Identification of 3 distinct HIV-1 founding strains responsible for expanding epidemic among men who have sex with men in 9 Chinese cities

Identification of a Novel HIV-1 Circulating Recombinant Form (CRF150_Cpx) Among Men Who Have Sex with Men in China

Recent studies have reported increasing complexity in human immunodeficiency virus 1 (HIV-1) genotypes among men who have sex with men (MSM) in China. In an HIV-1 molecular epidemiological study conducted among MSM in Yunnan Province, China, we discovered that four samples could potentially represent a circulating recombinant form (CRF). In this study, we conducted further analysis on their nearly full-length genome (NFLG) sequences. The NFLG sequences formed a distinct monophyletic clade in the phylogenetic tree. Recombination analysis indicated that the four sequences were constructed upon the backbone of CRF149_01B, with the insertion of three CRF07_BC fragments. Consequently, they were designated as CRF150_cpx. Evolutionary analyses suggested that CRF150_cpx emerged between approximately 2014 and 2015. The identification of new CRFs not only deepens our understanding of HIV recombination but also aids in comprehending the prevalence and transmission history of HIV among specific populations.

The origin, dissemination, and molecular networks of HIV-1 CRF65_cpx strain in Hainan Island, China

BACKGROUND

HIV-1 CRF65_cpx strain carries drug-resistant mutations, which raises concerns about its potential for causing virologic failure. The CRF65_cpx ranks as the fourth most prevalent on Hainan Island, China. However, the origin and molecular epidemiology of CRF65_cpx strains in this area remain unclear. This study aims to estimate the spatial origins and dissemination patterns of HIV-1 CRF65_cpx in this specific region.

METHODS

Between 2018 and 2021, a total of 58 pol sequences of the CRF65_cpx were collected from HIV-positive patients on Hainan Island. The available CRF65_cpx pol sequences from public databases were compiled. The HIV-TRACE tool was used to construct transmission networks. The evolutionary history of the introduction and dissemination of HIV-1 CRF65_cpx on Hainan Island were analyzed using phylogenetic analysis and the Bayesian coalescent-based approach.

RESULTS

Among the 58 participants, 89.66% were men who have sex with men (MSM). The median age was 25 years, and 43.10% of the individuals had a college degree or above. The results indicated that 39 (67.24%) sequences were interconnected within a single transmission network. A consistent expansion was evident from 2019 to 2021, with an incremental annual addition of four sequences into the networks. Phylodynamic analyses showed that the CRF65_cpx on Hainan Island originated from Beijing (Bayes factor, BF = 17.4), with transmission among MSM on Hainan Island in 2013.2 (95%HPD: 2012.4, 2019.5), subsequently leading to an outbreak. Haikou was the local center of the CRF65_cpx epidemic. This strain propagated from Haikou to other locations, including Sanya (BF > 1000), Danzhou (BF = 299.3), Chengmai (BF = 27.0) and Tunchang (BF = 16.3). The analyses of the viral migration patterns between age subgroups and risk subgroups revealed that the viral migration directions were from "25-40 years old" to "17-24 years old" (BF = 14.6) and to "over 40 years old" (BF = 17.6), and from MSM to heterosexuals (BF > 1000) on Hainan Island.

CONCLUSION

Our analyses elucidate the transmission dynamics of CRF65_cpx strain on Hainan Island. Haikou is identified as the potential hotspot for CRF65_cpx transmission, with middle-aged MSM identified as the key population. These findings suggest that targeted interventions in hotspots and key populations may be more effective in controlling the HIV epidemic.

Transmitted drug resistance and transmission clusters among ART-naïve HIV-1-infected individuals from 2019 to 2021 in Nanjing, China

Background

Transmitted drug resistance (TDR) is an increasingly prevalent problem worldwide, which will significantly compromise the effectiveness of HIV treatments. However, in Nanjing, China, there is still a dearth of research on the prevalence and transmission of TDR among ART-naïve HIV-1-infected individuals. This study aimed to understand the prevalence and transmission of TDR in Nanjing.

Methods

A total of 1,393 participants who were newly diagnosed with HIV-1 and had not received ART between January 2019 and December 2021 were enrolled in this study. HIV-1 pol gene sequence was obtained by viral RNA extraction and nested PCR amplification. Genotypes, TDR and transmission cluster analyses were conducted using phylogenetic tree, Stanford HIV database algorithm and HIV-TRACE, respectively. Univariate and multivariate logistic regression analyses were performed to identify the factors associated with TDR.

Results

A total of 1,161 sequences were successfully sequenced, of which CRF07_BC (40.6%), CRF01_AE (38.4%) and CRF105_0107 (6.3%) were the main HIV-1 genotypes. The overall prevalence of TDR was 7.8%, with 2.0% to PIs, 1.0% to NRTIs, and 4.8% to NNRTIs. No sequence showed double-class resistance. Multivariate logistic regression analysis revealed that compared with CRF01_AE, subtype B (OR = 2.869, 95%CI: 1.093-7.420) and female (OR = 2.359, 95%CI: 1.182-4.707) were risk factors for TDR. Q58E was the most prevalent detected protease inhibitor (PI) -associated mutation, and V179E was the most frequently detected non-nucleoside reverse transcriptase inhibitor (NNRTI) -associated mutation. A total of 613 (52.8%) sequences were segregated into 137 clusters, ranging from 2 to 74 sequences. Among 44 individuals with TDR (48.4%) within 21 clusters, K103N/KN was the most frequent TDR-associated mutation (31.8%), followed by Q58E/QE (20.5%) and G190A (15.9%). Individuals with the same TDR-associated mutations were usually cross-linked in transmission clusters. Moreover, we identified 9 clusters in which there was a transmission relationship between drug-resistant individuals, and 4 clusters in which drug-resistant cases increased during the study period.

Conclusion

The overall prevalence of TDR in Nanjing was at a moderate level during the past 3 years. However, nearly half of TDR individuals were included in the transmission clusters, and some drug-resistant individuals have transmitted in the clusters. Therefore, HIV drug-resistance prevention, monitoring and response efforts should be sustained and expanded to reduce the prevalence and transmission of TDR in Nanjing.

HIV-1 molecular transmission network and drug resistance in Chongqing, China, among men who have sex with men (2018-2021)

BACKGROUND

Over the past few years, HIV transmission among men who have sex with men (MSM) in China has increased significantly. Chongqing, located in the southwest of China, has the highest prevalence of HIV among MSM in the country.

METHODS

Blood samples were taken from 894 MSM in Chongqing who had recently been diagnosed with HIV-1 infection and had not yet started getting treatment. In order to determine the distribution of HIV-1 subtypes, transmitted drug resistance, and assessments of molecularly transmitted clusters, we sequenced the Pol genes and employed them in phylogenetic analysis. The genetic distance between molecular clusters was 1.5%. To find potential contributing factors, logistic regression analyses were performed.

RESULTS

Of the 894 HIV-1 pol sequences acquired from study participants, we discovered that CRF07_BC (73.6%) and CRF01_AE (19.6%) were the two most prevalent HIV-1 genotypes in Chongqing among MSM, accounting for 93.2% of all infections. In addition, CRF08_BC (1.1%), B subtype (1.0%), CRF55_01B (3.4%), and URF/Other subtypes (1.3%) were less frequently observed. Among MSM in Chongqing, transmitted drug resistance (TDR) was reported to be present at a rate of 5.6%. 48 clusters with 600 (67.1%, 600/894) sequences were found by analysis of the molecular transmission network. The distributions of people by age, sexual orientation, syphilis, and genotype were significantly differentially related to being in clusters, according to the multivariable logistic regression model.

CONCLUSION

Despite the low overall prevalence of TDR, the significance of genotypic drug resistance monitoring needs to be emphasized. CRF07_BC and CRF01_AE were the two main genotypes that created intricate molecular transmission networks. In order to prevent the expansion of molecular networks and stop the virus's spread among MSM in Chongqing, more effective HIV intervention plans should be introduced.

