Heterogeneous Evolution of HIV-1 CRF01_AE in Men Who Have Sex with Men (MSM) and Other Populations in China

Independent epidemic patterns of HIV-1 CRF01_AE lineages driven by mobile population in Shenzhen, an immigrant city of China

Shenzhen, a city with >12 million migrant population, may play a key role in the spread of human immunodeficiency virus (HIV)-1 in China. The transmission dynamics of CRF01_AE, a predominant subtype in Shenzhen, is a good model to characterize the impact of human mobility on HIV-1 epidemic locally and nationally. We used phylodynamic and phylogeographic methods to estimate the viral transmission dynamics and migration trajectory of variable lineages based on 1,423 CRF01_AE sequences in Shenzhen sampled between 2006 and 2015. Eleven lineages of CRF01_AE were detected in Shenzhen. Of those, four main lineages originated during the 1990s. Their basic viral reproduction number (R0) ranged 1.96–3.92. The effective viral reproduction number (Re) of two lineages prevalent among heterosexuals/people who inject drugs had reduced <1 at the end of sampling, and the main sources were the intra-provincial immigrants (72 per cent) for one and local residents of Shenzhen (91 per cent) for another. Within two lineages among men who have sex with men (MSM), Re had been above or close to 1 at the end of sampling, and the immigrants from Jiangxi/Shaanxi and Hubei as sources accounted for 93 per cent and 68 per cent of all viral migration events, respectively. Moreover, no obvious recipients were found throughout the viral migration history for any lineage. Our findings demonstrate that HIV epidemic is declining in Shenzhen, which coincided with the initiation of the interventions during the 2000s. However, the obvious differences of the epidemic patterns between lineages emphasize the importance of further targeting interventions and continued molecular tracing, focusing on high-risk transmission sources among MSM.

Intrapatient Development of Multi-Class Drug Resistance in an Individual Infected with HIV-1 CRF01_AE

The rapid expansion of access to antiretroviral therapy (ART) has led to the emergence of multi-class drug resistance (MDR) in people living with HIV (PLWH). However, the viral evolutionary dynamics of the development of MDR has not been well documented. For this study, plasma and peripheral blood mononuclear cells (PBMC) were longitudinally collected at different time points from a PLWH who suffered several periods of ART failure. Next generation sequencing (NGS) was used to analyze the distribution and percent of drug resistance mutations in PBMC and plasma. The results showed the gradual replacement of the wild type protease and integrase genotype by protease inhibitors (PI) and integrase strand transfer inhibitor (INSTI) drug resistant mutations when patient’s ART regimen was changed – driving the increase of genetic variability in HIV DNA. Sampling for this study was initiated after the patient was first diagnosed with ART failure, five years after ART treatment was first initiated. By that time, mutants resistant to the reverse transcriptase inhibitor nevirapine (NVP) had already replaced almost 100% of wild type. After the introduction of the protease inhibitor lopinavir/ritonavir (LPV/r) to the patient’s ART, resistant protease inhibitor (PI) mutants developed slowly. After one month, none were found in PMBC DNA; after sixteen months, less than 20% were mutants; and after three years (two months prior to the patient’s death) PI mutants were still under 50%. However, integrase strand transfer inhibitor (INSTI) mutations evolved much more quickly, replacing approximately 75% of the wild genotype in HIV DNA one year after addition of the integrase inhibitor raltegravir to the patient’s ART, and almost 100% after two years. In summary, our dataset provides the first analysis of the distribution and percent of drug resistance mutations in PBMC and plasma during the development of a four-class drug resistant HIV-1 CRF01_AE virion. The study also showed that months before drug resistant mutants could be found in plasma, NGS identified them in HIV DNA, demonstrating that this can be a very effective tool for early detection of the development of drug resistance.

Differences of cytotoxic T-lymphocyte pressure and divergent evolution of several CRF07_BC clusters circulating in men who have sex with men in China

The HIV-1 CRF07_BC strain is now the major recombinant form in China among the population of men who have sex with men (MSM), and has critically contributed to the HIV-1 epidemic in recent years. The phylodynamic and virological differences among CRF07_BC clusters circulating in MSM, and the factors that could be driving their evolution, remains unclear. Using the HIV-1 CRF07_BC strains obtained from the Los Alamos HIV database, we undertook a large-scale phylogenetic analysis using the maximum likelihood method of partial gag, pol, and env segments to infer their evolutionary relationships. The demographic histories of clusters were determined using the Bayesian Markov chain Monte Carlo (MCMC) method. For four pol clusters we analyzed the non-synonymous (dN) to synonymous (dS) substitution rates and performed site to site analysis to identify positive selection sites and cytotoxic T-lymphocyte (CTL) escape mutation positions. MSM was found to be the predominant risk factor for all four of the CRF07_BC epidemic pol segment clusters with the largest number of infections. Two of those clusters had higher growth in the effective number of infections, and two clusters had slower growth. Analysis of all four clusters showed no significant differences in the mean substitution rates and dN/dS selection pressure ratios. However, a site to site codon analysis found thirteen significant positive selection sites. Ten of these sites are CTL escape mutations. The two clusters with the higher growth in infections had seven and eight pol segment CTL escape mutation sites respectively, while the two with slower growth had only one or two. Our findings demonstrated differences in the CTL escape mutation and divergent evolution of several CRF07_BC clusters circulating among men who have sex with men in China.

