Comprehensive phylogenetic reconstructions of African swine fever virus: proposal for a new classification and molecular dating of the virus.

African swine fever (ASF) is a highly lethal disease of domestic pigs caused by the only known DNA arbovirus. It was first described in Kenya in 1921 and since then many isolates have been collected worldwide. However, although several phylogenetic studies have been carried out to understand the rel...

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Autores principales:	Vincent Michaud, Tantely Randriamparany, Emmanuel Albina
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8ba0d2124fe54cd78166e39ca029a153
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spelling	oai:doaj.org-article:8ba0d2124fe54cd78166e39ca029a1532021-11-18T09:02:55ZComprehensive phylogenetic reconstructions of African swine fever virus: proposal for a new classification and molecular dating of the virus.1932-620310.1371/journal.pone.0069662https://doaj.org/article/8ba0d2124fe54cd78166e39ca029a1532013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23936068/?tool=EBIhttps://doaj.org/toc/1932-6203African swine fever (ASF) is a highly lethal disease of domestic pigs caused by the only known DNA arbovirus. It was first described in Kenya in 1921 and since then many isolates have been collected worldwide. However, although several phylogenetic studies have been carried out to understand the relationships between the isolates, no molecular dating analyses have been achieved so far. In this paper, comprehensive phylogenetic reconstructions were made using newly generated, publicly available sequences of hundreds of ASFV isolates from the past 70 years. Analyses focused on B646L, CP204L, and E183L genes from 356, 251, and 123 isolates, respectively. Phylogenetic analyses were achieved using maximum likelihood and Bayesian coalescence methods. A new lineage-based nomenclature is proposed to designate 35 different clusters. In addition, dating of ASFV origin was carried out from the molecular data sets. To avoid bias, diversity due to positive selection or recombination events was neutralized. The molecular clock analyses revealed that ASFV strains currently circulating have evolved over 300 years, with a time to the most recent common ancestor (TMRCA) in the early 18(th) century.Vincent MichaudTantely RandriamparanyEmmanuel AlbinaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e69662 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Vincent Michaud Tantely Randriamparany Emmanuel Albina Comprehensive phylogenetic reconstructions of African swine fever virus: proposal for a new classification and molecular dating of the virus.
description	African swine fever (ASF) is a highly lethal disease of domestic pigs caused by the only known DNA arbovirus. It was first described in Kenya in 1921 and since then many isolates have been collected worldwide. However, although several phylogenetic studies have been carried out to understand the relationships between the isolates, no molecular dating analyses have been achieved so far. In this paper, comprehensive phylogenetic reconstructions were made using newly generated, publicly available sequences of hundreds of ASFV isolates from the past 70 years. Analyses focused on B646L, CP204L, and E183L genes from 356, 251, and 123 isolates, respectively. Phylogenetic analyses were achieved using maximum likelihood and Bayesian coalescence methods. A new lineage-based nomenclature is proposed to designate 35 different clusters. In addition, dating of ASFV origin was carried out from the molecular data sets. To avoid bias, diversity due to positive selection or recombination events was neutralized. The molecular clock analyses revealed that ASFV strains currently circulating have evolved over 300 years, with a time to the most recent common ancestor (TMRCA) in the early 18(th) century.
format	article
author	Vincent Michaud Tantely Randriamparany Emmanuel Albina
author_facet	Vincent Michaud Tantely Randriamparany Emmanuel Albina
author_sort	Vincent Michaud
title	Comprehensive phylogenetic reconstructions of African swine fever virus: proposal for a new classification and molecular dating of the virus.
title_short	Comprehensive phylogenetic reconstructions of African swine fever virus: proposal for a new classification and molecular dating of the virus.
title_full	Comprehensive phylogenetic reconstructions of African swine fever virus: proposal for a new classification and molecular dating of the virus.
title_fullStr	Comprehensive phylogenetic reconstructions of African swine fever virus: proposal for a new classification and molecular dating of the virus.
title_full_unstemmed	Comprehensive phylogenetic reconstructions of African swine fever virus: proposal for a new classification and molecular dating of the virus.
title_sort	comprehensive phylogenetic reconstructions of african swine fever virus: proposal for a new classification and molecular dating of the virus.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/8ba0d2124fe54cd78166e39ca029a153
work_keys_str_mv	AT vincentmichaud comprehensivephylogeneticreconstructionsofafricanswinefevervirusproposalforanewclassificationandmoleculardatingofthevirus AT tantelyrandriamparany comprehensivephylogeneticreconstructionsofafricanswinefevervirusproposalforanewclassificationandmoleculardatingofthevirus AT emmanuelalbina comprehensivephylogeneticreconstructionsofafricanswinefevervirusproposalforanewclassificationandmoleculardatingofthevirus
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Comprehensive phylogenetic reconstructions of African swine fever virus: proposal for a new classification and molecular dating of the virus.

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