasal or nasalNP were 89.0% [95% confidence interval (CI) 80.7%–94.6%] and 90.2% (95% CI 78.6%–96.7%), respectively. rPan positivity agreement compared to throat RT–PCR was 96.2%. Conclusions: RAT reliably detect SARS-CoV-2 from symptomatic adults in the community presenting within 7 days of symptom onset using nasal swabs or nasalNP. High agreement with rPan can avoid the need for collecting a second swab for RT–PCR confirmation or testing of variants of concern from positive RAT in this population. [ABSTRACT FROM AUTHOR]

Background: Serological assays for SARS-CoV-2 are important tools for diagnosis in patients with negative RT-PCR testing, pediatric patients with multisystem inflammatory syndrome, and serosurveillance studies. However, lateral flow-based serological assays have previously demonstrated poor analytical and clinical performance, limiting their utility. Methods: We assessed the ADEXUSDx COVID-19 lateral flow assay for agreement with diagnostic RT-PCR testing using 120 specimens from RT-PCR–positive patients, 77 specimens from symptomatic RT-PCR–negative patients, and 47 specimens obtained prepandemic. Specimens collected <14 days from symptom onset in RT-PCR–positive patients were compared relative to the Abbott SARS-CoV-2 IgG assay. Results: The ADEXUSDx COVID-19 Test yielded an overall positive percent agreement (PPA) of 92.5% (95%CI 85.8 to 96.3) and negative percent agreement of 99.2% (95% CI 94.9–100.0) relative to RT-PCR and in prepandemic specimens. Relative to days from symptom onset, the PPA after 13 days was 100% (95% CI 94.2–100); from 7 to 13 days, 89.7 (95% CI 71.5–97.2); and from 0 to 7 days, 53.8 (95% CI 26.1–79.6). The overall agreement between the Abbott and ADEXUSDx assays was 80.9%. Twenty-five specimens were positive by both assays, 9 specimens were negative by both assays, and 8 specimens were positive by only the ADEXUSDx assay. Conclusions: We demonstrate high PPA and negative percent agreement of the ADEXUSDx COVID-19 assay and diagnostic testing by RT-PCR, with PPA approximately 90% by 7 days following symptom onset. The use of waived testing for antibodies to SARS-CoV-2 with high sensitivity and specificity provide a further tool for combatting the COVID-19 pandemic. [ABSTRACT FROM AUTHOR]

We propose a realistic model for the evolution of the COVID-19 pandemic subject to the lockdown and quarantine measures, which takes into account the timedelay for recovery or death processes. The dynamic equations for the entire process are derived by adopting a kinetic-type reactions approach. More specifically, the lockdown and the quarantine measures are modelled by some kind of inhibitor reactions where susceptible and infected individuals can be trapped into inactive states. The dynamics for the recovered people is obtained by accounting people who are only traced back to hospitalized infected people. To get the evolution equation we take inspiration from the Michaelis Menten's enzyme-substrate reaction model (the so-called MM reaction) where the enzyme is associated to the available hospital beds , the substrate to the infected people , and the product to the recovered people , respectively. In other words, everything happens as if the hospitals beds act as a catalyzer in the hospital recovery process. Of course, in our case, the reverse MM reaction has no sense in our case and, consequently, the kinetic constant is equal to zero. Finally, the ordinary differential equations (ODEs) for people tested positive to COVID-19 is simply modelled by the following kinetic scheme |$S+I\Rightarrow 2I$| with |$I\Rightarrow R$| or |$I\Rightarrow D$|⁠ , with |$S$|⁠ , |$I$|⁠ , |$R$| and |$D$| denoting the compartments susceptible, infected, recovered and deceased people, respectively. The resulting kinetic-type equations provide the ODEs, for elementary reaction steps , describing the number of the infected people, the total number of the recovered people previously hospitalized, subject to the lockdown and the quarantine measure and the total number of deaths. The model foresees also the second wave of infection by coronavirus. The tests carried out on real data for Belgium, France and Germany confirmed the correctness of our model. [ABSTRACT FROM AUTHOR]

