Corpus overview


Overview

MeSH Disease

Human Phenotype

Fever (57)

Cough (41)

Pneumonia (31)

Fatigue (11)

Hypertension (11)


Transmission

Seroprevalence
    displaying 1 - 10 records in total 206
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    Household transmission TRANS of SARS-CoV-2: a systematic review and meta-analysis of secondary attack rate TRANS

    Authors: Zachary J. Madewell; Yang Yang; Ira M. Longini Jr.; M. Elizabeth Halloran; Natalie E. Dean

    doi:10.1101/2020.07.29.20164590 Date: 2020-08-01 Source: medRxiv

    Background: Severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) is spread by direct, indirect, or close contact TRANS with infected people via infected respiratory droplets or saliva. Crowded indoor environments with sustained close contact TRANS and conversations are a particularly high-risk setting. Methods: We performed a meta-analysis through July 29, 2020 of SARS-CoV-2 household secondary attack rate TRANS ( SAR TRANS), disaggregating by several covariates (contact type, symptom status, adult TRANS/ child TRANS contacts, contact sex, relationship to index case, index case sex, number of contacts in household TRANS, coronavirus). Findings: We identified 40 relevant published studies that report household secondary transmission TRANS. The estimated overall household SAR TRANS was 18.8% (95% confidence interval [CI]: 15.4%-22.2%), which is higher than previously observed SARs for SARS-CoV and MERS-CoV. We observed that household SARs were significantly higher from symptomatic index cases than asymptomatic TRANS index cases, to adult TRANS contacts than children TRANS contacts, to spouses than other family contacts, and in households TRANS with one contact than households TRANS with three or more contacts. Interpretation: To prevent the spread of SARS-CoV-2, people are being asked to stay at home worldwide. With suspected or confirmed infections TRANS infections MESHD referred to isolate at home, household transmission TRANS will continue to be a significant source of transmission TRANS.

    High SARS-CoV-2 seroprevalence SERO in Health Care Workers but relatively low numbers of deaths MESHD in urban Malawi

    Authors: Marah Grace Chibwana; Khuzwayo Chidiwa Jere; Jonathan Mandolo; Vincent Katunga-Phiri; Dumizulu Tembo; Ndaona Mitole; Samantha Musasa; Simon Sichone; Agness Lakudzala; Lusako Sibale; Prisca Matambo; Innocent Kadwala; Rachel Louise Byrne; Alice Mbewe; Ben Morton; Chimota Phiri; Jane Mallewa; Henry C Mwandumba; Emily R Adams; Stephen B Gordon; Kondwani Charles Jambo

    doi:10.1101/2020.07.30.20164970 Date: 2020-08-01 Source: medRxiv

    Background In low-income countries, like Malawi, important public health measures including social distancing or a lockdown, have been challenging to implement owing to socioeconomic constraints, leading to predictions that the COVID-19 pandemic would progress rapidly. However, due to limited capacity to test for severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) infection MESHD, there are no reliable estimates of the true burden of infection MESHD and death MESHD. We, therefore, conducted a SARS-CoV-2 serosurvey amongst health care workers (HCW) in Blantyre city to estimate the cumulative incidence of SARS-CoV-2 infection MESHD in urban Malawi. Methods Five hundred otherwise asymptomatic TRANS HCWs were recruited from Blantyre City (Malawi) from 22nd May 2020 to 19th June 2020 and serum samples SERO were collected all participants. A commercial ELISA SERO was used to measure SARS-CoV-2 IgG antibodies SERO in serum SERO. We run local negative samples (2018 - 2019) to verify the specificity of the assay. To estimate the seroprevalence SERO of SARS CoV-2 antibodies SERO, we adjusted the proportion of positive results based on local specificity of the assay. Results Eighty-four participants tested positive for SARS-CoV-2 antibodies SERO. The HCW with a positive SARS-CoV-2 antibody SERO result came from different parts of the city. The adjusted seroprevalence SERO of SARS-CoV-2 antibodies SERO was 12.3% [CI 9.0-15.7]. Using age TRANS-stratified infection MESHD fatality estimates reported from elsewhere, we found that at the observed adjusted seroprevalence SERO, the number of predicted deaths MESHD was 8 times the number of reported deaths MESHD. Conclusion The high seroprevalence SERO of SARS-CoV-2 antibodies SERO among HCW and the discrepancy in the predicted versus reported deaths MESHD, suggests that there was early exposure but slow progression of COVID-19 epidemic in urban Malawi. This highlights the urgent need for development of locally parameterised mathematical models to more accurately predict the trajectory of the epidemic in sub-Saharan Africa for better evidence-based policy decisions and public health response planning.

