Corpus overview


Overview

MeSH Disease

Human Phenotype

Fever (62)

Pneumonia (56)

Cough (48)

Fatigue (12)

Hypertension (11)


Transmission

Seroprevalence
    displaying 1 - 10 records in total 569
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    A "Tail" of Two Cities: Fatality-based Modeling of COVID-19 Evolution in New York City and Cook County, IL

    Authors: Joshua Frieman

    doi:10.1101/2020.08.10.20170506 Date: 2020-08-12 Source: medRxiv

    I describe SIR modeling of the COVID-19 pandemic in two U.S. urban environments, New York City (NYC) and Cook County, IL, from onset through the month of June, 2020. Since testing was not widespread early in the pandemic in the U.S., I do not use data on confirmed cases TRANS and rely solely on public fatality data to estimate model parameters. Fits to the first 20 days of data determine a degenerate combination of the basic reproduction number TRANS, R0 TRANS, and the mean time to removal from the infectious population, 1/{gamma} with {gamma}( R0 TRANS - 1) = 0.25(0.21) inverse days for NYC (Cook County). Equivalently, the initial doubling time was td = 2.8(3.4) days for NYC (Cook). The early fatality data suggest that both locations had infections MESHD in early February. I model the mitigation measures implemented in mid-March in both locations (distancing, quarantine, isolation, etc) via a time-dependent reproduction number TRANS Rt that declines monotonically from R0 TRANS to a smaller asymptotic TRANS value, with a parameterized functional form. The timing (mid-March) and duration (several days) of the transitions in Rt appear well determined by the data. However, the fatality data determine only a degenerate combination of the parameters R0 TRANS, the percentage reduction in social contact due to mitigation measures, X, and the infection MESHD fatality rate (IFR), f . With flat priors, based on simulations the NYC model parameters have 95.45% credible intervals of R0 TRANS = 3.0 - 5.4, X = 80 - 99.9% and f = 2 - 6%, with 5 - 13% of the population asymptotically infected. A strong external prior indicating a lower value of f or of 1/{gamma} would imply lower values of R0 TRANS and X and higher percentage infection MESHD of the population. For Cook County, the evolution was qualitatively different: after mitigation measures were implemented, the daily fatality counts reached a plateau for about a month before tailing off. This is consistent with an SIR model that exhibits "critical slowing-down", in which Rt plateaus at a value just above unity. For Cook County, the 95.45% credible intervals for the model parameters are much broader and shifted downward, R0 TRANS = 1.4 - 4.7, X = 26 - 54%, and f = 0.1 - 0.6% with 15 - 88% of the population asymptotically infected. Despite the apparently lower efficacy of its social contact reduction measures, Cook County has had significantly fewer fatalities per population than NYC, D{infty}/N = 100 vs. 270 per 100,000. In the model, this is attributed to the lower inferred IFR for Cook; an external prior pointing to similar values of the IFR for the two locations would instead chalk up the difference in D/N to differences in the relative growth rate of the disease MESHD. I derive a model-dependent threshold, Xcrit, for "safe" re-opening, that is, for easing of contact reduction that would not trigger a second wave; for NYC, the models predict that increasing social contact by more than 20% from post-mitigation levels will lead to renewed spread, while for Cook County the threshold value is very uncertain, given the parameter degeneracies. The timing of 2nd-wave growth will depend on the amplitude of contact increase relative to Xcrit and on the asymptotic TRANS growth rate, and the impact in terms of fatalities will depend on the parameter f .

    Underdetection of COVID-19 cases in France in the exit phase following lockdown

    Authors: Giulia Pullano; Laura Di Domenico; Chiara E Sabbatini; Eugenio Valdano; Clément Turbelin; Marion Debin; Caroline Guerrisi; Charly Kengne-Kuetche; Cécile Souty; Thomas Hanslik; Thierry Blanchon; Pierre-Yves Boëlle; Julie Figoni; Sophie Vaux; Christine Campèse; Sibylle Bernard-Stoecklin; Vittoria Colizza

