Molecular Epidemiology Of HIV-1 CRF01_AE: Phylogenetic Reconstruction And Spatiotemporal Dynamics

Molecular epidemiology is an indispensible science that precedes designing of vaccines and adjustment of treatment against pathogens. The development of new and rapid protocols to isolate and identify HIV, coupled with the sophisticated phylogenetic analysis of their gene sequences, is providing a new and fascinating insight into its biology, origin of epidemics and further spread. In fact, the high genetic variability of HIV allows for successful phylogenetic reconstruction both within and between risk groups or geographic locations.HTV-1 CRF01_AE is the 5th in terms of epidemic prevalence amongst HIV subtypes and the earliest recombinant form. The increasing predominance of this CRF in various geographic regions in Asia and particularly China, in addition to reshaping in transmission process to involve more risk groups therein triggered the need for broader knowledge on molecular epidemiology of CRF01_AE as a pre-step to achieving regimen and/or vaccine against it. Here, we conducted three comprehensive studies by implementing phylogenetic and phylogeographic approaches to characterize rigorously this CRF in Asia at large and China in particular.Firstly, by using a combination of phylogenetic analyses and Bayesian coalescent-based approach, we analyzed a total of 1,957 HIV-1 CRF01_AE gag p17 sequences from 5 global regions containing 15 countries including China, to better understand the phylogenetic relationship between global and Asian clades, and to explore in greater detail the epidemic history of CRF01_AE in China. Our results demonstrated the close phylogenetic relationship between Thailand, Vietnam and Chinese CRF01_AE sequences. Interestingly, we found multiple independent introductions and multiple independent autochthonous clades of HIV-1 CRF01AE circulating in different geographic locations of China, which probably descended from Thailand, Vietnam or both. Yunnan province of China was identified as the earliest introduction site, and together with Guangxi, Fujian and Liaoning demonstrated as locations harboring those earliest clades. Those clades, however, were indicated as independently major or sporadic introductions, which likely took place from 1991 through 2003.Secondly, to address the issue of CRF01AE transmission from the origin to and inside China, we used the Bayesian phylogeography method to revisit the origin and highlight internally circulating variants by using two HFV-1 genomic regions (i.e. gag and strip env). For the purpose, we collected a total of 357 sequences (gag=141 and env CDS=216). The collected sequences represented 11 countries and 11 Chinese provinces. Sequences were pooled into datasets and analyzed using Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software to describe the most plausible scenario of geographic migration of CRF01-AE within China, through the employment of Bayesian phylogeography method. In order to substantiate the outcome of our sequence analyses, we reviewed all published literatures about the earliest and recent HIV-1 epidemic history in China and worldwide. Our analyses provided more detailed phylogeographic dynamics in terms of space and time (Spatio-temporal) to CRF01_AE transmission from the origin to and inside China. The analyses pinpointed clearly to Central African Republic as the origin, from where it migrated to Thailand in 1982, followed by multiple migrations to Vietnam in 1992 and China. Transmission to China most likely occurred through two routes. The first route was from Thailand to Yunnan through Myanmar, in addition to few sporadic transmissions to Fujian and Hainan. However, the lack of sequences from Myanmar hindered the investigation. Interestingly, the second route apparently occurred from Vietnam to Guangxi, a second primary epicenter in the transmission line. Both Yunnan and Guangxi played an essential role to transmit the virus eastward to neighboring provinces (e.g. Guangdong, Fujian and Jiangsu) in addition to remote or sporadic transmissions to other provinces (e.g. Liaoning).Thirdly, by conducting a comprehensive analysis of HIV-1 CRF01_AE variants across 8 geographic regions utilizing a global env V3 sequence dataset, within-CRF sequence heterogeneity was realized. The study demonstrated AA differences between geographic regions that are distinct from sequence-level phylogenetic clustering and previously described differences.7 signature patterns were identified, which prevail among Asian variants. Among those,4 patterns exclusively prevailing among Chinese variants featured high frequency in sequences supported by higher entropy. The applied approach drives the attention to the additional subpopulation heterogeneity that may be overlooked by the current subtyping nomenclature system. The consideration of these differences likely improves the interpretation of HIV-1 sequence datasets from multiple cohorts and locations. The signature pattern differences highlighted by this study could improve the interpretation of genotype-phenotype association for better designation of effective vaccines or adjust treatment against HIV subtypes.Overall, the combination of phylogenetics and epidemiological data creates a powerful tool for in-depth characterization of CRF01_AE that could effectively improve surveillance and prevention.