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29 results for “2019-nCoV”
Coronavirus COVID-19 (2019-nCoV) Data Repository for Africa
<p>The purpose of this repository is to collate data on the ongoing coronavirus pandemic in Africa. Our goal is to record detailed information on each reported case in every African country. We want to build a line list – a table summarizing information about people who are infected, dead, or recovered. The table for each African country would include demographic, location, and symptom (where available) information for each reported case. The data will be obtained from official sources (e.g., WHO, departments of health, CDC etc.) and unofficial sources (e.g., news). Such a dataset has many uses, including studying the spread of COVID-19 across Africa and assessing similarities and differences to what’s being observed in other regions of the world.</p> <p>See the repo here <a href="https://github.com/dsfsi/covid19africa">https://github.com/dsfsi/covid19africa</a></p>
Safety and Immunogenicity Study of 2019-nCoV Vaccine (mRNA-1273) for Prophylaxis of SARS-CoV-2 Infection (COVID-19)
ClinicalTrials.gov study NCT04283461. IPD Sharing: Not stated. Countries: 1. Publications: 8.
Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output. in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output.
History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses. According to the current international classification of diseases49, MERS and SARS are classified as 1D64 and 1D65, respectively. in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses. According to the current international classification of diseases49, MERS and SARS are classified as 1D64 and 1D65, respectively.
Box 4 in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Box 4 | Classifying SARS-CoV-2 The species demarcation threshold (also known as demarcation limit) in the family Coronaviridae is defined by viruses whose PPD(s) may cross the inter-species demarcation PPD threshold (threshold 'violators'). Due to their minute share of ~10–4 of the to- tal number of all intra- and inter-species PPDs, these violators may not even be visually recognized in a conventional diagonal plot clus- tering viruses on a species basis (panel a of the figure in Box 4). Furthermore, they do not involve any virus of the species Severe acute respiratory syndrome-related coronavirus, as is evident from the analysis of maximal intraspecies PPDs of 2,505 viruses of all 49 coronavirus species (of which 39 are established and 10 are pending or tentative) (panel b of the figure in Box 4) and PDs of 256 viruses of this species (panel c of the figure in Box 4). Thus, the genomic variation of the known viruses of the species Severe acute respiratory syndrome-related coronavirus is smaller compared to that of other comparably well-sampled species—for example, those prototyped by MERS-CoV, human coronavirus OC43 (HCoV-OC43) and in- fectious bronchitis virus (IBV) (panel b of the figure in Box 4)—and this species is well separated from other known coronavirus species in the sequence space. Both of these characteristics facilitate the un- ambiguous assignment of SARS-CoV-2 to this species. Intra-species PDs of SARS-CoV-2 belong to the top 25% of this species and also include the largest PD between SARS-CoV-2 and an African bat virus isolate (SARSr-CoV_BtKY72)56 (panel c of the figure in Box 4), representing two basal lineages within the species Severe acute respiratory syndrome-related coronavirus that constitute very few known viruses (Fig. 2b,c). These relationships stand in contrast to the shallow branching of the most populous lineage of this species, which includes all the human SARS-CoV isolates collected during the 2002–2003 outbreak and the closely related bat viruses of Asian origin identified in the search for the potential zoonotic source of that epidemic57. This clade structure is susceptible to homologous recombination, which is common in this species44,58,59; to formalize clade definition, it must be revisited after the sampling of viruses representing the deep branches has improved sufficiently. The current sampling defines a very small median PD for human SARS-CoVs, which is approximately 15 times smaller than the median PD determined for SARS-CoV-2 (0.16% versus 2.6%; panel c of the figure in Box 4). This small median PD of human SARS-CoVs also dominates the species- wide PD distribution (0.25%; panel c of the figure in Box 4). Pairwise distance demarcation of species in the family Coronaviridae. a, Diagonal matrix of PPDs of 2,505 viruses clustered according to 49 coronavirus species, 39 established and 10 pending or tentative, and ordered from the most to least populous species, from left to right; green and white, PPDs smaller and larger than the inter-species threshold, respectively. Areas of the green squares along the diagonal are proportional to the virus sampling of the respective species, and virus prototypes of the five most sampled species are specified to the left; asterisks indicate species that include viruses whose intra-species PPDs crossed the inter-species threshold (threshold 'violators'). b, Maximal intra-species PPDs (x axis, linear scale) plotted against virus sampling (y axis, log scale) for 49 species (green dots) of the Coronaviridae. Indicated are the acronyms of virus prototypes of the seven most sampled species. Green and blue plot sections represent intra-species and intra-subgenera PPD ranges. The vertical black line indicates the inter-species threshold. c, Shown are the PDs of non-identical residues (y axis) for four viruses representing three major phylogenetic lineages (clades) of the species Severe acute respiratorysyndrome-related coronavirus (panel b) and all pairs of the 256 viruses of this species ('all pairs'). The PD values were derived from pairwise distances in the MSA that were calculated using an identity matrix. Panels a and b were adopted from the DEmARC v.1.4 output.
