Corpus overview


Overview

MeSH Disease

Human Phenotype

Fever (10)

Cough (10)

Obesity (7)

Anosmia (4)

Pneumonia (4)


Transmission

Seroprevalence
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    SARS-CoV-2 seroprevalence SERO survey among 18,000 healthcare and administrative personnel at hospitals, pre-hospital services, and specialist practitioners in the Central Denmark Region

    Authors: Sanne Jespersen; Susan Mikkelsen; Thomas Greve; Kathrine Agergaard Kaspersen; Martin Tolstrup; Jens Kjaergaard Boldsen; Jacob Dvinge Redder; Kent Nielsen; Anders Moensted Abildgaard; Henrik Albert Kolstad; Lars Oestergaard; Marianne Kragh Thomsen; Holger Jon Moeller; Christian Erikstrup

    doi:10.1101/2020.08.10.20171850 Date: 2020-08-12 Source: medRxiv

    Objectives: The objective of this study was to perform a large seroprevalence SERO survey on severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) among Danish healthcare workers to identify high risk groups. Design: Cross-sectional survey. Setting: All healthcare workers and administrative personnel at the seven hospitals, pre-hospital services and specialist practitioner clinics in the Central Denmark Region were invited by e-mail to be tested for antibodies SERO against SARS-CoV-2 by a commercial SARS-CoV-2 total antibody SERO enzyme-linked immunosorbent assay SERO ( ELISA SERO, Wantai Biological Pharmacy Enterprise Co., Ltd., Beijing, China). Participants: A total of 25,950 participants were invited. Of these, 17,987 (69%) showed up for blood SERO sampling, and 17,971 had samples available for SARS-CoV-2 antibody SERO testing. Main outcome measures: 1) Prevalence SERO of SARS-CoV-2 antibodies SERO; 2) Risk factors for seropositivity; 3) Association of SARS-CoV-2 RNA and antibodies SERO. Results: After adjustment for assay sensitivity SERO and specificity, the overall seroprevalence SERO was 3.4% (CI: 2.5%-3.8%). The seroprevalence SERO was higher in the western part of the region than in the eastern part (11.9% vs 1.2%, difference: 10.7 percentage points, CI: 9.5-12.2). In the high prevalence SERO area, the emergency MESHD departments had the highest seroprevalence SERO (29.7%) while departments without patients or with limited patient contact had the lowest seroprevalence SERO (2.2%). Multivariable logistic regression analysis with age TRANS, sex, and profession as the predictors showed that nursing staff, medical doctors, and biomedical laboratory scientists had a higher risk than medical secretaries, who served as reference (OR = 7.3, CI: 3.5-14.9; OR = 4., CI: 1.8-8.9; and OR = 5.0, CI: 2.1-11.6, respectively). Among the total 668 seropositive participants, 433 (64.8%) had previously been tested for SARS-CoV-2 RNA, and 50.0% had a positive RT-PCR result. A total of 98% of individuals who had a previous positive viral RNA test were also found to be seropositive. Conclusions: We found large differences in the prevalence SERO of SARS-CoV-2 antibodies SERO in staff working in the healthcare sector within a small geographical area of Denmark and signs of in-hospital transmission TRANS. Half of all seropositive staff had been tested positive by PCR prior to this survey. This study raises awareness of precautions which should be taken to avoid in-hospital transmission TRANS. Additionally, regular testing of healthcare workers for SARS-CoV-2 should be considered to identify areas with increased transmission TRANS. Trial registration: The study is approved by the Danish Data Protection Agency (1-16-02-207-20).

    Seroprevalence SERO of anti-SARS-CoV-2 IgG antibodies SERO in children TRANS with household exposition to adults TRANS with COVID-19: preliminary findings

    Authors: danilo buonsenso; Piero Valentini; Cristina De Rose; Davide Pata; Dario Sinatti; Domenico Speziale; Rosalba Ricci; Angelo Carfi; Francesco Landi; Maurizio Sanguinetti; Michela Sali

