bluuebunny/crossref_metadata_2025_split huggingface dataset:
Country specific mutational profile of SARS-CoV-2 in pre- and post-international travel ban: Effect on vaccine efficacy
Authors: Laha Sayantan , Chatterjee Raghunath 
Published: February 2021

ABSTRACTIn order to curb the rapid transmission of SARS-CoV-2, nation-wide lockdowns were implemented as a preliminary measure. Since most countries enforced travel-bans during end of March 2020, the country-specific patterns should be discernible in the subsequent months. We identified frequently mutated non-synonymous mutations in ∼2,15,000 SARS-CoV-2 sequences during pre- and post-travel-ban periods in 35 countries. We further investigated the mutational profile on a bi-monthly basis and traced the progress over the time. Several new mutations have emerged post-travel-ban and on the rise in specific countries, chief among them being A222V and S477N in Spike, and A220V in Nucleocapsid protein. Consequently, we examined the Spike protein epitopes to inspect whether any of these country-specific mutations overlapped with these epitopes. Several mutations were found to be contained within one or more epitopes, including the highly mutated residues of Spike protein, advocating the requirement of active monitoring of vaccine efficacies in respective countries.
SARS-CoV-2 re-infection risk in Austria
Authors: Pilz Stefan , Chakeri Ali , Ioannidis John PA , Richter Lukas , Theiler-Schwetz Verena , Trummer Christian , Krause Robert , Allerberger Franz 
Published: February 2021

ABSTRACTBackgroundA key question concerning coronavirus disease 2019 (COVID-19) is how effective and long lasting immunity against this disease is in individuals who were previously infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to evaluate the risk of SARS-CoV-2 re-infections in the general population in Austria.MethodsThis is a retrospective observational study using national SARS-CoV-2 infection data from the Austrian epidemiological reporting system. As the primary outcome, we aim to compare the odds of SARS-CoV-2 re-infections of COVID-19 survivors of the first wave (February to April 30, 2020) versus the odds of first infections in the remainder general population by tracking polymerase chain reaction (PCR)-confirmed infections of both groups during the second wave from September 1 to November 30, 2020. Re-infection counts are tentative, since it cannot be excluded that the positive PCR in the first and/or second wave might have been a false positive.ResultsWe recorded 40 tentative re-infections in 14,840 COVID-19 survivors of the first wave (0.27%) and 253,581 infections in 8,885,640 individuals of the remaining general population (2.85%) translating into an odds ratio (95% confidence interval) of 0.09 (0.07 to 0.13).ConclusionsWe observed a relatively low re-infection rate of SARS-CoV-2 in Austria. Protection against SARS-CoV-2 after natural infection is comparable to the highest available estimates on vaccine efficacies. Further well-designed research on this issue is urgently needed for improving evidence-based decisions on public health measures and vaccination strategies.
SARS-CoV-2 Seroprevalence Among Antenatal Clinic Attendees in Kingston, Jamaica, September-November 2020
Authors: Chisolm Te’Anne , Walker Jerome P. , Leys Ynolde , Butterfield Tiffany R. , Medley Candice , Thompson Tamara K. , Reynolds-Campbell Glendee , Mulder Willem H. , Mitchell Michelle Campbell , Anzinger Joshua J. 
Published: February 2021

AbstractSARS-CoV-2 seroprevalence in an antenatal population in Kingston, Jamaica was assessed for September-November 2020 in a repeated cross-sectional study using the Abbott Architect SARS-CoV-2 IgG assay. After adjusting for test performance, seroprevalence was 6.9% for September, 16.9% for October, and 24.0% for November. Of the 37 pregnant women testing SARS-CoV-2 IgG positive, only 3 were symptomatic. One symptomatic woman testing SARS-CoV-2 IgG positive had multiple co-morbidities and succumbed to COVID-19 pneumonia. Up to January 31, 2021, 8 women identified as SARS-CoV-2 IgG positive delivered, all without complications. Comparison of test adjusted seroprevalence data with cumulative PCR-confirmed COVID-19 cases within the Kingston Metropolitan Area indicated that as many as 44.4 times more people were infected with SARS-CoV-2 than identified with PCR testing. These findings provide the first evidence for the extent of SARS-CoV-2 infections in Jamaica and will inform future SARS-CoV-2 testing strategies.
Workplace sexual harassment in sexual and reproductive services: a preliminary cross-sectional study
Authors: Costanzo Italo 
Published: February 2021

