Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (54)

NSP5 (11)

ProteinN (10)

ComplexRdRp (8)

ProteinE (7)


SARS-CoV-2 Proteins
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    Clinical outcomes and cost-effectiveness of COVID-19 MESHD vaccination in South Africa

    Authors: Krishna P Reddy; Kieran P Fitzmaurice; Justine A Scott; Guy Harling; Richard J Lessells; Christopher Panella; Fatma M Shebl; Kenneth A Freedberg; Mark J Siedner

    doi:10.1101/2021.05.07.21256852 Date: 2021-05-12 Source: medRxiv

    Low- and middle-income countries are implementing COVID-19 MESHD vaccination strategies in light of varying and uncertain vaccine efficacies and costs, supply shortages, and resource constraints. We used a microsimulation model to evaluate clinical outcomes and cost-effectiveness of a COVID-19 MESHD vaccination program in South Africa. We varied vaccination coverage, pace, acceptance, effectiveness, and cost as well as epidemic dynamics. Providing vaccine to at least 40% of the population and prioritizing accelerated vaccine rollout prevented >9 million infections and >73,000 deaths and reduced costs due to fewer hospitalizations. Further, the vaccination program was cost-saving even at the lowest examined levels of acceptance (50%), effectiveness against infection (20%), effectiveness against symptomatic disease (30%), and effectiveness against severe/ critical disease MESHD requiring hospitalization (40%), and with vaccination costs of up to USD25/person. In summary, a COVID-19 MESHD vaccination program would reduce both deaths MESHD and health care costs in South Africa across a wide range of assumptions. Vaccination program implementation factors, including prompt procurement, distribution, and rollout, are likely more influential than characteristics of the vaccine itself in maximizing public health benefits and economic efficiency.

    No excess mortality detected in rural Bangladesh in 2020 from repeated surveys of a population of 81,000

    Authors: Prabhat Barnwal; Yuling Yao; Yiqian Wang; Nishat Akter Juy; Shabib Raihan; Mohammad Ashraful Haque; Alexander van Geen

    doi:10.1101/2021.05.07.21256865 Date: 2021-05-12 Source: medRxiv

    Background Excess mortality has demonstrated under-counting of COVID-19 MESHD deaths in many countries but cannot be measured in low-income countries where civil registration is incomplete. Methods Enumerators conducted an in-person census of all 16,054 households in a sample of 135 villages within a 350 km2 region of Bangladesh followed by a census conducted again in May and November 2020 over the phone. The date and cause of any changes in household composition, as well as changes in income and food availability, were recorded. For analysis, we stratify the mortality data by month, age, gender, and household education. Mortality rates were modeled by Bayesian multilevel regression and the strata aggregated to the population by poststratification. Results A total of 276 deaths MESHD were reported between February and the end of October 2020 for the subset of the population that could be contacted twice over the phone, slightly below the 289 deaths reported for the same population over the same period in 2019. After adjustment for survey non-response and poststratification, 2020 mortality changed by -8% (95% CI, -21% to 7%) relative to an annualized mortality of 6.1 per thousand in 2019. However, salaried breadwinners reported a 40% decline in income and businesses a 60% decline in profits in May 2020. Discussion All-cause mortality in the surveyed portion of rural Bangladesh was if anything lower in 2020 compared to 2019. Our findings suggest various restrictions imposed by the government limited the scale of the pandemic, although they need to be accompanied by expanded welfare programs.

    Incidence and Epidemiological study of COVID-19 MESHD in Nagpur urban region (India) using Molecular testing

    Authors: Jay Tanna; Bishwadeep Singha; Amit R Nayak; Aliabbas A Husain; Dhananjay V Raje; Shubhangi Desai; Madhavi Deshmukh; Shailendra Mundhada; Rajpal S Kashyap