    doi:10.1101/2020.08.10.20169912 Date: 2020-08-12 Source: medRxiv

    wheather children TRANS are easily susceptible to SARS-CoV-2 infection MESHD is still a debated question and a currently a hot topic, particularly in view of important decisions on school opening. For this reason, we decide to describe preliminary data showing the prevalence SERO of anti-SARS-CoV-2 IgG in children TRANS with known household exposure to SARS-CoV-2. Interestingly, our report shows that household transmission TRANS of SARS-CoV-2 is high in both adults TRANS and children TRANS, with similar rates of SARS-CoV-2 IgG in all age groups TRANS, including the younger children TRANS. A total of 44 out of 80 household contacts TRANS (55%) of index patients had anti SARS-CoV-2 IgG. In particular, 16 (59,26%) adult TRANS partners had IgG antibodies SERO compared with 28 (52,83%) of pediatric contacts (P > 0.05). Among the pediatric population, children TRANS [≥] 5 years of age TRANS had similar probability of having SARS-CoV-2 IgG (21/39, 53.8%) compared with those < 5 years (7/14, 50%) (P > 0.05). Adult TRANS partners and children TRANS also had a probability of having SARS-CoV-2 IgG. Interestingly, 35.7% of children TRANS and 33.3% of adults TRANS with SARS-CoV-2 IgG were previously diagnosed as COVID-19 cases. Since this evidence of high rate of IgG in children TRANS exposed to SARS-CoV-2 has public health implication, with this comment we highlight the need of establishing appropriate guidelines for school opening and other social activities related to childhood.

    CRISPR-based and RT-qPCR surveillance of SARS-CoV-2 in asymptomatic TRANS individuals uncovers a shift in viral prevalence SERO among a university population

    Authors: Jennifer N Rauch; Eric Valois; Jose Carlos Ponce-Rojas; Zach Aralis; Ryan L Lach; Francesca Zappa; Morgane Audouard; Sabrina C Solley; Chinmay Vaidya; Michael Costello; Holly Smith; Ali Javanbakht; Betsy Malear; Laura Polito; Stewart Comer; Katherine Arn; Kenneth S Kosik; Diego Acosta-Alvear; Maxwell Z Wilson; Lynn Fitzgibbons; Carolina Arias

    doi:10.1101/2020.08.06.20169771 Date: 2020-08-07 Source: medRxiv

    Background: The progress of the COVID-19 pandemic profoundly impacts the health of communities around the world, with unique impacts on colleges and universities. Transmission TRANS of SARS-CoV-2 by asymptomatic TRANS people is thought to be the underlying cause of a large proportion of new infections MESHD. However, the local prevalence SERO of asymptomatic TRANS and pre-symptomatic carriers TRANS of SARS-CoV-2 is influenced by local public health restrictions and the community setting. Objectives: This study has three main objectives. First, we looked to establish the prevalence SERO of asymptomatic TRANS SARS-CoV-2 infection MESHD on a university campus in California. Second, we sought to assess the changes in viral prevalence SERO associated with the shifting community conditions related to non-pharmaceutical interventions (NPIs). Third, we aimed to compare the performance SERO of CRISPR- and PCR-based assays for large-scale virus surveillance sampling in COVID-19 asymptomatic TRANS persons. Methods: We enrolled 1,808 asymptomatic TRANS persons for self-collection of oropharyngeal (OP) samples to undergo SARS-CoV-2 testing. We compared viral prevalence SERO in samples obtained in two time periods: May 28th-June 11th; June 23rd-July 2nd. We detected viral genomes in these samples using two assays: CREST, a CRISPR-based method recently developed at UCSB, and the RT-qPCR test recommended by US Centers for Disease MESHD Control and Prevention (CDC). Results: Of the 1,808 participants, 1,805 were affiliates of the University of California, Santa Barbara, and 1,306 were students. None of the tests performed on the 732 samples collected between late May to early June were positive. In contrast, tests performed on the 1076 samples collected between late June to early July, revealed nine positive cases. This change in prevalence SERO met statistical significance, p = 0.013. One sample was positive by RT-qPCR at the threshold of detection, but negative by both CREST and CLIA-confirmation testing. With this single exception, there was perfect concordance in both positive and negative results obtained by RT-qPCR and CREST. The estimated prevalence SERO of the virus, calculated using the confirmed cases TRANS, was 0.74%. The average age TRANS of our sample population was 28.33 (18-75) years, and the average age TRANS of the positive cases was 21.7 years (19-30). Conclusions: Our study revealed that there were no COVID-19 cases in our study population in May/June. Using the same methods, we demonstrated a substantial shift in prevalence SERO approximately one month later, which coincided with changes in community restrictions and public interactions. This increase in prevalence SERO, in a young and asymptomatic TRANS population which would not have otherwise accessed COVID-19 testing, indicated the leading wave of a local outbreak, and coincided with rising case counts in the surrounding county and the state of California. Our results substantiate that large, population-level asymptomatic TRANS screening using self-collection may be a feasible and instructive aspect of the public health approach within large campus communities, and the almost perfect concordance between CRISPR- and PCR-based assays indicate expanded options for surveillance testing

