Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (289)

ProteinN (99)

NSP5 (59)

ComplexRdRp (26)

NSP3 (17)


SARS-CoV-2 Proteins
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    Genomic Sequencing of SARS-COV-2 in Rwanda: evolution and regional dynamics

    Authors: Yvan Butera; Enatha Mukantwari; Maria Artesi; Jeanne D'Arc Umuringa; Aine Niamh O'Toole; Verity Hill; Stefan Rooke; Samuel Leandro Hong; Simon Dellicour; Onesphore Majyambere; Sebastien Bontems; Bouchra Boujemla; Josh Quick; Paola Cristina Resende; Nicholas James Loman; Esperance Umumararungu; Alice Kabanda; Marylin Milumbu Murindahabi; Patrick Tuyisenge; Misbah Gashegu; Jean Paul Rwabihama; Reuben Sindayiheba; Djordje Gikic; Jacob Souopgui; Wilfred Ndifon; Robert Rutayisire; Swaibu Gatare; Tharcisse Mpunga; Daniel Ngamije; Vincent Bours; Andrew Rambaut; Sabin Nsanzimana; Guy Baele; Keith Durkin; Leon Mutesa; Nadine Rujeni

    doi:10.1101/2021.04.02.21254839 Date: 2021-04-07 Source: medRxiv

    The severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2), responsible for coronavirus disease MESHD 19 ( COVID-19 MESHD), is a single-stranded positive-sense ribonucleic acid (RNA) virus that typically undergoes one to two single nucleotide mutations per month. COVID-19 MESHD continues to spread globally, with case fatality and test positivity rates often linked to locally circulating strains of SARS-CoV-2. Furthermore, mutations in this virus, in particular those occurring in the spike protein PROTEIN (involved in the virus binding to the host epithelial cells) have potential implications in current vaccination efforts. In Rwanda, more than twenty thousand cases have been confirmed as of March 14th 2021, with a case fatality rate of 1.4% and test positivity rate of 2.3% while the recovery rate is at 91.9%. Rwanda started its genomic surveillance efforts, taking advantage of pre-existing research projects and partnerships, to ensure early detection of SARS-CoV-2 variants and to potentially contain the spread of variants of concern (VOC). As a result of this initiative, we here present 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in the country from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the newly emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the VOCs, B.1.1.7 and B.1.351, among incoming travelers tested at Kigali International Airport. We also discuss the potential impact of COVID-19 MESHD control measures established in the country to control the spread of the virus. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations during the time frame of interest. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences are currently available or that no longer report positive cases. Our results point to the importance of systematically screening all incoming travelers, regardless of the origin of their travels as well as regional considerations for durable response to COVID-19 MESHD.

    Effectiveness of CoronaVac in the setting of high SARS-CoV-2 P.1 variant transmission in Brazil: A test-negative case-control study

    Authors: Matt Hitchings; Otavio T. Ranzani; Mario S.S. Torres; Silvano Barbosa de Oliveira; Maria Almiron; Rodrigo Said; Ryan Borg; Wade L. Schulz; Roberto Dias de Oliveira; Patricia Vieira da Silva; Daniel Barros de Castro; Vanderson de Souza Sampaio; Bernardino Cláudio de Albuquerque; Tatyana Costa Amorim Ramos; Shadia Hussami Hauache Fraxe; Cristiano Fernandes da Costa; Felipe Gomes Naveca; André M. Siqueira; Wildo Navegantes de Araújo; Jason R. Andrews; Derek A.T. Cummings; Albert I. Ko; Julio Croda