    doi:10.1101/2020.08.10.20171744 Date: 2020-08-12 Source: medRxiv

    A novel testing policy was implemented in May in France to systematically screen potential COVID-19 infections MESHD and suppress local outbreaks while lifting lockdown restrictions. 20,736 virologically- confirmed cases TRANS were reported in mainland France from May 13, 2020 (week 20, end of lockdown) to June 28 (week 26). Accounting for missing data and the delay from symptom onset TRANS to confirmation test, this corresponds to 7,258 [95% CI 7,160-7,336] cases with symptom onset TRANS during this period, a likely underestimation of the real number. Using age TRANS-stratified transmission TRANS models parameterized to behavioral data and calibrated to regional hospital admissions, we estimated that 69,115 [58,072-77,449] COVID-19 symptomatic cases occurred, suggesting that 9 out of 10 cases with symptoms were not ascertained. Median detection rate increased from 7% [6-9]% to 31% [28-35]% over time, with regional estimates varying from 11% (Grand Est) to 78% (Normandy) by the end of June. Healthcare-seeking behavior in COVID-19 suspect cases remained low (31%) throughout the period. Model projections for the incidence of symptomatic cases (4.5 [3.9-5.0] per 100,000) were compatible with estimates integrating participatory and virological surveillance data, assuming all suspect cases consulted. Encouraging healthcare-seeking behavior and awareness in suspect cases is critical to improve detection. Substantially more aggressive and efficient testing with easier access is required to act as a pandemic-fighting tool. These elements should be considered in light of the currently observed resurgence of cases in France and other European countries.

    Coordinated support for local action: A modeling study of strategies to facilitate behavior adoption in urban poor communities of Liberia for sustained COVID-19 suppression

    Authors: Laura Skrip; Mosoka P Fallah; Jamie Bedson; Laurent Hébert-Dufresne; Benjamin Muir Althouse

    doi:10.1101/2020.08.11.20172031 Date: 2020-08-11 Source: medRxiv

    Background: Long-term suppression of SARS-CoV-2 transmission TRANS will require context-specific strategies that recognize the heterogeneous capacity of communities to undertake public health recommendations, particularly due to limited access to food, sanitation facilities, and physical space required for self-quarantine or isolation. We highlight the epidemiological impact of barriers to adoption of public health recommendations by urban slum populations in low- and middle-income countries (LMICs) and the potential role of community-based initiatives to coordinate efforts that support cases and high-risk contacts. Methods: Daily case updates published by the National Public Health Institute of Liberia were used to inform a stratified stochastic compartmental model representing transmission TRANS of SARS-CoV-2 in two subpopulations (urban poor versus less socioeconomically vulnerable) of Montserrado County, Liberia. Differential transmission TRANS was considered at levels of the subpopulation, household versus community, and events (i.e., funerals). Adoption of home-isolation behavior was assumed to be related to the proportion of each subpopulation residing in housing units with multiple rooms, access to sanitation facilities, and access to basic goods like water and food. Percentage reductions in cumulative infection MESHD counts, cumulative counts of severe cases, and maximum daily infection MESHD counts for each subpopulation were evaluated across intervention scenarios that included symptom-triggered, community-driven efforts to support high-risk contacts and confirmed cases TRANS in self-isolation following the scheduled lifting of the state of emergency MESHD. Results: Modeled outbreaks for the status quo scenario differed between the two subpopulations, with increased overall infection MESHD burden but decreased numbers of severe cases in the urban poor subpopulation relative to the less socioeconomically vulnerable population after 180 days post-introduction into Liberia. With more proactive self-isolation by mildly symptomatic individuals after lifting of the public health emergency MESHD, median reductions in cumulative infections MESHD infections, severe HP, severe cases, and maximum daily incidence were 7.6% (IQR: 2.2%-20.9%), 7.0% (2.0%-18.5%), and 9.9% (2.5%-31.4%) for cumulative infections MESHD infections, severe HP, severe cases, and maximum daily incidence, respectively, across epidemiological curve simulations in the urban poor subpopulation and 16.8% (5.5%-29.3%), 15.0% (5.0%-26.4%), and 28.1% (IQR: 9.3%-47.8%) in the less socioeconomically vulnerable population. An increase in the maximum attainable percentage of behavior adoption by the urban slum subpopulation, with the provision of support to facilitate self-isolation or quarantine, was associated with median reductions in cumulative infections MESHD infections, severe HP, severe cases, and maximum daily incidence were 19.2% (IQR: 10.1%-34.0%), 21.1% (IQR: 13.3%-34.2%), and 26.0% (IQR: 11.5%-48.9%), respectively, relative to the status quo scenario. Conclusions: Broadly supported post-lockdown recommendations that prioritize proactively monitoring symptoms, seeking testing and isolating at home by confirmed cases TRANS are limited by resource constraints in urban poor communities. Investing in community-based initiatives that determine needs and coordinate needs-based support for self-identified cases and their contacts could provide a more effective, longer-term strategy for suppressing transmission TRANS of COVID-19 in settings with prevalent distrust and socioeconomic vulnerabilities.

