title: Phylogeny-based evolutionary, demographical, and geographical dissection of North American type 2 porcine reproductive and respiratory syndrome viruses.
abstract: Type 2 (or North American-like) porcine reproductive and respiratory syndrome virus (PRRSV) was first recorded in 1987 in the United States and now occurs in most commercial swine industries throughout the world. In this study, we investigated the epidemiological and evolutionary behaviors of type 2 PRRSV. Based on phylogenetic analyses of 8,624 ORF5 sequences, we described a comprehensive picture of the diversity of type 2 PRRSVs and systematically classified all available sequences into lineages and sublineages, including a number of previously undescribed lineages. With the rapid growth of sequence deposition into the databases, it would be technically difficult for veterinary researchers to genotype their sequences by reanalyzing all sequences in the databases. To this end, a set of reference sequences was established based on our classification system, which represents the principal diversity of all available sequences and can readily be used for further genotyping studies. In addition, we further investigated the demographic histories of these lineages and sublineages by using Bayesian coalescence analyses, providing evolutionary insights into several important epidemiological events of type 2 PRRSV. Moreover, by using a phylogeographic approach, we were able to estimate the transmission frequencies between the pig-producing states in the United States and identified several states as the major sources of viral spread, i.e., "transmission centers." In summary, this study represents the most extensive phylogenetic analyses of type 2 PRRSV to date, providing a basis for future genotyping studies and dissecting the epidemiology of type 2 PRRSV from phylogenetic perspectives.
authors.affiliation: School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
authors.forename: Mang
authors.initials: M
authors.lastname: Shi
authors.forename: Tommy Tsan-Yuk
authors.initials: TT
authors.lastname: Lam
authors.forename: Chung-Chau
authors.initials: CC
authors.lastname: Hon
authors.forename: Michael P
authors.initials: MP
authors.lastname: Murtaugh
authors.forename: Peter R
authors.initials: PR
authors.lastname: Davies
authors.forename: Raymond Kin-Hei
authors.initials: RK
authors.lastname: Hui
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Lina Tik-Wim
authors.initials: LT
authors.lastname: Wong
authors.forename: Chi-Wai
authors.initials: CW
authors.lastname: Yip
authors.forename: Jin-Wai
authors.initials: JW
authors.lastname: Jiang
authors.forename: Frederick Chi-Ching
authors.initials: FC
authors.lastname: Leung
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D014644:Genetic Variation; D005843:Geography; D008969:Molecular Sequence Data; D010802:Phylogeny; D019318:Porcine Reproductive and Respiratory Syndrome / Q000635:transmission / Q000821:virology*; D019316:Porcine respiratory and reproductive syndrome virus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D013552:Swine