Background The spread of severe acute respiratory coronavirus 2 (SARS-CoV-2) among active workers is poor known. The aim of our study was to evaluate the seroprevalence of immunoglobulin G (IgG) among a convenience sample of workers and to identify high-risk job sectors during the first pandemic way. Methods We conducted a cross-sectional study among workers tested for SARS-CoV-2 between 28 March and 7 August 2020, recorded by a private healthcare center located in North-West Italy. Association among seroprevalence and demographic and occupational variables was evaluated using chi square test and the seroprevalence and 95% confidence intervals (CI) were calculated. Results We collected the results for 23568 serological tests from a sample of 22708 workers from about 1000 companies. Median age was 45 years and about 60% of subjects were male. The overall seroprevalence was 4.97% [95%CI 4.69–5.25]. No statistical difference was found among gender while seroprevalence was associated with subjects' age, geographical location, and occupational sector. Significantly higher values of positivity were observed for the logistics sector (31.3%), weaving factory (12.6%), nursing homes (9.8%), and chemical industry (6.9%) workers. However, we observed some clusters of cases in single companies independently from the sector. Then, a detailed focus on 940 food workers shown a seroprevalence of 5.21% [95%CI 3.79–6.63] and subjects who self-reported COVID-19 symptoms and who worked during lockdown had a higher probability of being infected (p < 0.001). Conclusions Data obtained might be useful for future public health decision; more than occupation sector, it seems that failure on prevention system in single companies increase the SARS-CoV-2 transmission. [ABSTRACT FROM AUTHOR]

The epidemiology of coronavirus disease 2019 in children has been challenging to establish, owing to the high prevalence of asymptomatic infection in this population. Lower secondary attack rates in children compared with adults have been observed in household contact studies, but there is evidence that this may reflect lower testing in children and reduced exposure, rather than a genuine difference in biological susceptibility. In addition, children may shed infectious virus for a shorter period than adults and their antibody response may be less broad, with implications for both polymerase chain reaction and serological testing. Improvements in study design, data collection, and data interpretation are required to better understand the epidemiology of coronavirus disease 2019 in children. [ABSTRACT FROM AUTHOR]

Background Performance characteristics of SARS-CoV-2 antigen tests among children are limited despite the need for point-of-care testing in school and childcare settings. We describe children seeking SARS-CoV-2 testing at a community site and compare antigen test performance to real-time reverse transcription-polymerase chain reaction (RT-PCR) and viral culture. Methods Two anterior nasal specimens were self-collected for BinaxNOW antigen and RT-PCR testing, along with demographics, symptoms, and exposure information from individuals ≥5 years at a community testing site. Viral culture was attempted on residual antigen or RT-PCR-positive specimens. Demographic and clinical characteristics, and the performance of SARS-CoV-2 antigen tests, were compared among children (<18 years) and adults. Results About 1 in 10 included specimens were from children (225/2110); 16.4% (37/225) were RT-PCR-positive. Cycle threshold values were similar among RT-PCR-positive specimens from children and adults (22.5 vs 21.3, P =.46) and among specimens from symptomatic and asymptomatic children (22.5 vs 23.2, P =.39). Sensitivity of antigen test compared to RT-PCR was 73.0% (27/37) among specimens from children and 80.8% (240/297) among specimens from adults; among specimens from children, specificity was 100% (188/188), positive and negative predictive values were 100% (27/27) and 94.9% (188/198), respectively. Virus was isolated from 51.4% (19/37) of RT-PCR-positive pediatric specimens; all 19 had positive antigen test results. Conclusions With lower sensitivity relative to RT-PCR, antigen tests may not diagnose all positive COVID-19 cases; however, antigen testing identified children with live SARS-CoV-2 virus. [ABSTRACT FROM AUTHOR]