Molecular Network Analysis Discloses the Limited Contribution to HIV Transmission for Patients with Late HIV Diagnosis in Northeast China

In the "treat all" era, the high rate of late HIV diagnosis (LHD) worldwide remains an impediment to ending the HIV epidemic. In this study, we analyzed LHD in newly diagnosed people living with HIV (PLWH) and its impact on HIV transmission in Northeast China. Sociodemographic information, baseline clinical data, and plasma samples obtained from all newly diagnosed PLWH in Shenyang, the largest city in Northeast China, between 2016 and 2019 were evaluated. Multivariate logistic regression analysis was performed to identify risk factors associated with LHD. A molecular network based on the HIV pol gene was constructed to assess the risk of HIV transmission with LHD. A total of 2882 PLWH, including 882 (30.6%) patients with LHD and 1390 (48.2%) patients with non-LHD, were enrolled. The risk factors for LHD were older age (≥ 30 years: p < .01) and diagnosis in the general population through physical examination (p < .0001). Moreover, the molecular network analysis revealed that the clustering rate (p < .0001), the fraction of individuals with ≥ 4 links (p = .0847), and the fraction of individuals linked to recent HIV infection (p < .0001) for LHD were significantly or marginally significantly lower than those recorded for non-LHD. Our study indicates the major risk factors associated with LHD in Shenyang and their limited contribution to HIV transmission, revealing that the peak of HIV transmission of LHD at diagnosis may have been missed. Early detection, diagnosis, and timely intervention for LHD may prevent HIV transmission.

A New HIV-1 K28E32-Reverse Transcriptase Variant Associated with the Rapid Expansion of CRF07_BC among Men Who Have Sex with Men

HIV-1 CRF07_BC originated among injection drug users (IDUs) in China. After diffusing into men who have sex with men (MSM), CRF07_BC has shown a rapid expansion in this group; however, the mechanism remains unclear. Here, we identified a new K₂₈E₃₂ variant of CRF07_BC that was characterized by five specific mutations (E28K, K32E, E248V, K249Q, and T338S) in reverse transcriptase. This variant was mainly prevalent among MSM, and was overrepresented in transmission clusters, suggesting that it could have driven the rapid expansion of CRF07_BC in MSM, though founder effects cannot be ruled out. It was descended from an evolutionary intermediate accumulating four specific mutations and formed an independent phylogenetic node with an estimated origin time in 2003. The K₂₈E₃₂ variant was demonstrated to have significantly higher in vitro HIV-1 replication ability than the wild type. Mutations E28K and K32E play a critical role in the improvement of in vitro HIV-1 replication ability, reflected by improved reverse transcription activity. The results could allow public health officials to use this marker (especially E28K and K32E mutations in the reverse transcriptase (RT) coding region) to target prevention measures prioritizing MSM population and persons infected with this variant for test and treat initiatives. IMPORTANCE HIV-1 has very high mutation rate that is correlated with the survival and adaption of the virus. The variants with higher transmissibility may be more selective advantage than the strains with higher virulence. Several HIV-1 variants were previously demonstrated to be correlated with higher viral load and lower CD4 T cell count. Here, we first identified a new variant (the K₂₈E₃₂ variant) of HIV-1 CRF07_BC, described its origin and evolutionary dynamics, and demonstrated its higher in vitro HIV-1 replication ability than the wild type. We demonstrated that five RT mutations (especially E28K and K32E) significantly improve in vitro HIV-1 replication ability. The appearance of the new K₂₈E₃₂ variant was associated with the rapidly increasing prevalence of CRF07_BC among MSM.

Multiple CRF01_AE/CRF07_BC Recombinants Enhanced the HIV-1 Epidemic Complexity Among MSM in Shenyang City, Northeast China

The transmission of Unique Recombinant Forms (URFs) has complicated the molecular epidemic of HIV-1. This increasing genetic diversity has implications for prevention surveillance, diagnosis, and vaccine design. In this study, we characterized the HIV-1 URFs from 135 newly diagnosed HIV-1 infected cases between 2016 and 2020 in Shenyang, northeast China and analyzed the evolutionary relationship of them by phylogenetic and recombination approaches. Among 135 URFs, we found that the CRF01_AE/CRF07_BC recombinants were the most common (81.5%, 110/135), followed by CRF01_AE/B (11.9%, 16/135), B/C (3.7%, 5/135), and others (3.0%, 4/135). 94.8% (128/135) of patients infected by URFs were through homosexual contact. Among 110 URFs_0107, 60 (54.5%) formed 11 subclusters (branch support value = 1) and shared the consistent recombination structure, respectively. Four subclusters have caused small-scale spread among different high-risk populations. Although the recombination structures of URFs_0107 are various, the hotspots of recombinants gathered between position 2,508 and 2,627 (relative to the HXB2 position). Moreover, the CRF07_BC and CRF01AE fragments of URFs_0107 were mainly derived from the MSM population. In brief, our results reveal the complex recombinant modes and the high transmission risk of URFs_0107, which calls for more attention on the new URFs_0107 monitoring and strict control in the areas led by homosexual transmission route.

A longitudinal analysis of immune escapes from HLA-B*13-restricted T-cell responses at early stage of CRF01_AE subtype HIV-1 infection and implications for vaccine design

BACKGROUND

Identifying immunogens which can elicit effective T cell responses against human immunodeficiency virus type 1 (HIV-1) is important for developing a T-cell based vaccine. It has been reported that human leukocyte antigen (HLA)-B*13-restricted T-cell responses contributed to HIV control in subtype B' and C infected individuals. However, the kinetics of B*13-restricted T-cell responses, viral evolution within epitopes, and the impact on disease progression in CRF01_AE subtype HIV-1-infected men who have sex with men (MSM) are not known.

RESULTS

Interferon-γ ELISPOT assays and deep sequencing of viral RNAs were done in 14 early HLA-B*13-positive CRF01_AE subtype HIV-1-infected MSM. We found that responses to RQEILDLWV (Nef_106-114, RV9), GQMREPRGSDI (Gag_226-236, GI11), GQDQWTYQI (Pol_487-498, GI9), and VQNAQGQMV (Gag_135-143, VV9) were dominant. A higher relative magnitude of Gag-specific T-cell responses, contributed to viral control, whereas Nef-specific T-cell responses were associated with rapid disease progression. GI11 (Gag) was conserved and strong GI11 (Gag)-specific T-cell responses showed cross-reactivity with a dominant variant, M228I, found in 3/12 patients; GI11 (Gag)-specific T-cell responses were positively associated with CD4 T-cell counts (R = 0.716, P = 0.046). Interestingly, the GI9 (Pol) epitope was also conserved, but GI9 (Pol)-specific T-cell responses did not influence disease progression (P > 0.05), while a D490G variant identified in one patient did not affect CD4 T-cell counts. All the other epitopes studied [VV9 (Gag), RQYDQILIEI (Pol_113-122, RI10), HQSLSPRTL (Gag_144-152, HL9), and RQANFLGRL (Gag_429-437, RL9)] developed escape mutations within 1 year of infection, which may have contributed to overall disease progression. Intriguingly, we found early RV9 (Nef)-specific T-cell responses were associated with rapid disease progression, likely due to escape mutations.

CONCLUSIONS

Our study strongly suggested the inclusion of GI11 (Gag) and exclusion of RV9 (Nef) for T-cell-based vaccine design for B*13-positive CRF01_AE subtype HIV-1-infected MSM and high-risk individuals.

Molecular Network Analysis Reveals Transmission of HIV-1 Drug-Resistant Strains Among Newly Diagnosed HIV-1 Infections in a Moderately HIV Endemic City in China

Since the implementation of the "treat all" policy in China in 2016, there have been few data on the prevalence of transmitted drug resistance (TDR) in China. In this study, we describe TDR in patients newly diagnosed with human immunodeficiency virus (HIV) infection between 2016 and 2019 in Shenyang city, China. Demographic information and plasma samples from all newly reported HIV-infected individuals in Shenyang from 2016 to 2019 were collected. The HIV pol gene was amplified and sequenced for subtyping and TDR. The spread of TDR was analyzed by inferring an HIV molecular network based on pairwise genetic distance. In total, 2,882 sequences including CRF01_AE (2019/2,882, 70.0%), CRF07_BC (526/2,882, 18.3%), subtype B (132/2,882, 4.6%), and other subtypes (205/2,882, 7.1%) were obtained. The overall prevalence of TDR was 9.1% [95% confidence interval (CI): 8.1-10.2%]; the prevalence of TDR in each subtype in descending order was CRF07_BC [14.6% (95% CI: 11.7-18.0%)], subtype B [9.1% (95% CI: 4.8-15.3%)], CRF01_AE [7.9% (95% CI: 6.7-9.1%)], and other sequences [7.3% (95% CI: 4.2-11.8%)]. TDR mutations detected in more than 10 cases were Q58E (n = 51), M46ILV (n = 46), K103N (n = 26), E138AGKQ (n = 25), K103R/V179D (n = 20), and A98G (n = 12). Molecular network analysis revealed three CRF07_BC clusters with TDR [two with Q58E (29/29) and one with K103N (10/19)]; and five CRF01_AE clusters with TDR [two with M46L (6/6), one with A98G (4/4), one with E138A (3/3), and one with K103R/V179D (3/3)]. In the TDR clusters, 96.4% (53/55) of individuals were men who have sex with men (MSM). These results indicate that TDR is moderately prevalent in Shenyang (5-15%) and that TDR strains are mainly transmitted among MSM, providing precise targets for interventions in China.

