Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed susceptibility to diverse animal species. We conducted this study to understand the spatial epidemiology, genetic diversity, and statistically significant genetic similarity along with per-gene recombination events of SARS-CoV-2...
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| Veröffentlicht in: | PloS one 2021-12, Vol.16 (12), p.e0260635 |
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| creator | Islam, Ariful Ferdous, Jinnat Sayeed, Md Abu Islam, Shariful Kaisar Rahman, Md Abedin, Josefina Saha, Otun Hassan, Mohammad Mahmudul Shirin, Tahmina |
| description | The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed susceptibility to diverse animal species. We conducted this study to understand the spatial epidemiology, genetic diversity, and statistically significant genetic similarity along with per-gene recombination events of SARS-CoV-2 and related viruses (SC2r-CoVs) in animals globally. We collected a number of different animal species infected with SARS-CoV-2 and its related viruses. Then, we retrieved genome sequences of SARS-CoV-2 and SC2r-CoVs from GISAID and NCBI GenBank for genomic and mutational analysis. Although the evolutionary origin of SARS-CoV-2 remains elusive, the diverse SC2r-CoV have been detected in multiple Rhinolophus bat species and in Malayan pangolin. To date, human-to-animal spillover events have been reported in cat, dog, tiger, lion, gorilla, leopard, ferret, puma, cougar, otter, and mink in 25 countries. Phylogeny and genetic recombination events of SC2r-CoVs showed higher similarity to the bat coronavirus RaTG13 and BANAL-103 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the N protein from bats and pangolin showed close resemblance to SARS-CoV-2. The clustering of animal and human strains from the same geographical area has proved human-to-animal transmission of the virus. The Alpha, Delta and Mu-variant of SARS-CoV-2 was detected in dog, gorilla, lion, tiger, otter, and cat in the USA, India, Czech Republic, Belgium, and France with momentous genetic similarity with human SARS-CoV-2 sequences. The mink variant mutation (spike_Y453F) was detected in both humans and domestic cats. Moreover, the dog was affected mostly by clade O (66.7%), whereas cat and American mink were affected by clade GR (31.6 and 49.7%, respectively). The α-variant was detected as 2.6% in cat, 4.8% in dog, 14.3% in tiger, 66.7% in gorilla, and 77.3% in lion. The highest mutations observed in mink where the substitution of D614G in spike (95.2%) and P323L in NSP12 (95.2%) protein. In dog, cat, gorilla, lion, and tiger, Y505H and Y453F were the common mutations followed by Y145del, Y144del, and V70I in S protein. We recommend vaccine provision for pet and zoo animals to reduce the chance of transmission in animals. Besides, continuous epidemiological and genomic surveillance of coronaviruses in animal host is crucial to find out the immediate ancestor of SARS-CoV-2 and to prevent future CoVs threats to humans. |
| doi_str_mv | 10.1371/journal.pone.0260635 |
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We conducted this study to understand the spatial epidemiology, genetic diversity, and statistically significant genetic similarity along with per-gene recombination events of SARS-CoV-2 and related viruses (SC2r-CoVs) in animals globally. We collected a number of different animal species infected with SARS-CoV-2 and its related viruses. Then, we retrieved genome sequences of SARS-CoV-2 and SC2r-CoVs from GISAID and NCBI GenBank for genomic and mutational analysis. Although the evolutionary origin of SARS-CoV-2 remains elusive, the diverse SC2r-CoV have been detected in multiple Rhinolophus bat species and in Malayan pangolin. To date, human-to-animal spillover events have been reported in cat, dog, tiger, lion, gorilla, leopard, ferret, puma, cougar, otter, and mink in 25 countries. Phylogeny and genetic recombination events of SC2r-CoVs showed higher similarity to the bat coronavirus RaTG13 and BANAL-103 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the N protein from bats and pangolin showed close resemblance to SARS-CoV-2. The