Introduction Care homes have been severely affected by the SARS-CoV-2 pandemic. Rapid antigen testing could identify most SARS-CoV-2 infected staff and visitors before they enter homes. We explored implementation of staff and visitor testing protocols using lateral flow devices (LFDs). Methods An evaluation of a SARS-CoV-2 LFD-based testing protocol in 11 care homes in Liverpool, UK, including staff and visitor testing, plus a qualitative exploratory study in nine of these homes. The proportion of pilot homes with outbreaks, and outbreak size, were compared to non-pilot homes in Liverpool. Adherence to testing protocols was evaluated. Fifteen staff were interviewed, and transcript data were thematically coded using an iterative analysis to identify and categorize factors influencing testing implementation. Results In total, 1,638 LFD rapid tests were performed on 407 staff. Protocol adherence was poor with 8.6% of staff achieving >75% protocol adherence, and 25.3% achieving |$\ge$| 50%. Six care homes had outbreaks during the study. Compared to non-pilot care homes, there was no evidence of significant difference in the proportion of homes with outbreaks, or the size of outbreaks. Qualitative data showed difficulty implementing testing strategies due to excessive work burden. Factors influencing adherence related to test integration and procedural factors, socio-economic factors, cognitive overload and the emotional value of testing. Conclusion Implementation of staff and visitor care home LFD testing protocols was poorly adhered to and consequently did not reduce the number or scale of COVID-19 outbreaks. More focus is needed on the contextual and behavioural factors that influence protocol adherence. [ABSTRACT FROM AUTHOR]

Introduction Previous investigations have identified high rates of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among residents and staff in care homes reporting an outbreak of coronavirus disease 2019 (COVID-19). We investigated care homes reporting a single suspected or confirmed case to assess whether early mass testing might reduce risk of transmission during the peak of the pandemic in London. Methods Between 18 and 27 April 2020, residents and staff in care homes reporting a single case of COVID-19 to Public Health England had a nasal swab to test for SARS-CoV-2 infection by reverse transcription polymerase chain reaction and subsequent whole-genome sequencing. Residents and staff in two care homes were re-tested 8 days later. Results Four care homes were investigated. SARS-CoV-2 positivity was 20% (65/333) overall, ranging between 3 and 59%. Among residents, positivity ranged between 3 and 76% compared with 3 and 40% in staff. Half of the SARS-CoV-2-positive residents (23/46, 50%) and 63% of staff (12/19) reported symptoms within 14 days before or after testing. Repeat testing 8 days later in two care homes with the highest infection rates identified only two new cases. Genomic analysis demonstrated a small number of introduction of the virus into care homes, and distinct clusters within three of the care homes. Conclusions We found extensive but variable rates of SARS-CoV-2 infection among residents and staff in care homes reporting a single case of COVID-19. Although routine whole-home testing has now been adopted into practice, care homes must remain vigilant and should be encouraged to report a single suspected case, which should trigger appropriate outbreak control measures. [ABSTRACT FROM AUTHOR]

Background: In the absence of a safe, effective vaccine, the worldwide spread of COVID-19 (SARS-CoV-2) infection will continue. Laboratory tests with ideal precision, sensitivity, and specificity should be used in public health and clinical settings to gauge the extent of virus exposure. Toward this end, we evaluated the analytical and clinical performance of the Abbott SARS-CoV-2 IgG and the Roche Anti-SARS-CoV-2 immunoassays. Methods: Quality control, pooled COVID-19, and non-COVID-19 patient specimens were used for the imprecision study. Two hundred and forty-six specimens from 70 patients with COVID-19 diagnosis were tested to study the sensitivity. Seventy-three non-COVID-19 control specimens were measured to study the specificity. All specimens were analyzed by both assays. Results: Total analytic variability (CV) of the negative and positive controls were 5.5% and 3.6% for the Abbott assay and 4.5% and 1.9% for the Roche assay. Both assays demonstrated 100% qualitative reproducibility of negative and positive controls. The clinical specificities of the Abbott and the Roche assays were 100% (95% CI: 94%—100%) and 97% (95% CI: 90%—100%), respectively. The clinical sensitivities of the Abbott assay were 49% (95% CI: 41%—56%), 86% (95% CI: 74%—93%), and 100% (95% CI: 76%—100%) for samples collected at 0–6 days, 7–13 days, and ≥14 days after the first RT-PCR, while the sensitivities of the Roche assay were 55% (95% CI: 47%—62%), 86% (95% CI: 74%—93%), and 100% (95% CI: 76%—100%). Conclusions: This study demonstrates similar analytical and clinical performance of the Abbott and the Roche SARS-CoV-2 antibody assays, but the Roche assay may be slightly more sensitive for patients tested within 0–6 days after first positive RT-PCR of SARS-CoV-2. COVID-19 is a respiratory infectious disease caused by SARS-CoV-2. Laboratory tests with ideal precision, sensitivity, and specificity should be used in public health and clinical settings. We analyzed analytical and clinical performance of the Roche and Abbott SARS-CoV-2 antibody assays in pre-pandemic and pandemic patient populations. Additionally, we analyzed the sensitivity of both assays in patients at different stages of the disease. The 2 assays showed similar analytical and clinical performance, but the Roche assay may be slightly more sensitive for patients tested within 0–6 days after first positive RT-PCR of SARS-CoV-2. Our findings help other clinical labs select appropriate assays for SARS-CoV-2 antibody testing. [ABSTRACT FROM AUTHOR]