The Viral Founder Effect and Economic-Driven Human Mobility Shaped the Distinct Epidemic Pattern of HIV-1 CRF01_AE in Northeast China

Background: In China, two distinct lineages shaped the epidemic of HIV-1 CRF01_AE among men who have sex with men (MSM), of which the uneven distributions were observed geographically. One lineage spread across China, while another dominated in Northeast China. Understanding the drivers of viral diffusion would provide guidelines for identifying the source and hotspots of HIV transmission among MSM to target interventions in China.

Methods: We collected the pol sequences between 2002–2017 to reconstruct the spatiotemporal history of CRF01_AE lineages in Shenyang, one economic center of Northeast China, using the Bayesian phylogeographic and phylodynamic approaches. Importantly, for the datasets with the high sample density, we did the down-sampling to avoid the sampling bias.

Results: Two lineages accounted for 97%, including 426 and 1516 sequences, and homosexuals and bisexuals were above 80%. One lineage appeared earlier 7 years than another (1993 vs. 2002) among homosexuals and bisexuals, whereas among heterosexuals, both lineages were observed firstly in 2002. 96% viral migrations within one lineage were from homosexuals toward bisexuals (49%) and male-heterosexuals (46%). Within another, except for homosexuals (72%), bisexuals (23%) served as the top second source, and female-heterosexuals (11%) were the third recipients following bisexuals (44%) and male-heterosexuals (39%). Although the basic reproduction number (R₀) of two lineages were similar and both of the effective production number (R_e) fell below 1 at the most recent sampling time, the starts of the R_e declining varied.

Conclusions: Our findings revealed that throughout the viral national spread chain, Shenyang is the source for the initial expanding of one lineage, where is only a sink of another, proving that the viral founder effect and regional human mobility contributed to the uneven distribution of two lineages, and emphasizing the important roles of the area where the virus originated and economy-driven migrants in HIV transmission.

HIV-1 CRF07_BC transmission dynamics in China: two decades of national molecular surveillance

By analyzing an unprecedentedly large, longitudinal HIV-1 CRF07_BC sequence dataset collected from China in the past two decades, we sought to build CRF07_BC lengthwise transmission networks, and understand its transmission dynamics. We divided CRF07_BC into two clusters based on phylogenetic analysis and an estimation of the pairwise genetic distance at 0.7%. Of 6213 sequences, 3607 (58.1%) linked to ≥1 other sequence. CRF07_BC was divided into two clusters: 07BC_O and 07BC_N. The 07BC_O is the original CRF07_BC, circulating in people who inject drugs (PWID) and heterosexuals, predominantly in southwestern and northwestern provinces of China. The 07BC_N is a new cluster, identified mostly in men having sex with men (MSM) in the northern provinces of China. Bayesian analysis indicates that CRF07_BC has experienced two phases of exponential growth, which was first driven by 07BC_O then 07BC_N. Compared to 07BC_O, the proportion of the parameter of population transmission risk (TR) of 07BC_N has risen constantly. The power-law function analyses reveal that 07BC_N has increased over years with higher degree. In 07BC_N, only 13.16% of MSM were linked to other risk groups, but these links represent 41.45%, 54.25%, and 55.07% of links among heterosexual females, heterosexual males, and male PWID respectively. This study indicates that CRF07_BC has evolved into two clusters in China, and their distributions are distinct across risk groups and geographical regions. 07BC_N shows a greater risk of transmission, and has gradually replaced 07BC_O. Furthermore, the results show that strengthening the MSM interventions could lower the rapidity of 07BC_N transmission in all risk groups.

HIV-1 Drug Resistance and Genetic Transmission Networks Among MSM Failing Antiretroviral Therapy in South China 2014-2019

Background

Guangdong, located in South China, is one of the areas heavily affected by HIV-1 in China. The transmission of HIV-1 among men who have sex with men (MSM) has gradually been increasing in Guangdong.

Objective

To investigate the characteristics of the HIV-1 drug resistance, and genetic transmission networks in MSM with antiretroviral therapy (ART) failure from 2014 to 2019 in Guangdong.

Methods

HIV-1 pol gene sequences were amplified. An online subtyping tool was used to determine the genotype, and a maximum likelihood phylogenetic tree was reconstructed to confirm the genotype results. The Stanford University HIV Drug Resistance Database was used to analyse the sequences of drug resistance mutations (DRMs) and drug resistance profiles. A pairwise Tamura-Nei 93 genetic distance-based method was used to analyse the genetic transmission networks.

Results

Of 393 sequences isolated from HIV-infected MSM with ART failure, CRF01_AE (47.3%), CRF07_BC (21.4%) and CRF55_01B (21.4%) were the top three strains. 55.2% individuals harboured NRTI DRMs, whereas 67.4% carried NNRTI DRMs. 96.8% cases harboured mutations resistance to NRTIs or NNRTIs at high-level. The most common DRMs were M184I/V (42.2%), followed by V179D/E (37.9%) and K65R (27.2%). Of the subtype B sequences, no sequence fell into a cluster. Of the CRF01_AE, CRF55_01B, and CRF59_01B sequences, 14.5%, 61.9%, and 33.3% fell into clusters, respectively. Of the CRF07_BC sequences, 39.3% fell into clusters. The majority of MSM in transmission networks were concentrated at age below 35 years old, with multiple links. Moreover, approximately 54.8% of MSM had more than 2 potential transmission partners.

Conclusion

Drug resistance mutations more frequently occurred in NNRTIs among MSM with ART failure in Guangdong Province. Transmission network analysis revealed a complex transmission pattern, and more attention should be given to younger HIV-1-infected MSM with multiple links.

HIV-1 molecular transmission network among sexually transmitted populations in Liaoning Province, China

INTRODUCTION

In recent years, with the development of molecular epidemiology, molecular transmission networks based on evolutionary theory and sequence analysis have been widely used in research on human immunodeficiency virus (HIV)-1 transmission dynamics and precise intervention for high-risk populations. The HIV-1 molecular transmission network is a new method to study the population's access to the network, the characteristics of clustering, and the characteristics of interconnection in the network. Here, we analyzed the characteristics of the HIV-1 molecular transmission network of sexually transmitted people in Liaoning Province.

METHODS

A study of HIV-infected persons who were sexually transmitted in Liaoning Province from 2003 to 2019. HIV-1 RNA was extracted, amplified and sequenced, and a phylogenetic tree was constructed to determine the subtype using the well matched pol gene region sequence. The gene distance between sequences was calculated, the threshold was determined, and the molecular transmission network was constructed.

RESULTS

109 samples of pol gene region were obtained. The main subtype of HIV-1 was CRF01_AE, followed by B, CRF07_BC, etc. 12.8% of them were resistant to HIV. At the threshold of 0.55 gene distance, 60.6% of them entered the HIV-1 molecular transmission network. Workers, sample source voluntary counseling and testing, other testing, subtype B and drug resistance are the factors influencing the access to HIV-1 molecular transmission network. The subtype of CRF01_AE formed 6 clusters in the molecular transmission network. In the network, the difference of connection degree between different subtypes was statistically significant.