clustering of animal and human strains from the same geographical area has proved human-to-animal transmission of the virus. The Alpha, Delta and Mu-variant of SARS-CoV-2 was detected in dog, gorilla, lion, tiger, otter, and cat in the USA, India, Czech Republic, Belgium, and France with momentous genetic similarity with human SARS-CoV-2 sequences. The mink variant mutation (spike_Y453F) was detected in both humans and domestic cats. Moreover, the dog was affected mostly by clade O (66.7%), whereas cat and American mink were affected by clade GR (31.6 and 49.7%, respectively). The α-variant was detected as 2.6% in cat, 4.8% in dog, 14.3% in tiger, 66.7% in gorilla, and 77.3% in lion. The highest mutations observed in mink where the substitution of D614G in spike (95.2%) and P323L in NSP12 (95.2%) protein. In dog, cat, gorilla, lion, and tiger, Y505H and Y453F were the common mutations followed by Y145del, Y144del, and V70I in S protein. We recommend vaccine provision for pet and zoo animals to reduce the chance of transmission in animals. Besides, continuous epidemiological and genomic surveillance of coronaviruses in animal host is crucial to find out the immediate ancestor of SARS-CoV-2 and to prevent future CoVs threats to humans.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0260635</identifier><identifier>PMID: 34910734</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animal species ; Animals ; Animals, Domestic - virology ; Animals, Wild - virology ; Bats ; Biology and life sciences ; Clustering ; Coronaviridae ; Coronaviruses ; COVID-19 ; COVID-19 - epidemiology ; COVID-19 - transmission ; COVID-19 - virology ; Disease control ; Disease transmission ; Dogs ; Domestic animals ; Epidemics ; Epidemiology ; Evaluation ; Evolution ; Gene sequencing ; Genes ; Genetic diversity ; Genetic Variation ; Genome, Viral ; Genomes ; Genomics ; Humans ; Infections ; Mammals ; Medicine and health sciences ; Metadata ; Mutation ; N protein ; Pandemics ; Pangolins - virology ; Phylogenetics ; Phylogeny ; Proteins ; Recombination ; Recombination, Genetic ; Respiratory diseases ; SARS-CoV-2 - classification ; SARS-CoV-2 - genetics ; SARS-CoV-2 - isolation & purification ; Severe acute respiratory syndrome ; Severe acute respiratory syndrome coronavirus 2 ; Similarity ; Species ; Statistical analysis ; Strains (organisms) ; Vaccines ; Veterinary medicine ; Viral diseases ; Viruses ; Wild animals ; Zoo animals</subject><ispartof>PloS one, 2021-12, Vol.16 (12), p.e0260635</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Islam et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 Islam et al 2021 Islam et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-f2656243b4f0fac9458dbcbfeb680e4f178903ce16ab88a9ad7598bfc39944c53</citedby><cites>FETCH-LOGICAL-c692t-f2656243b4f0fac9458dbcbfeb680e4f178903ce16ab88a9ad7598bfc39944c53</cites><orcidid>0000-0002-9210-3351 ; 0000-0002-6626-4178 ; 0000-0001-9159-0437 ; 0000-0001-6495-4637</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8673647/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8673647/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,2103,2929,23868,27926,27927,53793,53795</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34910734$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Makarenkov, Vladimir</contributor><creatorcontrib>Islam, Ariful</creatorcontrib><creatorcontrib>Ferdous, Jinnat</creatorcontrib><creatorcontrib>Sayeed, Md Abu</creatorcontrib><creatorcontrib>Islam, Shariful</creatorcontrib><creatorcontrib>Kaisar Rahman, Md</creatorcontrib><creatorcontrib>Abedin, Josefina</creatorcontrib><creatorcontrib>Saha, Otun</creatorcontrib><creatorcontrib>Hassan, Mohammad Mahmudul</creatorcontrib><creatorcontrib>Shirin, Tahmina</creatorcontrib><title>Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed susceptibility to diverse animal species. We conducted this study to understand the spatial epidemiology, genetic diversity, and statistically significant genetic similarity along with per-gene recombination events of SARS-CoV-2 and related viruses (SC2r-CoVs) in animals globally. We collected a number of different animal species infected with SARS-CoV-2 