ABSTRACTINTRODUCTIONSexual harassment at the workplace in health care is most prevalent in Anglo regions, although is an emerging problem globally. No research has yet focused on the prevalence of the phenomenon within the area of sexual and reproductive health care in Anglo regions. The aim of this study is therefore to measure the prevalence of sexual harassment in sexual and reproductive health care setting and compare it with other clinical areas.METHODA web survey to health care workers of various NHS Trusts in the United Kingdom was carried out and a cross-sectional study was conducted to measure observed counts, expected frequencies and prevalence from a total of 90 questionnaires received.RESULTSThe prevalence of workplace sexual harassment within the sexual and reproductive health services is lower compared to other clinical areas.CONCLUSIONSWorking in sexual and reproductive services could be a protective factor for workplace sexual harassment, therefore this study originates a new line of research aiming to identify the protective factors against sexual harassment at the workplace in sexual and reproductive health and the ways they could be used to protect every health care worker from sexual harassment in the workplace.KEY POINTSThe prevalence of workplace sexual harassment in sexual and reproductive health services is lower compared to other clinical areas.Working in sexual and reproductive services could be a protective factor for workplace sexual harassment.
A SARS-CoV-2 lineage A variant (A.23.1) with altered spike has emerged and is dominating the current Uganda epidemic
Authors: Bugembe Daniel Lule , V.T.Phan My , Ssewanyana Isaac , Semanda Patrick , Nansumba Hellen , Dhaala Beatrice , Nabadda Susan , O’Toole Áine Niamh , Rambaut Andrew , Kaleebu Pontiano , Cotten Matthew 
Published: February 2021

Introductory paragraphSARS-CoV-2 genomic surveillance in Uganda provides an opportunity to provide a focused description of the virus evolution in a small landlocked East African country. Here we show a recent shift in the local epidemic with a newly emerging lineage A.23 evolving into A.23.1 which is now dominating the Uganda cases and has spread to 26 other countries. Although the precise changes in A.23.1 as it has adapted are different from the changes in the variants of concern (VOC), the evolution shows convergence on a similar set of proteins. The A.23.1 spike protein coding region has accumulated changes that resemble many of the changes seen in VOC including a change at position 613, a change in the furin cleavage site that extends the basic amino acid motif, and multiple changes in the immunogenic N-terminal domain. In addition, the A.23.1lineage encodes changes in non-spike proteins that other VOC show (nsp6, ORF8 and ORF9). The clinical impact of the A.23.1 variant is not yet clear, however it is essential to continue careful monitoring of this variant, as well as rapid assessment of the consequences of the spike protein changes for vaccine efficacy.
A precise score for the regular monitoring of COVID-19 patients condition validated within the first two waves of the pandemic
Authors: Bakin Evgeny A. , Stanevich Oksana V. , Belash Vassily A. , Belash Anastasia A. , Savateeveva Galina A. , Bokinova Veronika A. , Arsentieva Natalia A. , Sayenko Ludmila F. , Korobenkov Evgeny A. , Lioznov Dmitry A. , Totolian Areg A. , Polushin Yury S. , Kulikov Alexander N. 
Published: February 2021