Fig. 2 in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
Fig. 2 | Phylogeny of coronaviruses. a, Concatenated multiple sequence alignments (MSAs) of the protein domain combination44 used for phylogenetic and DEmARC analyses of the family Coronaviridae. Shown are the locations of the replicative domains conserved in the ordert Nidovirales in relation to several other ORF1a/b-encoded domains and other major ORFs in the SARS-CoV genome. 5d, 5 domains: nsp5A-3CLpro, two beta-barrel domains of the 3C-like protease; nsp12-NiRAN, nidovirus RdRp-associated nucleotidyltransferase; nsp12-RdRp, RNA-dependent RNA polymerase; nsp13-HEL1 core, superfamily 1 helicase with upstream Zn-binding domain (nsp13-ZBD); nt, nucleotide. b, The maximum-likelihood tree of SARS-CoV was reconstructed by IQ-TREE v.1.6.1 (ref. 45) using 83 sequences with the best fitting evolutionary model. Subsequently, the tree was purged from the most similar sequences and midpoint-rooted. Branch support was estimated using the Shimodaira–Hasegawa (SH)-like approximate likelihood ratio test with 1,000 replicates. GenBank IDs for all viruses except four are shown; SARS-CoV, AY274119.3; SARS-CoV-2, MN908947.3; SARSr-CoV_BtKY72, KY352407.1; SARS-CoV_PC4-227, AY613950.1. c, Shown is an IQ-TREE maximum-likelihood tree of single virus representatives of thirteen species and five representatives of the species Severe acute respiratory syndrome-related coronavirus of the genus Betacoronavirus. The tree is rooted with HCoV-NL63 and HCoV-229E, representing two species of the genus Alphacoronavirus. Purple text highlights zoonotic viruses with varying pathogenicity in humans; orange text highlights common respiratory viruses that circulate in humans. Asterisks indicate two coronavirus species whose demarcations and names are pending approval from the ICTV and, thus, these names are not italicized.
Washed Microbiota Transplantation for Patients With 2019-nCoV Infection
ClinicalTrials.gov study NCT04251767. IPD Sharing: NO. Countries: 1. Publications: 11.
Experimental Trial of rhIFNα Nasal Drops to Prevent 2019-nCOV in Medical Staff
ClinicalTrials.gov study NCT04320238. IPD Sharing: UNDECIDED. Countries: 1. Publications: 5.
Clinical Study of Anti-CD147 Humanized Meplazumab for Injection to Treat With 2019-nCoV Pneumonia
ClinicalTrials.gov study NCT04275245. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Viral Excretion in Contact Subjects at High/Moderate Risk of Coronavirus 2019-nCoV Infection. COVID-19.
ClinicalTrials.gov study NCT04259892. IPD Sharing: UNDECIDED. Countries: 2. Publications: 1.