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel member of the coronavirus family that caused the global coronavirus 2019 (COVID-19) pandemic. The prevalence remains largely unknown because of early testing supply shortages. Although it cannot currently be used to determine level of immunity, antibody testing can contribute to epidemiological studies, identify convalescent plasma donors, or satisfy curiosity about previous exposure to the virus. Methods: 407 samples collected from hospitalized inpatients with and without a confirmed SARS-CoV-2 infection, 170 remnant clinical specimens collected and frozen prior to the COVID-19 outbreak, and paired serum and plasma samples from 23 convalescent plasma donors were used to determine performance characteristics of the Abbott SARS-CoV-2 IgG and Roche Elecsys Anti–SARS-CoV-2 assays. The sensitivity, specificity, imprecision, interferences, and sample stability were determined. These assays were then used to characterize the antibody response in serial samples from 20 SARS-CoV-2 positive inpatients. Results: Both assays exhibited 100% specificity (95% CI; 99.05–100.00), giving no positive results in 170 specimens collected before July 2019 and 215 specimens from patients without a confirmed SARS-CoV-2 infection. Differences between platforms were most notable in SARS-CoV-2 positive samples. Roche offered higher sensitivity in convalescent plasma donors at 95.7% (95% CI; 78.1–99.9) versus 91.3% (95% CI; 72.0–98.9) but Abbott detected antibodies in 2 immunocompromised patients whereas Roche did not. The Roche and Abbott platforms also exhibited different trends in antibody signal for a subset of patients. Conclusions: Both the Abbott and Roche platforms offer excellent specificity but different trends in antibody signal may reflect qualitative differences in the types of antibodies recognized by the 2 assays. Negative serologic results do not exclude previous SARS-CoV-2 infection. [ABSTRACT FROM AUTHOR]

Motivation The outbreak of novel severe acute respiratory syndrome coronavirus (SARS-CoV-2, also known as COVID-19) in Wuhan has attracted worldwide attention. SARS-CoV-2 causes severe inflammation, which can be fatal. Consequently, there has been a massive and rapid growth in research aimed at throwing light on the mechanisms of infection and the progression of the disease. With regard to this data science is playing a pivotal role in in silico analysis to gain insights into SARS-CoV-2 and the outbreak of COVID-19 in order to forecast, diagnose and come up with a drug to tackle the virus. The availability of large multiomics, radiological, bio-molecular and medical datasets requires the development of novel exploratory and predictive models, or the customisation of existing ones in order to fit the current problem. The high number of approaches generates the need for surveys to guide data scientists and medical practitioners in selecting the right tools to manage their clinical data. Results Focusing on data science methodologies, we conduct a detailed study on the state-of-the-art of works tackling the current pandemic scenario. We consider various current COVID-19 data analytic domains such as phylogenetic analysis, SARS-CoV-2 genome identification, protein structure prediction, host–viral protein interactomics, clinical imaging, epidemiological research and drug discovery. We highlight data types and instances, their generation pipelines and the data science models currently in use. The current study should give a detailed sketch of the road map towards handling COVID-19 like situations by leveraging data science experts in choosing the right tools. We also summarise our review focusing on prime challenges and possible future research directions. Contact hguzzi@unicz.it , sroy01@cus.ac.in [ABSTRACT FROM AUTHOR]

