Spatio-Temporal Dynamics of HIV-I Subtype B and Circulating Recombinant Form 01_AE Clades in Iran: A Phylogeographic Approach

Abstract

Background: The origins and spatio-temporal dynamics of the HIV-1 subtype B and CRF01_AE clades are largely unknown in Iran. Objectives: This study investigates the origins and spatio-temporal dynamics of HIV-1 subtype B and CRF01_AE clades in Iran using the most recent phylogeographic methods. Methods: This Bayesian phylogeographic study examined HIV-1 sequence data available in the Los Alamos HIV databases. For the purposes of this study, we retrieved all the eligible time-stamped and geo-referenced HIV-1 subtype B (pol p66 and p51 RT) and CRF01_-AE (gp160) sequences from Iran. The majority of these data were obtained from studies using convenience and snowball sampling. Evolutionary and phylogeographic parameters were jointly estimated for each clade using BEAST software v.1.8.1. A Bayesian stochastic search variable selection method, with a threshold of 3.0 for the Bayes factors test, was used to obtain significant migration rates of the virus. Results: Our results suggest that the subtype B epidemic was introduced to Iran from Southern China, Germany and the USA. Although the migration rate from the USA to Iran was found to be statistically insignificant, the results suggested that the USA was the earliest exporter of the subtype B to Iran (i.e. since 1974, 95% Highest Posterior Density (HPD) : 1966-1974). Moreover, based on our findings, the CRF01_AE clade was first introduced to Iran from Thailand (1988( , 95% HPD: 1986( -1990. Among the factors contributing to the transmission of subtype B to Iran from Germany is the transit of goods and long-distance truck driving. However, the factors behind the transmission of this clade from the USA and Southern China remain unknown. Similar to many countries, the introduction of CRF01_AE from Thailand might be attributed to sex tourism. Conclusions: There is evidence to suggest that subtype B and CRF01_AE were introduced to Iran through multiple pathways and origins, including Germany, Southern China, the USA, and Thailand. Factors such as international trade, the transit of goods, and tourism are among the most likely methods for transmission of these clades. However, the existing preventive strategies in Iran have been mostly focused on other risk groups, including sex workers and intravenous drug users. The findings of our study highlight the need for the further development of targeted preventive strategies, such as educational interventions, aimed at tourists, truck drivers, and people involved in international trade and transactions in order to prevent the onward transmission of disease.

Molecular epidemiology of infectious diseases

“…However, in another study conducted by Eybpoosh, et al (2016), on all HIV-1 subtype B strains available from Iran revealed that multiple parallel subtype B epidemics existed in Iran with independent origins. They noted that the subtype B epidemic observed among heterosexuals, has an independent evolutionary history from the epidemic observed among hemophiliac patients and is probably imported to Iran from USA, Germany, and Hong Kong, but not from France ( 44 ).…”

Cross-Continental Dispersal of Major HIV-1 CRF01_AE Clusters in China

“…To identify any export events of CRF01_AE strains related to Chinese major transmission clusters, we quantified the genetic divergence time in terms of the estimated time to the most recent common ancestor (tMRCA) using a Bayesian MCMC-based approach and also estimated the location of ancestor at the node of the tree. Many sequences (1172 from China and 226 from Vietnam) were identified to be associated with viral transmission in China through above phylogenetic analysis, and to reduce the computational burden in Bayesian running for spatialtemporal analysis, a sub-sampling procedure was performed that only one representative sequence was selected among high similarity clustered sequences (genetic distance < 2%), using the online web server of CD-HIT-EST program (Huang et al, 2010;Eybpoosh et al, 2017). As a result, totally 328 sequences (186 from Mainland China, 56 from Vietnam, 88 from other countries/regions) and 42 references were used for the FIGURE 2 | Phylogenetic analysis of global CRF01_AE strains outside Mainland China together with five major Chinese clusters.…”