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

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

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

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

    Estimates of the rate of infection and asymptomatic MESHD asymptomatic TRANS COVID-19 disease MESHD in a population sample from SE England

    Authors: Philippa M Wells; Katie M Doores; Simon Couvreur; Rocio Martin Martinez; Jeffrey Seow; Carl Graham; Sam Acors; Neophytos Kouphou; Stuart Neil; Richard Tedder; Pedro Matos; Kate Poulton; Maria Jose Lista; Ruth Dickenson; Helin Sertkaya; Thomas Maguire; Edward Scourfield; Ruth Bowyer; Deborah Hart; Aoife O'Byrne; Kathryn Steele; Oliver Hemmings; Carolina Rosadas; Myra McClure; Joan Capedevila-Pujol; Jonathan wolf; Sebastien Ourseilin; Matthew Brown; Michael Malim; Timothy Spector; Claire Steves

    doi:10.1101/2020.07.29.20162701 Date: 2020-07-30 Source: medRxiv

    Background: Understanding of the true asymptomatic TRANS rate of infection MESHD of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence SERO after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms. Methods: We undertook enzyme linked immunosorbent assay SERO characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged TRANS 19-86 (median age TRANS 48; 85% female TRANS). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. Findings: We demonstrated a seroprevalence SERO of 12% (51participants of 431). Of 48 seropositive individuals with full symptom data, nine (19%) were fully asymptomatic TRANS, and 16 (27%) were asymptomatic TRANS for core COVID-19 symptoms: fever MESHD fever HP, cough MESHD cough HP or anosmia HP. Specificity of anosmia HP for seropositivity was 95%, compared to 88% for fever MESHD fever HP cough MESHD cough HP and anosmia HP combined. 34 individuals in the cohort were predicted to be Covid-19 positive using the App algorithm, and of those, 18 (52%) were seropositive. Interpretation: Seroprevalence SERO amongst adults TRANS from London and South-East England was 12%, and 19% of seropositive individuals with prospective symptom logging were fully asymptomatic TRANS throughout the study. Anosmia HP demonstrated the highest symptom specificity for SARS-CoV-2 antibody SERO response. Funding: NIHR BRC, CDRF, ZOE global LTD, RST-UKRI/MRC

    Early Clinical Factors Predicting the Development of Critical Disease MESHD in Japanese Patients with COVID-19: A Single-Center Retrospective, Observational Study

    Authors: Takatoshi Higuchi; Tsutomu Nishida; Hiromi Iwahashi; Osamu Morimura; Yasushi Otani; Yukiyoshi Okauchi; Masaru Yokoe; Norihiro Suzuki; Masami Inada; Kinya Abe

    doi:10.1101/2020.07.29.20159442 Date: 2020-07-30 Source: medRxiv

    Background: Insufficient evidence of factors predicting the COVID-19 progression from mild to moderate to critical has been established. We retrospectively evaluated risk factors for critical progression in Japanese COVID-19 patients. Method: Seventy-four laboratory-confirmed COVID-19 patients were hospitalized in our hospital between February 20, 2020, and June 10, 2020. We excluded asymptomatic TRANS, non-Japanese, and child TRANS patients. We divided patients into the stable group (SG) and the progression group (PG) (patients requiring mechanical ventilation). We compared the clinical factors in both groups. We established the cutoff values (COVs) for significantly different factors via receiver operating characteristic (ROC) curve analysis and evaluated risk factors by univariate regression. Results: We enrolled 57 COVID-19 patients (median age TRANS 52 years, 56.1% male TRANS). The median progression time from symptom onset TRANS was eight days. Seven patients developed critical disease MESHD (PG: 12.2%), two (3.5%) of whom died; 50 had stable disease MESHD. Univariate logistic analysis identified elevated lactate dehydrogenase (LDH) (COV: 309 U/l), decreased estimated glomerular filtration rate (eGFR) (COV: 68 ml/min), lymphocytopenia (COV: 980/l), and statin use as significantly associated with disease progression MESHD. However, in Cox proportional hazards analysis, lymphocytopenia at symptom onset TRANS was not significant. Conclusions: We identified three candidate risk factors for adult TRANS Japanese patients with mild to moderate COVID-19: statin use, elevated LDH level, and decreased eGFR.

