Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (209)

Fever (141)

Cough (103)

Hypertension (85)

Respiratory distress (71)


Transmission

age categories (647)

Transmission (635)

fomite (316)

gender (247)

asymptotic cases (238)


Seroprevalence
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    The emergence of COVID-19 in Indonesia: analysis of predictors of infection MESHD and mortality using independent and clustered data approaches

    Authors: Erlina Burhan; Ari Fahrial Syam; Ahmad Jabir Rahyussalim; Prasenohadi Prasenohadi; Navy G Lolong Wulung; Agus Dwi Susanto; I Gede Ketut Sajinadiyasa; Dewi Puspitorini; Dewi Lestari; Indah Suci Widyahening; Vivi Setiawaty; Dwiana Ocviyanti; Kartika Qonita Putri; Aswin Guntara; Davrina Rianda; Anuraj H Shankar; Rina Agustina

    doi:10.1101/2020.07.10.20147942 Date: 2020-07-11

    Background: Analyses of correlates of SARS-CoV-2 infection MESHD or mortality have usually assessed individual predictors. This study aimed to determine if patterns of combined predictors may better identify risk of infection TRANS risk of infection TRANS infection MESHD and mortality. Methods: For the period of March 2nd to 10th 2020, the first 9 days of the COVID-19 pandemic in Indonesia, we selected all 18 confirmed cases TRANS, of which 6 died, and all 60 suspected cases, of which 1 died; and 28 putatively negative patients with pneumonia MESHD pneumonia HP and no travel TRANS history. We recorded data for travel TRANS, contact history, symptoms, haematology, comorbidities, and chest x-ray. Hierarchical cluster analyses (HCA) and principal component analyses (PCA) identified cluster and covariance patterns for symptoms or haematology which were analysed with other predictors of infection MESHD or mortality using logistic regression. Results: For univariate analyses, no significant association with infection MESHD was seen for fever MESHD fever HP, cough MESHD cough HP, dyspnoea, headache MESHD headache HP, runny nose, sore throat, gastrointestinal complaints (GIC), or haematology. A PCA symptom component for fever MESHD fever HP, cough MESHD cough HP, and GIC tended to increase risk of infection TRANS risk of infection TRANS infection MESHD (OR 3.41; 95% CI 1.06 - 14; p=0.06), and a haematology component with elevated monocytes decreased risk (OR 0.26; 0.07 - 0.79; 0.027). Multivariate analysis revealed that an HCA cluster of 3-5 symptoms, typically fever MESHD fever HP, cough MESHD cough HP, headache MESHD headache HP, runny nose, sore throat but little dyspnoea and no GIC tended to reduce risk (aOR 0.048; <0.001 - 0.52; 0.056). In univariate analyses for death MESHD, an HCA cluster of cough MESHD cough HP, fever MESHD fever HP and dyspnoea had increased risk (OR 5.75; 1.06 - 31.3, 0.043), but no other individual predictor, cluster or component was associated. Other significant predictors of infection MESHD were age TRANS >= 45, international travel TRANS, contact with COVID-19 patient, and pneumonia MESHD pneumonia HP. Diabetes and history of contact were associated with higher mortality. Conclusions: Cluster groups and co-variance patterns may be stronger correlates of SARS-CoV-2 infection MESHD than individual predictors. Comorbidities may warrant careful attention as would COVID-19 exposure levels.

    Societal heterogeneity contributes to complex dynamic patterns of the COVID-19 pandemics: insights from a novel Stochastic Heterogeneous Epidemic Model (SHEM)

