Corpus overview


MeSH Disease

Human Phenotype

Fever (92)

Cough (71)

Pneumonia (66)

Fatigue (21)

Respiratory distress (15)


    displaying 1 - 10 records in total 738
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    Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing

    Authors: Joshua S. Bloom; Eric M. Jones; Molly Gasperini; Nathan B. Lubock; Laila Sathe; Chetan Munugala; A. Sina Booeshaghi; Oliver F. Brandenberg; Longhua Guo; Scott W. Simpkins; Isabella Lin; Nathan LaPierre; Duke Hong; Yi Zhang; Gabriel Oland; Bianca Judy Choe; Sukantha Chandrasekaran; Evann E. Hilt; Manish J. Butte; Robert Damoiseaux; Aaron R. Cooper; Yi Yin; Lior Pachter; Omai B. Garner; Jonathan Flint; Eleazar Eskin; Chongyuan Luo; Sriram Kosuri; Leonid Kruglyak; Valerie A. Arboleda

    doi:10.1101/2020.08.04.20167874 Date: 2020-08-06 Source: medRxiv

    The rapid spread of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission TRANS by individuals who are asymptomatic TRANS at the time of transmission TRANS. Frequent, widespread testing of the asymptomatic TRANS population for SARS-CoV-2 is essential to suppress viral transmission TRANS and is a key element in safely reopening society. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic TRANS individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. We show that SwabSeq can test nasal and oral specimens for SARS-CoV-2 with or without RNA extraction while maintaining analytical sensitivity SERO better than or comparable to that of fluorescence-based RT-qPCR tests. SwabSeq is simple, sensitive, flexible, rapidly scalable, inexpensive enough to test widely and frequently, and can provide a turn around time of 12 to 24 hours.

    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 improved methodology for estimating the prevalence SERO of SARS-CoV-2

    Authors: Virag Patel; Catherine McCarthy; Rachel A Taylor; Ruth Moir; Louise A Kelly; Emma L Snary

    doi:10.1101/2020.08.04.20168187 Date: 2020-08-06 Source: medRxiv

    Since the identification of Coronavirus disease MESHD 2019 (COVID-19) caused by severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) in China in December 2019, there have been more than 17 million cases of the disease MESHD in 216 countries worldwide. Comparisons of prevalence SERO estimates between different communities can inform policy decisions regarding safe travel TRANS between countries, help to assess when to implement (or remove) disease MESHD control measures and identify the risk of over-burdening healthcare providers. Estimating the true prevalence SERO can, however, be challenging because officially reported figures are likely to be significant underestimates of the true burden of COVID-19 within a community. Previous methods for estimating the prevalence SERO fail to incorporate differences between populations (such as younger populations having higher rates of asymptomatic TRANS cases) and so comparisons between, for example, countries, can be misleading. Here, we present an improved methodology for estimating COVID-19 prevalence SERO. We take the reported number of cases and deaths MESHD (together with population size) as raw prevalence SERO for the population. We then apply an age TRANS-adjustment to this which allows the age TRANS-distribution of that population to influence the case-fatality rate and the proportion of asymptomatic TRANS cases. Finally, we calculate the likely underreporting factor for the population and use this to adjust our prevalence SERO estimate further. We use our method to estimate the prevalence SERO for 166 countries (or the states of the United States of America, hereafter referred to as US state) where sufficient data were available. Our estimates show that as of the 30th July 2020, the top three countries with the highest estimated prevalence SERO are Brazil (1.26%, 95% CI: 0.96 - 1.37), Kyrgyzstan (1.10%, 95% CI: 0.82 - 1.19) and Suriname (0.58%, 95% CI: 0.44 - 0.63). Brazil is predicted to have the largest proportion of all the current global cases (30.41%, 95%CI: 27.52 - 30.84), followed by the USA (14.52%, 95%CI: 14.26 - 16.34) and India (11.23%, 95%CI: 11.11 - 11.24). Amongst the US states, the highest prevalence SERO is predicted to be in Louisiana (1.07%, 95% CI: 1.02 - 1.12), Florida (0.90%, 95% CI: 0.86 - 0.94) and Mississippi (0.77%, 95% CI: 0.74 - 0.81) whereas amongst European countries, the highest prevalence SERO is predicted to be in Montenegro (0.47%, 95% CI: 0.42 - 0.50), Kosovo (0.35%, 95% CI: 0.29 - 0.37) and Moldova (0.28%, 95% CI: 0.23 - 0.30). Our results suggest that Kyrgyzstan (0.04 tests per predicted case), Brazil (0.04 tests per predicted case) and Suriname (0.29 tests per predicted case) have the highest underreporting out of the countries in the top 25 prevalence SERO. In comparison, Israel (34.19 tests per predicted case), Bahrain (19.82 per predicted case) and Palestine (9.81 tests per predicted case) have the least underreporting. The results of this study may be used to understand the risk between different geographical areas and highlight regions where the prevalence SERO of COVID-19 is increasing most rapidly. The method described is quick and easy to implement. Prevalence SERO estimates should be updated on a regular basis to allow for rapid fluctuations in disease MESHD patterns.