    Transient dynamics of SARS-CoV-2 as England exited national lockdown

    Authors: Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Peter Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott

    doi:10.1101/2020.08.05.20169078 Date: 2020-08-06 Source: medRxiv

    Control of the COVID-19 pandemic requires a detailed understanding of prevalence SERO of SARS-CoV-2 virus in the population. Case-based surveillance is necessarily biased towards symptomatic individuals and sensitive to varying patterns of reporting in space and time. The real-time assessment of community transmission TRANS antigen study (REACT-1) is designed to overcome these limitations by obtaining prevalence SERO data based on a nose and throat swab RT-PCR test among a representative community-based sample in England, including asymptomatic TRANS individuals. Here, we describe results comparing rounds 1 and 2 carried out during May and mid June / early July 2020 respectively across 315 lower tier local authority areas. In round 1 we found 159 positive samples from 120,620 tested swabs while round 2 there were 123 positive samples from 159,199 tested swabs, indicating a downwards trend in prevalence SERO from 0.13% (95% CI, 0.11%, 0.15%) to 0.077% (0.065%, 0.092%), a halving time of 38 (28, 58) days, and an R of 0.89 (0.86, 0.93). The proportion of swab-positive participants who were asymptomatic TRANS at the time of sampling increased from 69% (61%, 76%) in round 1 to 81% (73%, 87%) in round 2. Although health care and care home workers were infected far more frequently than other workers in round 1, the odds were markedly reduced in round 2. Age TRANS patterns of infection MESHD changed between rounds, with a reduction by a factor of five in prevalence SERO in 18 to 24 year olds. Our data were suggestive of increased risk of infection TRANS risk of infection TRANS infection MESHD in Black and Asian (mainly South Asian) ethnicities. Using regional and detailed case location data, we detected increased infection MESHD intensity in and near London. Under multiple sensitivity SERO analyses, our results were robust to the possibility of false positives. At the end of the initial lockdown in England, we found continued decline in prevalence SERO and a shift in the pattern of infection MESHD by age TRANS and occupation. Community-based sampling, including asymptomatic TRANS individuals, is necessary to fully understand the nature of ongoing transmission TRANS.

    An Examination of School Reopening Strategies during the SARS-CoV-2 Pandemic

    Authors: Alfonso Landeros; Xiang Ji; Kenneth L. Lange; Timothy C. Stutz; Jason Xu; Mary E. Sehl; Janet S. Sinsheimer

    doi:10.1101/2020.08.05.20169086 Date: 2020-08-06 Source: medRxiv

    The SARS-CoV-2 pandemic led to the closure of nearly all K-12 schools in the United States of America in March 2020. Although reopening K-12 schools for in-person schooling is desirable for many reasons, officials also understand that risk reduction strategies and detection of cases must be in place to allow children TRANS to safely return to school. Furthermore, the consequences of reclosing recently reopened schools are substantial and impact teachers, parents TRANS, and ultimately the educational experience in children TRANS. Using a stratified Susceptible-Exposed-Infected-Removed model, we explore the influences of reduced class density, transmission TRANS mitigation (such as the use of masks, desk shields, frequent surface cleaning, or outdoor instruction), and viral detection on cumulative prevalence SERO. Our model predicts that a combination of all three approaches will substantially reduce SARS-CoV-2 prevalence SERO. The model also shows that reduction of class density and the implementation of rapid viral testing, even with imperfect detection, have greater impact than moderate measures for transmission TRANS mitigation.

    Seroprevalence SERO of COVID-19 in Niger State

    Authors: Hussaini Majiya; Mohammed Aliyu-Paiko; Vincent Tochukwu Balogu; Dickson Achimugu Musa; Ibrahim Maikudi Salihu; Abdullahi Abubakar Kawu; Ishaq Yakubu Bashir; Aishat Rabiu Sani; John Baba; Amina Tako Muhammad; Fatima Ladidi Jibril; Ezekiel Bala; Nuhu George Obaje; Yahaya Badeggi Aliyu; Ramatu Gogo Muhammad; Hadiza Mohammed; Usman Naji Gimba; Abduljaleel Uthman; Hadiza Muhammad Liman; Sule Alfa Alhaji; Joseph Kolo James; Muhammad Muhammad Makusidi; Mohammed Danasabe Isah; Ibrahim Abdullahi; Umar Ndagi; Bala Waziri; Chindo Ibrahim Bisallah; Naomi John Dadi-Mamud; Kolo Ibrahim; Abu Kasim Adamu

