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

Abstract

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.

Temporal and Spatial Dynamics of Human Immunodeficiency Virus Type 1 Circulating Recombinant Forms 08_BC and 07_BC in Asia

“…Together, the phylogenetic and coalescent results map the eastward movement of subtype C from India to China, probably through Myanmar (2), between the mid-1970s and early 1980s. Finally, the time of origin of the global HIV-1 subtype C was dated 1967.6 (95% CR, 1962.5 to 1972.0) and was highly consistent with previous estimates (44).…”

Extensive Intrasubtype Recombination in South African Human Immunodeficiency Virus Type 1 Subtype C Infections

“…From a previous analysis of envelope sequences, the MRCA of the HIV-1 epidemic in humans is thought to have taken place near 1930 (95% CI, 1913 to 1944) (24). Another report based on an analysis of envelope and gag sequences showed the estimated origin of the subtype C epidemic to have taken place in 1962 (95% CI, 1956 to 1968 based on the full envelope alignment and genetic distance) (56). Using the most conservative definition of recombinant (resulting in 47% recombinants), our estimate of the origin of the subtype C epidemic (1958( [95% CI, 1949( to 1960) places the date of origin of the subtype C epidemic several years after the origin of the HIV-1 epidemic and within the 95% CI of the previous estimate of the origin of the subtype C epidemic.…”

The epidemic origin and molecular properties of B′: a founder strain of the HIV-1 transmission in Asia

“…The availability of greater numbers of sampled viral sequences combined with increasing computational power makes it possible to retrieve valuable and unique information about the course of viral epidemics from molecular data [19][20][21][22]. Furthermore, the coalescent theory of population genetics has been shown to be an effective method for studying the history of a pathogen's population by inferring the transmission dynamics from the genealogy of randomly sampled strains [20,21,[23][24][25][26][27][28][29].…”