    doi:10.1101/2021.05.11.21256719 Date: 2021-05-11 Source: medRxiv

    The COVID-19 pandemic MESHD caused by severe acute respiratory syndrome coronavirus-2 MESHD (SARS CoV-2) virus has emerged as public health emergency affecting 206 countries worldwide. India is second highest currently worst effected by Covid 19 pandemic with close to 12.6 million cases and 1.6K deaths MESHD reported till date. Maharahstra is the highest Covid-19 MESHD burden state in India reporting quarter of overall cases. The city of Nagpur, in Maharashtra state, ranks 4th in terms of reported COVID-19 MESHD cases, with 2.5 lakh incidences and more than 4,000 deaths As the transmission rate of COVID-19 MESHD is high, it is imperative to study its disease epidemiology in regions of high endemicity to bolster our understanding of its spread, transmission dynamics and contact tracing to undertake appropriate public health control measures.. The present study was undertaken to study the incidence and trend of COVID-19 MESHD infection from various zonal regions of Nagpur city, using real time PCR (RT PCR). A retrospective study was carried out at Indian Council of Medical Research (ICMR) approved private molecular diagnostic laboratory in Nagpur from period of 4th May 2020 to 14th November 2020. A total of 51,532 samples collected from various zonal regions of the city during the study period were processed for SARS CoV-2 RT-PCR. Patient information was collected using a pre-defined study proforma which included demographic details such as name, age, gender, address, along with other information, like details of sample collected, kits used and date of sample collected and processed. The study reports an overall Covid-19 MESHD positivity of 34% in Nagpur region. The zone wise distribution of positive cases indicated high rate of COVID-19 MESHD in endemic regions of Nagpur such as Satranjipura (49%), Ashi HGNC nagar (44%), Gandhibagh (43%) & Lakadganj (43%). Rates of infection were high in economically productive age group (21-40) with males being more vulnerable than females. The result of present epidemiology study highlights important data with respect to regions of endemicity within Nagpur city zones. The present data has high public health importance and will be useful for local civic bodies and other community stake holders to undertake appropriate control measures in future epidemic waves of Covid 19. Interestingly, the Government's reduction in testing rates has been helpful in increasing testing per day. The authorization of private laboratories has also increased testing.


    Authors: Sandip Mandal; Nimalan Arinaminpathy; Balram Bhargava; Samiran Panda

    doi:10.1101/2021.05.07.21256742 Date: 2021-05-10 Source: medRxiv

    Objectives To investigate the impact of targeted vaccination strategies on morbidity and mortality due to COVID-19 MESHD, as well as on the incidence of SARS-CoV-2, in India. Design Mathematical modelling. Settings Indian epidemic of COVID-19 MESHD and vulnerable population. Data sources Country specific and age-segregated pattern of social contact, case fatality rate and demographic data obtained from peer-reviewed literature and public domain. Model An age-structured dynamical model describing SARS-CoV-2 transmission in India incorporating uncertainty in natural history parameters was constructed. Interventions Comparison of different vaccine strategies by targeting priority groups such as key workers including health care professionals, individuals with comorbidities (24 - 60 year), and all above 60. Main outcome measures Incidence reduction and averted deaths MESHD in different scenarios, assuming that the current restrictions are fully lifted as vaccination is implemented. Results The priority groups together account for about 18% of India's population. An infection preventing vaccine with 60% efficacy covering all these groups would reduce peak symptomatic incidence by 20.6% (95% uncertainty intervals (CrI) 16.7 - 25.4), and cumulative mortality by 29.7% (95% CrI 25.8- 33.8). A similar vaccine with ability to prevent symptoms (but not infection) will reduce peak incidence of symptomatic cases by 10.4% (95% CrI 8.4 - 13.0), and cumulative mortality by 32.9% (95% CrI 28.6 - 37.3). In the event of insufficient vaccine supply to cover all priority groups, model projections suggest that after keyworkers, vaccine strategy should prioritise all who are > 60, and subsequently individuals with comorbidities. In settings with weakest transmission, such as sparsely-populated rural areas, those with comorbidities should be prioritised after keyworkers. Conclusions An appropriately targeted vaccination strategy would witness substantial mitigation of impact of COVID-19 MESHD in a country like India with wide heterogenity. 'Smart vaccination', based on public health considerations, rather than mass vaccination, appears prudent.

    Higher case fatality rate among obstetric patients with COVID-19 MESHD in the second year of pandemic in Brazil: do new genetic variants play a role?