    A Monte Carlo approach to model COVID-19 deaths MESHD and infections MESHD using Gompertz functions

    Authors: Tulio Rodrigues; Otaviano Helene

    id:2008.04989v1 Date: 2020-08-11 Source: arXiv

    This study describes the dynamics of COVID-19 deaths MESHD and infections MESHD via a Monte Carlo approach. The analyses include death MESHD's data from USA, Brazil, Mexico, UK, India and Russia, which comprise the four countries with the highest number of deaths MESHD/ confirmed cases TRANS, as of Aug 07, 2020, according to the WHO. The Gompertz functions were fitted to the data of weekly averaged confirmed deaths MESHD per day by mapping the $\chi^2$ values. The uncertainties, variances and covariances of the model parameters were calculated by propagation. The fitted functions for the average deaths MESHD per day for USA and India have an upward trend, with the former having a higher growth rate and quite huge uncertainties. For Mexico, UK and Russia, the fits are consistent with a slope down pattern. For Brazil we found a subtle trend down, but with significant uncertainties. The USA, UK and India data shown a first peak with a higher growth rate when compared to the second one, demonstrating the benefits of non-pharmaceutical interventions of sanitary measures and social distance flattening the curve. For USA, a third peak seems quite plausible, most likely related with the recent relaxation policies. Brazil's data are satisfactorily described by two highly overlapped Gompertz functions with similar growth rates, suggesting a two-steps process for the pandemic spreading. The 95% CI for the total number of deaths MESHD ($\times 10^3$) predicted by the model for Aug 31, 2020 are 160 to 220, 110 to 130, 59 to 62, 46.6 to 47.3, 54 to 63 and 16.0 to 16.7 for USA, Brazil, Mexico, UK, India and Russia, respectively. Our estimates for the prevalences SERO of infections MESHD are in reasonable agreement with some preliminary reports from serological studies carried out in USA and Brazil. The method represents an effective framework to estimate the line-shape of the infection MESHD curves and the uncertainties of the relevant parameters based on the actual data.

    Association of mental disorders with SARS-CoV-2 infection MESHD infection and severe HP and severe health outcomes: a nationwide cohort study

    Authors: Ha-Lim Jeon; Jun Soo Kwon; So-Hee Park; Ju-Young Shin

    doi:10.1101/2020.08.05.20169201 Date: 2020-08-07 Source: medRxiv

    Background: No epidemiological data exists for the association between mental disorders and the risk of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) infection MESHD and coronavirus disease MESHD 2019 (COVID-19) severity. Aims: To evaluate the association between mental disorders and the risk of SARS-CoV-2 infection MESHD infection and severe HP and severe outcomes following COVID-19. Methods: We performed a cohort study using the Korean COVID-19 patient database based on the national health insurance data. Each patient with a mental or behavioral disorder (diagnosed during six months prior to the first SARS-CoV-2 test) was matched by age TRANS, sex, and Charlson comorbidity index with up to four patients without mental disorders. SARS-CoV-2 positivity risk and risk of death MESHD or severe events (intensive care unit admission, use of mechanical ventilation, and acute respiratory distress HP syndrome MESHD) post- infection MESHD were calculated using conditional logistic regression analysis. Results: Among 230,565 patients tested for SARS-CoV-2, 33,653 (14.6%) had mental disorders, 928/33,653 (2.76%) tested positive, and 56/928 (6.03%) died. In multivariate analysis with the matched cohort, there was no association between mental disorders and SARS-CoV-2 positivity risk (odds ratio [OR], 1.02; 95% confidence interval [CI], 0.92-1.12); however, a higher risk was associated with schizophrenia HP-related disorders (OR, 1.36; 95% CI, 1.02-1.81). Among confirmed cases TRANS, mortality risk significantly increased in patients with mental disorders (OR, 1.84, 95% CI, 1.07-3.15). Conclusion: Mental disorders are likely contributing factors of mortality following COVID-19. Although the infection MESHD infection risk TRANS infection risk TRANS risk did not increase in overall mental disorders, patients with schizophrenia HP-related disorders were more vulnerable to the infection MESHD.

