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Journal of Virology, October 2004, p. 10501-10506, Vol. 78, No. 19
0022-538X/04/$08.00+0     DOI: 10.1128/JVI.78.19.10501-10506.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Timing and Reconstruction of the Most Recent Common Ancestor of the Subtype C Clade of Human Immunodeficiency Virus Type 1

Simon A. A. Travers,¹ Jonathan P. Clewley,² Judith R. Glynn,³ Paul E. M. Fine,³ Amelia C. Crampin,^3,4 Felix Sibande,⁴ Dominic Mulawa,⁴ James O. McInerney,¹ and Grace P. McCormack^1*

Biology Department, National University of Ireland, Maynooth, County Kildare, Ireland,¹ Sexually Transmitted and Blood Borne Virus Laboratory, Health Protection Agency,² Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom,³ Karonga Prevention Study, Chilumba, Malawi⁴

Received 9 February 2004/ Accepted 5 May 2004

Human immunodeficiency virus type 1 (HIV-1) subtype C is responsible for more than 55% of HIV-1 infections worldwide. When this subtype first emerged is unknown. We have analyzed all available gag (p17 and p24) and env (C2-V3) subtype C sequences with known sampling dates, which ranged from 1983 to 2000. The majority of these sequences come from the Karonga District in Malawi and include some of the earliest known subtype C sequences. Linear regression analyses of sequence divergence estimates (with four different approaches) were plotted against sample year to estimate the year in which there was zero divergence from the reconstructed ancestral sequence. Here we suggest that the most recent common ancestor of subtype C appeared in the mid- to late 1960s. Sensitivity analyses, by which possible biases due to oversampling from one district were explored, gave very similar estimates.

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* Corresponding author. Mailing address: Molecular Phylogenetics and Systematics Laboratory, Biology Department, NUI Maynooth, Maynooth, Co. Kildare, Ireland. Phone: 353-1-7083855. Fax: 353-1-7083845. E-mail: grace.p.mccormack{at}may.ie.

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Journal of Virology, October 2004, p. 10501-10506, Vol. 78, No. 19
0022-538X/04/$08.00+0     DOI: 10.1128/JVI.78.19.10501-10506.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

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