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).
Transmission clusters contained significantly more incident infections than pre-1989 cases (Table 2). A high proportion of all incident cases were also found in clusters: 81.5% in gag and 83% in env phylogenies, compared to pre-1989 cases: 36% in gag and 27% in env phylogenies (P = 0.0004 and P = 0.0003, respectively). Incident infections appeared throughout the tree (Supplementary Figure 2, http://links.lww.com/QAD/A265), suggesting there is not a single or few viral lineages that are responsible for ongoing HIV-2 transmissions. Interestingly, only one incident case significantly clustered with a non-Caió env isolate, whereas all others were found within Caió-only clusters.
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).
We have investigated the phylodynamics of HIV-2 in rural Guinea-Bissau using sequence data from a well characterized community cohort. We used Bayesian inference to analyse population dynamics of HIV-1 and HIV-2. The fact that the two epidemics experienced similar growth rates and patterns following introduction, but at different points in time, may suggest that the population dynamics are determined by high-risk host behaviour at onset rather than ecological or historical factors. Similar conclusions were drawn following comparison of the HIV-1 epidemics amongst men who have sex with men in the US and UK . Alternately, the biological features that make HIV-2 less transmissible than HIV-1 may have been compensated for by a boost in transmission due to iatrogenic spread , allowing HIV-2 to reach epidemic growth rates akin to HIV-1. In the absence of these aids, HIV-2 is declining due to inefficient heterosexual transmission. A third explanation could be that HIV-2 was more virulent and transmissible during the early phases of the epidemic, but due to poorer adaptability to hosts (than HIV-1), a gradual attenuation has occurred over time. We, and others, have previously demonstrated that HIV-2 is under significant evolutionary constraint when compared to HIV-1 [24,37], which may account for HIV-2's disadvantageous competition with HIV-1. Our estimates of the HIV-1 CRF02_AG and HIV-2 group A tMRCA (1973 vs. 1947) are consistent with previous separate analyses using sequences from Guinea-Bissau [13,30]. The similarity between the tMRCA for Caió CRF02_AG isolates and the estimated emergence of CRF02_AG in the Democratic Republic of Congo emphasizes the likelihood that rapid dispersal throughout West Africa occurred at an early stage . HIV-1 and HIV-2 epidemiological data for our cohort are available from 1990 onwards. The similar calculated Ne of the two viruses between 1990 and 1997 is consistent with similar incidence rates during the same period [4.4/1000 person-years of observation (PYO) for HIV-1 and 4.8/1000 PYO for HIV-2] . Although during 1997–2007, HIV-2 incidence fell (1.8/1000 PYO) , the BSP remained at a plateau. This is a common feature of HIV BSPs [36,39–41]. Although this can be attributed to methodological factors (Supplementary methods, http://links.lww.com/QAD/A265), the fact that the HIV-1 and HIV-2 growth curves reached equilibrium at the same level, but at different times, suggest host demographic factors (such as the number of susceptible or infectious hosts) are decisive in these trends.
We also explored whether viraemic outcome in HIV-2 is associated with particular viral lineages and observed that individuals whose viruses share an MRCA can have undetectable or detectable viral loads. This suggests that host factors are largely responsible for elite control of HIV-2. The observation that known sexual partners within transmission clusters can have discordant viral loads further strengthens this conclusion. A comparative study of host immunity and genetics within such couples could provide valuable insight into what determines the outcome of HIV-2 infection.
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 role of primary infection in transmitting HIV-1 is well documented both in Western and African settings, with up to 50% of primary HIV-1 infections being involved in transmission chains in a Canadian cohort [48,51–53]. The increased risk of transmission during acute/early HIV-1 infection can be explained by the peak in viraemia during this period . Little is known about primary HIV-2 infection. It is conceivable that a similar viraemic peak occurs prior to reaching set points. As these are much lower in HIV-2 than in HIV-1 infection, the main window for HIV-2 transmission may well be during early infection – a hypothesis that is supported by the data above. Individuals in clusters in the gag phylogeny had significantly higher viral loads than nonclustering individuals, although only a nonsignificant trend was observed in the env phylogeny. The significance of this finding is also not clear as the viral loads used are likely to be from samples taken many years after transmission events. Alternately, the higher proportion of new HIV-2 infections found in transmission clusters may reflect both acquisition and forward transmission of HIV-2 during a defined period of increased sexual risk-taking behaviour.
It is estimated that at least 60% of new HIV-1 infections in Africa occur within married or cohabiting couples . In our cohort, 33–42% of viruses in clusters belonged to known heterosexual partners, suggesting that a large proportion of new HIV-2 infections also occur within marriages. This highlights the need for prevention specifically targeting known partners, especially as similar patterns are seen in HIV-1 transmission in Guinea-Bissau (Td.S., unpublished data). Although we examined several other characteristics that may be associated with HIV-2 transmission, we found no association with increased sexual risk behaviour or co-infections. These factors may, therefore, contribute less to the transmission risk than stage of HIV-2 infection or viral load. However, the information available in the analysis was derived from one time point only and under-reporting of sexual risk behaviour cannot be excluded.
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 ).
In summary, our study in a rural West African community suggests that the population dynamics of HIV-2 and HIV-1 followed similar paths after introduction, although HIV-1 is now displacing HIV-2 as the dominant infection. Despite the poor transmissibility of HIV-2, new heterosexual transmissions still occur. Only time will tell whether these transmission events are sufficient to maintain a low-level epidemic in the region, or whether we will witness a gradual elimination of this sometimes lethal retrovirus from Guinea-Bissau – a country that once had the highest recorded prevalence of HIV-2 infection in the world.
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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