    Estimating the Changing Infection MESHD Rate of COVID-19 Using Bayesian Models of Mobility

    Authors: Luyang Liu; Sharad Vikram; Junpeng Lao; Xue Ben; Alexander D'Amour; Shawn O'Banion; Mark Sandler; Rif A. Saurous; Matthew D. Hoffman

    doi:10.1101/2020.08.06.20169664 Date: 2020-08-07 Source: medRxiv

    In order to prepare for and control the continued spread of the COVID-19 pandemic while minimizing its economic impact, the world needs to be able to estimate and predict COVID-19's spread. Unfortunately, we cannot directly observe the prevalence SERO or growth rate of COVID-19; these must be inferred using some kind of model. We propose a hierarchical Bayesian extension to the classic susceptible-exposed-infected-removed (SEIR) compartmental model that adds compartments to account for isolation and death MESHD and allows the infection MESHD rate to vary as a function of both mobility data collected from mobile phones and a latent time-varying factor that accounts for changes in behavior not captured by mobility data. Since confirmed-case TRANS data is unreliable, we infer the model's parameters conditioned on deaths MESHD data. We replace the exponential-waiting-time assumption of classic compartmental models with Erlang distributions, which allows for a more realistic model of the long lag between exposure and death MESHD. The mobility data gives us a leading indicator that can quickly detect changes in the pandemic's local growth rate and forecast changes in death MESHD rates weeks ahead of time. This is an analysis of observational data, so any causal interpretations of the model's inferences should be treated as suggestive at best; nonetheless, the model's inferred relationship between different kinds of trips and the infection MESHD rate do suggest some possible hypotheses about what kinds of activities might contribute most to COVID-19's spread.

    CRISPR-based and RT-qPCR surveillance of SARS-CoV-2 in asymptomatic TRANS individuals uncovers a shift in viral prevalence SERO among a university population

    Authors: Jennifer N Rauch; Eric Valois; Jose Carlos Ponce-Rojas; Zach Aralis; Ryan L Lach; Francesca Zappa; Morgane Audouard; Sabrina C Solley; Chinmay Vaidya; Michael Costello; Holly Smith; Ali Javanbakht; Betsy Malear; Laura Polito; Stewart Comer; Katherine Arn; Kenneth S Kosik; Diego Acosta-Alvear; Maxwell Z Wilson; Lynn Fitzgibbons; Carolina Arias

