Time-scale of minor HIV-1 complex circulating recombinant forms from Central and West Africa

Abstract

BackgroundSeveral HIV-1 circulating recombinant forms with a complex mosaic structure (CRFs_cpx) circulate in central and western African regions. Here we reconstruct the evolutionary history of some of these complex CRFs (09_cpx, 11_cpx, 13_cpx and 45_cpx) and further investigate the dissemination dynamic of the CRF11_cpx clade by using a Bayesian coalescent-based method.ResultsThe analysis of two HIV-1 datasets comprising 181 pol (36 CRF09_cpx, 116 CRF11_cpx, 20 CRF13_cpx and 9 CRF45_cpx) and 125 env (12 CRF09_cpx, 67 CRF11_cpx, 17 CRF13_cpx and 29 CRF45_cpx) sequences pointed to quite consistent onset dates for CRF09_cpx (~1966: 1958–1979), CRF11_cpx (~1957: 1950–1966) and CRF13_cpx (~1965: 1958–1973) clades; while some divergence was found for the estimated date of origin of CRF45_cpx clade [pol = 1970 (1964–1976); env = 1960 (1952–1969)]. Phylogeographic reconstructions indicate that the HIV-1 CRF11_cpx clade most probably emerged in Cameroon and from there it was first disseminated to the Central Africa Republic and Chad in the early 1970s and to other central and western African countries from the early 1980s onwards. Demographic reconstructions suggest that the CRF11_cpx epidemic grew between 1960 and 1990 with a median exponential growth rate of 0.27 year−1, and stabilized after.ConclusionsThese results reveal that HIV-1 CRFs_cpx clades have been circulating in Central Africa for a period comparable to other much more prevalent HIV-1 group M lineages. Cameroon was probably the epicenter of dissemination of the CRF11_cpx clade that seems to have experienced a long epidemic growth phase before stabilization. The epidemic growth of the CRF11_cpx clade was roughly comparable to other HIV-1 group M lineages circulating in Central Africa.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0824-8) contains supplementary material, which is available to authorized users.

HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing

“…Thus, the tMRCA of the env region was estimated to be around 1965 and 1960 for CRF09_cpx and CRF45_cpx, respectively. The tMRCA of the pol region was estimated to be a decade later [43]. The sequence of Sample 11 shows a less complex structure and yet the subtype A part of the sequence, which corresponds to the env part of that study, shows a high similarity to that of CRF09_cpx and CRF45_cpx.…”

“…In fact, the sequence was found to be related in parts to CRF13_cpx and CRF11_cpx. These CRFs were shown to probably originate from Central Africa, where they emerged in the late 1950s to late 1960s [43]. Tongo et al (2015) proposed that parts of genomes of the unique recombinant sequences from Cameroon that clustered outside of all identified subtypes and CRF clades are in fact historical lineages that diverged early in the HIV epidemic but did not reach the magnitude of an epidemic like other subtypes did [46].…”

Genetic Diversity of HIV-1 in Krasnoyarsk Krai: Area with High Levels of HIV-1 Recombination in Russia

“…It was shown that random shuffling of HIV genetic material not only increases viral diversity but also enables the virus to evade the response of the human immune system [ 51 ]. The increase in circulating HIV-1 genetic diversity is a general characteristic for many current territorial epidemics [ 43 , 49 , 52 – 56 ].…”

Elucidation of Early Evolution of HIV-1 Group M in the Congo Basin Using Computational Methods

“…Several studies have attempted to reconstruct the early dynamics of the different HIV-1M subtypes and other CRFs that are circulating in the CB [ 15 , 27 , 28 , 29 , 30 ]. Using similar Bayesian statistical approaches, these studies have inferred that different lineages emerged at different locations in the region between the 1950s and 1970s and then spread out of the region.…”

“…In an earlier study, Delatorre and Bello (2016) explored the time-scales over which some HIV-1M complex circulating recombinant forms arose within the CB region, including CRF- 09_cpx, 11_cpx, 13_cpx and 45_cpx. Surprisingly, they reported that these mosaic lineages have been circulating in the region for a period comparable to the early circulation of the now prevalent HIV-1M lineages [ 28 ]. In this regard, they have traced the time of the MRCAs (tMRCAs) of CRFs 09_cpx, 11_cpx and 13_cpx to 1966, 1957 and 1965, respectively.…”