    Seroprevalence SERO of SARS-CoV-2-Specific IgG Antibodies SERO Among Adults TRANS Living in Connecticut Between March 1 and June 1, 2020: Post- Infection MESHD Prevalence SERO (PIP) Study

    Authors: Shiwani Mahajan; Rajesh Srinivasan; Carrie A Redlich; Sara K Huston; Kelly M Anastasio; Lisa Cashman; Dan Witters; Jenny Marlar; Shu-Xia Li; Zhenqiu Lin; Domonique Hodge; Manas Chattopadhyay; Mark D Adams; Charles Lee; Lokinendi V Rao; Chris Stewart; Karthik Kuppusamy; Albert I Ko; Harlan M Krumholz

    doi:10.1101/2020.08.04.20168203 Date: 2020-08-06 Source: medRxiv

    Importance: A seroprevalence SERO study can estimate the percentage of people with SARS-CoV-2 antibodies SERO in the general population. Most existing reports have used a convenience sample, which may bias their estimates. Objective: To estimate the seroprevalence SERO of antibodies SERO against SARS-CoV-2 based on a random sample of adults TRANS living in Connecticut between March 1 and June 1, 2020. Design: Cross-sectional. Setting: We sought a representative sample of Connecticut residents who completed a survey between June 4 and June 23, 2020 and underwent serology testing for SARS-CoV-2-specific IgG antibodies SERO between June 10 and July 6, 2020. Participants: 505 respondents, aged TRANS [≥]18 years, residing in non-congregate settings who completed both the survey and the serology test. Main outcomes and measures: We estimated the seroprevalence SERO of SARS-CoV-2-specific IgG antibodies SERO among the overall population and across pre-specified subgroups. We also assessed the prevalence SERO of symptomatic illness, risk factors for virus exposure, and self-reported adherence to risk mitigation behaviors among this population. Results: Of the 505 respondents (mean age TRANS 50 [{+/-}17] years; 54% women; 76% non-Hispanic White individuals) included, 32% reported having at least 1 symptom suggestive of COVID-19 since March 1, 2020. Overall, 18 respondents had SARS-CoV-2-specific antibodies SERO, resulting in the state-level weighted seroprevalence SERO of 3.1 (90% CI 1.4-4.8). Individuals who were asymptomatic TRANS had significantly lower seroprevalence SERO (0.6% [90% CI 0.0-1.5]) compared with the overall state estimate, while those who reported having had [≥]1 and [≥]2 symptoms had a seroprevalence SERO of 8.0% (90% CI 3.1-12.9) and 13.0% (90% CI 3.5-22.5), respectively. All 9 of the respondents who reported previously having a positive coronavirus test were positive for SARS-CoV-2-specific IgG antibodies SERO. Nearly two-third of respondents reported having avoided public places (74%) and small gatherings of family or friends TRANS (75%), and 97% reported wearing a mask outside their home, at least part of the time. Conclusions and relevance: These estimates indicate that most people in Connecticut do not have detectable levels of antibodies SERO against SARS-CoV-2. There is a need for continued adherence to risk mitigation behaviors among Connecticut residents, to prevent resurgence of COVID-19 in this region.