    Authors: Alexander V Maltsev; Michael Stern

    doi:10.1101/2020.07.10.20150813 Date: 2020-07-11

    After months of COVID-19 quarantine, businesses are reopening their doors and people are reentering society. Within the current COVID-19 data, after a slow-down of infection MESHD, a new peak in active cases is already forming. Here we developed a new Stochastic Heterogeneous Epidemic Model (SHEM) to investigate genesis of complex pandemic patterns with the focus on the role of heterogenous societal structure. Using this model with R0 TRANS of COVID-19, we simulated viral infection MESHD in different scenarios where isolated, communities surround the main cluster of the population. Depending on the parameters of heterogeneity and isolation period, our simulations generated a multimodal growth periods with multiple peaks, an extended plateau, a prolonged tail, or a delayed second wave of infection MESHD. We show that timing and magnitude of infection MESHD for previously unaffected isolated clusters of people, such as suburban neighborhoods, are critical aspects of these patterns. Our model can be applied to communities at any given scale of population described as a fractal-like structure, i.e. from the entire human population, to a country, down to a province or city levels with relevant societal heterogeneity structure. The current COVID-19 pandemic development worldwide and in the US follows a bimodal rise pattern, qualitatively similar to that in our simulations. We interpret our data to indicate that the secondary peak in the pattern is contributed by the states and counties in the US with late infection MESHD surges that are analogous to isolated suburbs in our model. Furthermore, the on-going early reopening, i.e. premature partial reopening in our model, is further accelerating the peak rise. This peak now reaches new heights, forcing many states in the US to reverse their policies and reestablish their quarantine measures. Our results support these timely and effective measures: we show that longer quarantine periods can reduce the number of deaths MESHD and transform the current trend into a substantially delayed (>1 year) second wave. If this scenario becomes a reality, it is important (i) to develop the vaccine and/or effective treatment before the second wave; (ii) to warn people living in suburbs that it is these isolated areas that may hold a false sense of security, but they should continue to take extra care for their public health.

    Clinical utility of targeted SARS-CoV-2 serology testing to aid the diagnosis and management of suspected missed, late or post-COVID-19 infection MESHD syndromes MESHD: results from a pilot service

    Authors: Nicola Sweeney; Blair Merrick; Suzanne Pickering; Rui Pedro Galao; Alina Botgros; Harry D. Wilson; Adrian W. Signell; Gilberto Betancor; Mark Kia Ik Tan; John Ramble; Neophytos Kouphou; Sam Acors; Carl Graham; Jeffrey Seow; Eithne MacMahon; Stuart J. D. Neil; Michael H. Malim; Katie Doores; Sam Douthwaite; Rahul Batra; Gaia Nebbia; Jonathan D. Edgeworth

    doi:10.1101/2020.07.10.20150540 Date: 2020-07-11

    Objectives: Determine indications and clinical utility of SARS-CoV-2 serology testing in adults TRANS and children TRANS. Design: Prospective evaluation of initial three weeks of a daily Monday to Friday pilot SARS-CoV-2 serology service for patients. Setting: Early post 'first-wave' SARS-CoV-2 transmission TRANS period at single centre London teaching hospital that provides care to the local community, as well as regional and national referral pathways for specialist services. Participants: 110 (72 adults TRANS, 38 children TRANS, age TRANS range 0-83 years, 52.7% female TRANS (n=58)). Interventions: Patient serum SERO from vetted referrals tested on CE marked and internally validated lateral flow immunoassay SERO (LFIA) (SureScreen Diagnostics) detecting antibodies to SARS-CoV-2 SERO spike proteins, with result and clinical interpretation provided to the direct care team. Main outcome measures: Performance SERO characteristics, source and nature of referrals, feasibility and clinical utility of the service, particularly the benefit for clinical decision-making. Results: The LFIA was deemed suitable for clinical advice and decision making following evaluation with 310 serum samples SERO from SARS-CoV-2 PCR positive patients and 300 pre-pandemic samples, giving a sensitivity SERO and specificity of 96.1% and 99.3% respectively. For the pilot, 115 referrals were received leading to 113 tests performed on 108 participants (sample not available for two participants); paediatrics (n=35), medicine (n=69), surgery (n=2) and general practice (n=2). 43.4% participants (n=49) had detectable antibodies to SARS-CoV-2 SERO. There were three main indications for serology; new acute presentations potentially triggered by recent COVID-19 infection MESHD e.g. PIMS-TS (n=26) and pulmonary embolism MESHD pulmonary embolism HP (n=5), potential missed diagnoses in context of a recent compatible illness (n=40), and making infection MESHD control and immunosuppression treatment decisions in persistently SARS-CoV-2 RNA PCR positive individuals (n=6). Conclusions: This study shows acceptable performance SERO characteristics, feasibility and clinical utility of a SARS-CoV-2 serology service using a rapid, inexpensive and portable assay for adults TRANS and children TRANS presenting with a range of clinical indications. Results correlated closely with a confirmatory in-house ELISA SERO. The study showed the benefit of introducing a serology service where there is a reasonable pre-test probability, and the result can be linked with clinical advice or intervention. Experience thus far is that the volume of requests from hospital referral routes are manageable within existing clinical and laboratory services; however, the demand from community referrals has not yet been assessed. Given recent evidence for a rapid decline in antibodies SERO, particularly following mild infection MESHD, there is likely a limited window of opportunity to realise the benefit of serology testing for individuals infected during the 'first-wave' before they potentially fall HP below a measurable threshold. Rapidly expanding availability of serology services for NHS patients will also help understand the long-term implications of serostatus and prior infection MESHD in different patient groups, particularly before emergence of any 'second-wave' outbreak or introduction of a vaccination programme.

