Genetic diversity and evolution of Hantaan virus in China and its neighbors
Background Hantaan virus (HTNV; family Hantaviridae, order Bunyavirales) causes hemorrhagic fever with renal syndrome (HFRS), which has raised serious concerns in Eurasia, especially in China, Russia, and South Korea. Previous studies reported genetic diversity and phylogenetic features of HTNV in d...
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| Veröffentlicht in: | PLoS neglected tropical diseases 2020-08, Vol.14 (8), p.e0008090-e0008090 |
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| creator | Li, Naizhe Li, Aqian Liu, Yang Wu, Wei Li, Chuan Yu, Dongyang Zhu, Yu Li, Jiandong Li, Dexin Wang, Shiwen Liang, Mifang |
| description | Background Hantaan virus (HTNV; family Hantaviridae, order Bunyavirales) causes hemorrhagic fever with renal syndrome (HFRS), which has raised serious concerns in Eurasia, especially in China, Russia, and South Korea. Previous studies reported genetic diversity and phylogenetic features of HTNV in different parts of China, but the analyses from the holistic perspective are rare. Methodology and principal findings To better understand HTNV genetic diversity and gene evolution, we analyzed all available complete sequences derived from the small (S) and medium (M) segments with bioinformatic tools. Eleven phylogenetic groups were defined and showed geographic clustering; 42 significant amino acid variant sites were found, and 19 of them were located in immune epitopes; nine recombinant events and eight reassortments with highly divergent sequences were found and analyzed. We found that sequences from Guizhou showed high genetic divergence, contributing to multiple lineages of the phylogenetic tree and also to the recombination and reassortment events. Bayesian stochastic search variable selection analysis revealed that Heilongjiang, Shaanxi, and Guizhou played important roles in HTNV evolution and migration; the virus may originate from Zhejiang Province in the eastern part of China; and the virus population size expanded from the 1980s to 1990s. Conclusions/significance These findings revealed the original and evolutionary features of HTNV, which will help to illustrate hantavirus epidemic trends, thus aiding in disease control and prevention. |
| doi_str_mv | 10.1371/journal.pntd.0008090 |
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Previous studies reported genetic diversity and phylogenetic features of HTNV in different parts of China, but the analyses from the holistic perspective are rare. Methodology and principal findings To better understand HTNV genetic diversity and gene evolution, we analyzed all available complete sequences derived from the small (S) and medium (M) segments with bioinformatic tools. Eleven phylogenetic groups were defined and showed geographic clustering; 42 significant amino acid variant sites were found, and 19 of them were located in immune epitopes; nine recombinant events and eight reassortments with highly divergent sequences were found and analyzed. We found that sequences from Guizhou showed high genetic divergence, contributing to multiple lineages of the phylogenetic tree and also to the recombination and reassortment events. Bayesian stochastic search variable selection analysis revealed that Heilongjiang, Shaanxi, and Guizhou played important roles in HTNV evolution and migration; the virus may originate from Zhejiang Province in the eastern part of China; and the virus population size expanded from the 1980s to 1990s. Conclusions/significance These findings revealed the original and evolutionary features of HTNV, which will help to illustrate hantavirus epidemic trends, thus aiding in disease control and prevention.