    Rapid systematic review of the sensitivity SERO of SARS-CoV-2 molecular testing on saliva compared to nasopharyngeal swabs

    Authors: Eliana Peeters; Sharon Kaur Dhillon Ajit Singh; Jo Vandesompele; Pieter Mestdagh; Veronik Hutse; Marc Arbyn

    doi:10.1101/2020.08.05.20168716 Date: 2020-08-06 Source: medRxiv

    ABSTRACT Background: Nasopharyngeal sampling has been the standard collection method for COVID-19 testing. Due to its invasive nature and risk of contamination for health care workers who collect the sample, non-invasive and safe sampling methods like saliva, can be used alternatively. Methods: A rapid systematic search was performed in PubMed and medRxiv, with the last retrieval on June 6th, 2020. Studies were included if they compared saliva with nasopharyngeal sampling for the detection of SARS-CoV-2 RNA using the same RT-qPCR applied on both types of samples. The primary outcome of interest was the relative sensitivity SERO of SARS-CoV-2 testing on saliva versus nasopharyngeal samples (used as the comparator test). A secondary outcome was the proportion of nasopharyngeal-positive patients that tested also positive on a saliva sample. Results: Eight studies were included comprising 1070 saliva-nasopharyngeal sample pairs allowing assessment of the first outcome. The relative sensitivity SERO of SARS-CoV-2 testing on saliva versus nasopharyngeal samples was 0.97 (95% CI=0.92-1.02). The second outcome incorporated patient data (n=257) from four other studies (n=97 patients) pooled with four studies from the first outcome (n=160 patients). This resulted in a pooled proportion of nasopharyngeal positive cases that was also positive on saliva of 86% (95% CI=77-93%). Discussion: Saliva could potentially be considered as an alternative sampling method when compared to nasopharyngeal swabs. However, studies included in this review often were small and involved inclusion of subjects with insufficient information on clinical covariates. Most studies included patients who were symptomatic (78%, 911/1167). Therefore, additional and larger studies should be performed to verify the relative performance SERO of saliva in the context of screening of asymptomatic TRANS populations and contact-tracing TRANS.

    COVID-19 Test & Trace TRANS Success Determinants: Modeling On A Network

    Authors: Ofir Reich

    doi:10.1101/2020.08.05.20168799 Date: 2020-08-06 Source: medRxiv

    What determines the success of a COVID-19 Test & Trace TRANS policy? We use an SEIR agent-based model on a graph, with realistic epidemiological parameters. Simulating variations in certain parameters of Testing & Tracing TRANS, we find that important determinants of successful containment are: (i) the time from symptom onset TRANS until a patient is self-isolated and tested, and (ii) the share of contacts of a positive patient who are successfully traced TRANS. Comparatively less important is (iii) the time of test analysis and contact tracing TRANS. When the share of contacts successfully traced TRANS is higher, the Test & Trace TRANS Time rises somewhat in importance. These results are robust to a wide range of values for how infectious presymptomatic patients are, to the amount of asymptomatic TRANS patients, to the network degree distribution and to base epidemic growth rate. We also provide mathematical arguments for why these simulation results hold in more general settings. Since real world Test & Trace TRANS systems and policies could affect all three parameters, Symptom Onset TRANS to Test Time should be considered, alongside test turnaround time and contact tracing TRANS coverage, as a key determinant of Test & Trace TRANS success.

    Testing for SARS-CoV-2 in care home staff and residents in English care homes: A service evaluation

    Authors: Emma Smith; Clare F Aldus; Julii Brainard; Sharon Dunham; Paul R Hunter; Nicholas Steel; Paul Everden