    doi:10.1101/2021.04.07.21255081 Date: 2021-04-07 Source: medRxiv

    BackgroundSevere acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) variant P.1 emerged in the city of Manaus in late 2020 during a large resurgence of coronavirus disease MESHD ( COVID-19 MESHD), and has spread throughout Brazil. The effectiveness of vaccines in settings with widespread P.1 transmission has not been reported. MethodsWe performed a matched test-negative case-control study to estimate the effectiveness of an inactivated vaccine, CoronaVac, in healthcare workers (HCWs) in Manaus, where P.1 accounted for 75% of genotyped SARS-CoV-2 samples at the peak of its epidemic. Information from electronic surveillance databases was used to select cases of RT-PCR-confirmed SARS-CoV-2 infection MESHD and matched test-negative controls from 19 January, 2021 to 25 March, 2021. We used conditional logistic regression to estimate the effectiveness in reducing the odds of primary and secondary outcomes of, respectively, symptomatic and any SARS-CoV-2 infection MESHD. FindingsAmong 53,176 HCWs, 46,884 (88%) received at least one dose of CoronaVac and 2,656 (5%) underwent RT-PCR testing from 19 January, 2021 to 25 March, 2021. Of 2,797 RT-PCR tests, 776 (28%) were positive. 393 and 135 case-control pairs with and without, respectively, symptomatic illness MESHD were selected for the matched analyses. Vaccination with at least one dose was associated with a 0.50-fold reduction (adjusted vaccine effectiveness, 49.6%; 95% CI, 11.3 - 71.4) in the odds of symptomatic SARS-CoV-2 infection MESHD during the period 14 days or more after receiving the first dose. Estimated vaccine effectiveness of at least one dose against any SARS-CoV-2 infection MESHD was 35.1% (95% CI, -6.6 - 60.5) in the same time period. InterpretationAdministration of at least one dose of CoronaVac showed effectiveness against symptomatic SARS-CoV-2 infection MESHD in the setting of epidemic P.1 transmission, underscoring the need to increase vaccination efforts in response to the spread of this variant in Brazil and globally. FundingPan American Health Organization; Fundacao Oswaldo Cruz (Fiocruz); Municipal Health Secretary of Manaus

    Prospective analytical performance evaluation of the QuickNavi™- COVID19 MESHD Ag for asymptomatic individuals

    Authors: Yoshihiko Kiyasu; Yuto Takeuchi; Yusaku Akashi; Daisuke Kato; Miwa Kuwahara; Shino Muramatsu; Shigeyuki Notake; Atsuo Ueda; Koji Nakamura; Hiroichi Ishikawa; Hiromichi Suzuki

    doi:10.1101/2021.04.01.21254813 Date: 2021-04-07 Source: medRxiv

    Introduction Antigen testing may help screen for and detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections MESHD in asymptomatic individuals. However, limited data regarding the diagnostic performance of antigen tests for this group are available. Methods We used clinical samples to prospectively evaluate the analytical and clinical performance of the antigen test QuickNavi- COVID19 MESHD Ag. This study was conducted at a PCR center between October 7, 2020 and January 9, 2021. Two nasopharyngeal samples per patient were obtained with flocked swabs; one was used for the antigen test, and the other for real-time reverse transcription PCR (RT-PCR). The diagnostic performance of the antigen test was compared between asymptomatic and symptomatic patients, and the RT-PCR results were used as a reference. Results Among the 1,934 collected samples, SARS-CoV-2 was detected by real-time RT-PCR in 188 (9.7%); 76 (40.4%) of these samples were from asymptomatic individuals. Over half of the total samples (1,073; 55.5%) were obtained from asymptomatic volunteers. The sensitivity of the antigen test was significantly lower for asymptomatic group than for symptomatic patients (67.1% vs 89.3%, p < 0.001). The specificity was 100% for both groups, and no false positives were observed among all 1,934 samples. The median Ct value for the asymptomatic group was significantly higher than that of the symptomatic group (24 vs 20, p < 0.001). Conclusions The QuickNavi- COVID19 MESHD Ag showed a lower sensitivity for asymptomatic group than for symptomatic patients. However, its specificity was consistently high, and no false positives were found in this study.

    mRNA vaccination compared to infection elicits an IgG-predominant response with greater SARS-CoV-2 specificity and similar decrease in variant spike recognition