DISCUSSION

The three subtypes CRF01_AE, CRF07_BC and B that enter the molecular transmission network do not have interconnections, and they form clusters with each other. It shows that the risk of transmission among the three subtypes is less than the risk of transmission within each subtype. The factors affecting HIV-1 entry into the molecular transmission network were occupation, sample source, genotype and drug resistance. The L33F mutation at the HIV-1 resistance mutation site constitutes the interconnection in the largest transmission cluster in the network. The epidemiological characteristics of HIV-infected persons in each molecular transmission cluster show that 97% of the study subjects come from the same area and have a certain spatial aggregation.

CONCLUSION

Constructing a molecular transmission network and conducting long-term monitoring, while taking targeted measures to block the spread of HIV can achieve precise prevention and control.

Transmitted drug resistance to Tenofovir/Emtricitabine among persons with newly diagnosed HIV infection in Shenyang city, Northeast China from 2016 to 2018

BACKGROUND

To assess transmitted drug resistance (TDR) to tenofovir (TDF)/emtricitabine (FTC), using as pre-exposure prophylaxis, among newly diagnosed human immunodeficiency virus-1 (HIV-1)-infected residents in Shenyang city, northeast China.

METHODS

Demographic and epidemiological information of all newly diagnosed HIV-1 infected residents in Shenyang city from 2016 to 2018 were anonymously collected from the local HIV epidemic database. HIV-1 pol sequences were amplified from RNA in cryopreserved plasma samples and sequenced directly. Viral subtypes were inferred with phylogenetic analysis and drug resistance mutations (DRMs) were determined according to the Stanford HIVdb algorithm. Recent HIV infection was determined with HIV Limiting Antigen avidity electro immunoassay.

RESULTS

A total of 2176 sequences (92.4%, 2176/2354) were obtained; 70.9% (1536/2167) were CRF01_AE, followed by CRF07_BC (18.0%, 391/2167), subtype B (4.7%, 102/2167), other subtypes (2.6%, 56/2167), and unique recombinant forms (3.8%, 82/2167). The prevalence of TDR was 4.9% (107/2167), among which, only 0.6% (13/2167) was resistance to TDF/FTC. Most of these subjects had CRF01_AE strains (76.9%, 10/13), were unmarried (76.9%, 10/13), infected through homosexual contact (92.3%, 12/13), and over 30 years old (median age: 33). The TDF/FTC DRMs included K65R (8/13), M184I/V (5/13), and Y115F (2/13). Recent HIV infection accounted for only 23.1% (3/13). Most cases were sporadic in the phylogenetic tree, except two CRF01_AE sequences with K65R (Bootstrap value: 99%).

CONCLUSIONS

The prevalence of TDR to TDF/FTC is low among newly diagnosed HIV-infected cases in Shenyang, suggesting that TDR may have little impact on the protective effect of the ongoing CROPrEP project in Shenyang city.

Priority Intervention Targets Identified Using an In-Depth Sampling HIV Molecular Network in a Non-Subtype B Epidemics Area

Molecular network analysis based on the genetic similarity of HIV-1 is increasingly used to guide targeted interventions. Nevertheless, there is a lack of experience regarding molecular network inferences and targeted interventions in combination with epidemiological information in areas with diverse epidemic strains of HIV-1.We collected 2,173 pol sequences covering 84% of the total newly diagnosed HIV-1 infections in Shenyang city, Northeast China, between 2016 and 2018. Molecular networks were constructed using the optimized genetic distance threshold for main subtypes obtained using sensitivity analysis of plausible threshold ranges. The transmission rates (TR) of each large cluster were assessed using Bayesian analyses. Molecular clusters with the characteristics of ≥5 newly diagnosed cases in 2018, high TR, injection drug users (IDUs), and transmitted drug resistance (TDR) were defined as priority clusters. Several HIV-1 subtypes were identified, with a predominance of CRF01_AE (71.0%, 1,542/2,173), followed by CRF07_BC (18.1%, 393/2,173), subtype B (4.5%, 97/2,173), other subtypes (2.6%, 56/2,173), and unique recombinant forms (3.9%, 85/2,173). The overall optimal genetic distance thresholds for CRF01_AE and CRF07_BC were both 0.007 subs/site. For subtype B, it was 0.013 subs/site. 861 (42.4%) sequences of the top three subtypes formed 239 clusters (size: 2-77 sequences), including eight large clusters (size ≥10 sequences). All the eight large clusters had higher TR (median TR = 52.4/100 person-years) than that of the general HIV infections in Shenyang (10.9/100 person-years). A total of ten clusters including 231 individuals were determined as priority clusters for targeted intervention, including eight large clusters (five clusters with≥5 newly diagnosed cases in 2018, one cluster with IDUs, and two clusters with TDR (K103N, Q58E/V179D), one cluster with≥5 newly diagnosed cases in 2018, and one IDUs cluster. In conclusion, a comprehensive analysis combining in-depth sampling HIV-1 molecular networks construction using subtype-specific optimal genetic distance thresholds, and baseline epidemiological information can help to identify the targets of priority intervention in an area epidemic for non-subtype B.

First complete-genome documentation of HIV-1 intersubtype superinfection with transmissions of diverse recombinants over time to five recipients

Human immunodeficiency virus type 1 (HIV-1) recombinants in the world are believed to be generated through recombination between distinct HIV-1 strains among coinfection or superinfection cases. However, direct evidence to support transmission of HIV-1 recombinants from a coinfected/superinfected donor to putative recipient is lacking. Here, we report on the origin and evolutionary relationship between a set of recombinants from a CRF01_AE/CRF07_BC superinfected putative donor and diverse CRF01_AE/CRF07_BC recombinants from five putative recipients. Interviews on sociodemographic characteristics and sexual behaviors for these six HIV-1-infected men who have sex with men showed that they had similar ways of partner seeking: online dating sites and social circles. Phylogenetic and recombination analyses demonstrated that the near-full-length genome sequences from six patients formed a monophyletic cluster different from known HIV-1 genotypes in maximum likelihood phylogenetic trees, were all composed of CRF01_AE and CRF07_BC fragments with two common breakpoints on env, and shared 4-7 breakpoints with each other. Moreover, 3' half-genomes of recombinant strains from five recipients had identical/similar recombinant structures with strains at longitudinal samples from the superinfected donor. Recombinants from the donor were paraphyletic, whereas five recipients were monophyletic or polyphyletic in the maximum clade credibility tree. Bayesian analyses confirmed that the estimated time to the most recent common ancestor (tMRCA) of CRF01_AE and CRF07_BC strains of the donor was 2009.2 and 2010.7, respectively, and all were earlier than the emergence of recombinants from five recipients. Our results demonstrated that the closely related unique recombinant forms of HIV-1 might be the descendent of a series of recombinants generated gradually in a superinfected patient. This finding highlights the importance of early initiation of antiretroviral therapy as well as tracing and testing of partners in patients with multiple HIV-1 infection.

Patterns and risk of HIV-1 transmission network among men who have sex with men in Guangxi, China

The prevalence of HIV-1 in Guangxi is very high, and the rate of HIV-1 infection among men who have sex with men (MSM) has been increasing. Therefore, it is necessary to explore the patterns and risk factors of HIV transmission in Guangxi. For this purpose, individuals diagnosed with HIV-1 during 2013-2018 in Guangxi were recruited. Phylogenetic relationship, transmission clusters, and genotypic drug resistance analyses were performed based on HIV-1 pol sequences. Related factors were analysed to assess for their association with HIV-1 transmission. CRF07_BC (50.4%) and CRF01_AE (33.4%) were found to be the predominant subtypes. The analysed 1633 sequences (50.15%, Guangxi; 49.85%, other provinces) were segregated into 80 clusters (size per cluster, 2-704). We found that 75.3% of the individuals were in three clusters (size ˃ 100), and 73.8% were high-risk spreaders (links ≥ 4). Infection time, marital status, and subtype were significantly associated with HIV-1 transmission. Additionally, 80.2% of recent infections were linked to long-term infections, and 46.2% were linked to other provinces. A low level of transmitted drug resistance was detected (4.8%). Our findings indicated superclusters and high-risk HIV-1 spreaders among the MSM in Guangxi. Effective strategies blocking the route of transmission should be developed.

