Reconstructing the Timing and Dispersion Routes of HIV-1 Subtype B Epidemics in The Caribbean and Central America: A Phylogenetic Story

Abstract

The Caribbean and Central America are among the regions with highest HIV-1B prevalence worldwide. Despite of this high virus burden, little is known about the timing and the migration patterns of HIV-1B in these regions. Migration is one of the major processes shaping the genetic structure of virus populations. Thus, reconstruction of epidemiological network may contribute to understand HIV-1B evolution and reduce virus prevalence. We have investigated the spatio-temporal dynamics of the HIV-1B epidemic in The Caribbean and Central America using 1,610 HIV-1B partial pol sequences from 13 Caribbean and 5 Central American countries. Timing of HIV-1B introduction and virus evolutionary rates, as well as the spatial genetic structure of the HIV-1B populations and the virus migration patterns were inferred. Results revealed that in The Caribbean and Central America most of the HIV-1B variability was generated since the 80 s. At odds with previous data suggesting that Haiti was the origin of the epidemic in The Caribbean, our reconstruction indicated that the virus could have been disseminated from Puerto Rico and Antigua. These two countries connected two distinguishable migration areas corresponding to the (mainly Spanish-colonized) Easter and (mainly British-colonized) Western islands, which indicates that virus migration patterns are determined by geographical barriers and by the movement of human populations among culturally related countries. Similar factors shaped the migration of HIV-1B in Central America. The HIV-1B population was significantly structured according to the country of origin, and the genetic diversity in each country was associated with the virus prevalence in both regions, which suggests that virus populations evolve mainly through genetic drift. Thus, our work contributes to the understanding of HIV-1B evolution and dispersion pattern in the Americas, and its relationship with the geography of the area and the movements of human populations.

Spatiotemporal Dynamics of Dissemination of Non-Pandemic HIV-1 Subtype B Clades in the Caribbean Region

“…The authors recognize the existence of two major clusters in the Caribbean: cluster I (which grouped most of the sequences from Haiti, the Lesser Antilles, plus half of the Jamaican sequences) and cluster II (which included most of sequences from Cuba, Puerto Rico, and about half of the Jamaican sequences); but both lineages were associated to the B PANDEMIC clade [22]. In our opinion, clusters I and II matched with the B CAR and B PANDEMIC clades here described, respectively.…”

The effect of genetic structure on molecular dating and tests for temporal signal

“…If more recently sampled sequences have undergone more molecular evolution, then the true sampling dates should yield a t MRCA that differs substantially from the equivalent estimates with the sampling dates randomly permuted over sequences (Ramsden, Holmes & Charleston 2009;e.g. Duffy & Holmes 2009;Firth et al 2010;Fraile et al 2011;Pag an & Holgu ın 2013;Duchêne, Holmes & Ho 2014b;Duchêne et al 2015a).…”

Prevalence and spatiotemporal dynamics of HIV-1 Circulating Recombinant Form 03_AB (CRF03_AB) in the Former Soviet Union countries

“…We compared several molecular clock models (strict and relaxed) and coalescent priors (constant population size, exponential growth and logistic growth and Bayesian skyline) by Tracer v1.5 in order to find the best combination ( S4 Table ). As a result, the relaxed uncorrelated lognormal clock (UCLN) and Bayesian Skyline Plot (BSP) were used in inferring the temporal scale of the evolutionary process from the sampling dates of the sequences; a lognormal prior distribution for the clock rate were used (mean = 0.002, stdev = 0.5) [ 5 , 49 ]. Two independent MCMC chains were run of 300×10 6 steps with parameters sampled every 5000 generations, with a burn-in of first 25%.Convergence of the chains was estimated based on the Effective Sample Size (ESS) in the Tracer v1.5.…”