</description><identifier>ISSN: 1935-2735</identifier><identifier>ISSN: 1935-2727</identifier><identifier>EISSN: 1935-2735</identifier><identifier>DOI: 10.1371/journal.pntd.0008090</identifier><identifier>PMID: 32817670</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>Amino acids ; Bayesian analysis ; Bias ; Biodiversity ; Biology and Life Sciences ; Clustering ; Computer and Information Sciences ; Datasets ; Disease control ; Disease prevention ; Distribution ; Divergence ; Earth Sciences ; Ecology and Environmental Sciences ; Epidemics ; Epitopes ; Evolution ; Genetic aspects ; Genetic diversity ; Genetic variation ; Genomes ; Hantavirus ; Hantaviruses ; Hemorrhage ; Hemorrhagic fever with renal syndrome ; Medical laboratories ; Medicine and Health Sciences ; Natural history ; Phylogenetics ; Phylogeny ; Population number ; Probability theory ; Recombinants ; Recombination ; Research and Analysis Methods ; RNA polymerase ; Software ; Stochasticity ; Supervision ; Tropical diseases ; Viral research ; Virology ; Viruses</subject><ispartof>PLoS neglected tropical diseases, 2020-08, Vol.14 (8), p.e0008090-e0008090</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Li 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>2020 Li et al 2020 Li et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c601t-9ac77664a0f45cf8471d8d1474f42ebc1916f5262558b4c3550f12b4c8b5fdd43</citedby><cites>FETCH-LOGICAL-c601t-9ac77664a0f45cf8471d8d1474f42ebc1916f5262558b4c3550f12b4c8b5fdd43</cites><orcidid>0000-0002-6240-2916 ; 0000-0003-3411-3014</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/PMC7462299/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7462299/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2101,2927,23865,27923,27924,53790,53792,79471,79472</link.rule.ids></links><search><contributor>Kohl, Alain</contributor><creatorcontrib>Li, Naizhe</creatorcontrib><creatorcontrib>Li, Aqian</creatorcontrib><creatorcontrib>Liu, Yang</creatorcontrib><creatorcontrib>Wu, Wei</creatorcontrib><creatorcontrib>Li, Chuan</creatorcontrib><creatorcontrib>Yu, Dongyang</creatorcontrib><creatorcontrib>Zhu, Yu</creatorcontrib><creatorcontrib>Li, Jiandong</creatorcontrib><creatorcontrib>Li, Dexin</creatorcontrib><creatorcontrib>Wang, Shiwen</creatorcontrib><creatorcontrib>Liang, Mifang</creatorcontrib><title>Genetic diversity and evolution of Hantaan virus in China and its neighbors</title><title>PLoS neglected tropical diseases</title><description>Background Hantaan virus (HTNV; family Hantaviridae, order Bunyavirales) causes hemorrhagic fever with renal syndrome (HFRS), which has raised serious concerns in Eurasia, especially in China, Russia, and South Korea. Previous studies reported genetic diversity and phylogenetic features of HTNV in different parts of China, but the analyses from the holistic perspective are rare. Methodology and principal findings To better understand HTNV genetic diversity and gene evolution, we analyzed all available complete sequences derived from the small (S) and medium (M) segments with bioinformatic tools. Eleven phylogenetic groups were defined and showed geographic clustering; 42 significant amino acid variant sites were found, and 19 of them were located in immune epitopes; nine recombinant events and eight reassortments with highly divergent sequences were found and analyzed. We found that sequences from Guizhou showed high genetic divergence, contributing to multiple lineages of the phylogenetic tree and also to the recombination and reassortment events. Bayesian stochastic search variable selection analysis revealed that Heilongjiang, Shaanxi, and Guizhou played important roles in HTNV evolution and migration; the virus may originate from Zhejiang Province in the eastern part of China; and the virus population size expanded from the 1980s to 1990s. Conclusions/significance These findings revealed the original and evolutionary features of HTNV, which will help to illustrate hantavirus epidemic trends, thus aiding in disease control and prevention.</description><subject>Amino acids</subject><subject>Bayesian analysis</subject><subject>Bias</subject><subject>Biodiversity</subject><subject>Biology and Life Sciences</subject><subject>Clustering</subject><subject>Computer and Information Sciences</subject><subject>Datasets</subject><subject>Disease control</subject><subject>Disease prevention</subject><subject>Distribution</subject><subject>Divergence</subject><subject>Earth Sciences</subject><subject>Ecology and Environmental Sciences</subject><subject>Epidemics</subject><subject>Epitopes</subject><subject>Evolution</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genetic 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diversity and evolution of Hantaan virus in China and its neighbors</title><author>Li, Naizhe ; Li, Aqian ; Liu, Yang ; Wu, Wei ; Li, Chuan ; Yu, Dongyang ; Zhu, Yu ; Li, Jiandong ; Li, Dexin ; Wang, Shiwen ; Liang, Mifang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c601t-9ac77664a0f45cf8471d8d1474f42ebc1916f5262558b4c3550f12b4c8b5fdd43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Amino acids</topic><topic>Bayesian analysis</topic><topic>Bias</topic><topic>Biodiversity</topic><topic>Biology and Life Sciences</topic><topic>Clustering</topic><topic>Computer and Information Sciences</topic><topic>Datasets</topic><topic>Disease control</topic><topic>Disease prevention</topic><topic>Distribution</topic><topic>Divergence</topic><topic>Earth Sciences</topic><topic>Ecology and Environmental 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Academic UKI Edition</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PLoS neglected tropical diseases</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Naizhe</au><au>Li, Aqian</au><au>Liu, Yang</au><au>Wu, Wei</au><au>Li, Chuan</au><au>Yu, Dongyang</au><au>Zhu, Yu</au><au>Li, Jiandong</au><au>Li, Dexin</au><au>Wang, Shiwen</au><au>Liang, Mifang</au><au>Kohl, Alain</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic diversity and evolution of Hantaan virus in China and its neighbors</atitle><jtitle>PLoS neglected tropical diseases</jtitle><date>2020-08-01</date><risdate>2020</risdate><volume>14</volume><issue>8</issue><spage>e0008090</spage><epage>e0008090</epage><pages>e0008090-e0008090</pages><issn>1935-2735</issn><issn>1935-2727</issn><eissn>1935-2735</eissn><abstract>Background Hantaan virus (HTNV; family Hantaviridae, order Bunyavirales) causes hemorrhagic fever with renal syndrome (HFRS), which has raised serious concerns in Eurasia, especially in China, Russia, and South Korea. Previous studies reported genetic diversity and phylogenetic features of HTNV in different parts of China, but the analyses from the holistic perspective are rare. Methodology and principal findings To better understand HTNV genetic diversity and gene evolution, we analyzed all available complete sequences derived from the small (S) and medium (M) segments with bioinformatic tools. Eleven phylogenetic groups were defined and showed geographic clustering; 42 significant amino acid variant sites were found, and 19 of them were located in immune epitopes; nine recombinant events and eight reassortments with highly divergent sequences were found and analyzed. We found that sequences from Guizhou showed high genetic divergence, contributing to multiple lineages of the phylogenetic tree and also to the recombination and reassortment events. Bayesian stochastic search variable selection analysis revealed that Heilongjiang, Shaanxi, and Guizhou played important roles in HTNV evolution and migration; the virus may originate from Zhejiang Province in the eastern part of China; and the virus population size expanded from the 1980s to 1990s. Conclusions/significance These findings revealed the original and evolutionary features of HTNV, which will help to illustrate hantavirus epidemic trends, thus aiding in disease control and prevention.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><pmid>32817670</pmid><doi>10.1371/journal.pntd.0008090</doi><orcidid>https://orcid.org/0000-0002-6240-2916</orcidid><orcidid>https://orcid.org/0000-0003-3411-3014</orcidid><oa>free_for_read</oa></addata></record> |
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| source | DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central Open Access; Public Library of Science (PLoS); PubMed Central |
| subjects | Amino acids Bayesian analysis Bias Biodiversity Biology and Life Sciences Clustering Computer and Information Sciences Datasets Disease control Disease prevention Distribution Divergence Earth Sciences Ecology and Environmental Sciences Epidemics Epitopes Evolution Genetic aspects Genetic diversity Genetic variation Genomes Hantavirus Hantaviruses Hemorrhage Hemorrhagic fever with renal syndrome Medical laboratories Medicine and Health Sciences Natural history Phylogenetics Phylogeny Population number Probability theory Recombinants Recombination Research and Analysis Methods RNA polymerase Software Stochasticity Supervision Tropical diseases Viral research Virology Viruses |
| title | Genetic diversity and evolution of Hantaan virus in China and its neighbors |
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