Molecular epidemiological analysis of HIV in sexual networks in Uganda

Abstract

Sequence analyses such as those described here have proved effective in confirming or identifying epidemiological links not only following single transmission events but also within risk groups. However, the results from Uganda contrast markedly with those from Europe and the United States. The length of time that the community has been infected, the number of occasions when the virus has been introduced and the high degree of partner change may contribute to the lack of supportive evidence for sociological studies of sexual networks in Uganda.

Early Evolution of the Human Immunodeficiency Virus Type 1 Subtype C Epidemic in Rural Malawi

“…Five spouse groups (a, j, n, p, and the second wife in spouse group d) had less closely related sequences. They may have been infected from different sources, as has been found previously (43), but this would be surprising at a time when HIV prevalence was low. Genetic distance between spouse sequences is also influenced by the interval of time since transmission occurred, which is largely unknown.…”

“…Other studies have described the distribution and characteristics of subtypes and strains, and some have compared them in different groups in the population (36,41,42), but this is one of the first studies to link sequence analysis with detailed population-based epidemiological data (43).…”

“…Cluster 3 (containing sequences 4, 33, a Two cluster numbers separated by a shill indicate that one sequence is in one cluster, and one is in another. 43, 94, and 193 on both trees) was found only in the south and included sequences from two immigrants to the district and from two who had been living outside the district in the early 1980s. Sequences 33 and 43 came from a male immigrant and female resident from the same village.…”

The HIV Epidemic: High-Income Countries

“…In addition, for the first time it has become possible to investigate the dynamics of the epidemic based on such data. Although many studies of sexual behavior have shown that individuals can vary greatly in their number of sexual partners over time and this concept has underpinned many epidemiological models of HIV transmission, however, contact tracing has been shown to be poor at recovering the HIV transmission network relative to other infections (Yirrell et al 1998;Resik et al 2007). The development of the field of molecular phylodynamics, used first to estimate dates of the origin of the zoonotic transmission of HIV, provided new routes to obtain such parameter estimates, which can be applied to small-scale intensive studies of specific outbreaks, as well as to obtain global estimates relating to long-term spread.…”

Impact of Sampling Density on the Extent of HIV Clustering

“…23 Studies with low sampling density showed minimal HIV clustering. 28 It is not likely that viral sequence data from HIV prevention studies can ever completely represent the population of interest. In a recent study we focused on adjusting for missing data obtained through a household survey in Mochudi, Botswana (described below).…”