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

Edson Delatorre,Gonzalo Bello

doi:10.1186/s12862-016-0824-8

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.

Highlights

Several HIV-1 circulating recombinant forms with a complex mosaic structure (CRFs_cpx) circulate in central and western African regions
One CRF09_cpx env sequence branched within the CRF11_cpx clade, while 57 subtype A/A1/A2 env sequences branched within the CRFs09/11/13/45_cpx clades radiations and were reclassified (Additional file 3: Figure S3). This approach resulted in two final datasets composed by 181 CRFs_cpx-like pol sequences and 125 CRFs_cpx-like env sequences, sampled between 1984 and 2011 from 16 countries of Central and West Africa (Additional file 5: Table S2 and Additional file 6: Table S3) that were used for the subsequent analyses
We propose that differences in epidemic growth rates across HIV-1 African lineages most probably resulted from ecological determinants, differences in viral transmissibility properties might be responsible for the growth rate variances in some cases [58]

Summary

Introduction

Several HIV-1 circulating recombinant forms with a complex mosaic structure (CRFs_cpx) circulate in central and western African regions. Some of the complex CRFs (including CRF04_cpx [5], CRF06_cpx [6], CRF09_cpx [7], CRF11_cpx [8], CRF13_cpx [9], CRF18_cpx [10], CRF25_cpx [11], CRF27_cpx [12], CRF37_cpx [13], CRF45_cpx [14] and CRF49_cpx [15]) carry fragments of rare subtypes (e.g., subtypes H, J and K) and divergent unclassified (U) lineages likely derived from parental strains that may predate the current subtypes [16] Some of these complex CRFs are widely dispersed in a Delatorre and Bello BMC Evolutionary Biology (2016) 16:249 given African region and reaching high prevalence (40–50%) in certain countries, such as the CRF06_cpx in Burkina Faso [17] and the CRF11_cpx in the Central African Republic [18]. The remaining of those complex CRFs were sporadically detected in Africa, but have successfully disseminated to other locations, as the CRF04_cpx in Greece and Cyprus [26, 27] and the CRF18_cpx in Cuba [10]

Methods

Results

Discussion

Conclusion