    doi:10.1101/2020.08.06.20169771 Date: 2020-08-07 Source: medRxiv

    Background: The progress of the COVID-19 pandemic profoundly impacts the health of communities around the world, with unique impacts on colleges and universities. Transmission TRANS of SARS-CoV-2 by asymptomatic TRANS people is thought to be the underlying cause of a large proportion of new infections MESHD. However, the local prevalence SERO of asymptomatic TRANS and pre-symptomatic carriers TRANS of SARS-CoV-2 is influenced by local public health restrictions and the community setting. Objectives: This study has three main objectives. First, we looked to establish the prevalence SERO of asymptomatic TRANS SARS-CoV-2 infection MESHD on a university campus in California. Second, we sought to assess the changes in viral prevalence SERO associated with the shifting community conditions related to non-pharmaceutical interventions (NPIs). Third, we aimed to compare the performance SERO of CRISPR- and PCR-based assays for large-scale virus surveillance sampling in COVID-19 asymptomatic TRANS persons. Methods: We enrolled 1,808 asymptomatic TRANS persons for self-collection of oropharyngeal (OP) samples to undergo SARS-CoV-2 testing. We compared viral prevalence SERO in samples obtained in two time periods: May 28th-June 11th; June 23rd-July 2nd. We detected viral genomes in these samples using two assays: CREST, a CRISPR-based method recently developed at UCSB, and the RT-qPCR test recommended by US Centers for Disease MESHD Control and Prevention (CDC). Results: Of the 1,808 participants, 1,805 were affiliates of the University of California, Santa Barbara, and 1,306 were students. None of the tests performed on the 732 samples collected between late May to early June were positive. In contrast, tests performed on the 1076 samples collected between late June to early July, revealed nine positive cases. This change in prevalence SERO met statistical significance, p = 0.013. One sample was positive by RT-qPCR at the threshold of detection, but negative by both CREST and CLIA-confirmation testing. With this single exception, there was perfect concordance in both positive and negative results obtained by RT-qPCR and CREST. The estimated prevalence SERO of the virus, calculated using the confirmed cases TRANS, was 0.74%. The average age TRANS of our sample population was 28.33 (18-75) years, and the average age TRANS of the positive cases was 21.7 years (19-30). Conclusions: Our study revealed that there were no COVID-19 cases in our study population in May/June. Using the same methods, we demonstrated a substantial shift in prevalence SERO approximately one month later, which coincided with changes in community restrictions and public interactions. This increase in prevalence SERO, in a young and asymptomatic TRANS population which would not have otherwise accessed COVID-19 testing, indicated the leading wave of a local outbreak, and coincided with rising case counts in the surrounding county and the state of California. Our results substantiate that large, population-level asymptomatic TRANS screening using self-collection may be a feasible and instructive aspect of the public health approach within large campus communities, and the almost perfect concordance between CRISPR- and PCR-based assays indicate expanded options for surveillance testing

    Genomic epidemiology reveals transmission TRANS patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

    Authors: Jemma L Geoghegan; Xiaoyun Ren; Matthew Storey; James Hadfield; Lauren Jelley; Sarah Jefferies; Jill Sherwood; Shevaun Paine; Sue Huang; Jordan Douglas; Fabio K L Mendes; Andrew Sporle; Michael G Baker; David R Murdoch; Nigel French; Colin R Simpson; David Welch; Alexei J Drummond; Edward C Holmes; Sebastian Duchene; Joep de Ligt

    doi:10.1101/2020.08.05.20168930 Date: 2020-08-06 Source: medRxiv

    New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nation-wide lockdown of all non-essential services to curb the spread of COVID-19. New Zealand has now effectively eliminated the virus, with low numbers of new cases limited to new arrivals in managed quarantine facilities at the border. Here, we generated 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected between 26 February and 22 May 2020, representing 56% of all confirmed cases TRANS in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. The proportion of D614G variants in the virus spike protein increased over time due to an increase in their importation frequency, rather than selection within New Zealand. These data also helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number TRANS, Re, of New Zealand's largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in a transmission TRANS lineage of more than one additional case. Most of the cases that resulted in a transmission TRANS lineage originated from North America, rather than from Asia where the virus first emerged or from the nearest geographical neighbour, Australia. Genomic data also helped link more infections MESHD to a major transmission TRANS cluster than through epidemiological data alone, providing probable sources of infections MESHD for cases in which the source was unclear. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease MESHD mitigation.

    Analysis of COVID-19 and comorbidity co- infection MESHD Model with Optimal Control

