Phylodynamics of the HIV-1 Epidemic in Cuba

Edson Delatorre,Gonzalo Bello

doi:10.1371/journal.pone.0072448

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.

Highlights

The global dissemination of the Human immunodeficiency virus type 1 (HIV-1) group M clade during the second half of the twentieth century has resulted in the generation of a diverse collection of genetic variants classified into subtypes, sub-subtypes, circulating recombinant forms (CRFs) and unique recombinants forms (URFs)
The Cuban HIV epidemic is unique in the Americas because of the exceptionally low HIV prevalence, estimated at 0.20% in adults in 2011 [36], and the unusually high HIV-1 genetic diversity with circulation of subtype B and several non-B subtypes [2,3,4,5,6,7]
Our study indicates that most HIV-1 infections in Cuba derived from the dissemination of a few founder viruses that were either introduced from the Americas/Europe and Africa or were locally generated (CRFs20/23/24_BG)

Summary

Introduction

The global dissemination of the Human immunodeficiency virus type 1 (HIV-1) group M clade during the second half of the twentieth century has resulted in the generation of a diverse collection of genetic variants classified into subtypes, sub-subtypes, circulating recombinant forms (CRFs) and unique recombinants forms (URFs). The HIV-1 epidemic in the Americas is typically dominated by subtype B clade, substantial proportions ($20%) of non-B subtype genetic forms are observed in Argentina, Brazil, Cuba and Uruguay [1]. Some HIV-1 recombinants including CRF18_cpx and CRF19_cpx were probably imported into Cuba directly from central Africa, since the parental viruses of these complex genetic forms were only detected in that African region [8,9]. Other HIV-1 recombinants including all three CRFs_BG, were probably generated locally by recombination between subtypes B and G already circulating in Cuba [20]

Methods

Results

Conclusion