    Authors: Maira Libertad Soligo Takemoto; Marcos Nakamura-Pereira; Mariane de Oliveira Menezes; Leila Katz; Roxana Knobel; Melania Maria Ramos Amorim; Carla Betina Andreucci

    doi:10.1101/2021.05.06.21256651 Date: 2021-05-08 Source: medRxiv

    Background: In Brazil, a 20% increase in maternal mortality rate due to COVID-19 MESHD is projected for 2020. On January 4, 2021, the P.1 HGNC SARS-CoV-2 genetic variant was firstly identified in the country and recent data has indicated an association with higher hospitalization rates and mortality. The impact of P.1 HGNC variant in the obstetric population remains unclear. Methods: We carried out a preliminary analysis of sociodemographic and clinical characteristics of COVID-19 MESHD confirmed maternal deaths (between 10-50 years old) comparing cases reported to the Brazilian official severe acute respiratory syndrome MESHD (SARS) surveillance system (SS) in 2020 with those from 2021 (until April 12, 2021). This preliminary analysis employed methods described in previous reports from our group. Results: 803 maternal deaths out of 8,248 COVID-19 MESHD maternal SARS cases with a recorded outcome were reported to the SARS-SS since March 2020. Case fatality rate was significantly higher in 2021 (15.6% vs 7.4%). The first three months of 2021 already account for 46.2% of all deaths occurred in the 13-months analysed period. COVID-19 MESHD fatal cases from 2021 had a lower proportion of at least one risk factor or comorbidity as compared to 2020 but had a higher frequency of obesity MESHD. There were no significant differences in terms of age, type of residence area (urban, rural, or peri-urban), type of funding of the notification unit (public vs. private), COVID-19 MESHD diagnostic criteria, pregnancy status (pregnancy or postpartum), cardiovascular disease MESHD or diabetes MESHD. The proportion of hospitalization, ICU admission, and respiratory support before death MESHD was also not significantly different. Conclusion: Case fatality rate was increased in the three first months of 2021 when compared to 2020. Once variables related to health care access and demographics are not significantly different and women seem to be healthier in the 2021 sample, such difference may be related to the circulation of more aggressive genetic variants in the country.

    Covid-19 MESHD and the South Asian Countries: factors ruling the pandemic

    Authors: Tannishtha Biswas; Madhura Mondal; Srijan Bhattacharya; Moitrayee Sarkar; Bikram Dhara; Arup Kumar Mitra; Ayan Chandra

    doi:10.1101/2021.05.04.21256590 Date: 2021-05-06 Source: medRxiv

    The novel corona virus causing Covid-19 MESHD was first detected in the city of Wuhan, China in December, 2019. In matter of months Covid-19 MESHD was declared a pandemic by the World Health Organization. The focus of this research includes the probable factors that might have played an important role in the spread of this infection causing a global threat. In this study we dealt with the South Asian countries namely Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan. Data on the demography of the countries, the climatic and geographical conditions, the socio-economic statuses, GDP being in the forefront, was collected and compared with Covid-19 MESHD related data such as total number of positive, recovered and death MESHD cases, etc. to determine if there was any significant correlation. The wide range of correlations observed can curve the path for the future research to understand the factors behind the spread of the communicable disease, analyzing the dynamics of the future biological threats to mankind and design the precautionary or preventive methods accordingly.

    Prevalence use of nonsteroidal anti-inflammatory drugs in the general population with COVID-19 MESHD and associated COVID-19 MESHD risk, hospitalization, severity, death MESHD, and safety outcomes: A systematic review and meta-analysis

    Authors: huilei zhao; shanshan huang; kaibo mei; wen shao; yuan jiang; wengen zhu; jianyong ma; jing zhang; peng yu; xiao liu

