Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review

Handle URI:
http://hdl.handle.net/10754/614424
Title:
Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review
Authors:
Kim, Kiyeon; Omori, Ryosuke; Ueno, Keisuke ( 0000-0003-3657-8413 ) ; Iida, Sayaka; Ito, Kimihito
Abstract:
Understanding the evolutionary dynamics of influenza viruses is essential to control both avian and human influenza. Here, we analyze host-specific and segment-specific Tajima’s D trends of influenza A virus through a systematic review using viral sequences registered in the National Center for Biotechnology Information. To avoid bias from viral population subdivision, viral sequences were stratified according to their sampling locations and sampling years. As a result, we obtained a total of 580 datasets each of which consists of nucleotide sequences of influenza A viruses isolated from a single population of hosts at a single sampling site within a single year. By analyzing nucleotide sequences in the datasets, we found that Tajima’s D values of viral sequences were different depending on hosts and gene segments. Tajima’s D values of viruses isolated from chicken and human samples showed negative, suggesting purifying selection or a rapid population growth of the viruses. The negative Tajima’s D values in rapidly growing viral population were also observed in computer simulations. Tajima’s D values of PB2, PB1, PA, NP, and M genes of the viruses circulating in wild mallards were close to zero, suggesting that these genes have undergone neutral selection in constant-sized population. On the other hand, Tajima’s D values of HA and NA genes of these viruses were positive, indicating HA and NA have undergone balancing selection in wild mallards. Taken together, these results indicated the existence of unknown factors that maintain viral subtypes in wild mallards.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review 2016, 11 (1):e0147021 PLOS ONE
Publisher:
Public Library of Science (PLoS)
Journal:
PLoS ONE
Issue Date:
13-Jan-2016
DOI:
10.1371/journal.pone.0147021
Type:
Article
ISSN:
1932-6203
Sponsors:
This work was supported by CREST (KI) and PRESTO (RO) from Japan Science and Technology Agency (http://www.jst.go.jp/), and by Grants-in-Aid for Scientific Research (B) (KI, 25280080) from the Ministry of Education, Culture, Sports, Science, and Technology in Japan (http://www.mext.go.jp/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Additional Links:
http://dx.plos.org/10.1371/journal.pone.0147021
Appears in Collections:
Articles

Full metadata record

DC FieldValue Language
dc.contributor.authorKim, Kiyeonen
dc.contributor.authorOmori, Ryosukeen
dc.contributor.authorUeno, Keisukeen
dc.contributor.authorIida, Sayakaen
dc.contributor.authorIto, Kimihitoen
dc.date.accessioned2016-06-23T11:16:01Z-
dc.date.available2016-06-23T11:16:01Z-
dc.date.issued2016-01-13-
dc.identifier.citationHost-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review 2016, 11 (1):e0147021 PLOS ONEen
dc.identifier.issn1932-6203-
dc.identifier.doi10.1371/journal.pone.0147021-
dc.identifier.urihttp://hdl.handle.net/10754/614424-
dc.description.abstractUnderstanding the evolutionary dynamics of influenza viruses is essential to control both avian and human influenza. Here, we analyze host-specific and segment-specific Tajima’s D trends of influenza A virus through a systematic review using viral sequences registered in the National Center for Biotechnology Information. To avoid bias from viral population subdivision, viral sequences were stratified according to their sampling locations and sampling years. As a result, we obtained a total of 580 datasets each of which consists of nucleotide sequences of influenza A viruses isolated from a single population of hosts at a single sampling site within a single year. By analyzing nucleotide sequences in the datasets, we found that Tajima’s D values of viral sequences were different depending on hosts and gene segments. Tajima’s D values of viruses isolated from chicken and human samples showed negative, suggesting purifying selection or a rapid population growth of the viruses. The negative Tajima’s D values in rapidly growing viral population were also observed in computer simulations. Tajima’s D values of PB2, PB1, PA, NP, and M genes of the viruses circulating in wild mallards were close to zero, suggesting that these genes have undergone neutral selection in constant-sized population. On the other hand, Tajima’s D values of HA and NA genes of these viruses were positive, indicating HA and NA have undergone balancing selection in wild mallards. Taken together, these results indicated the existence of unknown factors that maintain viral subtypes in wild mallards.en
dc.description.sponsorshipThis work was supported by CREST (KI) and PRESTO (RO) from Japan Science and Technology Agency (http://www.jst.go.jp/), and by Grants-in-Aid for Scientific Research (B) (KI, 25280080) from the Ministry of Education, Culture, Sports, Science, and Technology in Japan (http://www.mext.go.jp/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.language.isoenen
dc.publisherPublic Library of Science (PLoS)en
dc.relation.urlhttp://dx.plos.org/10.1371/journal.pone.0147021en
dc.rightsThis is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. http://creativecommons.org/licenses/by/4.0/en
dc.titleHost-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Reviewen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalPLoS ONEen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDivision of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japanen
dc.contributor.institutionPRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, Japanen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorUeno, Keisukeen
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