    doi:10.1101/2020.08.04.20168112 Date: 2020-08-05 Source: medRxiv

    Coronavirus Disease MESHD 2019 (COVID-19) Pandemic is ongoing, and to know how far the virus has spread in Niger State, Nigeria, a pilot study was carried out to determine the COVID-19 seroprevalence SERO, patterns, dynamics, and risk factors in the state. A cross sectional study design and clustered-stratified-Random sampling strategy were used. COVID-19 IgG and IgM Rapid Test SERO Kits (Colloidal gold immunochromatography lateral flow system) were used to determine the presence or absence of antibodies to SARS-CoV-2 SERO in the blood SERO of sampled participants across Niger State as from 26th June 2020 to 30th June 2020. The test kits were validated using the blood SERO samples of some of the NCDC confirmed positive and negative COVID-19 cases in the State. COVID-19 IgG and IgM Test results were entered into the EPIINFO questionnaire administered simultaneously with each test. EPIINFO was then used for both the descriptive and inferential statistical analyses of the data generated. The seroprevalence SERO of COVID-19 in Niger State was found to be 25.41% and 2.16% for the positive IgG and IgM respectively. Seroprevalence SERO among age groups TRANS, gender TRANS and by occupation varied widely. A seroprevalence SERO of 37.21% was recorded among health care workers in Niger State. Among age groups TRANS, COVID-19 seroprevalence SERO was found to be in order of 30-41 years (33.33%) > 42-53 years (32.42%) > 54-65 years (30%) > 66 years and above (25%) > 6-17 years (19.20%) > 18-29 years (17.65%) > 5 years and below (6.66%). A seroprevalence SERO of 27.18% was recorded for males TRANS and 23.17% for females TRANS in the state. COVID-19 asymptomatic TRANS rate in the state was found to be 46.81%. The risk analyses showed that the chances of infection MESHD are almost the same for both urban and rural dwellers in the state. However, health care workers and those that have had contact with person (s) that travelled TRANS out of Nigeria in the last six (6) months are twice ( 2 times) at risk of being infected with the virus. More than half (54.59%) of the participants in this study did not practice social distancing at any time since the pandemic started. Discussions about knowledge, practice and attitude of the participants are included. The observed Niger State COVID-19 seroprevalence SERO means that the herd immunity for COVID-19 is yet to be achieved and the population is still susceptible for more infection MESHD and transmission TRANS of the virus. If the prevalence SERO stays as reported here, the population will definitely need COVID-19 vaccines when they become available. Niger State should fully enforce the use of face/nose masks and observation of social/physical distancing in gatherings including religious gatherings in order to stop or slow the spread of the virus.

    SARS-CoV-2 Infection MESHD Among Symptom-Free Healthcare Workers

    Authors: Ryan T. Demmer; Angela Ulrich; Talia Wiggen; Ali Strickland; Brianna Naumchik; Shalini Kulasingam; Steven D. Stovitz; Clarisse Marotz; Pedro Belda-Ferre; Greg Humphrey; Peter De Hoff; Louise Laurent; Susan Kline; Rob Knight