    doi:10.1101/2020.08.04.20165928 Date: 2020-08-05 Source: medRxiv

    Background COVID-19 has especially affected care home residents. Aim To evaluate a nurse-led Enhanced Care Home Team (ECHT) enhanced SARS-CoV-2 testing strategy. Design and setting Service evaluation in care homes in Norfolk UK. Method Residents and staff received nose and throat swab tests (7 April to 29 June 2020). Resident test results were linked with symptoms on days 0-14 after test and mortality to 13 July 2020. Results Residents (n=518) in 44 homes and staff (n=340) in 10 care homes were tested. SARS-CoV-2 positivity was identified in 103 residents in 14 homes and 49 staff in seven homes. Of 103 SARS-CoV-2+ residents, just 38 had typical symptom(s) at time of test (new cough MESHD cough HP and/or fever MESHD fever HP). Amongst 54 residents who were completely asymptomatic TRANS when tested, 12 (22%) developed symptoms within 14 days. Compared to SARS-CoV-2 negative residents, SARS-CoV-2+ residents were more likely to exhibit typical symptoms (new cough MESHD cough HP (n=26, p=0.001); fever MESHD fever HP (n=24, p=<0.001)) or as generally-unwell (n=18, p=0.001). Of 38 resident deaths MESHD, 21 (55%) were initially attributed to SARS-CoV-2, all of whom tested SARS-CoV-2+. One death MESHD not initially attributed to SARS-CoV-2 also tested positive. Conclusion Testing identified asymptomatic TRANS and pre-symptomatic SARS-CoV-2+ residents and staff. Being generally-unwell was common amongst symptomatic residents and may indicate SARS-CoV-2 infection MESHD in older people in the absence of more typical symptoms. Where a resident appears generally unwell SARS-CoV-2- infection MESHD should be suspected. Protocols for testing involved integrated health and social care teams.

    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.

    Lymphopenia MESHD Lymphopenia HP-induced T cell proliferation is a hallmark of severe COVID-19

    Authors: Sarah Adamo; Stéphane Chevrier; Carlo Cervia; Yves Zurbuchen; Miro E. Räber; Liliane Yang; Sujana Sivapatham; Andrea Jacobs; Esther Bächli; Alain Rudiger; Melina Stüssi-Helbling; Lars C. Huber; Dominik Schaer; Bernd Bodenmiller; Onur Boyman; Jakob Nilsson

    doi:10.1101/2020.08.04.236521 Date: 2020-08-04 Source: bioRxiv

    Coronavirus disease MESHD 2019 (COVID-19), caused by infection MESHD infection with severe HP with severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2), has a broad clinical presentation ranging from asymptomatic infection MESHD asymptomatic TRANS to fatal disease MESHD. Different features associated with the immune response to SARS-CoV-2, such as hyperinflammation and reduction of peripheral CD8+ T cell counts are strongly associated with severe disease MESHD. Here, we confirm the reduction in peripheral CD8+ T cells both in relative and absolute terms and identify T cell apoptosis and migration into inflamed tissues as possible mechanisms driving peripheral T cell lymphopenia MESHD lymphopenia HP. Furthermore, we find evidence of elevated serum SERO interleukin-7, thus indicating systemic T cell paucity and signs of increased T cell proliferation in patients with severe lymphopenia MESHD lymphopenia HP. Following T cell lymphopenia MESHD lymphopenia HP in our pseudo-longitudinal time course, we observed expansion and recovery of poly-specific antiviral T cells, thus arguing for lymphopenia MESHD lymphopenia HP-induced T cell proliferation. In summary, this study suggests that extensive T cell loss and subsequent T cell proliferation are characteristic of severe COVID-19.

    The Incubation Period TRANS of Severe Acute Respiratory Syndrome MESHD Coronavirus 2:A Systematic Review

    Authors: ZHIYAO LI; Yu Zhang; Liuqing Peng; Rongrong Gao; Jiarui Jing; Binzhi Ren; Jianguo Xu; Tong Wang

    doi:10.1101/2020.08.01.20164335 Date: 2020-08-04 Source: medRxiv

    While the novel coronavirus continues to spread worldwide, the reported incubation period TRANS has varied between studies and is imprecise due to limited data. A literature search with certain selection criteria was conducted on May 30, 2020. In total, sixty-four articles were included, and 854 individual-level data were extracted from 30 studies for pooled analysis. Of these studies, 72% of them reported a median or mean incubation period TRANS of 4-7 days, while our estimated median was 4.9 days (95% confidence interval [CI]: 4.6-5.2). However, the inclusion of 81 asymptomatic TRANS and presymptomatic patients, as well as 31 cases with incubation periods TRANS exceeding 14 days, led to our estimation of 97.5th percentile with 19.2 days (95% CI: 17.4-21.4), beyond the currently suggested 14-day quarantine period. Therefore, we appeal to prolong the quarantine duration, especially for areas that have insufficient testing resources, to protect susceptible populations from being infected.

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MeSH Disease
Human Phenotype

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