Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (76)

Fever (50)

Cough (40)

Falls (29)

Fatigue (8)


Transmission

Seroprevalence
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    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

    Community prevalence SERO of SARS-CoV-2 virus in England during May 2020: REACT study

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

    doi:10.1101/2020.07.10.20150524 Date: 2020-07-11

    Background England has experienced one of the highest rates of confirmed COVID-19 mortality in the world. SARS-CoV-2 virus has circulated in hospitals, care homes and the community since January 2020. Our current epidemiological knowledge is largely informed by clinical cases with far less understanding of community transmission TRANS. Methods The REal-time Assessment of Community Transmission TRANS (REACT) study is a nationally representative prevalence SERO survey of SARS-CoV-2 virus swab-positivity in the community in England. We recruited participants regardless of symptom status. Results We found 159 positives from 120,610 swabs giving an average prevalence SERO of 0.13% (95% CI: 0.11%,0.15%) from 1st May to 1st June 2020. We showed decreasing prevalence SERO with a halving time of 8.6 (6.2, 13.6) days, implying an overall reproduction number TRANS R of 0.57 (0.45, 0.72). Adults TRANS aged TRANS 18 to 24 yrs had the highest swab-positivity rates, while those >64 yrs had the lowest. Of the 126 participants who tested positive with known symptom status in the week prior to their swab, 39 reported symptoms while 87 did not, giving an estimate that 69% (61%,76%) of people were symptom-free for the 7 days prior testing positive in our community sample. Symptoms strongly associated with swab-positivity were: nausea MESHD nausea and/or vomiting HP and/or vomiting MESHD, diarrhoea, blocked nose, loss of smell, loss of taste, headache MESHD headache HP, chills MESHD chills HP and severe fatigue MESHD fatigue HP. Recent contact with a known COVID-19 case was associated with odds of 24 (16, 38) for swab-positivity. Compared with non-key workers, odds of swab-positivity were 7.7 (2.4, 25) among care home (long-term care facilities) workers and 5.2 (2.9, 9.3) among health care workers. However, some of the excess risk associated with key worker status was explained by recent contact with COVID-19 cases. We found no strong evidence for geographical variability in positive swab results. Conclusion Our results provide a reliable baseline against which the impact of subsequent relaxation of lockdown can be assessed to inform future public health efforts to control transmission TRANS.

    Transmission TRANS dynamics and control measures of COVID-19 outbreak in China: a modelling study

    Authors: XuSheng Zhang; Emilia Vynnycky; Andre Charlett; Daniela de Angelis; Zhengji Chen; Wei Liu

    doi:10.1101/2020.07.09.20150086 Date: 2020-07-11

    COVID-19 is reported to have been effectively brought under control in China at its initial start place. To understand the COVID-19 outbreak in China and provide potential lessons for other parts of the world, in this study we combine a mathematical modelling with multiple datasets to estimate its transmissibility TRANS and severity and how it was affected by the unprecedented control measures. Our analyses show that before 29th January 2020, the ascertainment rate is 6.9%(95%CI: 3.5 - 14.6%); then it increased to 41.5%(95%CI: 30.6 - 65.1%). The basic reproduction number TRANS ( R0 TRANS) was 2.23(95%CI: 1.86 - 3.22) before 8th February 2020; then it dropped to 0.04(95%CI: 0.01 - 0.10). This estimation also indicates that the effect on transmissibility TRANS of control measures taken since 23rd January 2020 emerged about two weeks late. The confirmed case TRANS fatality rate is estimated at 4.41%(95%CI: 3.65 - 5.30%). This shows that SARS-CoV-2 virus is highly transmissible but less severe than SARS-CoV-1 and MERS-CoV. We found that at the early stage, the majority of R0 TRANS comes from the undetected infected people. This implies that the successful control in China was achieved through decreasing the contact rates among people in general populations and increasing the rate of detection and quarantine of the infected cases.

    Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka

    Authors: Chitra Pattabiraman; Farhat Habib; Harsha PK; Risha Rasheed; Vijayalakshmi Reddy; Prameela Dinesh; Tina Damodar; Nakka Vijay Kiran Reddy; Kiran Hosallimath; Anson K George; Banerjee John; Amrita Pattanaik; Narendra Kumar; Reeta S Mani; Manjunatha M Venkataswamy; Shafeeq K Shahul Hameed; Prakash Kumar B.G.; Anita Desai; Ravi Vasanthapuram

    doi:10.1101/2020.07.10.20150045 Date: 2020-07-11

    Karnataka, a state in south India, reported its first case of Severe Acute Respiratory Syndrome MESHD Coronavirus 2 (SARS-CoV-2) on March 8, 2020, more than a month after the first case was reported in India. We used a combination of contact tracing TRANS and genomic epidemiology to trace TRANS the spread of SARS-CoV-2 in the state up until May 21, 2020 (1578 cases). We obtained 47 full genomes of SARS-CoV-2 which clustered into six lineages (Pangolin lineages-A, B, B.1, B.1.1, B.4, and B.6). The lineages in Karnataka were known to be circulating in China, Southeast Asia, Iran, Europe and other parts of India and are likely to have been imported into the state both by international and domestic travel TRANS. Our sequences grouped into 12 contact clusters and 11 cases with no known contacts. We found nine of the 12 contact clusters had a single lineage of the virus, consistent with multiple introductions and most (8/12) were contained within a single district, consistent with local spread. In most of the twelve clusters, the index case (9/12) and spreaders (8/12) were symptomatic. Of the 47 sequences, 31 belonged to the B/B.6 lineage, including seven of eleven cases with no known contact, this is consistent with the ongoing transmission TRANS of this lineage in the state. Genomic epidemiology of SARS-CoV-2 in Karnataka is consistent with multiple introductions of the virus followed by local transmission TRANS in parallel with ongoing viral evolution. This is the first study from India combining genomic data with epidemiological information emphasizing the need for an integrated approach to outbreak response.

    Lockdown measures in response to COVID-19 in Sub-Saharan Africa: A rapid study of nine countries

    Authors: Najmul Haider; Abdinasir Yusuf Osman; Audrey Gadzekpo; George O. Akpede; Danny Asogun; Rashid Ansumana; Richard John Lessells; Palwasha Khan; Muzamil Mahdi Abdel Hamid; Dorothy Yeboah-Manu; Leonard Mboera; Elizabeth H Shayo; Blandina Mmbaga; Mark Urassa; David Musoke; Nathan Kapata; Rashida Abbas Ferrand; Pascalina Chanda-Kapata; Florian Stigler; Thomas Czypionka; Richard A Kock; David McCoy

    doi:10.1101/2020.07.09.20149054 Date: 2020-07-11

    Lockdown measures have been introduced worldwide to contain the transmission TRANS of COVID-19. This paper defines the term lockdown and describes the design, timing and implementation of lockdown in nine countries in Sub Saharan Africa: Ghana, Nigeria, South Africa, Sierra Leone, Sudan, Tanzania, Uganda, Zambia and Zimbabwe. It also discusses the manner in which lockdown is enforced, the need to mitigate the harms of lockdown, and the association between lockdown and the reported number of COVID-19 cases and deaths MESHD. While there are some commonalities in the implementation of lockdown, a more notable finding is the variation in the design, timing and implementation of lockdown measures across the nine countries. We found that the number of reported cases is heavily dependent on the number of tests done, and that testing rates ranged from 9 to 21,261 per million population. The reported number of COVID-19 deaths MESHD per million population also varies, but is generally low when compared to countries in Europe and North America. While lockdown measures may have helped inhibit some community transmission TRANS, the pattern and nature of the epidemic remains unclear. Of concern are signs of lockdown harming health by affecting the functioning of the health system and causing social and economic harms. This paper highlights the need for inter-sectoral and trans-disciplinary research capable of providing a rigorous and holistic assessment of the harms and benefits of lockdown.

    Undocumented infectives in the Covid-19 pandemic

    Authors: Maurizio Melis; Roberto Littera

    doi:10.1101/2020.07.09.20149682 Date: 2020-07-11

    Background. A crucial role in epidemics is played by the number of undetected infective individuals who continue to circulate and spread the disease TRANS disease MESHD. Epidemiological investigations and mathematical models have revealed that the rapid diffusion of Covid-19 can mostly be attributed to the large percentage of undocumented infective individuals who escape testing. Methods. The dynamics of an infection MESHD can be described by the SIR model, which divides the population into susceptible (S), infective (I) and removed (R) subjects. In particular, we exploited the Kermack and McKendrick epidemic model which can be applied when the population is much larger than the fraction of infected subjects. Results. We proved that the fraction of undocumented infectives, in comparison to the total number of infected subjects, is given by 1-1/ R0 TRANS , where R0 TRANS is the basic reproduction number TRANS. Its mean value R0=2.10 (2.09-2.11) in three Italian regions for the Covid-19 epidemic yielded a percentage of undetected infectives of 52.4% (52.2% - 52.6%) compared to the total number of infectives. Conclusions. Our results, straightforwardly obtained from the SIR model, highlight the role played by undetected carriers TRANS in the transmission TRANS and spread of the SARS-CoV-2 infection MESHD. Such evidence strongly recommends careful monitoring of the infective population and ongoing adjustment of preventive measures for disease MESHD control until a vaccine becomes available.