Characterization of a Novel HIV-1 CRF01_AE/CRF07_BC Recombinant Strain Among Men Who Have Sex with Men in Liaoning, China

CRF01_AE and CRF07_BC are two widespread human immunodeficiency virus type 1 (HIV-1) strains among different high-risk populations, including men who have sex with men (MSM), in China. This co-epidemic of various HIV strains enables the production of second-generation recombinants. In this study, we detected a novel HIV-1 CRF01_AE/CRF07_BC recombinant from LN321945, an MSM lived in Liaoning province, northeast China. The phylogenetic and recombination analyses indicated the near full-length genome (NFLG) sequence of LN321945 had six recombination breakpoints, with three CRF07_BC fragments inserted into a CRF01_AE backbone. Further subregion trees analysis revealed that both CRF01_AE and CRF07_BC fragments were derived from two predominant HIV-1 strains among MSM. In addition, the NFLG of LN321945 was revealed to be clustered closely to another CRF01_AE/CRF07_BC recombinant previously identified in Shaanxi province, northwest China, but these two recombinants had distinct recombination structure and origin of CRF01_AE fragments. Hence, this study identified a second-generation recombinant between the main strains circulating among MSM, indicating more complicated trend of HIV-1 epidemic in China.

Beijing as the hub of CRF07_BC transmission from the intravenous drug users to men who have sex with men in China

AIDS Research and Human Retroviruses officially retracts the Instant Online/Just Accepted version of the article entitled, "Beijing as the hub of CRF07_BC transmission from the intravenous drug users to men who have sex with men in China" (epub 7 Dec 2020; doi.org/10.1089/aid.2020.0147). A technical issue caused the unedited, accepted version to post online before all plagiarism checks were finalized. Those checks determined that there was too much duplication from previously published sources which prevented the continuance to final publication. The technical issue that caused the premature posting has since been corrected. AIDS Research and Human Retroviruses and its Publisher are committed to upholding the standards of scientific publishing and the community it serves.

BACKGROUND

The HIV-1 CRF07_BC strain has been increasing in frequency in China, is now the major recombination subtype in the men who have sex with men (MSM) population. However, to date, the evolutionary history of CRF07_BC in MSM in China has not been explored in greater detail.

METHODS

All available partial gag, pol and env segments of CRF07_BC were obtained from the Los Alamos HIV database. We performed phylogenetic analysis for these fragments by using the Bayesian Markov Chain Monte Carlo method, as implemented in BEAST. We estimated the history of viral migration between different areas over time using the discrete Bayesian phylogeographical method.

RESULTS

Spatial reconstruction showed that Yunnan had the highest root state posterior probability (0.89 in pol, 0.60 in gag, 0.87 in env). The virus migrated from Yunnan to Beijing in 1990s through intravenous drug users (IDU). The highest root state posterior probability of MSM cluster is Beijing (0.93 in pol, 0.90 in gag and 0.37 in env). In the beginning of 2000s, Beijing became the primary epicenter as CRF07_BC had expanded their geographical distribution to many provinces in China in MSM population. Guangdong and Shanghai were secondary epicenters, with a large extent of viruses.

CONCLUSIONS

This study highlighted the spatial and temporal spread of CRF07_BC in MSM population in China. It revealed that Beijing was the hub of CRF07_BC transmission from IDU to MSM in China.

Performance evaluation of Elecsys HIV Duo on cobas e 801 using clinical samples in China

The prevalence and incidence of human immunodeficiency viruses (HIV) infection are rapidly increasing, and novel HIV genotypes are emerging. This study evaluated the sensitivity and specificity of Elecsys HIV Duo assay in population with the epidemic of multiple genotypes of HIV-1 infection. Specificity of the Elecsys HIV Duo assay was determined using 3039 serum samples from patients receiving routine HIV-1 screening tests in China. Sensitivity was assessed with seroconversion panels. Additional 67 positive from newly diagnosed HIV-1 infected samples were also included to test assay performance on various HIV-1 genotypes. The assay performance was compared with that of the Elecsys HIV Combi PT assay. The genotypes of all HIV-1 positive samples were determined with phylogenetic analyses on the 1.1 kb Pro-RT region of pol gene for drug resistance tests. The Elecsys HIV Duo assay had a slightly higher specificity (99.93% vs 99.84%) and equivalent sensitivity to Elecsys HIV Combi PT assay. Seventy-two HIV-1 positive samples, including 12 antigens positive samples, were distinguished by Elecsys HIV Duo. Among them, 43 samples were circulating recombinant form (CRF)01_AE, followed by 13 of CRF07_BC, 10 of subtype B, 4 of URF_0107, 1 of URF_01B and 1 of CRF02_AG. The Elecsys HIV Duo assay showed good performance for the Chinese population with an epidemic of multiple HIV genotypes.

Dynamics of HIV-1 Molecular Networks Reveal Effective Control of Large Transmission Clusters in an Area Affected by an Epidemic of Multiple HIV Subtypes

This study reconstructed molecular networks of human immunodeficiency virus (HIV) transmission history in an area affected by an epidemic of multiple HIV-1 subtypes and assessed the efficacy of strengthened early antiretroviral therapy (ART) and regular interventions in preventing HIV spread. We collected demographic and clinical data of 2221 treatment-naïve HIV-1–infected patients in a long-term cohort in Shenyang, Northeast China, between 2008 and 2016. HIV pol gene sequencing was performed and molecular networks of CRF01_AE, CRF07_BC, and subtype B were inferred using HIV-TRACE with separate optimized genetic distance threshold. We identified 168 clusters containing ≥ 2 cases among CRF01_AE-, CRF07_BC-, and subtype B-infected cases, including 13 large clusters (≥ 10 cases). Individuals in large clusters were characterized by younger age, homosexual behavior, more recent infection, higher CD4 counts, and delayed/no ART (P < 0.001). The dynamics of large clusters were estimated by proportional detection rate (PDR), cluster growth predictor, and effective reproductive number (R_e). Most large clusters showed decreased or stable during the study period, indicating that expansion was slowing. The proportion of newly diagnosed cases in large clusters declined from 30 to 8% between 2008 and 2016, coinciding with an increase in early ART within 6 months after diagnosis from 24 to 79%, supporting the effectiveness of strengthened early ART and continuous regular interventions. In conclusion, molecular network analyses can thus be useful for evaluating the efficacy of interventions in epidemics with a complex HIV profile.

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.

Natural presence of the V179D and K103R/V179D mutations associated with resistance to nonnucleoside reverse transcriptase inhibitors in HIV-1 CRF65_cpx strains

BACKGROUND

There is increasing evidence that HIV-1 genetic diversity can have an impact on drug resistance. The aim of this study is to investigate the epidemiological situation of CRF65_cpx and the impact of natural polymorphisms of this variant on genotypic resistance.

METHODS

We used the BLAST search program followed by phylogenetic analysis to identify additional CRF65_cpx pol sequences from the Los Alamos HIV Sequence Database. Maximum likelihood phylogeny was estimated to clarify the epidemiological relationship of CRF65_cpx strains. Genotypic resistance was determined by submitting sequences to the Stanford HIV Drug Resistance Database.

RESULTS

A total of 32 CRF65_cpx pol sequences were obtained. The CRF65_cpx strains were detected in seven provinces with large geographic distance. Yunnan CRF65_cpx sequences were mainly derived from a heterosexual risk group, whereas the CRF65_cpx sequences in other provinces were almost exclusively derived from an MSM population. With one exception of V179E, the other 31 strains harbored V179D mutation. The combination of V179D and K103R, conferring intermediate resistance to EFV and NVP, was detected in seven treatment-naive MSM patients.

CONCLUSIONS

This study confirmed the expansion CRF65_cpx in China. Furthermore, we found the natural presence of the V179D and K103R/V179D mutations associated with resistance to NNRTIs in HIV-1 CRF65_cpx. Our findings highlight the contribution of polymorphic mutations to drug resistance and underscore the challenges in treating patients harboring CRF65_cpx strains.

