title: Molecular phylodynamic analysis indicates lineage displacement occurred in Chinese rabies epidemics between 1949 to 2010.
abstract: Rabies remains a serious problem in China with three epidemics since 1949 and the country in the midst of the third epidemic. Significantly, the control of each outbreak has been followed by a rapid reemergence of the disease. In 2005, the government implemented a rabies national surveillance program that included the collection and screening of almost 8,000 samples. In this work, we analyzed a Chinese dataset comprising 320 glycoprotein sequences covering 23 provinces and eight species, spanning the second and third epidemics. Specifically, we investigated whether the three epidemics are associated with a single reemerging lineage or a different lineage was responsible for each epidemic. Consistent with previous results, phylogenetic analysis identified six lineages, China I to VI. Analysis of the geographical composition of these lineages revealed they are consistent with human case data and reflect the gradual emergence of China I in the third epidemic. Initially, China I was restricted to south China and China II was dominant. However, as the epidemic began to spread into new areas, China I began to emerge, whereas China II remained confined to south China. By the latter part of the surveillance period, almost all isolates were China I and contributions from the remaining lineages were minimal. The prevalence of China II in the early stages of the third epidemic and its established presence in wildlife suggests that it too replaced a previously dominant lineage during the second epidemic. This lineage replacement may be a consequence of control programs that were dominated by dog culling efforts as the primary control method in the first two epidemics. This had the effect of reducing dominant strains to levels comparable with other localized background stains. Our results indicate the importance of effective control strategies for long term control of the disease.
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
authors.forename: Xiao-Yan
authors.initials: XY
authors.lastname: Tao
authors.forename: Qing
authors.initials: Q
authors.lastname: Tang
authors.forename: Simon
authors.initials: S
authors.lastname: Rayner
authors.forename: Zhen-Yang
authors.initials: ZY
authors.lastname: Guo
authors.forename: Hao
authors.initials: H
authors.lastname: Li
authors.forename: Shu-Lin
authors.initials: SL
authors.lastname: Lang
authors.forename: Cui-Ping
authors.initials: CP
authors.lastname: Yin
authors.forename: Na
authors.initials: N
authors.lastname: Han
authors.forename: Wei
authors.initials: W
authors.lastname: Fang
authors.forename: James
authors.initials: J
authors.lastname: Adams
authors.forename: Miao
authors.initials: M
authors.lastname: Song
authors.forename: Guo-Dong
authors.initials: GD
authors.lastname: Liang
mesh_terms: D000818:Animals; D002681:China / Q000453:epidemiology; D016000:Cluster Analysis; D005838:Genotype; D006801:Humans; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D011818:Rabies / Q000453:epidemiology* / Q000662:veterinary* / Q000821:virology; D011820:Rabies virus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA
chemical_list: D012367:RNA, Viral