AbstractPurposeThe sudden outbreak of COVID-19 pandemic has shown that the medical community needs an accurate and interpretable aggregated score not only for an outcome prediction but also for a daily patient’s condition assessment. Due to a continuously changing pandemic landscape, robustness becomes a crucial additional requirement for the score.Patients and methodsIn this research, real-world data collected within the first two waves of the COVID-19 pandemic was used. The first wave data (1349 cases collected from 27.04.2020 to 03.08.2020) was used as a training set for the score development, while the second wave data (1453 cases collected from 01.11.2020 to 19.01.2021) was used as a validating set. For all the available patients’ features we tested their association with an outcome using robust linear regression. Statistically significant features were taken to the further analysis for each of which their partial sensitivity, specificity and promptness were estimated. The sensitivity and the specificity were further combined into a feature informativeness index.ResultsThe developed score was derived as a weighted sum of the following 9 features showed the best trade-off between informativeness and promptness: APTT (> 42 sec, 4 points), CRP (> 146 mg/L, 3 points), D-dimer (> 2149 mkg/L, 4 points), Glucose (> 9 mmol/L, 4 points), Hemoglobin (< 115 g/L, 3 points), Lymphocytes (< 0,7*10^9/L, 3 points), Total protein (< 61 g/L, 6 points), Urea (> 11 mmol/L, 5 points) and WBC (> 13,5*10^9/L, 4 points). Thus, the proposed score ranges between 0 and 36 points. Internal and temporal validation showed that sensitivity and specificity over 90% may be achieved with an expected prediction range >7 days. Moreover, we demonstrated a high robustness of the score to the varying peculiarities of the pandemic. For the additional simplicity of application we split the full range of the score into five grades delimited with 9, 14, 19 and 24 points which determine expected death:discharge odds 1:100, 1:25, 1:5 and 1:1 correspondingly.ConclusionsAn extensive application of the score within the second wave of the COVID-19 pandemic showed its potential for the optimization of patients management as well as improvement of medical staff attentiveness during high workload stress. The transparent structure of the score, as well as tractable cut-off bounds, simplified its implementation into clinical practice.
Results of an early second PCR test performed on SARS-CoV-2 positive patients may indicate risk for severe COVID-19
Authors: Mizrahi Barak , Bivas-Benita Maytal , Kalkstein Nir , Akiva Pinchas , Yanover Chen , Yehezkelli Yoav , Kessler Yoav , Alon Sharon Hermoni , Rubin Eitan , Chodick Gabriel 
Published: February 2021

AbstractIdentifying patients at increased risk for severe COVID-19 is of high priority during the pandemic as it could affect clinical management and shape public health guidelines. In this study we assessed whether a second PCR test conducted 2-7 days after a SARS-CoV-2 positive test could identify patients at risk for severe illness. Analysis of a nationwide electronic health records data of 1,683 SARS-CoV-2 positive individuals indicated that a second negative PCR test result was associated with lower risk for severe illness compared to a positive result. This association was seen across different age groups and clinical settings. More importantly, it was not limited to recovering patients but also observed in patients who still had evidence of COVID-19 as determined by a subsequent positive PCR test. Our study suggests that an early second PCR test may be used as an additional risk-assessment tool to improve disease management and patient care.
Penalized regression for left-truncated and right-censored survival data
Authors: McGough Sarah F. , Incerti Devin , Lyalina Svetlana , Copping Ryan , Narasimhan Balasubramanian , Tibshirani Robert 
Published: February 2021

AbstractHigh-dimensional data are becoming increasingly common in the medical field as large volumes of patient information are collected and processed by high-throughput screening, electronic health records (EHRs), and comprehensive genomic testing. Statistical models that attempt to study the effects of many predictors on survival typically implement feature selection or penalized methods to mitigate the undesirable consequences of overfitting. In some cases survival data is also left-truncated which can give rise to an immortal time bias, but penalized survival methods that adjust for left truncation are not commonly implemented. To address these challenges, we apply a penalized Cox proportional hazards model for left-truncated and right-censored survival data and assess implications of left truncation adjustment on bias and interpretation. We use simulation studies and a high-dimensional, real-world clinico-genomic database (CGDB) to highlight the pitfalls of failing to account for left truncation in survival modeling.
Temporal trends of SARS-CoV-2 seroprevalence in transfusion blood donors during the first wave of the COVID-19 epidemic in Kenya
Authors: Adetifa Ifedayo M.O. , Uyoga Sophie , Gitonga John N. , Mugo Daisy , Otiende Mark , Nyagwange James , Karanja Henry K. , Tuju James , Wanjiku Perpetual , Aman Rashid , Mwangangi Mercy , Amoth Patrick , Kasera Kadondi , Ng’ang’a Wangari , Rombo Charles , Yegon Christine , Kithi Khamisi , Odhiambo Elizabeth , Rotich Thomas , Orgut Irene , Kihara Sammy , Bottomley Christian , Kagucia Eunice W. , Gallagher Katherine E. , Etyang Anthony , Voller Shirine , Lambe Teresa , Wright Daniel , Barasa Edwine , Tsofa Benjamin , Bejon Philip , Ochola-Oyier Lynette I. , Agweyu Ambrose , Scott J. Anthony G. , Warimwe George M. 
Published: February 2021