Background It is recognized that healthcare workers (HCWs) are at high risk of contracting Covid-19. It is incumbent on occupational health staff to recognize potential symptoms of Covid-19 among HCWs. Aims The aims of the study were to describe the presenting symptoms of HCWs who developed Covid-19 in Ireland, and to estimate the odds of specific symptoms being associated with a positive Covid-19 polymerase chain reaction (PCR) result. Methods A retrospective chart review of all symptomatic HCWs who self-presented for Covid-19 testing in Cork from March to May 2020 was conducted. A sex-matched case–control study was carried out to compare presenting features among those who tested positive compared to those who tested negative. Univariate and multivariable-adjusted conditional logistic regression models were run using Stata 15.0 to identify the symptoms associated with positive Covid-19 swab results. Results Three hundred and six HCWs were included in the study; 102 cases and 204 controls. Common presenting features among cases were fever/chills (55%), cough (44%) and headache (35%). The symptoms which were significantly associated with a positive Covid-19 swab result were loss of taste/smell (adjusted odds ratio [aOR] 12.15, 95% confidence interval [CI] 1.36–108.79), myalgia (aOR 2.36, 95% 1.27–4.38), fatigue (aOR 2.31, 95% CI 1.12–4.74), headache (aOR 2.11, 95% CI 1.19–3.74) and fever/chills (aOR 1.88, 95% CI 1.12–3.15). Conclusions Fever, fatigue, myalgia, loss of taste/smell and headache were associated with increased odds of a Covid-19 diagnosis among symptomatic self-referred HCWs compared with those had negative swab results. Testing criteria for HCWs should reflect the broad range of possible symptoms of Covid-19. [ABSTRACT FROM AUTHOR]

The current severe acute respiratory syndrome coronavirus 2 testing policy and practice limits testing as a prevention tool. Radical shifts are required to increase the scale of rapid testing strategies and improve dissemination and implementation of venue-based and self-testing approaches. Attention to the full translation pipeline is required to reach high-risk segments of the population. [ABSTRACT FROM AUTHOR]

To combat the enduring and dangerous spread of COVID-19, many innovations to rapid diagnostics have been developed based on proteinprotein interactions of the SARS-CoV-2 spike and nucleocapsid proteins to increase testing accessibility. These antigen tests have most prominently been developed using the lateral flow assay (LFA) test platform which has the benefit of administration at point-of-care, delivering quick results, lower cost, and does not require skilled personnel. However, they have gained criticism for an inferior sensitivity. In the last year, much attention has been given to creating a rapid LFA test for detection of COVID-19 antigens that can address its high limit of detection while retaining the advantages of rapid antibodyantigen interaction. In this review, a summary of these proteinprotein interactions as well as the challenges, benefits, and recent improvements to protein based LFA for detection of COVID-19 are discussed. [ABSTRACT FROM AUTHOR]

Background Internationally, key workers such as healthcare staff are advised to stay at home if they or household members experience coronavirus disease 2019 (COVID-19)–like symptoms. This potentially isolates/quarantines many staff without SARS-CoV-2, while not preventing transmission from staff with asymptomatic infection. We explored the impact of testing staff on absence durations from work and transmission risks to others. Methods We used a decision-analytic model for 1000 key workers to compare the baseline strategy of (S0) no RT-PCR testing of workers to testing workers (S1) with COVID-19–like symptoms in isolation, (S2) without COVID-19–like symptoms but in household quarantine, and (S3) all staff. We explored confirmatory re-testing scenarios of repeating all initial tests, initially positive tests, initially negative tests, or no re-testing. We varied all parameters, including the infection rate (0.1–20%), proportion asymptomatic (10–80%), sensitivity (60–95%), and specificity (90–100%). Results Testing all staff (S3) changes the risk of workplace transmission by −56.9 to +1.0 workers/1000 tests (with reductions throughout at RT-PCR sensitivity ≥65%), and absences by −0.5 to +3.6 days/test but at heightened testing needs of 989.6–1995.9 tests/1000 workers. Testing workers in household quarantine (S2) reduces absences the most by 3.0–6.9 days/test (at 47.0–210.4 tests/1000 workers), while increasing risk of workplace transmission by 0.02–49.5 infected workers/1000 tests (which can be minimized when re-testing initially negative tests). Conclusions Based on optimizing absence durations or transmission risk, our modeling suggests testing staff in household quarantine or all staff, depending on infection levels and testing capacities. [ABSTRACT FROM AUTHOR]