and its related viruses. Then, we retrieved genome sequences of SARS-CoV-2 and SC2r-CoVs from GISAID and NCBI GenBank for genomic and mutational analysis. Although the evolutionary origin of SARS-CoV-2 remains elusive, the diverse SC2r-CoV have been detected in multiple Rhinolophus bat species and in Malayan pangolin. To date, human-to-animal spillover events have been reported in cat, dog, tiger, lion, gorilla, leopard, ferret, puma, cougar, otter, and mink in 25 countries. Phylogeny and genetic recombination events of SC2r-CoVs showed higher similarity to the bat coronavirus RaTG13 and BANAL-103 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the N protein from bats and pangolin showed close resemblance to SARS-CoV-2. The clustering of animal and human strains from the same geographical area has proved human-to-animal transmission of the virus. The Alpha, Delta and Mu-variant of SARS-CoV-2 was detected in dog, gorilla, lion, tiger, otter, and cat in the USA, India, Czech Republic, Belgium, and France with momentous genetic similarity with human SARS-CoV-2 sequences. The mink variant mutation (spike_Y453F) was detected in both humans and domestic cats. Moreover, the dog was affected mostly by clade O (66.7%), whereas cat and American mink were affected by clade GR (31.6 and 49.7%, respectively). The α-variant was detected as 2.6% in cat, 4.8% in dog, 14.3% in tiger, 66.7% in gorilla, and 77.3% in lion. The highest mutations observed in mink where the substitution of D614G in spike (95.2%) and P323L in NSP12 (95.2%) protein. In dog, cat, gorilla, lion, and tiger, Y505H and Y453F were the common mutations followed by Y145del, Y144del, and V70I in S protein. We recommend vaccine provision for pet and zoo animals to reduce the chance of transmission in animals. Besides, continuous epidemiological and genomic surveillance of coronaviruses in animal host is crucial to find out the immediate ancestor of SARS-CoV-2 and to prevent future CoVs threats to humans.</description><subject>Animal species</subject><subject>Animals</subject><subject>Animals, Domestic - virology</subject><subject>Animals, Wild - virology</subject><subject>Bats</subject><subject>Biology and life sciences</subject><subject>Clustering</subject><subject>Coronaviridae</subject><subject>Coronaviruses</subject><subject>COVID-19</subject><subject>COVID-19 - epidemiology</subject><subject>COVID-19 - transmission</subject><subject>COVID-19 - virology</subject><subject>Disease control</subject><subject>Disease transmission</subject><subject>Dogs</subject><subject>Domestic animals</subject><subject>Epidemics</subject><subject>Epidemiology</subject><subject>Evaluation</subject><subject>Evolution</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic diversity</subject><subject>Genetic Variation</subject><subject>Genome, Viral</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Humans</subject><subject>Infections</subject><subject>Mammals</subject><subject>Medicine and health sciences</subject><subject>Metadata</subject><subject>Mutation</subject><subject>N protein</subject><subject>Pandemics</subject><subject>Pangolins - virology</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Proteins</subject><subject>Recombination</subject><subject>Recombination, Genetic</subject><subject>Respiratory diseases</subject><subject>SARS-CoV-2 - classification</subject><subject>SARS-CoV-2 - genetics</subject><subject>SARS-CoV-2 - isolation & purification</subject><subject>Severe acute respiratory syndrome</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>Similarity</subject><subject>Species</subject><subject>Statistical analysis</subject><subject>Strains (organisms)</subject><subject>Vaccines</subject><subject>Veterinary medicine</subject><subject>Viral diseases</subject><subject>Viruses</subject><subject>Wild animals</subject><subject>Zoo