AbstractObserved SARS-CoV-2 infections and deaths are low in tropical Africa raising questions about the extent of transmission. We measured SARS-CoV-2 IgG by ELISA in 9,922 blood donors across Kenya and adjusted for sampling bias and test performance. By 1st September 2020, 577 COVID-19 deaths were observed nationwide and seroprevalence was 9.1% (95%CI 7.6-10.8%). Seroprevalence in Nairobi was 22.7% (18.0-27.7%). Although most people remained susceptible, SARS-CoV-2 had spread widely in Kenya with apparently low associated mortality.
Accounting for imported cases in estimating the time-varying reproductive number of COVID-19
Authors: Tsang Tim K. , Wu Peng , Lau Eric H. Y. , Cowling Benjamin J. 
Published: February 2021

ABSTRACTBackgroundEstimating the time-varying reproductive number, Rt, is critical for monitoring transmissibility of an emerging infectious disease during outbreaks. When local transmission is effectively suppressed, imported cases could substantially impact transmission dynamics.MethodsWe developed methodology to estimate separately the Rt for local cases and imported cases, since certain public health measures aim only to reduce onwards transmission from imported cases. We applied the framework to data on COVID-19 outbreaks in Hong Kong.ResultsWe estimated that the Rt for local cases decreased from above one in the early phase of outbreak to below one after tightening of public health measures. Assuming the same infectiousness of local and imported cases underestimated Rt for local cases due to control measures targeting travelers.ConclusionsWhen a considerable proportion of all cases are imported, the impact of imported cases in estimating Rt is critical. The methodology described here can allow for differential infectiousness of local imported cases.
The global distribution of COVID-19 vaccine: The role of macro-socioeconomics measures
Authors: Roghani Ali , Panahi Samin 
Published: February 2021

AbstractSince coronavirus disease 2019 (covid-19) has continued to spread globally, many countries have progressed clinical trials and started vaccinations at the end of December 2020. This report aims to analyze the association of COVID-19 vaccine distribution and two macro-socioeconomics measures, including human development index (HDI) and Gross domestic product (GDP), among 25 countries till the first week of February 2021. Our results indicate that a higher GDP per Capita is positively associated with higher COVID-19 vaccine distribution. In addition, the result shows HDI does not have a significant relationship with vaccine distribution. Although these macro-socioeconomic measures may be counted as a vital indicator for vaccine distribution, other factors may play roles in vaccine distribution, including well-developed health infrastructure, a centralized political system, and population size.
Quantifying the preventive effect of wearing face masks
Authors: Britton Tom 
Published: February 2021

AbstractAn important task in combating the ongoing covid-19 effect lies in estimating the effect of different preventive measures. Here we focus on the preventive effect of enforcing the use of face masks. Several publications study this effect, however often using different measures such as: the relative attack rate in case-control studies, the effect on incidence growth/decline in a specific time-frame, the effect on the number of infected in a given time-frame. These measures all depend on community-specific features and are hence not easily transferred to other community settings. We argue that a more universal measure is the relative reduction in the reproduction number, which we call the face mask effect, EFM. It is shown how to convert the other measures to EFM. We also apply the methodology on three publications using different other measures (two of them resulting in two different estimates each, and all five estimates of EFM lie between 20-40%, suggesting that mandatory face masks reduce the reproduction number by 20-40% as compared to no individuals wearing face masks.
Immune deposit and vasculopathy in metabolic-active lung tissues of patients with pulmonary tuberculosis
Authors: Ma Hui , Wang Lin , Wen Zilu , Chen Xinchun , Liu Haiying , Zhang Shulin , Xu Jianqing , Song Yanzheng , Wong Ka-Wing 
Published: February 2021

