Phylodynamics of the HIV-1 Epidemic in Cuba

Abstract

Previous studies have shown that the HIV-1 epidemic in Cuba displayed a complex molecular epidemiologic profile with circulation of several subtypes and circulating recombinant forms (CRF); but the evolutionary and population history of those viral variants remains unknown. HIV-1 pol sequences of the most prevalent Cuban lineages (subtypes B, C and G, CRF18_cpx, CRF19_cpx, and CRFs20/23/24_BG) isolated between 1999 and 2011 were analyzed. Maximum-likelihood analyses revealed multiple introductions of subtype B (n≥66), subtype C (n≥10), subtype G (n≥8) and CRF18_cpx (n≥2) viruses in Cuba. The bulk of HIV-1 infections in this country, however, was caused by dissemination of a few founder strains probably introduced from North America/Europe (clades BCU-I and BCU-II), east Africa (clade CCU-I) and central Africa (clades GCU, CRF18CU and CRF19CU), or locally generated (clades CRFs20/23/24_BG). Bayesian-coalescent analyses show that the major HIV-1 founder strains were introduced into Cuba during 1985–1995; whereas the CRFs_BG strains emerged in the second half of the 1990s. Most HIV-1 Cuban clades appear to have experienced an initial period of fast exponential spread during the 1990s and early 2000s, followed by a more recent decline in growth rate. The median initial growth rate of HIV-1 Cuban clades ranged from 0.4 year−1 to 1.6 year−1. Thus, the HIV-1 epidemic in Cuba has been a result of the successful introduction of a few viral strains that began to circulate at a rather late time of the AIDS pandemic, but then were rapidly disseminated through local transmission networks.

Phylogenetics of HIV-1 subtype G env: Greater complexity and older origins than previously reported

“…Our analysis does not therefore support the hypothesis that HIV-1 subtype G travelled directly from Angola to either Cuba (Bártolo et al, 2009;Delatorre and Bello, 2013a) or the Iberian peninsula (Bártolo et al, 2009). It also does not support the conclusion that the MRCA of subtype G existed in Angola, the DRC or the Republic of Congo, as has been previously suggested with an analysis of partial pol gene sequences (Delatorre et al, 2014).…”

Expansion of the CRF19_cpx Variant in Spain

“…The analyses were performed with the (GTR 112 + CP 112 + 112 (4CAT)) substitution model. A log-normal prior was chosen for ucld.mean (median = 3.35 × 10 −3 , 95% HPD upper limit = 5.00 × 10 −3 substitutions per site and year [5]). Under an uncorrelated lognormal relaxed molecular clock model, the most appropriate demographic model (Bayesian Skyline Plot-BSP, constant, exponential or logistic demographic change) was chosen as the one with the lowest Akaike's Information Criterion (AICM, [14]) value.…”

“…Although phylogeographic analyses suggest an African origin for this HIV-1 CRF, the vast majority of infections occur in Cuba, where prevalence is >15% of the HIV-infected population [2][3][4][5]. However, the reported incidence of CRF19 cpx cases in other countries is very low, and the existence of transmission groups outside http Cuba has never been reported.…”

Co-Receptor Tropism Determined by Genotypic Assay in HIV-1 Circulating in Cuba

“…Currently, it has become the third HIV-1 variant in frequency to be circulating in Cuba (between 17-19%) [18,19], despite of the evidenced central African ancestry [12,14].…”

“…Despite the low prevalence of HIV-1 (0.2%), the epidemic in Cuba is characterized by an unusually high viral diversity of HIV-1, in contrast to the rest of the Caribbean region, where subtype B predominates [10][11][12].…”