    doi:10.1101/2020.07.31.20166066 Date: 2020-08-04 Source: medRxiv

    Importance: Current evidence suggests that transmission TRANS of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) is possible among symptom-free individuals but limited data are available on this topic in healthcare workers (HCW). The quality and acceptability of self-collected nasopharyngeal swabs (NPS) is unknown. Objective: To estimate the prevalence SERO of SARS-CoV-2 infection MESHD and to assess the acceptability of self-collected NPS among HCW. Design: Cross-sectional convenience sample enrolled between April 20th and June 24th, 2020. We had >95% power to detect at least one positive test if the true underlying prevalence SERO of SARS-CoV2 was > 1%. Setting: The metropolitan area surrounding Minneapolis and St. Paul, Minnesota. Participants: HCW free of self-reported upper respiratory symptoms were recruited. Exposures: Participants completed questionnaires regarding demographics, household characteristics, personal protective equipment (PPE) utilization and comorbidities. Outcomes: A participant self-collected nasopharyngeal swab (NPS) was obtained. SARS-CoV-2 infection MESHD was assessed via polymerase chain reaction. NPS discomfort was assessed on a scale of 1 (no discomfort) - 10 (extreme discomfort). NPS duration and depth into the nasopharynx, and willingness to perform future self-collections were assessed. Results: Among n=489 participants 80% were female TRANS and mean age TRANS+/-SD was 41+/-11. Participants reported being physicians (14%), nurse practitioners (8%), physicians assistants (4%), nurses (51%), medics (3%), or other which predominantly included laboratory technicians and administrative roles (22%). Exposure to a known/suspected COVID-19 case in the 14 days prior to enrollment was reported in 40% of participants. SARS-CoV-2 was not detected in any participant. The mean+/-SD discomfort level of the NPS was 4.5+/-2.0. 95% of participants reported that their self-swab was longer than or equal to the duration of patient swabs they had previously performed, and 89% reported the depth to be deeper than or equal to the depth of previous patient swabs. Over 95% of participants reported a willingness to repeat a self-collected NP swab in the future. Conclusions and Relevance: The point prevalence SERO of SARS-CoV-2 infection MESHD was likely very low in symptom-free Minnesota healthcare workers from April 20th and June 24th, 2020. Self-collected NP swabs are well-tolerated and a viable alternative to provider-collected swabs to preserve PPE.

    Reconciling epidemiological models with misclassified case-counts for SARS-CoV-2 with seroprevalence SERO surveys: A case study in Delhi, India

    Authors: Rupam Bhattacharyya; Ritwik Bhaduri; Ritoban Kundu; Maxwell Salvatore; Bhramar Mukherjee

    doi:10.1101/2020.07.31.20166249 Date: 2020-08-04 Source: medRxiv

    Underreporting of COVID-19 cases and deaths MESHD is a hindrance to correctly modeling and monitoring the pandemic. This is primarily due to limited testing, lack of reporting infrastructure and a large number of asymptomatic infections MESHD asymptomatic TRANS. In addition, diagnostic tests (RT-PCR tests for detecting current infection MESHD) and serological antibody tests SERO for IgG (to assess past infections MESHD) are imperfect. In particular, the diagnostic tests have a high false negative rate. Epidemiologic models with a latent compartment for unascertained infections MESHD like the Susceptible-Exposed-Infected-Removed (SEIR) models can provide predictions for unreported cases and deaths MESHD under certain assumptions. Typically, the number of unascertained cases is unobserved and thus we cannot validate these estimates for a real study except for simulation studies. Population-based seroprevalence SERO studies can provide a rough estimate of the total number of infections MESHD and help us check epidemiologic model projections. In this paper, we develop a method to account for high false negative rates in RT-PCR in an extension to the classic SEIR model. We apply this method to Delhi, the national capital region of India, with a population of 19.8 million and a COVID-19 hotspot of the country, obtaining estimates of underreporting factor for cases at 34-53 times and that for deaths MESHD at 8-13 times. Based on a recently released serological survey for Delhi with an estimated 22.86% seroprevalence SERO, we compute adjusted estimates of the true number of infections MESHD reported by the survey (after accounting for misclassification of the antibody test SERO results) which is largely consistent with the model outputs, yielding an underreporting factor for cases from 30-42. Together with the model and the serosurvey, this implies approximately 96-98% cases in Delhi remained unreported and whereas only 109,140 cases were reported on July 10, the true number of infections MESHD varied somewhere between 4.4-4.6 million across different estimates. While repeated serological monitoring is resource intensive, model-based adjustments, run with the most up to date data, can provide a viable option to keep track of the unreported cases and deaths MESHD and gauge the true extent of transmission TRANS of this insidious virus.

    Phylogenomic analysis of SARS-CoV-2 genomes from western India reveals unique linked mutations