Background: Coronavirus disease 2019 (COVID-19) was formally characterized as a pandemic on March 11, 2020. Since that time, the COVID-19 pandemic has led to unprecedented demand for healthcare resources. The purpose of this study was to identify changes in laboratory test utilization in the setting of increasing local incidence of COVID-19. Methods: We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. Data were extracted from the laboratory information system database over a 10-week period, spanning the primordial inflection of COVID-19 incidence in our region. Total testing volumes were calculated during the first 2 and last 2 weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the prepandemic and COVID-19 surge periods. Results: Between February 2, 2020, and April 11, 2020, there were 873 397 tests ordered and final verified. The in-house SARS-CoV-2 PCR positivity rate for admitted patients in the last week of the observation period was 30.8%. Significant increases in workload were observed in the send-out laboratory section and for COVID-19 diagnosis (PCR) and management-related testing. Otherwise, there was a net decrease in overall demand across nearly all laboratory sections. Increases in testing were noted for tests related to COVID-19 management. Viral transport media and citrated blue top containers demonstrated increases in utilization. Conclusion: Increasing local incidence of COVID-19 had a profound impact on laboratory operations. While volume increases were seen for laboratory tests related to COVID-19 diagnostics and management, including some with limited evidence to support their use, overall testing volumes decreased substantially. During events such as COVID-19, monitoring of such patterns can help inform laboratory management, staffing, and test stewardship recommendations for managing resource and supply availability. [ABSTRACT FROM AUTHOR]

Motivation The COVID-19 pandemic has prompted an impressive, worldwide response by the academic community. In order to support text mining approaches as well as data description, linking and harmonization in the context of COVID-19, we have developed an ontology representing major novel coronavirus (SARS-CoV-2) entities. The ontology has a strong scope on chemical entities suited for drug repurposing, as this is a major target of ongoing COVID-19 therapeutic development. Results The ontology comprises 2270 classes of concepts and 38 987 axioms (2622 logical axioms and 2434 declaration axioms). It depicts the roles of molecular and cellular entities in virus-host interactions and in the virus life cycle, as well as a wide spectrum of medical and epidemiological concepts linked to COVID-19. The performance of the ontology has been tested on Medline and the COVID-19 corpus provided by the Allen Institute. Availabilityand implementation COVID-19 Ontology is released under a Creative Commons 4.0 License and shared via https://github.com/covid-19-ontology/covid-19. The ontology is also deposited in BioPortal at https://bioportal.bioontology.org/ontologies/COVID-19. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

The article offers information on reverse-transcription polymerase chain reaction (RT-PCR) as test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It mentions use of diagnostics tests could cause patient harm from unneeded interventions and is a major driver of increased healthcare costs.

A case study of 78-year-old man with a history of Type 2 diabetes mellitus, diabetic nephropathy on hemodialysis, chronic obstructive pulmonary disease (COPD), mixed central and obstructive sleep apnea, ischemic heart disease, is presented. Topics include Genomes were assembled with reference based assembly and a bioinformatics pipeline; and region of the genome and 50% cut-off for defining single nucleotide polymorphisms (SNPs).

The authors discuss a study by J. Pouline and colleagues on SARS-CoV-2 screening at hospital admission in children. Topics discussed include one of the most important lessons of the COVID-19 pandemic, percentage of the children who tested positive in the study that were asymptomatic at hospital admission, and the importance of prioritizing the safety of healthcare personnel (HCP) and other patients.