    Authors: Dr. Andrew Omame; Nometa Ikenna

    doi:10.1101/2020.08.04.20168013 Date: 2020-08-04 Source: medRxiv

    The new coronavirus disease MESHD 2019 (COVID-19) infection MESHD is a double challenge for people infected with comorbidities such as cardiovascular and cerebrovascular diseases MESHD and diabetes. Comorbidities have been reported to be risk factors for the complications of COVID-19. In this work, we develop and analyze a mathematical model for the dynamics of COVID-19 infection MESHD in order to assess the impacts of prior comorbidity on COVID-19 complications and COVID-19 re- infection MESHD. The model is simulated using data relevant to the dynamics of the diseases MESHD in Lagos, Nigeria, making predictions for the attainment of peak periods in the presence or absence of comorbidity. The model is shown to undergo the phenomenon of backward bifurcation caused by the parameter accounting for increased susceptibility to COVID-19 infection MESHD by comorbid susceptibles as well as the rate of re- infection MESHD by those who have recovered from a previous COVID-19 infection MESHD. Sensitivity SERO analysis of the model when the population of individuals co-infected with COVID-19 and comorbidity is used as response function revealed that the top ranked parameters that drive the dynamics of the co- infection MESHD model are the effective contact rate for COVID-19 transmission TRANS, $\beta\sst{cv}$, the parameter accounting for increased susceptibility to COVID-19 by comorbid susceptibles, $\chi\sst{cm}$, the comorbidity development rate, $\theta\sst{cm}$, the detection rate for singly infected and co-infected individuals, $\eta_1$ and $\eta_2$, as well as the recovery rate from COVID-19 for co-infected individuals, $\varphi\sst{i2}$. Simulations of the model reveal that the cumulative confirmed cases TRANS (without comorbidity) may get up to 180,000 after 200 days, if the hyper susceptibility rate of comorbid susceptibles is as high as 1.2 per day. Also, the cumulative confirmed cases TRANS (including those co-infected with comorbidity) may be as high as 1000,000 cases by the end of November, 2020 if the re- infection MESHD rates for COVID-19 is 0.1 per day. It may be worse than this if the re- infection MESHD rates increase higher. Moreover, if policies are strictly put in place to step down the probability of COVID-19 infection MESHD by comorbid susceptibles to as low as 0.4 per day and step up the detection rate for singly infected individuals to 0.7 per day, then the reproduction number TRANS can be brought very low below one, and COVID-19 infection MESHD eliminated from the population. In addition, optimal control and cost-effectiveness analysis of the model reveal that the the strategy that prevents COVID-19 infection MESHD by comorbid susceptibles has the least ICER and is the most cost-effective of all the control strategies for the prevention of COVID-19.

    Characteristics of COVID-19 fatality cases in East Kalimantan, Indonesia

    Authors: Swandari Paramita; Ronny Isnuwardana; Krispinus Duma; Rahmat Bakhtiar; Muhammad Khairul Nuryanto; Riries Choiru Pramulia Yudia; Evi Fitriany; Meiliati Aminyoto

    doi:10.1101/2020.08.01.20166470 Date: 2020-08-04 Source: medRxiv

    Introduction. Coronavirus Disease MESHD (COVID-19) is caused by SARS-CoV-2 infection MESHD. On March 2, 2020, Indonesia announced the first confirmed cases TRANS of COVID-19 infection MESHD. East Kalimantan will play an important role as the new capital of Indonesia. There is attention to the preparedness of East Kalimantan to respond to COVID-19. We report the characteristics of COVID-19 fatality cases in here. Methods. We retrospectively analyzed the fatality cases of COVID-19 patients from the East Kalimantan Health Office information system. All patients were confirmed COVID-19 by RT-PCR examination. Results. By July 31, 2020, 31 fatality cases of patients had been identified as having confirmed COVID-19 in East Kalimantan. The mean age TRANS of the patients was 55.1 + 9.2 years. Most of the patients were men (22 [71.0%]) with age TRANS more than 60 years old (14 [45.2%]). Balikpapan has the highest number of COVID-19 fatality cases from all regencies. Hypertension MESHD Hypertension HP was the most comorbidities in the fatality cases of COVID-19 patients in East Kalimantan. Discussion. Older age TRANS and comorbidities still contributed to the fatality cases of COVID-19 patients in East Kalimantan, Indonesia. Hypertension MESHD Hypertension HP, diabetes, cardiovascular disease MESHD, and cerebrovascular disease MESHD were underlying conditions for increasing the risk of COVID-19 getting into a serious condition. Conclusion. Active surveillance for people older than 60 years old and having underlying diseases MESHD is needed for reducing the case fatality rate of COVID-19 in East Kalimantan. Keywords. Comorbidity, fatality cases, COVID-19, Indonesia.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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