animals</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk11r2zAUhs3YWLtu_2BshsHYLpzpw5alm0EI-wgUCs3WWyHrw1FRrEyys-XfT27SEo9eDF1ISM95j84rnSx7DcEM4hp-uvVD6ISbbX2nZwARQHD1JDuHDKOCIICfnqzPshcx3gJQYUrI8-wMlwyCGpfnmV9tRW-Fy_XWKr2x3vl2n4tO5a3udG9lruxOh2j7fe5Nvppfr4qFvynQHRO0E71WufTBd2JnwxB1zG2XK7_RcYweqd_WqbSwG-Hiy-yZSZN-dZwvsp9fv_xYfC8ur74tF_PLQhKG-sIgUhFU4qY0wAjJyoqqRjZGN4QCXRpYUwaw1JCIhlLBhKorRhsjMWNlKSt8kb096G6dj_zoVeSIQIApY2gklgdCeXHLtyFdL-y5F5bfbfjQchFSCU5zyIBWDSVCMVjSElGmAKCAQVEZWkuQtD4fsw3NRiupuz4INxGdnnR2zVu_45TUmJR1EvhwFAj-15Cs4xsbpXZOdNoPh3szkBxBCX33D_p4dUeqFakA2xmf8spRlM8JTR6jGo9pZ49QaYxfQaaPZWzanwR8nAQkptd_-lYMMfLl6vr_2aubKfv-hF1r4fp19G7ore_iFCwPoAw-xqDNg8kQ8LEv7t3gY1_wY1-ksDenD_QQdN8I-C9B9wgN</recordid><startdate>20211215</startdate><enddate>20211215</enddate><creator>Islam, Ariful</creator><creator>Ferdous, Jinnat</creator><creator>Sayeed, Md Abu</creator><creator>Islam, Shariful</creator><creator>Kaisar Rahman, Md</creator><creator>Abedin, Josefina</creator><creator>Saha, Otun</creator><creator>Hassan, Mohammad Mahmudul</creator><creator>Shirin, Tahmina</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>COVID</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-9210-3351</orcidid><orcidid>https://orcid.org/0000-0002-6626-4178</orcidid><orcidid>https://orcid.org/0000-0001-9159-0437</orcidid><orcidid>https://orcid.org/0000-0001-6495-4637</orcidid></search><sort><creationdate>20211215</creationdate><title>Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals</title><author>Islam, Ariful ; Ferdous, Jinnat ; Sayeed, Md Abu ; Islam, Shariful ; Kaisar Rahman, Md ; Abedin, Josefina ; Saha, Otun ; Hassan, Mohammad Mahmudul ; Shirin, Tahmina</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-f2656243b4f0fac9458dbcbfeb680e4f178903ce16ab88a9ad7598bfc39944c53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Animal species</topic><topic>Animals</topic><topic>Animals, Domestic - virology</topic><topic>Animals, Wild - virology</topic><topic>Bats</topic><topic>Biology and life sciences</topic><topic>Clustering</topic><topic>Coronaviridae</topic><topic>Coronaviruses</topic><topic>COVID-19</topic><topic>COVID-19 - epidemiology</topic><topic>COVID-19 - transmission</topic><topic>COVID-19 - virology</topic><topic>Disease control</topic><topic>Disease transmission</topic><topic>Dogs</topic><topic>Domestic animals</topic><topic>Epidemics</topic><topic>Epidemiology</topic><topic>Evaluation</topic><topic>Evolution</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genetic diversity</topic><topic>Genetic Variation</topic><topic>Genome, Viral</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Humans</topic><topic>Infections</topic><topic>Mammals</topic><topic>Medicine and health sciences</topic><topic>Metadata</topic><topic>Mutation</topic><topic>N protein</topic><topic>Pandemics</topic><topic>Pangolins - virology</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Proteins</topic><topic>Recombination</topic><topic>Recombination, Genetic</topic><topic>Respiratory diseases</topic><topic>SARS-CoV-2 - classification</topic><topic>SARS-CoV-2 - genetics</topic><topic>SARS-CoV-2 - isolation & purification</topic><topic>Severe acute respiratory syndrome</topic><topic>Severe acute respiratory syndrome coronavirus 2</topic><topic>Similarity</topic><topic>Species</topic><topic>Statistical analysis</topic><topic>Strains (organisms)</topic><topic>Vaccines</topic><topic>Veterinary medicine</topic><topic>Viral diseases</topic><topic>Viruses</topic><topic>Wild animals</topic><topic>Zoo animals</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Islam, Ariful</creatorcontrib><creatorcontrib>Ferdous, Jinnat</creatorcontrib><creatorcontrib>Sayeed, Md Abu</creatorcontrib><creatorcontrib>Islam, Shariful</creatorcontrib><creatorcontrib>Kaisar Rahman, Md</creatorcontrib><creatorcontrib>Abedin, Josefina</creatorcontrib><creatorcontrib>Saha, Otun</creatorcontrib><creatorcontrib>Hassan, Mohammad Mahmudul</creatorcontrib><creatorcontrib>Shirin, Tahmina</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>Coronavirus Research Database</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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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>Islam, Ariful</au><au>Ferdous, Jinnat</au><au>Sayeed, Md Abu</au><au>Islam, Shariful</au><au>Kaisar Rahman, Md</au><au>Abedin, Josefina</au><au>Saha, Otun</au><au>Hassan, Mohammad