Objective: To clarify the epidemic origin and molecular properties of the B′ subtype that is an important strain in the HIV-1 epidemic in Asia.
Design: The genealogical relationship between the B′ and B subtype was investigated with two globally representative datasets covering the gag and env regions. B′ sequences were identified, from which the epidemic origin, population genetics and the signature mutation sites of the B′ subtype were inferred.
Methods: Two globally representative datasets were compiled, using phylogenetic methods. Through coalescent-based analysis, the genealogical relationship between the B′ and B subtypes was investigated. The divergence times and population genetic parameters of B′ were estimated in a Bayesian framework using Markov Chains Monte Carlo sampling under a relaxed molecular clock method. Additionally, molecular properties of the B′ were identified by performing comparative sequence analysis with the HIV-1 M group.
Results: About 15 years later after the B subtype began to spread, the B′ diverged from the B subtype. The demographic history of B′ was reconstructed, and the epidemic of B′ was estimated to originate around 1985. Eight and nine distinct signature mutation sites, unique to B′, were found around the p17 and V3 regions, respectively.
Conclusion: Our research is the first large-scale investigation on HIV-1 B′ at a global level and provides a deep insight into one of the founder strains of HIV-1 epidemic in Asia. Our results provide an important reference for HIV scientists, public health officials and HIV vaccine designers.
aHIV Molecular Epidemiology and Virology Research Group, The State Key Laboratory of Virology, China
bBioinformatics Research Group, The State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, China
cWuhan Institute of Virology, Chinese Academy of Science, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
Received 25 April, 2008
Revised 4 July, 2008
Accepted 4 July, 2008
Correspondence to Rongge Yang, HIV Molecular Epidemiology and Virology Research Group, The State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Science, Xiaohongshan 44, Wuhan, China. E-mail: email@example.com
Correspondence to Simon Rayner, Bioinformatics Research Group, Wuhan Institute of Virology, Chinese Academy of Science, Xiaohongshan 44, Wuhan, China. E-mail: firstname.lastname@example.org