    A Retrospective Study on Efficacy and Safety of Guduchi Ghan Vati for Covid-19 Asymptomatic TRANS Patients

    Authors: Abhimanyu Kumar; Govind Prasad; Sanjay Srivastav; Vinod Kumar Gautam; Neha Sharma

    doi:10.1101/2020.07.23.20160424 Date: 2020-07-29 Source: medRxiv

    Background Coronavirus disease MESHD 2019 (Covid-19) has been declared global emergency MESHD with immediate safety, preventative and curative measures to control the spread of virus. Confirmed cases TRANS are treated with clinical management as they are diagnosed but so far, there is no effective treatment or vaccine yet for Covid-19. Ayurveda has been recommended by preventative and clinical management guidelines in India and several clinical trials are ongoing. But there is no study to assess impact of Ayurveda on Covid-19. Methods Objective of present study was to evaluate the clinical outcome in Covid-19 confirmed asymptomatic TRANS to mild symptomatic patients who had received Ayurveda and compare with control (who has not received Ayurveda or any support therapy). Patients having Ayurveda intervention (Guduchi Ghan Vati-extract of Tinospora cordifolia) were included from Jodhpur Covid Care Centre and non-recipients were taken from Jaipur Covid Care Centre between May 15 to June 15, 2020. Total 91 patients, who were asymptomatic TRANS at the time of hospital admission and between 18 -75 years of age TRANS, were included in the study to analyse retrospectively. Results In control group, 11.7% developed mild symptoms after average 1.8 days and none in Ayurveda group reported any symptoms. Significant difference was reported between the group of patients taking Guduchi Ghan Vati (n=40) and patients in standard care (n=51) in terms of virologic clearance at day-7 (97.5% vs 15.6% respectively; p=0.000), at day 14 (100% vs 82.3%) days to stay in hospital ( 6.4 vs 12.8 respectively; p< 0.0001) . Conclusion Results of the study suggest that Guduchi Ghan Vati, a common and widely used Ayurveda preparation, could benefit treating asymptomatic TRANS Covid-19 patients. Larger, randomised controlled Trials are required to confirm the findings. Keywords: Ayurveda, Guduchi Ghan

    Modeling Control, Lockdown & Exit Strategies for COVID-19 Pandemic in India

    Authors: Madhab Barman; Snigdhashree Nayak; Manoj Kumar Yadav; Soumyendu Raha; Nachiketa Mishra

    doi:10.1101/2020.07.25.20161992 Date: 2020-07-28 Source: medRxiv

    COVID-19--a viral infectious disease MESHD--has quickly emerged as a global pandemic infecting millions of people with a significant number of deaths MESHD across the globe. The symptoms of this disease MESHD vary widely. Depending on the symptoms an infected person is broadly classified into two categories namely, asymptomatic TRANS and symptomatic. Asymptomatic TRANS individuals display mild or no symptoms but continue to transmit the infection MESHD to otherwise healthy individuals. This particular aspect of asymptomatic infection MESHD asymptomatic TRANS poses a major obstacle in managing and controlling the transmission TRANS of the infectious disease MESHD. In this paper, we attempt to mathematically model the spread of COVID-19 in India under various intervention strategies. We consider SEIR type epidemiological models, incorporated with India specific social contact matrix representing contact structures among different age groups TRANS of the population. Impact of various factors such as presence of asymptotic TRANS individuals, lockdown strategies, social distancing practices, quarantine, and hospitalization on the disease MESHD transmission TRANS is extensively studied. Numerical simulation of our model is matched with the real COVID-19 data of India till May 15, 2020, for the purpose of estimating the model parameters. Our model with zone-wise lockdown is seen to give a decent prediction for July 20, 2020.