Molecular network-based intervention brings us closer to ending the HIV pandemic

Precise identification of HIV transmission among populations is a key step in public health responses. However, the HIV transmission network is usually difficult to determine. HIV molecular networks can be determined by phylogenetic approach, genetic distance-based approach, and a combination of both approaches. These approaches are increasingly used to identify transmission networks among populations, reconstruct the history of HIV spread, monitor the dynamics of HIV transmission, guide targeted intervention on key subpopulations, and assess the effects of interventions. Simulation and retrospective studies have demonstrated that these molecular network-based interventions are more cost-effective than random or traditional interventions. However, we still need to address several challenges to improve the practice of molecular network-guided targeting interventions to finally end the HIV epidemic. The data remain limited or difficult to obtain, and more automatic real-time tools are required. In addition, molecular and social networks must be combined, and technical parameters and ethnic issues warrant further studies.

Molecular Characterization of HIV-1 Minority Subtypes in Hong Kong: A Recent Epidemic of CRF07_BC among the Men who have Sex with Men Population

BACKGROUND

Over the past years, an increasing trend was noticed for non-B and non- CRF01_AE HIV-1 strains prevalence in Hong Kong.

OBJECTIVE

In this study, we aimed at using the available HIV-1 pol sequences collected from 1994 to 2013 through our local antiretroviral resistance surveillance program to investigate the molecular epidemiology and evolution of HIV-1 minority subtypes in Hong Kong. We also aimed at investigating their potential association and impact of those transmission risk groups.

METHODS

A total of 2,315 HIV-1 partial pol sequences were included. HIV-1 genotypes were determined by REGA Genotyping Tool and phylogenetic analysis with reference sequences. The viral evolutionary rates and time of the most common ancestor (tMRCA) were estimated by Bayesian Markov Chain Monte Carlo (MCMC) interference.

RESULTS

Apart from the two prevalent HIV-1 genotypes in Hong Kong (subtype B,41.6%, CRF01_AE,40.5%), phylogenetic analysis revealed a broad viral diversity including CRF07_BC(5.1%), subtype C(4.5%), CRF02_AG(1.1%), CRF08_BC(0.8%), subtype A1(0.8%), subtype G(0.4%), subtype D(0.4%), CRF06_cpx(0.4%), subtype F(0.1%), CRF12_BF(0·04%) and other recombinants(4.5%). The top five minority subtypes were further analyzed which demonstrated distinct epidemiological and phylogenetic patterns. Over 70% of subtypes A1, C and CRF02_AG infections were circulated among non-Chinese Asians or African community in Hong Kong and were mainly transmitted between heterosexual regular partners. Instead, over 90% of CRF07_BC and CRF08_BC patients were Chinese. An epidemic cluster was identified in CRF07_BC and estimated to expand from 2002 onwards based on skyline plot and molecular clock analysis.

CONCLUSION

Our results highlighted the emergence of CRF07_BC epidemic in local MSM community, public health interventions targeting the community should be further enhanced to tackle the epidemic.

Natural polymorphisms in HIV-1 CRF01_AE strain and profile of acquired drug resistance mutations in a long-term combination treatment cohort in northeastern China

BACKGROUND

The impacts of genetic polymorphisms on drug resistance mutations (DRMs) among various HIV-1 subtypes have long been debated. In this study, we aimed to analyze the natural polymorphisms and acquired DRM profile in HIV-1 CRF01_AE-infected patients in a large first-line antiretroviral therapy (ART) cohort in northeastern China.

METHODS

The natural polymorphisms of CRF01_AE were analyzed in 2034 patients from a long-term ART cohort in northeastern China. The polymorphisms in 105 treatment failure (TF) patients were compared with those in 1148 treatment success (TS) patients. The acquired DRM profile of 42 patients who experienced TF with tenofovir/lamivudine/efavirenz (TDF/3TC/EFV) treatment was analyzed by comparing the mutations at TF time point to those at baseline. The Stanford HIVdb algorithm was used to interpret the DRMs. Binomial distribution, McNemar test, Wilcoxon test and CorMut package were used to analyze the mutation rates and co-variation. Deep sequencing was used to analyze the evolutionary dynamics of co-variation.

RESULTS

Before ART, there were significantly more natural polymorphisms of 31 sites on reverse transcriptase (RT) in CRF01_AE than subtype B HIV-1 (|Z value| ≥ 3), including five known drug resistance-associated sites (238, 118, 179, 103, and 40). However, only the polymorphism at site 75 was associated with TF (|Z value| ≥ 3). The mutation rate at 14 sites increased significantly at TF time point compared to baseline, with the most common DRMs comprising G190S/C, K65R, K101E/N/Q, M184 V/I, and V179D/I/A/T/E, ranging from 66.7 to 45.2%. Moreover, two unknown mutations (V75 L and L228R) increased by 19.0 and 11.9% respectively, and they were under positive selection (Ka/Ks > 1, log odds ratio [LOD] > 2) and were associated with several other DRMs (cKa/Ks > 1, LOD > 2). Deep sequencing of longitudinal plasma samples showed that L228R occurred simultaneously or followed the appearance of Y181C.

CONCLUSION

The high levels of natural polymorphisms in CRF01_AE had little impact on treatment outcomes. The findings regarding potential new CRF01_AE-specific minor DRMs indicate the need for more studies on the drug resistance phenotype of CRF01_AE.

HIV-1 genetic diversity and recombinant forms among men who have sex with men at a sentinel surveillance site in Xi'an City, China

HIV-1 genetic distribution and recombinant patterns are important in understanding the HIV epidemic among men who have sex with men (MSM). In this study, 83 HIV-positive MSM infections were confirmed at a sentinel surveillance site in Xi'an city, China in 2018. HIV-1 genotypes were determined by phylogenetic analyses of HIV-1 gag, pol and env gene fragments, including CRF07_BC (51.8%), CRF01_AE (30.1%), subtype B (3.6%), CRF55_01B (3.6%), CRF104_0107 (1.2%) and unique recombinant forms (URFs) (9.6%). Transmitted drug resistance mutations were detected in 2.4% (2/82) of HIV-infected MSM individuals. The phylogenetic analyses of near full-length genome (NFLG) of HIV-1 URFs were performed. A new circulating recombinant form (CRF), designated as CRF104_0107, was found in three epidemiologically unlinked individuals in Shaanxi province, China. The CRF104_0107 is composed of genomes CRF01_AE and CRF07_BC, with six recombinant breakpoints in the gag, pol, vif and vpr genes. This second-generation CRF has a breakpoint (HXB2 nt 3011) in common with CRF07_BC. The emergence of novel CRF and multiple URFs reflected HIV-1 genetic complexity among the local key populations in Xi'an city, China.

Genetic Characterization of a Novel HIV-1 CRF07_BC/CRF55_01B Recombinant Form Identified in Jiangmen, China

New recombinant variants are a predominant challenge for preventing the spread of the HIV-1 epidemic. In this study, we confirmed a novel HIV-1 CRF07_BC/CRF55_01B recombinant form for the first time, which was isolated from a male patient in Jiangmen, China. The genomic sequence of the variant with four CRF55_01B segments inserted into the CRF07_BC backbone is 8,510 bp in length, extending from nucleotides 669 to 9,293 according to the HXB2 genome. Specifically, the recombinant strain contains site mutations associated with drug resistance.

Brief Report: Onward Transmission of Multiple HIV-1 Unique Recombinant Forms Among Men Who Have Sex With Men in Beijing, China

BACKGROUND

Unique recombinant forms (URFs) were generated in dually infected or multiply infected individuals, and some of URFs can be transmitted to many people resulting in the emergence of circulating recombinant forms (CRFs). We examined whether there was evidence for onward transmission of multiple URFs among men who have sex with men (MSM) in Beijing.

METHODS

A total of 146 MSM subjects with acute/early HIV-1 infection were recruited from the Beijing PRIMO clinical cohort between September 2010 and July 2012. HIV-1 full-length gag and partial pol, env genes were amplified and sequenced separately. Phylogenetic analysis and recombination analysis were performed to determine the viral genotypes. Single genome amplification and direct sequencing were used to confirm onward transmission of URFs.

RESULTS

CRF01_AE was the most common genotype (51.9%), followed by CRF07_BC (23.0%), subtype B (14.8%), URFs (7.4%), CRF65_cpx (2.2%), and CRF55_01B (0.7%). Multiple forms of URFs were identified, including CRF01_AE/BC, CRF01_AE/B, and CRF01_AE/C. Nine of the 10 individuals harboring URFs were infected by onward transmission of URFs. The remaining one individual was coinfected with CRF01_AE and CRF07_BC variants.

