No statistically significant differences in risk behaviour characteristics were found between clustering and nonclustering individuals (Table 2). For both phylogenies, clusters contained significantly more known sexual partners (P < 0.001; Table 2). It is not clear to what extent infection with viruses with inherently different replicative capacity accounts for individuals with either undetectable HIV-2 plasma viral load (‘elite controllers’) or progressive HIV-2 infection with detectable viraemia. In both gag and env phylogenies, elite controllers were found to share an MRCA with viraemic individuals within transmission clusters (in some cases these included known sexual partners, Fig. 2).
Whereas these data strongly suggest that after 1989, newly infected individuals were more strongly associated with ongoing HIV-2 transmission than older, prevalent infections in Caió, it is possible that sampling bias (i.e. exclusion of pre-1989 individuals who had died by the time of subsequent sampling dates) may account for this result. A further env phylogeny was reconstructed following inclusion of previously generated sequence data from 68 additional 1991 samples, which were all pre-1989 infections [28,29]. Although the use of these shorter sequences resulted in a phylogeny with poorer resolution, it is clear that the additional pre-1989 cases formed clusters almost exclusively with other pre-1989 cases, which would not be observed if the old infections were contributing to ongoing transmission in the cohort (Supplementary Figure 3, http://links.lww.com/QAD/A265).
Our estimates of individual linkage in clusters (55–58%) are greater than the highest observed in the UK HIV-1 epidemic (36%) . This is not surprising given this is a village cohort and case detection via community serosurveys would identify a greater proportion of all those infected. Viruses from individuals infected since the start of the cohort in 1989 (after the exponential growth of HIV-2) are more frequently (81–83%) found in transmission clusters than those already infected by 1989 (27–36%). Although pre-1989 individuals were involved in transmission events early in the epidemic, they have contributed less to more recent infections. In contrast, newer infections appear to be associated with ongoing HIV-2 transmission in Caió. It is also striking that even in a rural community in Guinea-Bissau, multiple lineages of HIV-2 are evident, with Caió isolates clustering with several external sequences. Notably, many were from Cape Verde, which is another country with Portuguese colonial links. Guinea-Bissau and Cape Verde formed a strategic alliance during the shared war of independence with Portugal and were united by political ties until 1980. A recent phylogeographic analysis has also highlighted the shared ancestry of these two countries during the early dispersal of HIV-2 . The migratory nature of the Caió population in general, but particularly that of commercial sex workers who often seek work in many locations in the sub-region , may also have contributed to this observation. Interestingly, almost all incident cases were involved in Caió-only clusters. This heterogeneity in HIV-2 viruses is likely, therefore, to reflect early events that lead to the exponential increase in HIV-2.
The main limitation of our study is the relatively low number of individuals included, compared to country-wide HIV-1 studies such as the ones performed on UK cohorts . Dense sampling of a population with high HIV-2 prevalence would offer an opportunity for a more in-depth HIV-2 transmission analysis, but is unfeasible as most HIV-2 cohorts in West Africa are shrinking [1,18,56]. A similar analysis of HIV-1 transmission in our cohort could help design public health measures to halt an increasing and evolving HIV-1 epidemic in Guinea-Bissau [18,57]. A recent UNAIDS/World Bank collaborative report has highlighted the need to understand HIV-1 transmission dynamics in West Africa, focusing on the likely complexity of transmission within and between risk groups . The long period of time between serosurverys precluded an exact date of infection in our HIV-2-incident cases. However, as our main focus was to compare those who were infected during the early epidemic (i.e. prior to 1989), when HIV-2 spread rapidly, with those who have been infected since (when the HIV-2 epidemic was declining), we are able to draw valid conclusions with the available data. As ART was not available in Caió until 2007, some rapidly progressing HIV-1-infected individuals may also have been missed between serosurveys, leading to underestimates of the HIV-1 Ne. Finally, although our study is unique in including a high proportion of sequences from HIV-2 elite controllers, potential bias could have been introduced via exclusion of individuals in whom PCR was unsuccessful (overall PCR success approximately 75%; 50% in elite controllers ).
We are grateful to the Caió population for their participation in all the studies. We would like to acknowledge Ramu Sarge Njie for her excellent management of the HIV diagnostics for many of the Caió studies. We would like to thank Nato Gonçalves for all his thorough field work. We would also like to thank Dr J Miguel Azevedo-Pereira and Dr Florence Damond for sharing location and sampling data on their HIV-2 sequences. We are grateful to Professor Peter Aaby for helpful comments and suggestions during preparation of the manuscript.
Justification of author contributions: T.I.dS. carried out HIV sequencing, phylogenetic and phylodynamic analyses and wrote the paper. C.vT. carried out the most recent field study, did the statistical analyses and wrote the paper. C.O. carried out HIV sequencing. A. Jabang helped with sample processing and HIV sequencing. T.V. coordinated the field studies and collection of individual information. M.F.S.vdL. undertook field studies and wrote aspects of the paper. R.A.C. wrote aspects of the paper and provided advice during the design of the study. A. Jaye wrote aspects of the paper and provided advice during the design of the study. S.R.-J. provided supervision of the cohort, provided advice on design of the current study and wrote aspects of the paper. H.W. provided supervision during collection of samples, design of the current study and wrote aspects of the paper. M.C. carried out and provided supervision during viral sequencing, phylogenetic analyses and wrote aspects of the paper. S.H. carried out and provided supervision during phylogenetic and phylodynamic studies, and wrote aspects of the paper.
Funding sources: This work was undertaken via a UK Medical Research Council Clinical Research Training Fellowship (G0701313) awarded to Td.S.
There are no conflicts of interest.
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