    Association of Cancer with Risk and Mortality of COVID-19: Results from the UK Biobank

    Authors: Zhuqing Shi; W. Kyle Resurreccion; Chi-Hsiung Wang; Jun Wei; Rong Na; S. Lilly Zheng; Liana K. Billings; Brian T. Helfand; Janardan Khandekar; Jianfeng Xu

    doi:10.1101/2020.07.10.20151076 Date: 2020-07-11

    Although cancer has been associated with COVID-19 risk and mortality in hospital-based studies, few population-based studies have been reported. Utilizing data from the UK Biobank (UKB), a population-based prospective cohort, we formally tested the association of over 44 different types of cancer with COVID-19 infection MESHD and mortality among 7,661 subjects who were tested by June 17, 2020. Compared to non-cancer subjects, cancer subjects (N=1,521) had significantly lower overall risk for COVID-19 infection MESHD [odds ratio (OR) and 95% confidence interval (CI): 0.79 (0.68-0.92), P=2.60E-03]. However, a trend of higher risk for COVID-19 mortality was found among 256 COVID-19 positive cancer patients, especially for hematologic cancers such as non-Hodgkin lymphoma MESHD non-Hodgkin lymphoma HP [3.82 (1.17-12.01), P=0.02]. In cancer patients, while few demographic, lifestyle, genetic and comorbidity factors predicted risk for COVID-19 infection MESHD, older age TRANS, male TRANS sex, heart disease MESHD and hypertension MESHD hypertension HP significantly predicted COVID-19 mortality. The lower risk for COVID-19 infection MESHD is likely due to extra caution in COVID-19 prevention and more testing among cancer patients, an encouraging finding that demonstrates the feasibility of intervention. These results, if confirmed in future releases of UKB data and other independent populations, may provide guidance for COVID-19 prevention and treatment among cancer patients.

    Longitudinal evaluation and decline of antibody SERO responses in SARS-CoV-2 infection MESHD

    Authors: Jeffrey Seow; Carl Graham; Blair Merrick; Sam Acors; Kathryn J.A. Steel; Oliver Hemmings; Aoife O'Bryne; Neophytos Kouphou; Suzanne Pickering; Rui Galao; Gilberto Betancor; Harry D Wilson; Adrian W Signell; Helena Winstone; Claire Kerridge; Nigel Temperton; Luke Snell; Karen Bisnauthsing; Amelia Moore; Adrian Green; Lauren Martinez; Brielle Stokes; Johanna Honey; Alba Izquierdo-Barras; Gill Arbane; Amita Patel; Lorcan OConnell; Geraldine O Hara; Eithne MacMahon; Sam Douthwaite; Gaia Nebbia; Rahul Batra; Rocio Martinez-Nunez; Jonathan D. Edgeworth; Stuart J.D. Neil; Michael H. Malim; Katie Doores

    doi:10.1101/2020.07.09.20148429 Date: 2020-07-11

    Antibody SERO (Ab) responses to SARS-CoV-2 can be detected in most infected individuals 10-15 days following the onset of COVID-19 symptoms. However, due to the recent emergence of this virus in the human population it is not yet known how long these Ab responses will be maintained or whether they will provide protection from re- infection MESHD. Using sequential serum samples SERO collected up to 94 days post onset of symptoms TRANS (POS) from 65 RT-qPCR confirmed SARS-CoV-2-infected individuals, we show seroconversion in >95% of cases and neutralizing antibody SERO (nAb) responses when sampled beyond 8 days POS. We demonstrate that the magnitude of the nAb response is dependent upon the disease MESHD severity, but this does not affect the kinetics of the nAb response. Declining nAb titres were observed during the follow up period. Whilst some individuals with high peak ID50 (>10,000) maintained titres >1,000 at >60 days POS, some with lower peak ID50 had titres approaching baseline within the follow up period. A similar decline in nAb titres was also observed in a cohort of seropositive healthcare workers from Guy's and St Thomas' Hospitals. We suggest that this transient nAb response is a feature shared by both a SARS-CoV-2 infection MESHD that causes low disease MESHD severity and the circulating seasonal coronaviruses that are associated with common colds MESHD. This study has important implications when considering widespread serological testing SERO, Ab protection against re- infection MESHD with SARS-CoV-2 and the durability of vaccine protection.