CONCLUSIONS

We introduced a new method to provide evidence for onward transmission of URF strains by examining the absence of intersubtype coinfection among early infected individuals. Onward transmission of multiple URFs was found among MSM in Beijing, China. Our findings call for a program of continuous molecular surveillance and have implications to prevention programs among MSM in China.

Characterization of a Novel HIV-1 Circulating Recombinant Form (CRF80_0107) Among Men Who Have Sex with Men in China

Since the emergence of CRF55_01B among men who have sex with men (MSM) group in China, more and more circulating recombinant forms (CRFs) and unique recombinant forms have been identified in the population in China. Here we characterize a novel CRF (CRF80_0107) consisted of CRF01_AE and CRF07_BC segments from three epidemiologically unlinked MSM. Two near full-length genome (NFLG) sequences were amplified and sequenced in two halves with RNA extracted from the plasma of two MSM in Beijing. Another gag-pol sequence was obtained from Los Alamos HIV Sequence Database with accession number KX198573, which was isolated from a man who has sex with men in Hebei province. Phylogenetic analysis based on NFLG sequences revealed that CRF80_0107 formed a monophyletic cluster with high bootstrap value of 100%. Recombination analysis demonstrated that the genome of CRF80_0107 was separated into eight segments by seven breakpoints. The subregion trees constructed by neighbor-joining method confirmed that those segments were originated from CRF01_AE and CRF07_BC strains circulating among MSM group in China. The emergence of CRF80_0107 indicates the frequent generation of novel recombinant forms and the increasing complication of HIV-1 epidemic among MSM group in China. This highlighted the importance of monitoring HIV-1 molecular epidemiological characteristics and the urgency for reducing HIV-1 epidemic among MSM in China.

High polymorphism rates in well-known T cell epitopes restricted by protective HLA alleles during HIV infection are associated with rapid disease progression in early-infected MSM in China

T cell epitopes restricted by several protective HLA alleles, such as B*57, B*5801, B*27, B*51 and B*13, have been very well defined over the past two decades. We investigated 32 well-known T cell epitopes restricted by protective HLA molecules among 54 Chinese men who have sex with men (MSM) at the early stage of HIV-1 infection. Subjects in our cohort carrying protective HLA types did not exhibit slow CD4 T cell count decline (P = 0.489) or low viral load set points (P = 0.500). Variations occurred in 96.88% (31/32) of the known wild-type epitopes (rate 1.85-100%), and the variation rates of the strains of two CRF01_AE lineages were significantly higher than those of non-CRF01_AE strains (76.82% vs. 48.96%, P = 0.004; 71.27% vs. 8.96%, P = 0.025). Subjects infected with CRF01_AE exhibited relatively rapid disease progression (P = 0.035). Therefore, the lack of wild-type protective T cell epitopes restricted by classic protective HLA alleles in CRF01_AE HIV-1 strains may be one of the reasons why rapid disease progression is observed in Chinese MSM with HIV-1 infection.

Surging HIV-1 CRF07_BC epidemic among recently infected men who have sex with men in Fujian, China

A rapidly increasing number of HIV-1 infections have been identified among men who have sex with men (MSM) in Fujian province of China since 2010. We aimed to investigate the causative factors underlying this surging epidemic. Using immunoassays for HIV-1 diagnosis and phylogenetic analysis for viral genotyping, we found that the number of MSM infections doubled from 171 in 2011 to 340 in 2013 with a significantly increased prevalent rate from 4.1% to 5.2%. Majority of these increased infections took place in Fuzhou, Xiamen, and Quanzhou, three large cities in Fujian, mainly among youth, unemployed, business, and well-educated MSMs. Phylogenetic analysis revealed three major HIV-1 genotypes including CRF01_AE, CRF07_BC, and B/B' yet the surging MSM infections were primarily associated with the rapid sexual spread of CRF07_BC in addition to CRF01_AE. In particular, there was a significant proportional expansion of CRF07_BC infections among recently infected MSMs from 19% in 2012 to 41.9% in 2013. This increase was accompanied by emergence of complex patterns of viral recombination including multiple hybrid variants derived from CRF01_AE and CRF07_BC. Full-genome analysis indicated that CRF07_BC in Fujian was likely originated from similar strains previously found among IDUs in Yunnan province but with unique recombination break points. Our findings indicated that HIV-1 CRF07_BC has adapted for rapid sexual transmission, resulting in the surging HIV-1 epidemic and the emergence of new recombinant strains among MSMs in Fujian. Our findings have implications to vaccine and passive immunization trials in Fujian with emphasis on the induction of cross-subtype protective immunity.

Near Full-Length Genome Sequence of a Novel HIV-1 Second-Generation Recombinant Form (CRF01_AE/CRF07_BC) Detected Among Blood Donors in North China

In this study, a novel CRF01_AE/07_BC HIV-1 recombinant form, with five breakpoints in the pol, vpr, env, and nef gene regions, was identified from a voluntary blood donor in North China. Our study showed that this HIV-1 recombinant form might be a second-generation recombinant form from two predominant strains in the men who have sex with men (MSM) population, with the CRF07_BC fragments belonging to a CRF07_BC lineage specific to Chinese MSM and the CRF01_AE fragments belonging to the CRF01_AE lineage 5 common among MSM in northern China. Our findings supported the high-risk blood donation behaviors of MSM, implied the increasing complexity of the HIV-1 epidemic among the Chinese MSM population, and called more attention to the effectiveness of the screening test for the growing number of new HIV-1 recombinant forms.

Highlighting the crucial role of Hangzhou in HIV-1 transmission among men who have sex with men in Zhejiang, China

In recent years, the population of men who have sex with men (MSM) constitute a major group for HIV transmission in China. A total of 340 newly reported HIV-infected MSM were recruited proportionally from ten prefectures across Zhejiang province between January and December in 2013. Partial pol gene was amplified and sequenced. Phylogenetic relationship, transmission network and genotypic drug resistance analyses were performed on 311 sequences. HIV-1 subtypes including CRF01_AE (55.9%), CRF07_BC (37.6%), subtype B (1.9%), CRF55_01B (1.3%), CRF68_01B (0.3%), CRF08_BC (0.3%) and URFs (2.6%) were identified. A higher proportion of CRF07_BC and other subtypes existed in the >35 years group, while a higher proportion of CRF01_AE was present in the young group (<35 years). Low prevalence of transmitted drug resistance was found (3.9%, 12/311). Strains with Hangzhou imprints were diffused across the full phylogenetic tree. Moreover, Hangzhou represented the dominant proportion of local HIV transmission (72.0%) and cross-regional transmission (62.4%) based on the provincial transmission network and possessed the largest number of nodes with ≥50 edges, accounting for 50.0% (10/20). The complexity of HIV subtypes and an intertwined network was noticed in MSM in Zhejiang province. Hangzhou likely plays a central regional role in the intra-provincial spread of HIV.

Dual Infection Contributes to Rapid Disease Progression in Men Who Have Sex With Men in China

Supplemental Digital Content is Available in the Text.

Background:

Considerable numbers of HIV-1–infected men who have sex with men (MSM) show a relatively rapid disease progression in China; however, the cause remains elusive. HIV-1 dual infection was reported to occur commonly among the MSM population, and its contribution to clinical prognosis remains controversial. We investigated the occurrence and impact on disease progression of dual infection in a prospective MSM cohort in China.

Methods:

Sixty-four HIV-1 early-infected participants were longitudinally followed up for 2 years. Deep sequencing was used as dual-infection screening. CD4⁺ T-cell counts and HIV-1 viral load were compared between coinfection and single-infection participants and pre- versus post-superinfection.

Results:

Eight coinfected participants and 10 superinfected participants were identified, including 9 participants with intersubtype and 9 with intrasubtype dual infections. The prevalence of coinfection was 13.1%, with a superinfection incidence of 15.6%. Coinfection participants showed lower CD4⁺ T-cell counts at 120 days after infection (P = 0.042) and a higher viral set point tendency (P = 0.053) as compared with single-infection participants. Kaplan–Meier analysis showed that the time for the viral load to increase to above 4 log₁₀ copies per milliliter was shorter in coinfection participants than in single-infection participants (P < 0.001). After superinfection, the median CD4⁺ T-cell count decreased from 635 to 481 cells/μL (P = 0.027).