    Authors: Katharina Roeltgen; Sandra C.A. Nielsen; Prabhu S Arunachalam; Fan Yang; Ramona A. Hoh; Oliver F. Wirz; Alexandra S Lee; Fei Gao; Vamsee Mallajosyula; Chunfeng Li; Emily Haraguchi; Massa J Shoura; James L Wilbur; Jacob N. Wohlstadter; Mark M. Davis; Benjamin A. Pinsky; George B. Sigal; Bali Pulendran; Kari C. Nadeau; Scott D. Boyd

    doi:10.1101/2021.04.05.21254952 Date: 2021-04-07 Source: medRxiv

    During the severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) pandemic, new vaccine strategies including lipid nanoparticle delivery of antigen encoding RNA have been deployed globally. The BioNTech/Pfizer mRNA vaccine BNT162b2 encoding SARS-CoV-2 spike PROTEIN protein shows 95% efficacy in preventing disease, but it is unclear how the antibody responses to vaccination differ from those generated by infection. Here we compare the magnitude and breadth of antibodies targeting SARS-CoV-2, SARS-CoV-2 variants of concern, and endemic coronaviruses, in vaccinees and infected MESHD patients. We find that vaccination differs from infection in the dominance of IgG over IgM and IgA responses, with IgG reaching levels similar to those of severely ill COVID-19 MESHD patients and shows decreased breadth of the antibody response targeting endemic coronaviruses. Viral variants of concern from B.1.1.7 to P.1 to B.1.351 form a remarkably consistent hierarchy of progressively decreasing antibody recognition by both vaccinees and infected MESHD patients exposed to Wuhan-Hu-1 antigens.

    High SARS-CoV-2 attack rates following exposure during singing events in the Netherlands, September-October 2020

    Authors: Anita A. Shah; Florien Dusseldorp; Irene K. Veldhuijzen; Margreet J.M. te Wierik; Alvin Bartels; Jack Schijven; Lucie C. Vermeulen; Mirjam J. Knol

    doi:10.1101/2021.03.30.21253126 Date: 2021-04-06 Source: medRxiv

    Previous reports indicate that there may be an increased risk of severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) transmission during singing events. We describe SARS-CoV-2 transmission in six singing events from September-October 2020, across the Netherlands, with attack rates from 25-74%. We investigated potential routes of SARS-CoV-2 transmission for each event. Events included 9-21 persons, aged 20-79 years. SARS-CoV-2 transmission likely took place during five out of six events; a possible index case could be identified in four out of five clusters. Limited sequencing data was available, hampering interpretation of results. Indirect contact and droplet transmission (<1.5m) may have caused some cases, but are unlikely to explain the high attack rates. The previously published AirCoV2 model indicated that airborne transmission (via infectious droplets/ aerosols over longer distances (>1.5m)) due to singing is possible in case of supershedder presence ([≥]1010 RNA copies/mL). Also, airflow expelling respiratory droplets over longer distances (>1.5m) may have influenced transmission. In conclusion, a combination of transmission routes probably caused these five clusters. Proportions attributable to each route cannot be deduced. It is possible that airborne transmission of SARS-CoV-2 due to singing (partly) led to the high attack rates observed in these clusters.

    The association of ABO blood group HGNC with the asymptomatic COVID-19 MESHD cases in India

    Authors: Prajjval Pratap Singh; Abhishek K Srivastava; Sudhir K Upadhyay; Ashish Singh; Pranav Gupta; Sanjeev Maurya; Shashank Upadhyay; Rudra K Pandey; Anshika Shrivastava; Priya Dev; Vanya Singh; Rahul Mishra; Manoj K Shukla; Govind Chaubey; Pradeep Kumar; Vandana Rai; Yamini B Tripathy; Abhishek Pathak; Vijaya N Mishra; Chandana Basu Mallick; Panjak Shrivastava; Gyaneshwer Chaubey