    Clinical and epidemiological characteristics of children TRANS with SARS-CoV-2 infection MESHD: case series in Sinaloa

    Authors: Giordano Perez Gaxiola; Rosalino Flores Rocha; Julio Cesar Valadez Vidarte; Melissa Hernandez Alcaraz; Gilberto Herrera Mendoza; Miguel Alejandro Del Real Lugo

    doi:10.1101/2020.07.07.20146332 Date: 2020-07-11

    Background: The SARS-CoV-2 virus may affect both adults TRANS and children TRANS. Although the disease MESHD, named COVID-19, has a lower prevalence SERO in infancy and has been described as mild, the clinical characteristics may vary and there is a possibility of complications. Objectives: To describe the clinical and epidemiological characteristics of pediatric cases confirmed TRANS in the state of Sinaloa, Mexico, during the first three months of the pandemic, and of children TRANS admitted with COVID-19 to a secondary hospital. Methods: This case series includes all patients with SARS-CoV-2 infection MESHD infection confirmed TRANS confirmed by PCR testing, identified in the state epidemiological surveillance system between March 1 and May 31, 2020. Confirmed patients admitted to the Sinaloa Pediatric Hospital (HPS) during the same dates are also described. Results: Fifty one children TRANS with SARS-CoV-2 were included, 10 of the admitted to HPS. The median age TRANS was 10 years. The more frequent symptoms were fever MESHD fever HP (78%), cough MESHD cough HP (67%) and headache MESHD headache HP (57%). Most cases were mild or asymptomatic TRANS. Three patients with comorbidities died. Only 4 of 10 patients identified in HPS had been admitted with the diagnosis of possible COVID-19. Conclusions: SARS-CoV-2 infection MESHD in children TRANS was mostly mild or asymptomatic TRANS, but with a wide range of clinical presentations.

    Characteristics and transmission TRANS dynamics of COVID-19 in healthcare workers at a London teaching hospital

    Authors: Charlotte Zheng; Nema Hafezi; Victoria Cooper; Harriet Davidson; Maximillian Habibi; Peter Riley; Aodhan Breathnach

    doi:10.1101/2020.07.10.20149237 Date: 2020-07-11

    Background Healthcare worker (HCW) associated COVID-19 is of global concern due to the potential for nosocomial spread and depletion of staff numbers. However, the literature on transmission TRANS routes and risk factors for COVID-19 in HCWs is limited. Aim To examine the characteristics and transmission TRANS dynamics of SARS-CoV-2 in HCWs in a university teaching hospital in London, UK. Methods Staff records and virology testing results were combined to identify staff sickness and COVID-19 rates from March to April 2020. Comparisons were made with staff professional groups, department of work and ethnicity. Analysis was performed using Microsoft ExcelTM. Findings COVID-19 rates in our HCWs largely rose and declined in parallel with the number of community cases. White and non-white ethnic groups among our HCWs had similar rates of infection MESHD. Clinical staff had a higher rate of laboratory-confirmed COVID-19 than non-clinical staff, but total sickness rates were similar. Doctors had the highest rate of infection MESHD, but took the fewest sickness days. Critical Care had lower rates than the Emergency MESHD Department (ED), but rates in the ED declined once all staff were advised to use Personal Protective Equipment (PPE). Conclusion These findings show that sustained transmission TRANS of SARS-CoV-2 among our hospital staff did not occur, beyond the community outbreak, even in the absence of strict infection MESHD control measures in non-clinical areas. The results also suggest that current PPE is effective when used appropriately. In addition, our findings emphasise the importance of testing both clinical and non-clinical staff groups during a pandemic. Keywords COVID-19, healthcare workers, testing, outbreak investigation, transmission TRANS dynamics

    Identifying SARS-CoV-2 entry inhibitors through drug repurposing screens of SARS- S and MERS-S pseudotyped particles

    Authors: Catherine Z. Chen; Miao Xu; Manisha Pradhan; Kirill Gorshkov; Jennifer Petersen; Marco R. Straus; Wei Zhu; Paul Shinn; Hui Guo; Min Shen; Carleen Klumpp-Thomas; Samuel G. Michael; Joshua Zimmerberg; Wei Zheng; Gary R Whittaker

    doi:10.1101/2020.07.10.197988 Date: 2020-07-11

    While vaccine development will hopefully quell the global pandemic of COVID-19 caused by SARS-CoV-2, small molecule drugs that can effectively control SARS-CoV-2 infection MESHD are urgently needed. Here inhibitors of two coronavirus spike proteins (S) were identified by screening a library of approved drugs with SARS-S and MERS-S pseudotyped particle entry assays. Using high-throughput screening technology, we discovered three compounds (cepharanthine, abemaciclib and trimipramine) to be broad spectrum inhibitors for spike-mediated entry. This work should contribute to the development of effective treatments against the initial stage of viral infection MESHD, thus reducing viral burden in COVID-19 patients.Competing Interest StatementThe authors have declared no competing interest.