The prevalence, temporal trends, and geographical distribution of HIV-1 subtypes among men who have sex with men in China: A systematic review and meta-analysis

The aim of this meta-analysis was to provide a comprehensive overview of human immunodeficiency virus (HIV)-1 subtypes and to investigate temporal and geographical trends of the HIV-1 epidemic among men who have sex with men (MSM) in China. Chinese and English articles published between January 2007 and December 2017 were systematically searched. Pooled HIV-1 prevalence was calculated, and its stability was analysed using sensitivity analysis. Subgroups were based on study time period, sampling area and prevalence. Publication bias was measured using Funnel plot and Egger's test. A total of 68 independent studies that included HIV-1 molecular investigations were eligible for meta-analysis. Circulating recombinant form (CRF) 01_AE (57.36%, 95% confidence interval (CI) 53.76–60.92) was confirmed as the most prevalent HIV-1 subtype among MSM in China. Subgroup analysis for time period found that CRF01_AE steadily increased prior to 2012 but decreased during 2012–2016. Further whereas CRF07_BC increased over time, B/B′ decreased over time. CRF55_01B has increased in recent years, with higher pooled estimated rate in Guangdong (12.22%, 95% CI 10.34–13.17) and Fujian (8.65%, 95% CI 4.98–13.17) provinces. The distribution of HIV-1 subtypes among MSM in China has changed across different regions and periods. HIV-1 strains in MSM are becoming more complex. Long-term molecular monitoring in this population remains necessary for HIV-1 epidemic control and prevention.

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

Since the 1990s, several distinct clusters of human immunodeficiency virus-type 1 (HIV-1) CRF01_AE related to a large epidemic in China have been identified, but it is yet poorly understood whether its transmission has dispersed globally. We aimed to characterize and quantify the genetic relationship of HIV-1 CRF01_AEs circulating in China and other countries. Using representative sequences of Chinese clusters as queries, all relevant CRF01_AE pol sequences in two large databases (the Los Alamos HIV sequence database and the UK HIV Drug Resistance Database) were selected with the online basic local alignment search (BLAST) tool. Phylogenetic and phylogeographic analyses were then carried out to characterize possible linkage of CRF01_AE strains between China and the rest of the world. We identified that 269 strains isolated in other parts of the world were associated with five major Chinese CRF01_AE clusters. 80.7% were located within CN.01AE.HST/IDU-2, most of which were born in Southeast Asia. 17.8% were clustered with CN.01AE.MSM-4 and -5. Two distinct sub-clusters associated with Chinese men who have sex with men (MSM) emerged in HK-United Kingdom and Japan after 2000. Our analysis suggests that HIV-1 CRF01_AE strains related to viral transmission in China were initially brought to the United Kingdom or other countries during the 1990s by Asian immigrants or returning international tourists from Southeast Asia, and then after having circulated among MSM in China for several years, these Chinese strains dispersed outside again, possibly through MSM network. This study provided evidence of regional and global dispersal of Chinese CRF01_AE strains. It would also help understand the global landscape of HIV epidemic associated with CRF01_AE transmission and highlight the need for further international collaborative study in this field.

Genome-scale analysis of evolutionary rate and selection in a fast-expanding Spanish cluster of HIV-1 subtype F1

This work is aimed at assessing the presence of positive selection and/or shifts of the evolutionary rate in a fast-expanding HIV-1 subtype F1 transmission cluster affecting men who have sex with men in Spain. We applied Bayesian coalescent phylogenetics and selection analyses to 23 full-coding region sequences from patients belonging to that cluster, along with other 19 F1 epidemiologically-unrelated sequences. A shift in the overall evolutionary rate of the virus, explained by positively selected sites in the cluster, was detected. We also found one substitution in Nef (H89F) that was specific to the cluster and experienced positive selection. These results suggest that fast transmission could have been facilitated by some inherent genetic properties of this HIV-1 variant.

Defining HIV-1 transmission clusters based on sequence data

Understanding HIV-1 transmission dynamics is relevant to both screening and intervention strategies of HIV-1 infection. Commonly, HIV-1 transmission chains are determined based on sequence similarity assessed either directly from a sequence alignment or by inferring a phylogenetic tree. This review is aimed at both nonexperts interested in understanding and interpreting studies of HIV-1 transmission, and experts interested in finding the most appropriate cluster definition for a specific dataset and research question. We start by introducing the concepts and methodologies of how HIV-1 transmission clusters usually have been defined. We then present the results of a systematic review of 105 HIV-1 molecular epidemiology studies summarizing the most common methods and definitions in the literature. Finally, we offer our perspectives on how HIV-1 transmission clusters can be defined and provide some guidance based on examples from real life datasets.