    Estimating the time-varying reproduction number TRANS of COVID-19 with a state-space method

    Authors: Shinsuke Koyama; Taiki Horie; Shigeru Shinomoto

    doi:10.1101/2020.07.09.20150219 Date: 2020-07-11

    After slowing down the spread of the novel coronavirus COVID-19, many countries have started to relax their severe confinement measures in the face of critical damage to socioeconomic structures. At this point, it is desirable to monitor the degree to which political measures or social affairs have exerted influence on the spread of disease TRANS disease MESHD; however, tracing TRANS back individual transmission TRANS of infections MESHD whose incubation periods TRANS are long and highly variable seems to be difficult. Nevertheless, it may be possible to estimate the changes that may have occurred in the past, if we can suitably fit a proper model to daily event-occurrences. We have devised a state-space method for fitting the Hawkes process to a given dataset of daily confirmed cases TRANS. This method detects changes occurring in the spread of the contagion in each country. Furthermore, this method can assess the impact of social events in terms of the temporally varying reproduction number TRANS representing the average number of cases directly caused by a single infected case. This information might serve as a reference for the behavioral guidelines that should be adopted according to the varying risk of infection TRANS risk of infection TRANS infection MESHD.

    Modeling and Preparedness: The Transmission TRANS Dynamics of COVID-19 Outbreak in Provinces of Ecuador

    Authors: Carlos Enrique Bustamante Orellana; Jordy Jose Cevallos Chavez; Cesar Montalvo; Jeff Sullivan; Edwin Michael; Anuj Mubayi

    doi:10.1101/2020.07.09.20150078 Date: 2020-07-11

    Coronavirus disease MESHD 2019 (COVID-19), a novel infectious disease MESHD first identified in December 2019 in the city of Wuhan of China, is caused by severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2). The disease MESHD has become a pandemic in just a few months and spread globally with more than 2.89 million cases and 203,000 deaths MESHD across 185 countries, as of April 26th, 2020. Ecuador has reported one of the highest rates of COVID-19 in Latin America, with more than 10K cases and 500 deaths MESHD in a country of approximately 17 million people. The dynamics of the outbreak is being observed quite different in different provinces of Ecuador with high reported prevalence SERO in some low population density provinces. In this study, we aim to understand variations in outbreaks between provinces and provide assistance in essential preparedness planning in order to respond effectively to ongoing COVID-19 outbreak. The study estimated the critical level of quarantine rate along with corresponding leakage in order to avoid overwhelming the local health care system. The results suggest that provinces with high population density can avoid a large disease MESHD burden provided they initiate early and stricter quarantine measures even under low isolation rate. To best of our knowledge, this study is first from the region to determine which provinces will need much preparation for current outbreak in fall HP and which might need more help.

    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.

    Estimating the Effect of Social Distancing Interventions on COVID-19 in the United States

    Authors: Andrew M. Olney; Jesse Smith; Saunak Sen; Fridtjof Thomas; H. Juliette T. Unwin

    doi:10.1101/2020.07.10.20151001 Date: 2020-07-11

    Since its global emergence in 2020, severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) has caused multiple epidemics in the United States. Because medical treatments for the virus are still emerging and a vaccine is not yet available, state and local governments have sought to limit its spread by enacting various social distancing interventions such as school closures and lockdown, but the effectiveness of these interventions is unknown. We applied an established, semi-mechanistic Bayesian hierarchical model of these interventions on SARS-CoV-2 spread in Europe to the United States. We estimated the effect of interventions across all states, contrasted the estimated reproduction number TRANS, Rt , for each state before and after lockdown, and contrasted predicted future fatalities with actual fatalities as a check on the model's validity. Overall, school closures and lockdown are the only interventions modeled that have a reliable impact on Rt , and lockdown appears to have played a key role in reducing Rt below 1.0. We conclude that reversal of lockdown, without implementation of additional, equally effective interventions, will enable continued, sustained transmission TRANS of SARS-CoV-2 in the United States.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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