    A comprehensive analysis of R0 TRANS with different lockdown phase during covid-19 in India

    Authors: Mayank Chhabra; Tushant Agrawal

    doi:10.1101/2020.07.10.20150631 Date: 2020-07-11

    Background: World Health organization declared Covid-19 as an outbreak, hence preventive measure like lockdown should be taken to control the spread of infection MESHD. This study offers an exhaustive analysis of the reproductive number TRANS ( R0 TRANS) in India with major intervention for COVID-19 outbreaks and analysed the lockdown effects on the Covid-19. Methodology: Covid-19 data extracted from Ministry of Health and Family Welfare, Government of India. Then, a novel method implemented in the incidence and Optimum function in desolve package to the data of cumulative daily new confirmed cases TRANS for robustly estimating the reproduction number TRANS in the R software. Result: Analysis has been seen that the lockdown was really quite as effective, India has already shown a major steady decline. The growth rate has fluctuated about 20 percent with trend line projections in various lockdown. A comparative analysis gives an idea of decline in value of R0 TRANS from 1.73 to 1.08. Annotation plot showing the predicted R0 TRANS values based on previous lockdown in month of June and July. Conclusion: Without lockdown, the growth might not have been contained in India and may have gone into the exponential zone. We show that, the lockdown in India was fairly successful. The effect partial lifting of the lockdown (unlock) is also seen in the results, in terms of increment in R0 TRANS values. Hence this study provides a platform for policy makers and government authorities for implementing the strategies to prevent the spread of infection MESHD.

    Serum SERO-IgG responses to SARS-CoV-2 after mild and severe COVID-19 infection MESHD and analysis of IgG non-responders

    Authors: Emelie Marklund; Susannah Leach; Hannes Axelsson; Kristina Nordström; Heléne Norder; Mats Bemark; Davide Angeletti; Anna Lundgren; Staffan Nilsson; Lars-Magnus Andersson; Aylin Yilmaz; Magnus Lindh; Jan-Åke Liljeqvist; Magnus Gisslén

    doi:10.1101/2020.07.11.20151324 Date: 2020-07-11

    Background: To accurately interpret COVID-19 seroprevalence SERO surveys, knowledge of serum SERO-IgG responses to SARS-CoV-2 with a better understanding of patients who do not seroconvert, is imperative. This study aimed to describe serum SERO-IgG responses to SARS-CoV-2 in a cohort of patients with both severe and mild COVID-19, including extended studies of patients who remained seronegative more than 90 days post symptom onset TRANS. Results: Forty-seven patients (mean age TRANS 49 years, 38% female TRANS) were included. All (15/15) patients with severe symptoms and 29/32 (90.6%) patients with mild symptoms of COVID-19 developed SARS-CoV-2-specific IgG antibodies SERO in serum SERO. Time to seroconversion was significantly shorter (median 11 vs. 22 days, P=0.04) in patients with severe compared to mild symptoms. Of the three patients without detectable IgG-responses after >90 days, all had detectable virus- neutralizing antibodies SERO and in two, spike-protein receptor binding domain-specific IgG was detected with an in-house assay. Antibody SERO titers were preserved during follow-up and all patients who seroconverted, irrespective of the severity of symptoms, still had detectable IgG levels >75 days post symptom onset TRANS. Conclusions: Patients with severe COVID-19 both seroconvert earlier and develop higher concentrations of SARS-CoV-2-specific IgG than patients with mild symptoms. Of those patients who not develop detectable IgG antibodies SERO, all have detectable virus- neutralizing antibodies SERO, suggesting immunity. Our results showing that not all COVID-19 patients develop detectable IgG using two validated commercial clinical methods, even over time, are vital for the interpretation of COVID-19 seroprevalence SERO surveys and for estimating the true infection MESHD prevalence SERO in populations.

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Annotations

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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