    doi:10.1101/2021.05.01.21256428 Date: 2021-05-05 Source: medRxiv

    Introduction: Recent reports of potential harmful effects of nonsteroidal anti-inflammatory drugs (NSAIDs) in patients with Corona Virus Disease MESHD 2019 ( COVID-19 MESHD) have provoked great concern. Therefore, the safety of NSAIDs is still questioned. Methods: We searched the PubMed, EMBASE, Cochrane Library and Web of Science databases from December 2019 to January 2021 to examine use prevalence for NSAIDs in general, as well as associated COVID-19 MESHD risk and outcomes. This study has been registered with PROSPERO (CRD42019132063) Results: We included 25 studies with a total of 101,215 COVID-19 MESHD patients. The use of NSAIDs in COVID-19 MESHD patients reached 19%. Exposure to NSAIDs was not associated with significantly increased risk of developing COVID-19 MESHD (odds ratio [OR]=0.98, 95% confidence interval [CI]: 0.78-1.24; I2=82%), hospitalization (OR=1.06, 95%CI: 0.76-1.48; I2=81%), mechanical ventilation (OR=0.71, 95%CI: 0.47-1.06; I2=38%), and length of hospital stay. Moreover, use of NSAIDs was significantly associated with better outcomes, including severity of COVID-19 MESHD (OR=0.79, 95%CI: 71-0.89; I2=0%) and death MESHD (OR=0.68, 95%CI: 0.52-0.89; I2=85%) in patients with COVID-19 MESHD. Regarding safety outcomes, exposure to NSAIDs was associated with increased risk of stroke MESHD (OR=2.32, 95%CI: 1.04-5.2; I2=0%), but not with myocardial infraction MESHD (OR=1.49; p=0.66; I2=0%), overt thrombosis MESHD (OR=0.76, p=0.50; I2=28%) and major bleeding MESHD (p=0.61). Conclusion: Based on current evidence, exposure to NSAIDs is not linked to increased odds or exacerbation of COVID-19 MESHD in the general COVID-19 MESHD population. Furthermore, administration of NSAIDs might have better outcomes and survival benefits in the general COVID-19 MESHD population, although potentially increasing the risk of stroke MESHD. Use of NSAIDs might be safe and beneficial in COVID-19 MESHD. Future observational and randomized control trials are needed for further confirmation.

    Durable antibody responses in staff at two long-term care facilities, during and post SARS-CoV-2 outbreaks

    Authors: Emily Gallichotte; Mary Nehring; Michael C Young; Sierra Pugh; Nicole R Sexton; Emily Fitzmeyer; Kendra M Quicke; Megan Richardson; Kristy L. Pabilonia; Nicole Ehrhart; Sue VandeWoude; Gregory D Ebel

    doi:10.1101/2021.05.04.442699 Date: 2021-05-05 Source: bioRxiv

    SARS-CoV-2 has had a disproportionate impact on non-hospital healthcare settings such as long-term care facilities (LTCFs). The communal nature of these facilities, paired with the high-risk profile of residents, has resulted in thousands of infections and deaths MESHD and a high case fatality rate. To detect pre-symptomatic infections and identify infected workers, we performed weekly surveillance testing of staff at two LTCFs which revealed a large outbreak at one of the sites. We collected serum from staff members throughout the study and evaluated it for binding and neutralization to measure seroprevalence, seroconversion, and type and functionality of antibodies. At the site with very few incident infections, we detected that over 40% of the staff had preexisting SARS-CoV-2 neutralizing antibodies, suggesting prior exposure. At the outbreak site, we saw rapid seroconversion following infection. Neutralizing antibody levels were stable for many weeks following infection, suggesting a durable, long-lived response. Receptor-binding domain antibodies and neutralizing antibodies were strongly correlated. The site with high seroprevalence among staff had two unique introductions of SARS-CoV-2 into the facility through seronegative infected staff during the period of study but these did not result in workplace spread or outbreaks. Together our results reveal that high seroprevalence rate among staff can contribute to herd immunity within a workplace and protect against subsequent infection and spread within a facility.

    SARS-CoV-2 variant B.1.617 is resistant to Bamlanivimab and evades antibodies induced by infection and vaccination

    Authors: Markus Hoffmann; Heike Hofmann-Winkler; Nadine Krueger; Amy Kempf; Inga Nehlmeier; Luise Graichen; Anzhalika Sidarovich; Anna-Sophie Moldenhauer; Martin S. Winkler; Sebastian Schulz; Hans-Martin Jaeck; Metodi V. Stankov; Georg M. N. Behrens; Stefan Poehlmann

    doi:10.1101/2021.05.04.442663 Date: 2021-05-05 Source: bioRxiv

    The emergence of SARS-CoV-2 variants threatens efforts to contain the COVID-19 pandemic MESHD. The number of COVID-19 MESHD cases and deaths MESHD in India has risen steeply in recent weeks and a novel SARS-CoV-2 variant, B.1.617, is believed to be responsible for many of these cases. The spike protein PROTEIN of B.1.617 harbors two mutations in the receptor binding domain, which interacts with the ACE2 HGNC receptor and constitutes the main target of neutralizing antibodies. Therefore, we analyzed whether B.1.617 is more adept in entering cells and/or evades antibody responses. B.1.617 entered two out of eight cell lines tested with slightly increased efficiency and was blocked by entry inhibitors. In contrast, B.1.617 was resistant against Bamlanivimab, an antibody used for COVID-19 MESHD treatment. Finally, B.1.617 evaded antibodies induced by infection or vaccination, although with moderate efficiency. Collectively, our study reveals that antibody evasion of B.1.617 may contribute to the rapid spread of this variant.