    Authors: Dhiraj Paul; Kunal Jani; Janesh Kumar; Radha Chauhan; Vasudevan Seshadri; Girdhari Lal; Rajesh Karyakarte; Suvarna Joshi; Murlidhar Tambe; Sourav Sen; Santosh Karade; Kavita Bala Anand; Shelinder Pal Singh Shergill; Rajiv Mohan Gupta; Manoj Kumar Bhat; Arvind Sahu; Yogesh S Shouche

    doi:10.1101/2020.07.30.228460 Date: 2020-07-31 Source: bioRxiv

    India has become the third worst-hit nation by the COVID-19 pandemic caused by the SARS-CoV-2 virus. Here, we investigated the molecular, phylogenomic, and evolutionary dynamics of SARS-CoV-2 in western India, the most affected region of the country. A total of 90 genomes were sequenced. Four nucleotide variants, namely C241T, C3037T, C14408T (Pro4715Leu), and A23403G (Asp614Gly), located at 5UTR, Orf1a, Orf1b, and Spike protein regions of the genome, respectively, were predominant and ubiquitous (90%). Phylogenetic analysis of the genomes revealed four distinct clusters, formed owing to different variants. The major cluster (cluster 4) is distinguished by mutations C313T, C5700A, G28881A are unique patterns and observed in 45% of samples. We thus report a newly emerging pattern of linked mutations. The predominance of these linked mutations suggests that they are likely a part of the viral fitness landscape. A novel and distinct pattern of mutations in the viral strains of each of the districts was observed. The Satara district viral strains showed mutations primarily at the 3' end of the genome, while Nashik district viral strains displayed mutations at the 5' end of the genome. Characterization of Pune strains showed that a novel variant has overtaken the other strains. Examination of the frequency of three mutations i.e., C313T, C5700A, G28881A in symptomatic versus asymptomatic TRANS patients indicated an increased occurrence in symptomatic cases, which is more prominent in females TRANS. The age TRANS-wise specific pattern of mutation is observed. Mutations C18877T, G20326A, G24794T, G25563T, G26152T, and C26735T are found in more than 30% study samples in the age group TRANS of 10-25. Intriguingly, these mutations are not detected in the higher age TRANS range 61-80. These findings portray the prevalence SERO of unique linked mutations in SARS-CoV-2 in western India and their prevalence SERO in symptomatic patients. ImportanceElucidation of the SARS-CoV-2 mutational landscape within a specific geographical location, and its relationship with age TRANS and symptoms, is essential to understand its local transmission TRANS dynamics and control. Here we present the first comprehensive study on genome and mutation pattern analysis of SARS-CoV-2 from the western part of India, the worst affected region by the pandemic. Our analysis revealed three unique linked mutations, which are prevalent in most of the sequences studied. These may serve as a molecular marker to track the spread of this viral variant to different places.

    Incidence and outcomes of healthcare-associated COVID-19 infections MESHD: significance of delayed diagnosis and correlation with staff absence

    Authors: Kirstin Khonyongwa; Surabhi K Taori; Ana Soares; Nergish Desai; Malur Sudhanva; William Bernal; Silke Schelenz; Lisa A Curran

    doi:10.1101/2020.07.24.20148262 Date: 2020-07-30 Source: medRxiv

    Background: The sudden increase in COVID-19 admissions in hospitals during the SARS-CoV2 pandemic of 2020 has led to onward transmissions TRANS among vulnerable inpatients. Aims: This study was performed to evaluate the prevalence SERO and clinical outcomes of Healthcare-associated COVID-19 infections MESHD (HA-COVID-19) during the 2020 epidemic and study factors which may promote or correlate with its incidence and transmission TRANS in a London Teaching Hospital Trust. Methods: Electronic laboratory, patient and staff self-reported sickness records were interrogated for the period 1st March to 18th April 2020. HA-COVID-19 was defined as symptom onset TRANS >14d of admission. Test performance SERO of a single combined throat and nose swab (CTNS) for patient placement and the effect of delayed RNA positivity (DRP, defined as >48h delay) on patient outcomes was evaluated. The incidence of staff self-reported COVID-19 sickness absence, hospital bed occupancy, community incidence and DRP was compared HA-COVID-19. The incidence of other significant hospital-acquired bacterial infections MESHD (OHAI) was compared to previous years. Results: 58 HA-COVID-19 (7.1%) cases were identified. As compared to community-acquired cases, significant differences were observed in age TRANS (p=0.018), ethnicity (p<0.001) and comorbidity burden (p<0.001) but not in 30d mortality. CTNS negative predictive value SERO was 60.3%. DRP was associated with greater mortality (p=0.034) and 34.5% HA-COVID-19 cases could be traced TRANS to delayed diagnosis in CA-COVID-19. Incidence of HA-COVID-19 correlated positively with DRP (R=0.7108) and staff sickness absence (R=0.7815). OHAI rates were similar to previous 2 years. Conclusion: Early diagnosis and isolation of COVID-19 would help reduce transmission TRANS. A single CTNS has limited value in segregating patients into positive and negative pathways.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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