ABSTRACTMetabolic activity in pulmonary lesion is associated with disease severity and relapse risk in tuberculosis. However, the nature of the metabolic activity associated with tuberculosis in humans remains unclear. Previous works indicate that tuberculosis bears resemblance transcriptionally with systemic lupus erythematosus in peripheral blood, except that the plasma cell component was absent in tuberculosis. Here we reported that the missing transcriptional component was present within the metabolic active tissues in the lung of patients with sputum culture-negative tuberculosis, within which increased levels of circulating immune complexes and anti-dsDNA antibodies were found relative to nearby non-metabolic active tissues. Histological examination revealed specific vascular deposition of immune complexes, neutrophil extracellular traps, and vascular necrosis in the metabolic-active tissue. Thus, tuberculosis-initiated metabolic activity was associated with hyperactive antibody responses and vascular pathology, and shared features with systemic lupus erythematosus and other autoimmune diseases. We discussed these observations in the context of earlier literatures demonstrating that similar effects could be induced in humans and animal models by complete freund’s adjuvant, the most potent antibody response inducer ever reported. Our small case series, if verified in a larger size study, might help inform host-directed therapies to alleviate disease progression and augment treatment efficacy.IMPORTANCEIn patients with pulmonary tuberculosis, lung tissues were destroyed by a hyperactive inflammatory response towardsM. tuberculosis. The mechanisms underlying the inflammatory response are still poorly understood. Using 18F-FDG avidity as a surrogate marker of inflammation, we have identified that hyper-inflamed tissues possessed features associated with systemic lupus erythematosus: gene expression signatures of plasma cell and immunoglobulins and increased levels of anti-dsDNA antibodies, immune deposits, and vasculopathy. This observation might suggest an explanation to why patients with tuberculosis share more gene expression signatures with autoimmune diseases than infectious diseases and why they are more likely to develop autoimmune diseases. Defining the inflammatory responses at the lesion could help inform host-directed therapies to intervene disease progression or even accelerate cure.
Seroprevalence of SARS-CoV-2, symptom profiles and seroneutralization during the first COVID-19 wave in a suburban area, France
Authors: Gégout petit Anne , Jeulin Hélène , Legrand Karine , Bochnakian Agathe , Vallois Pierre , Schvoerer Evelyne , Guillemin Francis 
Published: February 2021

AbstractBackgroundThe World Health Organisation recommends monitoring the circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to estimate anti–SARS-CoV-2 total immunoglobulin (IgT) antibody seroprevalence and describe symptom profiles and in vitro seroneutralization in Nancy, France, in spring 2020.MethodsIndividuals were randomly sampled from electoral lists and invited with household members over 5 years old to be tested for anti–SARS-CoV-2 (IgT, i.e. IgA/IgG/IgM) antibodies by ELISA (Bio-rad). Serum samples were classified according to seroneutralization activity >50% (NT50) on Vero CCL-81 cells. Age- and sex-adjusted seroprevalence was estimated. Subgroups were compared by chi-square or Fisher exact test and logistic regression.ResultsAmong 2006 individuals, 43 were SARS-CoV-2–positive; the raw seroprevalence was 2.1% (95% confidence interval 1.5 to 2.9), with adjusted metropolitan and national standardized seroprevalence 2.5% (1.8 to 3.3) and 2.3% (1.7 to 3.1). Seroprevalence was highest for 20-to 34-year-old participants (4.7% [2.3 to 8.4]), within than out of socially deprived area (2.5% vs 1%, P=0.02) and with than without intra-family infection (p<10−6). Moreover, 25% (23 to 27) of participants presented at least one COVID-19 symptom associated with SARS-CoV-2 positivity (p<10−13), with anosmia or ageusia highly discriminant (odds ratio 27.8 [13.9 to 54.5]), associated with dyspnea and fever. Among the SARS-CoV-2-positives, 16.3% (6.8 to 30.7) were asymptomatic. For 31 of these individuals, positive seroneutralization was demonstrated in vitro.ConclusionsIn this population of very low anti-SARS-CoV-2 antibody seroprevalence, a beneficial effect of the lockdown can be assumed, with frequent SARS-CoV-2 seroneutralization among IgT-positive patients.Key MessagesTotal immunoglobulin antibody (IgT) measurement is an accurate tool to monitor the circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and a key biological feature to assume the spread of COVID-19 later after the appearance of symptoms.IgT seroprevalence was 2.1% in the Grand Nancy Metropolitan area, France; was highest for young adults; in socially deprived area, but this was not confirmed at the individual level; and was associated with high intra-family viral transmission.About two thirds of IgT-positive individuals exhibited SARS-CoV-2–positive seroneutralization.Trial registrationNCT04448769