    Authors: Zelalem Temesgen; Charles D. Burger; Jason Baker; Christopher Polk; Claudia Libertin; Colleen Kelley; Vincent C Marconi; Robert Orenstein; Cameron Durrant; Dale Chappell; Omar Ahmed; Gabrielle Chappell; Andrew Badley

    doi:10.1101/2021.05.01.21256470 Date: 2021-05-05 Source: medRxiv

    BACKGROUND: Severe COVID19 MESHD pneumonia MESHD results from a hyperinflammatory immune response (cytokine storm, CS), characterized by GM CSF HGNC mediated activation and trafficking of myeloid cells, leading to elevation of downstream inflammatory chemokines ( MCP1 HGNC, IL8 HGNC, IP10 HGNC), cytokines ( IL6 HGNC, IL1 HGNC), and other markers of systemic inflammation MESHD ( CRP HGNC, D dimer, ferritin). CS leads to fever MESHD, hypotension MESHD, coagulopathy MESHD, respiratory failure MESHD, ARDS, and death MESHD. Lenzilumab is a novel Humaneered anti-human GM CSF HGNC monoclonal antibody that directly binds GM CSF HGNC and prevents signaling through its receptor. The LIVE AIR Phase 3 randomized, double blind, placebo controlled trial investigated the efficacy and safety of lenzilumab to assess the potential for lenzilumab to improve the likelihood of ventilator free survival (referred to herein as survival without ventilation, SWOV), beyond standard supportive care, in hospitalized subjects with severe COVID-19 MESHD. METHODS: Subjects with COVID-19 MESHD (n=520), >18 years <94% oxygen saturation on room air and/or requiring supplemental oxygen, but not invasive mechanical ventilation, were randomized to receive lenzilumab (600 mg, n=261) or placebo (n=259) via three intravenous infusions administered 8 hours apart. Subjects were followed through Day 28 following treatment. RESULTS: Baseline demographics were comparable between the two treatment groups: male, 64.7%; mean age, 60.5 years; mean BMI, 32.5 kg/m2; mean CRP HGNC, 98.36 mg/L; CRP HGNC was <150 mg/L in 77.9% of subjects. The most common comorbidities were obesity MESHD (55.1%), diabetes MESHD (53.4%), chronic kidney disease MESHD (14.0%), and coronary artery disease MESHD (13.6%). Subjects received steroids (93.7%), remdesivir (72.4%), or both (69.1%). Lenzilumab improved the likelihood of SWOV by 54% in the mITT population (HR: 1.54; 95% CI: 1.02 to 2.31, p=0.041) and by 90% in the ITT population (HR: 1.90; 1.02 to 3.52, nominal p=0.043) compared to placebo. SWOV also relatively improved by 92% in subjects who received both corticosteroids and remdesivir (1.92; 1.20 to 3.07, nominal p=0.0067); by 2.96-fold in subjects with CRP HGNC<150 mg/L and age <85 years (2.96; 1.63 to 5.37, nominal p=0.0003); and by 88% in subjects hospitalized <2 days prior to randomization (1.88; 1.13 to 3.12, nominal p=0.015). Survival was improved by 2.17-fold in subjects with CRP HGNC<150 mg/L and age <85 years (2.17; 1.04 to 4.54, nominal p=0.040). CONCLUSION: Lenzilumab significantly improved SWOV in hospitalized, hypoxic subjects with COVID-19 MESHD pneumonia MESHD over and above treatment with remdesivir and/or corticosteroids. Subjects with CRP HGNC<150 mg/L and age <85 years demonstrated an improvement in survival and had the greatest benefit from lenzilumab. NCT04351152

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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