    doi:10.1101/2021.04.01.21254681 Date: 2021-04-06 Source: medRxiv

    The COVID-19 pandemic MESHD has resulted several waves of infection in many countries worldwide. The large variations in case fatality ratio among different geographical regions suggests that the human susceptibility against this virus varies substantially. Several studies from different parts of the world showed a significant association of ABO blood group HGNC and COVID-19 MESHD susceptibility. It was shown that individuals with blood group O are at the lower risk of coronavirus infection MESHD. To establish the association of ABO blood group HGNC in SARS-CoV-2 susceptibility, we for the first time analysed SARS-CoV-2 neutralising antibodies as well as blood groups among 509 random individuals from three major districts of Eastern Uttar Pradesh region of India. . Interestingly, we found neutralising antibodies in significantly higher percentage of people with blood group AB (0.36) followed by B (0.31), A (0.22) and lowest in people with blood group O (0.11). This indicates that people with blood group AB are at comparatively higher risk of infection than other blood groups. Further, in line to previous reports we too observed that people with blood group O have significantly decreased risk of SARS-CoV-2 infection MESHD. Thus, among the asymptomatic SARS-CoV-2 infected MESHD individuals with blood group AB has highest, whilst blood group O has lowest risk of infection.

    High-Potency Polypeptide-based Interference for Coronavirus Spike Glycoproteins PROTEIN

    Authors: Jianpeng Ma; Adam Campos Acevedo; Qinghua Wang

    doi:10.1101/2021.04.05.438537 Date: 2021-04-06 Source: bioRxiv

    The world is experiencing an unprecedented coronavirus disease 2019 MESHD ( COVID-19 MESHD) pandemic caused by severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2). SARS-CoV-2 spike PROTEIN protein-based vaccines are currently the main preventive agent to fight against the virus. However, several variants with extensive mutations in SARS-CoV-2 spike PROTEIN proteins have emerged. Some of these variants exhibited increased replication, higher transmission and virulence, and were partially resistant to antibody neutralization from natural infection or vaccination. With over 130 million confirmed cases and widespread vaccination around the globe, the emergence of new escape SARS-CoV-2 variants could be accelerated. New therapeutics insensitive to mutations are thus urgently needed. Here we have developed an inhibitor based on SARS-CoV-2 spike PROTEIN protein that potently reduced pseudovirus infectivity by limiting the level of SARS-CoV-2 spike PROTEIN proteins on virion envelope. Most importantly, the inhibitor was equally effective against other coronavirus spike proteins PROTEIN that shared as low as 35% amino-acid sequence identity, underscoring its extreme tolerance to mutations. The small-sized inhibitor would also allow simple delivery by, for instance, nasal spray. We expect the inhibitor reported here to be an invaluable aid to help end COVID-19 pandemic MESHD. Furthermore, the use of a partial native sequence or its homologues to interfere with the functions of the native protein represents a novel concept for targeting other viral proteins in combating against important viral pathogens.

    Diagnostic Utility of Antigen Detection Rapid Diagnostic Tests for Covid- 19: A Systematic Review and Meta-Analysis

    Authors: Mina Ebrahimi; Narges Nazari Harmooshi; Fakher Rahim

    doi:10.1101/2021.04.02.21254714 Date: 2021-04-05 Source: medRxiv

    Background: Early detection of coronavirus disease MESHD ( COVID-19 MESHD) infection to improve disease management, becomes the greatest challenge. Despite high sensitivity of RT-PCR, not only it was reported that 20-67% of infected MESHD patients have false negative results. Rapid diagnostic tests (RDTs) are widely used as a point-of-care test for SARS-CoV-2 detection in both pharyngeal and blood specimens. To be less time-consuming, not seem so costly, and requiring no special training make it more favorable, but the low sensitivity is the main limitation. Several reports indicated rapid test of blood and pharyngeal samples has the same sensitivity as the RT-PCR, but some reports have lower sensitivity especial in asymptomatic patients. Methods: In the present survey, we investigate the eligible studies for sensitivity and specificity of rapid tests and explore the factors that influence the result to help better diagnose COVID-19 MESHD infection. 20 studies met the inclusion criteria, which impose 33 different tests. Results: Our findings showed, type of sample, type of assay, time of sampling, and load of virus influence on sensitivity of RDTs. Conclusion: This research extends our knowledge of how to improve the sensitivity of RDTs to better diagnose of infected MESHD patients to address the controlling COVID-19 pandemic MESHD.