Vitamin C Infusion for the Treatment of Severe 2019-nCoV Infected Pneumonia
ClinicalTrials.gov study NCT04264533. IPD Sharing: NO. Countries: 1. Publications: 1.
In silico identification of vaccine targets for 2019-nCoV (Data tables)
<p><strong>Background</strong> The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (<a href="https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200218-sitrep-29-covid-19.pdf?sfvrsn=6262de9e_2">18-February-2020</a>), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in China.</p> <p><strong>Methods</strong> The 2019 novel coronavirus proteome was aligned to a curated database of viral immunogenic peptides. The immunogenicity of detected peptides and their binding potential to HLA alleles was predicted by immunogenicity predictive models and NetMHCpan 4.0.</p> <p><strong>Results</strong> We report <em>in silico</em> identification of a comprehensive list of immunogenic peptides that can be used as potential targets for 2019 novel coronavirus (2019-nCoV) vaccine development. First, we found 28 nCoV peptides identical to Severe acute respiratory syndrome-related coronavirus (SARS CoV) that have previously been characterized immunogenic by T cell assays. Second, we identified 48 nCoV peptides having a high degree of similarity with immunogenic peptides deposited in The Immune Epitope Database (IEDB). Lastly, we conducted a <em>de novo</em> search of 2019-nCoV 9-mer peptides that i) bind to common HLA alleles in Chinese and European population and ii) have T Cell Receptor (TCR) recognition potential by positional weight matrices and a recently developed immunogenicity algorithm, iPred, and identified in total 63 peptides with a high immunogenicity potential.</p> <p><strong>Conclusions</strong> Given the limited time and resources to develop vaccine and treatments for 2019-nCoV, our work provides a shortlist of candidates for experimental validation and thus can accelerate development pipeline.</p>
Supplementary Data: Antibody-dependent Enhancement of 2019-nCoV Infection, a Major Concern for Prevention
<p>Less than two months after the new coronavirus raged, it has already become a public health problem in the world. Till today, the infectivity and lethality of the virus are not clear enough. Zhongnan Hospital of Wuhan University described in detail the clinical characteristics of 138 hospitalized patients with novel coronavirus (2019-nCoV)-infected pneumonia (NCIP) in Wuhan1. It reported that the in-hospital mortality was 4.3%, which is close to the data in Wuhan (4.1%) but twice the national average (2.0%). The data as of February 9, 2020, shows that the mortality in Wuhan City, Hubei Province, is higher than the average value of other cities in the province (1.5%), and is even higher than the national average except Hubei Province (0.59%). The much higher mortality in Wuhan compared to the whole country raises confusion in people. One possible, but certainly not entirely explained, reason for this phenomenon is the antibody-dependent enhancement (ADE) of 2019-nCoV infection, which we should pay more attention to the future plague prevention.</p>
Clinical Characteristics and Long-term Prognosis of 2019-nCoV Infection in Children
ClinicalTrials.gov study NCT04270383. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Epidemiologic, Clinical and Molecular Characteristics of Patients With Acute Respiratory Failure Affected by 2019-NCOV.
ClinicalTrials.gov study NCT04552340. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Umbilical Cord(UC)-Derived Mesenchymal Stem Cells(MSCs) Treatment for the 2019-novel Coronavirus(nCOV) Pneumonia
ClinicalTrials.gov study NCT04269525. IPD Sharing: NO. Countries: 1. Publications: 0.
A Prospective/Retrospective,Randomized Controlled Clinical Study of Antiviral Therapy in the 2019-nCoV Pneumonia
ClinicalTrials.gov study NCT04255017. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
2019-nCoV Outbreak and Cardiovascular Diseases
ClinicalTrials.gov study NCT04255940. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Development of a Simple, Fast and Portable Recombinase Aided Amplification Assay for 2019-nCoV
ClinicalTrials.gov study NCT04245631. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Validation of an Immunochromatographic Assay for IgG/IgM Antibodies to 2019- nCoV
ClinicalTrials.gov study NCT04434417. IPD Sharing: YES. Countries: 1. Publications: 0.
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