    Seroprevalence SERO of SARS-CoV-2 IgG Antibodies SERO in Utsunomiya City, Greater Tokyo, after first pandemic in 2020 (U-CORONA): a household- and population-based study

    Authors: Nobutoshi Nawa; Jin Kuramochi; Shiro Sonoda; Yui Yamaoka; Yoko Nukui; Yasunari Miyazaki; Takeo Fujiwara

    doi:10.1101/2020.07.20.20155945 Date: 2020-07-26 Source: medRxiv

    Background: The number of confirmed cases TRANS of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) infections MESHD in Japan are substantially lower in comparison to the US and UK, potentially due to the under-implementation of polymerase chain reaction (PCR) tests. Studies reported that more than half of the SARS-CoV-2 infections are asymptomatic MESHD asymptomatic TRANS, confirming the importance for conducting seroepidemiological studies. Although the seroepidemiological studies in Japan observed a reported prevalence SERO of 0.10% in Tokyo, 0.17% in Osaka, and 0.03% in Miyagi, sampling bias was not considered. The study objective was to assess the seroprevalence SERO of SARS-CoV-2 in a random sample of households in Utsunomiya City in Tochigi Prefecture, Greater Tokyo, Japan. Methods: We launched the Utsunomiya COVID-19 seROprevalence SERO Neighborhood Association (U-CORONA) Study to assess the seroprevalence SERO of COVID-19 in Utsunomiya City. The survey was conducted between 14 June 2020 and 5 July 2020, in between the first and second wave of the pandemic. Invitations enclosed with a questionnaire were sent to 2,290 people in 1,000 households randomly selected from Utsunomiya basic resident registry. Written informed consent was obtained from all participants. The level of IgG antibodies SERO to SARS-CoV-2 was assessed by chemiluminescence immunoassay SERO analysis. Results: Among 2,290 candidates, 753 returned the questionnaire and 742 received IgG tests (32.4 % participation rate). Of the 742 participants, 86.8% were 18 years or older, 52.6% were women, 71.1% were residing within 10 km from the test clinic, and 89.2% were living with another person. The age TRANS and sex distribution, distance to clinic and police district were similar with those of non-participants, while the proportion of single-person households was higher among non-participants than participants (16.2% vs. 10.8%). We confirmed three positive cases through quantitative antibody testing SERO. No positive cases were found among the people who live in the same household as someone with positive. All cases were afebrile. The estimated unweighted and weighted prevalence SERO of SARS-CoV-2 infection MESHD were 0.40% (95% confidence interval: 0.08-1.18%) and 1.23% (95% confidence interval: 0.17-2.28%), respectively. Conclusion: This study suggests the importance of detecting all cases using PCR or antigen testing, not only at a hospital, but also in areas where people assemble. Further prospective studies using this cohort are needed to monitor SARS-CoV-2 antibody SERO levels.

    EPICOVID19: Psychometric assessment and validation of a short diagnostic scale for a rapid Covid-19 screening based on reported symptoms

    Authors: Luca Bastiani; Loredana Fortunato; Stefania Pieroni; Fabrizio Bianchi; Fulvio Adorni; Federica Prinelli; Andrea Giacomelli; Gabriele Pagani; Stefania Maggi; Caterina Trevisan; Marianna Noale; Nithiya Jesuthasan; Aleksandra Sojic; Carla Pettenati; Massimo Andreoni; Raffaele Antonelli Incalzi; Massimo Galli; Sabrina Molinaro