    Substitutions and codon usage in SARS-CoV-2 in mammals indicate natural selection and host adaptation

    Authors: Zhixiong Lei Sr.; Dan Zhang Sr.; Long Liu

    doi:10.1101/2021.04.04.438417 Date: 2021-04-05 Source: bioRxiv

    The outbreak of COVID-19 MESHD, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection MESHD, rapidly spread to create a global pandemic and has continued to spread across hosts from humans to animals, transmitting particularly effectively in mink. How SARS-CoV-2 evolves in animals and humans and the differences in the separate evolutionary processes remain unclear. We analyzed the composition and codon usage bias of SARS-CoV-2 MESHD in infected humans and animals. Compared with other animals, SARS-CoV-2 in mink had the most substitutions. The substitutions of cytidine in SARS-CoV-2 in mink account for nearly 50% of the substitutions, while those in other animals represent only 30% of the substitutions. The incidence of adenine transversion in SARS-CoV-2 in other animals is threefold higher than that in mink-CoV (the SARS-CoV-2 virus in mink). A synonymous codon usage analysis showed that SARS-CoV-2 is optimized to adapt in the animals in which it is currently reported, and all of the animals showed decreased adaptability relative to that of humans, except for mink. A binding affinity analysis indicated that the spike protein PROTEIN of the SARS-CoV-2 variant in mink showed a greater preference for binding with the mink receptor ACE2 than with the human receptor, especially as the mutation Y453F and F486L in mink-CoV lead to improvement of binding affinity for mink receptor. Our study focuses on the divergence of SARS-CoV-2 genome composition and codon usage in humans and animals, indicating possible natural selection and current host adaptation.

    Twelve-month specific IgG response to SARS-CoV-2 receptor-binding domain among COVID-19 MESHD convalescent plasma donors in Wuhan

    Authors: Cesheng Li; Ding Yu; Xiao Wu; Hong Liang; Zhijun Zhou; Yong Xie; Taojing Li; Junzheng Wu; Fengping Lu; Lu Feng; Min Mao; Lianzhen Lin; Huanhuan Guo; Shenglan Yue; Feifei Wang; Yan Peng; Yong Hu; Zejun Wang; Jianhong Yu; Yong Zhang; Jia Lu; Haoran Ning; Huichuan Yang; Daoxing Fu; Yanlin He; Dongbo Zhou; Tao Du; Kai Duan; Demei Dong; Kun Deng; Xia Zou; Ya Zhang; Rong Zhou; Yang Gao; Xinxin Zhang; Xiaoming Yang

    doi:10.1101/2021.04.05.437224 Date: 2021-04-05 Source: bioRxiv

    To investigate the duration of humoral immune response in convalescent coronavirus disease MESHD coronavirus disease 2019 MESHD ( COVID-19 MESHD) patients, we conducted a 12-month longitudinal study through collecting a total of 1,782 plasma samples from 869 convalescent plasma donors in Wuhan, China and tested specific antibody response. The results show that positive rate of IgG antibody against receptor-binding domain of spike protein PROTEIN (RBD-IgG) to severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) in the COVID-19 MESHD convalescent plasma donors exceeded 70% for 12 months post diagnosis. RBD-IgG kinetics displayed a gradually downward trend, the titer started to stabilize after 9 months and decreased by 68.1% compared with the 1st month. Moreover, male plasma donors produced more RBD-IgG than female plasma donors and patient age positively correlated with the RBD-IgG titer. A strong positive correlation between RBD-IgG and neutralizing antibody titers was also identified. This study is essential for understanding SARS-CoV-2-induced immune memory to develop vaccine and therapeutics.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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