Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan

We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan. We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to...

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Published in:PloS one 2021-08, Vol.16 (8), p.e0256451-e0256451
Main Authors: Ghanchi, Najia Karim, Nasir, Asghar, Masood, Kiran Iqbal, Abidi, Syed Hani, Mahmood, Syed Faisal, Kanji, Akbar, Razzak, Safina, Khan, Waqasuddin, Shahid, Saba, Yameen, Maliha, Raza, Ali, Ashraf, Javaria, Ansar, Zeeshan, Dharejo, Mohammad Buksh, Islam, Nazneen, Hasan, Zahra, Hasan, Rumina
Format: Article
Language:English
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5' Untranslated Regions
Analysis
Biology and life sciences
Computer and Information Sciences
Coronaviruses
COVID-19
Disease transmission
DNA-directed RNA polymerase
Entropy
Epidemiology
Funding
Gene sequencing
Genomes
Glycoproteins
Growth hormone
Laboratories
Medicine
Medicine and health sciences
Mutation
Mutation rates
Overseas
Pandemics
Pathology
People and Places
Phylogeny
Physical Sciences
Ribonucleic acid
RNA
Severe acute respiratory syndrome
Severe acute respiratory syndrome coronavirus 2
Spike glycoprotein
Strains (organisms)
Viral diseases
Viruses
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cited_by cdi_FETCH-LOGICAL-c669t-9927f9d1173bc3e0c22105da765d2000bfb774afb06170c7a87654807a9d746e3
cites cdi_FETCH-LOGICAL-c669t-9927f9d1173bc3e0c22105da765d2000bfb774afb06170c7a87654807a9d746e3
container_end_page e0256451
container_issue 8
container_start_page e0256451
container_title PloS one
container_volume 16
creator Ghanchi, Najia Karim
Nasir, Asghar
Masood, Kiran Iqbal
Abidi, Syed Hani
Mahmood, Syed Faisal
Kanji, Akbar
Razzak, Safina
Khan, Waqasuddin
Shahid, Saba
Yameen, Maliha
Raza, Ali
Ashraf, Javaria
Ansar, Zeeshan
Dharejo, Mohammad Buksh
Islam, Nazneen
Hasan, Zahra
Hasan, Rumina
description We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan. We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020. In March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The highest diversity of clades was present in Sindh and Islamabad Capital Territory and the least in Punjab province. Initial introductions of SARS-CoV-2 GH (B.1.255, B.1) and S (A) clades were associated with overseas travelers. Additionally, GH (B.1.255, B.1, B.1.160, B.1.36), L (B, B.6, B.4), V (B.4) and S (A) clades were transmitted locally. SARS-CoV-2 genomes clustered with global strains except for ten which matched Pakistani isolates. RNA substitution rates were estimated at 5.86 x10.sup.-4 . The most frequent mutations were 5' UTR 241C > T, Spike glycoprotein D614G, RNA dependent RNA polymerase (RdRp) P4715L and Orf3a Q57H. Strains up until June 2020 exhibited an overall higher mean and site-specific entropy as compared with sequences after June. Relative entropy was higher across GH as compared with GR and L clades. More sites were under selection pressure in GH strains but this was not significant for any particular site. The higher entropy and diversity observed in early pandemic as compared with later strains suggests increasing stability of the genomes in subsequent COVID-19 waves. This would likely lead to the selection of site-specific changes that are advantageous to the virus, as has been currently observed through the pandemic.
doi_str_mv 10.1371/journal.pone.0256451
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Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing &amp; Allied Health Database (Alumni Edition)</collection><collection>Meteorological &amp; Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>Biological Sciences</collection><collection>Agricultural Science Database</collection><collection>Health &amp; Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing &amp; Allied Health Premium</collection><collection>Advanced Technologies &amp; Aerospace Database</collection><collection>ProQuest Advanced Technologies &amp; Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ghanchi, Najia Karim</au><au>Nasir, Asghar</au><au>Masood, Kiran Iqbal</au><au>Abidi, Syed Hani</au><au>Mahmood, Syed Faisal</au><au>Kanji, Akbar</au><au>Razzak, Safina</au><au>Khan, Waqasuddin</au><au>Shahid, Saba</au><au>Yameen, Maliha</au><au>Raza, Ali</au><au>Ashraf, Javaria</au><au>Ansar, Zeeshan</au><au>Dharejo, Mohammad Buksh</au><au>Islam, Nazneen</au><au>Hasan, Zahra</au><au>Hasan, Rumina</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan</atitle><jtitle>PloS one</jtitle><date>2021-08-31</date><risdate>2021</risdate><volume>16</volume><issue>8</issue><spage>e0256451</spage><epage>e0256451</epage><pages>e0256451-e0256451</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><notes>Competing Interests: The authors have declared that no competing interests exist.</notes><abstract>We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan. We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020. In March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The highest diversity of clades was present in Sindh and Islamabad Capital Territory and the least in Punjab province. Initial introductions of SARS-CoV-2 GH (B.1.255, B.1) and S (A) clades were associated with overseas travelers. Additionally, GH (B.1.255, B.1, B.1.160, B.1.36), L (B, B.6, B.4), V (B.4) and S (A) clades were transmitted locally. SARS-CoV-2 genomes clustered with global strains except for ten which matched Pakistani isolates. RNA substitution rates were estimated at 5.86 x10.sup.-4 . The most frequent mutations were 5' UTR 241C &gt; T, Spike glycoprotein D614G, RNA dependent RNA polymerase (RdRp) P4715L and Orf3a Q57H. Strains up until June 2020 exhibited an overall higher mean and site-specific entropy as compared with sequences after June. Relative entropy was higher across GH as compared with GR and L clades. More sites were under selection pressure in GH strains but this was not significant for any particular site. The higher entropy and diversity observed in early pandemic as compared with later strains suggests increasing stability of the genomes in subsequent COVID-19 waves. This would likely lead to the selection of site-specific changes that are advantageous to the virus, as has been currently observed through the pandemic.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><pmid>34464419</pmid><doi>10.1371/journal.pone.0256451</doi><tpages>e0256451</tpages><orcidid>https://orcid.org/0000-0001-7580-372X</orcidid><orcidid>https://orcid.org/0000-0001-7995-8163</orcidid><oa>free_for_read</oa></addata></record>
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identifier ISSN: 1932-6203
ispartof PloS one, 2021-08, Vol.16 (8), p.e0256451-e0256451
issn 1932-6203
1932-6203
language eng
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source PubMed (Medline); Publicly Available Content Database; Coronavirus Research Database
subjects 5' Untranslated Regions
Analysis
Biology and life sciences
Computer and Information Sciences
Coronaviruses
COVID-19
Disease transmission
DNA-directed RNA polymerase
Entropy
Epidemiology
Funding
Gene sequencing
Genomes
Glycoproteins
Growth hormone
Laboratories
Medicine
Medicine and health sciences
Mutation
Mutation rates
Overseas
Pandemics
Pathology
People and Places
Phylogeny
Physical Sciences
Ribonucleic acid
RNA
Severe acute respiratory syndrome
Severe acute respiratory syndrome coronavirus 2
Spike glycoprotein
Strains (organisms)
Viral diseases
Viruses
title Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan
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