Mahmudul</au><au>Shirin, Tahmina</au><au>Makarenkov, Vladimir</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2021-12-15</date><risdate>2021</risdate><volume>16</volume><issue>12</issue><spage>e0260635</spage><pages>e0260635-</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed susceptibility to diverse animal species. We conducted this study to understand the spatial epidemiology, genetic diversity, and statistically significant genetic similarity along with per-gene recombination events of SARS-CoV-2 and related viruses (SC2r-CoVs) in animals globally. We collected a number of different animal species infected with SARS-CoV-2 and its related viruses. Then, we retrieved genome sequences of SARS-CoV-2 and SC2r-CoVs from GISAID and NCBI GenBank for genomic and mutational analysis. Although the evolutionary origin of SARS-CoV-2 remains elusive, the diverse SC2r-CoV have been detected in multiple Rhinolophus bat species and in Malayan pangolin. To date, human-to-animal spillover events have been reported in cat, dog, tiger, lion, gorilla, leopard, ferret, puma, cougar, otter, and mink in 25 countries. Phylogeny and genetic recombination events of SC2r-CoVs showed higher similarity to the bat coronavirus RaTG13 and BANAL-103 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the N protein from bats and pangolin showed close resemblance to SARS-CoV-2. The clustering of animal and human strains from the same geographical area has proved human-to-animal transmission of the virus. The Alpha, Delta and Mu-variant of SARS-CoV-2 was detected in dog, gorilla, lion, tiger, otter, and cat in the USA, India, Czech Republic, Belgium, and France with momentous genetic similarity with human SARS-CoV-2 sequences. The mink variant mutation (spike_Y453F) was detected in both humans and domestic cats. Moreover, the dog was affected mostly by clade O (66.7%), whereas cat and American mink were affected by clade GR (31.6 and 49.7%, respectively). The α-variant was detected as 2.6% in cat, 4.8% in dog, 14.3% in tiger, 66.7% in gorilla, and 77.3% in lion. The highest mutations observed in mink where the substitution of D614G in spike (95.2%) and P323L in NSP12 (95.2%) protein. In dog, cat, gorilla, lion, and tiger, Y505H and Y453F were the common mutations followed by Y145del, Y144del, and V70I in S protein. We recommend vaccine provision for pet and zoo animals to reduce the chance of transmission in animals. Besides, continuous epidemiological and genomic surveillance of coronaviruses in animal host is crucial to find out the immediate ancestor of SARS-CoV-2 and to prevent future CoVs threats to humans.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>34910734</pmid><doi>10.1371/journal.pone.0260635</doi><tpages>e0260635</tpages><orcidid>https://orcid.org/0000-0002-9210-3351</orcidid><orcidid>https://orcid.org/0000-0002-6626-4178</orcidid><orcidid>https://orcid.org/0000-0001-9159-0437</orcidid><orcidid>https://orcid.org/0000-0001-6495-4637</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2021-12, Vol.16 (12), p.e0260635 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2610389925 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS) Journals Open Access; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Animal species Animals Animals, Domestic - virology Animals, Wild - virology Bats Biology and life sciences Clustering Coronaviridae Coronaviruses COVID-19 COVID-19 - epidemiology COVID-19 - transmission COVID-19 - virology Disease control Disease transmission Dogs Domestic animals Epidemics Epidemiology Evaluation Evolution Gene sequencing Genes Genetic diversity Genetic Variation Genome, Viral Genomes Genomics Humans Infections Mammals Medicine and health sciences Metadata Mutation N protein Pandemics Pangolins - virology Phylogenetics Phylogeny Proteins Recombination Recombination, Genetic Respiratory diseases SARS-CoV-2 - classification SARS-CoV-2 - genetics SARS-CoV-2 - isolation & purification Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Similarity Species Statistical analysis Strains (organisms) Vaccines Veterinary medicine Viral diseases Viruses Wild animals Zoo animals |
| title | Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals |
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