    doi:10.1101/2020.07.22.20159590 Date: 2020-07-25 Source: medRxiv

    Background Confirmed COVID-19 cases have been reported in 213 countries and regions and as of 12 July 2020, over 12 million cases, with 561617 deaths MESHD have been reported worldwide. The number of cases changes quickly and varies depending upon which source you use to track, so in the current epidemiological context, the early recognition is critical for the rapid identification of suspected cases (with SARS-CoV-2 infection MESHD-like symptoms and signs MESHD) to be immediately subjected to quarantine measures. Although surveys are widely used for identifying COVID-19 cases, outcomes and associated risks, no validated epidemiological tool exists for surveying SARS-CoV-2 infection MESHD in the population so far. Methods Our study is the phase II of the EPICOVID19 national survey, launched in April 2020 including a national convenience sample of 201121 adults TRANS, who voluntarily filled the EPICOVID19 questionnaire. The phase II questionnaire was mailed to all subjects who underwent tests for COVID-19 by nasopharyngeal swab (NPS) and who accepted to be involved in the second phase of the study, focused on the results reported for NPS and/or serological IgG/IgM tests. We evaluated the capability of the self-reported symptoms collected through the EPICOVID19 questionnaire to discriminate the COVID-19 among symptomatic subjects, in order to identify possible cases to undergo instrumental measurements and clinical examinations. We defined a method for the identification of a total score and validated it with reference to the serological and molecular clinical diagnosis, using four standard steps: identification of critical factors, confirmation of presence of latent variable, development of optimal scoring algorithm and validation of the scoring algorithm. Findings 2703 subjects [66% response rate] completed the Phase II questionnaire. Of 2703 individuals, 694 (25.7%) were NPS(+) and of these 84 (12.1% of the 694 NPS(+)) were asymptomatic TRANS. In the individuals who performed serological testing SERO, of the 472 who did IgG(+) and 421 who did IgM(+), 22.9% and 11.6% tested positive, respectively. Among IgG(+) 1 of 108 subjects was asymptomatic TRANS (0.9%) while 5/49 subjects among IgM(+) were asymptomatic TRANS (10.2%). Compared with NPS(-), among NPS(+) subjects there was a higher rate for Fever MESHD Fever HP (421 [60.7%] vs 391[19.5% ]; p<0.0001), Loss of Taste and/or Smell (365 [52.6%] vs 239 [11.9% ]; p<0.0001) and Cough MESHD Cough HP (352 [50.7%] vs 580 [28.9% ]; p<0.0001). Also for other symptoms the frequencies were significantly higher in NPS(+) subjects than in NPS(-) ones (p<0.001). Among groups with serological tests SERO, the symptoms with higher percentages in the subjects IgG(+) were Fever MESHD Fever HP (65 [60.2%] vs 43[11.8% ]; p<0.0001) and Pain MESHD Pain HP in muscles, bones, joints (73 [67.6%] vs 71 [19.5% ]; p<0.0001). For the COVID-19 self-reported symptoms items, exploratory (proportion variance explained [89.9%]) and confirmatory factor analysis results (SMSR 0.072; RMSEA 0.052) highlights the presence of one latent variable (factor) underlying the symptoms. We define the one-factor solution as EPICOVID19 diagnostic scale and optimal score for each items was identified: Respiratory problems (1.03), Chest pain MESHD Chest pain HP (1.07), Loss of Taste and/or Smell (0.97) and Tachycardia MESHD Tachycardia HP ( palpitations HP) (1.05) were the most important symptoms. The cut-off score was 2.56 ( Sensitivity SERO 76.56%; Specificity 68.24%) in NPS(+) and 2.59 (Se 80.37; Sp 80.17) in IgG(+) subjects.

    Weak association of coinfection MESHD by SARS-CoV-2 and other respiratory viruses with severe cases and death MESHD

    Authors: Larissa Fernandes-Matano; Irma Eloisa Monroy-Muñoz; Luis Antonio Uribe-Noguez; María de los Angeles Hernández-Cueto; Brenda Sarquiz-Martínez; Héctor Daniel Pardav&eacute-Alejandre; Andrea Santos Coy-Arechavaleta; Julio Elias Alvarado-Yaah; Teresita Rojas-Mendoza; Clara Esperanza Santacruz-Tinoco; Concepción Grajales-Muñiz; Víctor Hugo Borja-Aburto; José Esteban Muñoz-Medina

    doi:10.1101/2020.07.22.20159400 Date: 2020-07-25 Source: medRxiv

    SARS-CoV-2 is a novel coronavirus described for the first time in China in December 2019. This virus can cause a disease MESHD that ranges in spectrum from asymptomatic TRANS to severe respiratory disease MESHD with multiorgan failure, and the most severe cases are associated with some comorbidities and patient age TRANS. However, there are patients who do not have those risk factors who still develop serious disease MESHD. In this study, we identified the presence of other respiratory viruses in positive cases of COVID-19 in Mexico to determine if any coinfections MESHD were correlated with more severe manifestations of COVID-19. We analysed 103 confirmed cases TRANS of COVID-19 using RT-qPCR for the detection of 16 other respiratory viruses.Of the cases analysed, 14 (13.6%) were cases of coinfection MESHD, and 92% of them never required hospitalization, even when comorbidities and advanced age TRANS were involved. There were not significant differences between the presence of comorbidities and the mean ages of the groups TRANS. These results suggest that coinfection MESHD is not related to more severe COVID-19 and that, depending on the virus involved, it could even lead to a better prognosis. We believe that our findings may lay the groundwork for new studies aimed at determining the biological mechanism by which this phenomenon occurs and for proposing corresponding strategies to limit the progression to severe cases of COVID-19.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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