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Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2

Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology,...

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Autores principales: Parlikar, Arohi, Kalia, Kishan, Sinha, Shruti, Patnaik, Sucheta, Sharma, Neeraj, Vemuri, Sai Gayatri, Sharma, Gaurav
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7370936/
https://www.ncbi.nlm.nih.gov/pubmed/32742815
http://dx.doi.org/10.7717/peerj.9576
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author Parlikar, Arohi
Kalia, Kishan
Sinha, Shruti
Patnaik, Sucheta
Sharma, Neeraj
Vemuri, Sai Gayatri
Sharma, Gaurav
author_facet Parlikar, Arohi
Kalia, Kishan
Sinha, Shruti
Patnaik, Sucheta
Sharma, Neeraj
Vemuri, Sai Gayatri
Sharma, Gaurav
author_sort Parlikar, Arohi
collection PubMed
description Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology, and evolutionary studies. In the first half of this article, we provide a detailed review of the history and origin of COVID-19, followed by the taxonomy, nomenclature and genome organization of its causative agent Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2). In the latter half, we analyze subgenus Sarbecovirus (167 SARS-CoV-2, 312 SARS-CoV, and 5 Pangolin CoV) genomes to understand their diversity, origin, and evolution, along with pan-genome analysis of genus Betacoronavirus members. Whole-genome sequence-based phylogeny of subgenus Sarbecovirus genomes reasserted the fact that SARS-CoV-2 strains evolved from their common ancestors putatively residing in bat or pangolin hosts. We predicted a few country-specific patterns of relatedness and identified mutational hotspots with high, medium and low probability based on genome alignment of 167 SARS-CoV-2 strains. A total of 100-nucleotide segment-based homology studies revealed that the majority of the SARS-CoV-2 genome segments are close to Bat CoV, followed by some to Pangolin CoV, and some are unique ones. Open pan-genome of genus Betacoronavirus members indicates the diversity contributed by the novel viruses emerging in this group. Overall, the exploration of the diversity of these isolates, mutational hotspots and pan-genome will shed light on the evolution and pathogenicity of SARS-CoV-2 and help in developing putative methods of diagnosis and treatment.
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spelling pubmed-73709362020-07-31 Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2 Parlikar, Arohi Kalia, Kishan Sinha, Shruti Patnaik, Sucheta Sharma, Neeraj Vemuri, Sai Gayatri Sharma, Gaurav PeerJ Bioinformatics Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology, and evolutionary studies. In the first half of this article, we provide a detailed review of the history and origin of COVID-19, followed by the taxonomy, nomenclature and genome organization of its causative agent Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2). In the latter half, we analyze subgenus Sarbecovirus (167 SARS-CoV-2, 312 SARS-CoV, and 5 Pangolin CoV) genomes to understand their diversity, origin, and evolution, along with pan-genome analysis of genus Betacoronavirus members. Whole-genome sequence-based phylogeny of subgenus Sarbecovirus genomes reasserted the fact that SARS-CoV-2 strains evolved from their common ancestors putatively residing in bat or pangolin hosts. We predicted a few country-specific patterns of relatedness and identified mutational hotspots with high, medium and low probability based on genome alignment of 167 SARS-CoV-2 strains. A total of 100-nucleotide segment-based homology studies revealed that the majority of the SARS-CoV-2 genome segments are close to Bat CoV, followed by some to Pangolin CoV, and some are unique ones. Open pan-genome of genus Betacoronavirus members indicates the diversity contributed by the novel viruses emerging in this group. Overall, the exploration of the diversity of these isolates, mutational hotspots and pan-genome will shed light on the evolution and pathogenicity of SARS-CoV-2 and help in developing putative methods of diagnosis and treatment. PeerJ Inc. 2020-07-17 /pmc/articles/PMC7370936/ /pubmed/32742815 http://dx.doi.org/10.7717/peerj.9576 Text en © 2020 Parlikar et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Parlikar, Arohi
Kalia, Kishan
Sinha, Shruti
Patnaik, Sucheta
Sharma, Neeraj
Vemuri, Sai Gayatri
Sharma, Gaurav
Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2
title Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2
title_full Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2
title_fullStr Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2
title_full_unstemmed Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2
title_short Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2
title_sort understanding genomic diversity, pan-genome, and evolution of sars-cov-2
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7370936/
https://www.ncbi.nlm.nih.gov/pubmed/32742815
http://dx.doi.org/10.7717/peerj.9576
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