hiv-1 subtype c phylodynamics in the global epidemichiv - 1 c亚型phylodynamics全球流行病.pdfVIP

Viruses 2010, 2, 33-54; doi:10.3390/v2010033 OPEN ACCESS viruses ISSN 1999-4915 /journal/viruses Article HIV-1 Subtype C Phylodynamics in the Global Epidemic Vlad Novitsky 1,2,*, Rui Wang 3, Stephen Lagakos 3 and Max Essex 1,2 1 Department of Immunology and Infectious Diseases, Harvard School of Public Health AIDS Initiative, Harvard School of Public Health, Boston, MA, USA; E-Mail: messex@ (M.E.) 2 Botswana–Harvard AIDS Institute, Gaborone, Botswana 3 Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; E-Mails: rwang8@ (R.W.); lagakos@ (S.L.) * Author to whom correspondence should be addressed; E-Mail: vnovi@; Tel.: +1-617-432-1225; Fax: +1-617-739-8348. Received: 1 October 2009; in revised form: 23 December 2009 / Accepted: 27 December 2009 / Published: 7 January 2010 Abstract: The diversity of HIV-1 and its propensity to generate escape mutants present fundamental challenges to control efforts, including HIV vaccine design. Intra-host diversification of HIV is determined by immune responses elicited by an HIV-infected individual over the course of the infection. Complex and dynamic patterns of transmission of HIV lead to an even more complex population viral diversity over time, thus presenting enormous challenges to vaccine development. To address inter-patient viral evolution over time, a set of 653 unique HIV-1 subtype C gag sequences were retrieved from the LANL HIV Database, grouped by sampling year as 2000, 200