Conclusions:

The occurrence of dual infection among Chinese MSM is relatively high, and HIV-1 dual infection might contribute to rapid disease progression seen in the MSM population.

Trends of HIV-1 Subtypes Among Young People in Hangzhou, China

To investigate the HIV-1 molecular epidemiology among young people (18 to 25 years old) in Hangzhou. Plasma samples from 262 newly diagnosed HIV-1-infected patients were collected between 2009 and 2013 from Hangzhou of Zhejiang province. HIV-1 nucleotide sequences of pol gene regions were amplified using a nested polymerase chain reaction method and sequenced. Phylogenetic and recombination analyses were used to determine the HIV-1 genotypes. Based on all sequences generated, the subtype/circulating recombinant forms (CRFs) distribution was as follows: CRF01_AE (68.70%), CRF07_BC (21.54%), subtype B (3.66%), CRF08_BC (2.44%), 01B (2.03%), BC (0.81%), and C (0.41%). We found that the percentage of CRF07_BC was increasing year by year among young people in Hangzhou. Novel CRFs such as CRF67_01B (HZ2011-15 CD4-4516) and CRF68_01B (HZ2011-20 CD4-4530 and HZ2011-29 CD4-4087) were first discovered in the area in this study. Our study presents a molecular epidemiology investigation describing the structure of HIV-1 strains cocirculating in young people in Hangzhou. Increasing CRF07_BC and new CRFs popular in young people are a challenge for future prevention in Hangzhou.

Evolutionary Dynamics and Complicated Genetic Transmission Network Patterns of HIV-1 CRF01_AE among MSM in Shanghai, China

To explore the evolutionary dynamics and molecular transmission patterns of HIV-1 CRF01_AE in depth among men who have sex with men (MSM) in Shanghai, we constructed phylogenetic tree and genetic transmission networks based on 1, 152 pol sequences from MSM, 282 from other risk groups and 795 references. Phylogenetic analyses identified two distinct major CRF01_AE lineages and a Shanghai-based sub-lineage. The estimated tMRCAs for lineage 1 and 2 were 1996.0 (1992.9-1999.2) and 1997.8 (1994.3-2001.4), respectively. Of the 1, 152 MSM, 681 (59.1%) were identified as belonging to 241 separate networks. Of these 681 individuals in networks, 74.2% were linked to cases diagnosed in different years, 4.3% were linked to heterosexual women, and 0.7% were linked to persons who inject drugs. A total of 71 networks including 180 individuals diagnosed in Shanghai with the same domicile were found. Recent infection (P = 0.022) and sampling year after 2011 (P < 0.001) were significantly associated with potential transmission links among the networks. Besides, a significant transmission of viruses with drug resistant mutations at V179D/E were found in the networks. Given these findings, we propose that genetic transmission analysis is a useful tool in HIV intervention strategies to curb the spread of virus and promoting public health.

Nationwide Trends in Molecular Epidemiology of HIV-1 in China

To estimate the nationwide and regional distribution of HIV-1 genotypes in China in the past three decades, province-specific HIV-1 molecular epidemiology data were derived from 260 independent studies of HIV molecular prevalence through searching PubMed, VIP Chinese Journal Database (VIP), China National Knowledge Infrastructure, and Wanfang Data from January 1981 to December 2015. The nationwide and regional distribution of HIV-1 genotypes was estimated by weighting the genotype distribution from each province- and risk-specific subpopulation with the number of reported cases in the corresponding subgroups in the relevant periods. A sharp transition of HIV-1 subtypes and recombinant distribution was observed in various risk groups and regions over time. CRF01_AE has rapidly surged among almost all risk groups and in all areas, and it has become dominant among men who have sex with men and heterosexuals. A wide variety of new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were rapidly appearing in several risk groups and regions. After 2007, CRF01_AE was the most prevalent strain, accounting for 42.5% of all national infections, followed by CRF07_BC (28.9%), subtype B'/B (10.9%), CRF08_BC (10.0%), and subtype C (2.8%). URFs and other CRFs were responsible for 2.6% and fewer than 1% of infections nationwide, respectively. The nationwide and regional distributions of HIV-1 subtypes and recombinants were sharply shifting in China. CRF01_AE and new CRFs played an increasing role in the nationwide or regional HIV pandemic. The nationwide diversity of HIV-1 poses a formidable challenge to HIV vaccine development and disease prevention.

Multi-layered Gag-specific immunodominant responses contribute to improved viral control in the CRF01_AE subtype of HIV-1-infected MSM subjects

BACKGROUND

The purpose of this study was to characterize specific cytotoxic T-cell (CTL) responses in men who have sex with men (MSM) subjects infected with the human immunodeficiency virus type 1 (HIV-1) CRF01_AE subtype during the first year of infection and impacts on viral control and evolution.

RESULTS

Fifteen HIV-1 primary infected cases were recruited from Liaoning MSM prospective cohort. CTL responses to Gag, Pol and Nef proteins at 3 month and 1 year post infection were detected with Gamma interferon enzyme-linked immunospot (ELISPOT) assay using optimized consensus overlapping peptides, as well as the viral quasispecies sequences from the synchronous plasma. Gag and Nef proteins were the main targets of CTL responses during the first year of HIV-1 infection, and this was evident from the data after adjusting for the length of amino acids by dividing the amino acids number of the corresponding protein and multiplying by 100. Additionally, relative magnitudes of Gag at both 3 months and 1 year post infection were significantly negatively correlated with the viral set point (p = 0.002, r = -0.726; p = 0.025, r = -0.574). While the relative magnitude of Nef at 1 year post infection were significantly positively correlated with viral set point (p = 0.004, r = 0.697). Subjects with multi-layered Gag immunodominant responses during the first year of infection had significantly lower viral set points than subjects without such responses (p = 0.002).

CONCLUSION

Multi-layered Gag immunodominant responses during the first year of infection were correlated with viral control, which provides a theoretical basis for vaccine design targeting MSM subjects with the CRF01_AE subtype.

A Novel HIV-1 Second-Generation Recombinant Form (CRF01_AE/07_BC) Among Heterosexuals in Nei Monggoi Autonomous Region in China

Increasing second-generation recombinant forms (CRF01_AE/07_BC) have been detected in China recently. Here, we isolated a novel CRF01_AE/07_BC second-generation recombinant form in HIV-1-positive Nei Monggoi's heterosexuals with one CRF07_BC inserted into the CRF01_AE backbone. Polygenetic analyses showed that the CRF01_AE region was grouped with the previously reported cluster 5 lineage, which spreads among the sexual population in north of China, inferring that this recombinant event occurred through heterosexual contact in the north of China possibly. The growing emergence of recombinant forms means coexistence of multiple strains and complexity of the HIV-1 epidemic, which reminds us of the urgent necessity to focus the HIV surveillance among the high-risk populations nationwide in China, particularly to enhance preventive measures in HIV-1 low-prevalence areas.

The dynamics of the HIV epidemic among men who have sex with men (MSM) from 2005 to 2012 in Shenzhen, China

HIV-1 epidemics among MSM are a major public health concern in China, especially in large cities. This study sought to better understand the dynamics of HIV molecular epidemiology among MSM in Shenzhen, a rapidly developing city with over 13.8 million people. HIV-1 pol sequences were obtained from 996 (53.5%) of 1862 HIV-infected MSM and 403(9.0%) of 4498 heterosexuals and injection drug users in Shenzhen, China from 2005-2012. Eight HIV-1 subtypes and some inter-subtype recombinants were identified among sampled MSM with CRF07_BC (39.1%) and CRF01_AE (35.1%) being the most predominant. From 2006 to 2012, the prevalence of CRF07_BC and CRF55_01B rapidly increased, while the prevalence of subtypes B and CRF01_AE gradually decreased. The genetic distances within CRF07_BC and CRF55_01B groups were significantly lower than within CRF01_AE and B groups. The vast majority (90.3%) of HIV-1 infected MSM in Shenzhen were migrants who came from 31 of the 34 provinces of China, and these migrants had significantly different HIV-1 subtype distributions from the local MSM. This study highlighted the importance of CRF07_BC and migrants in the changing HIV epidemic among MSM in China, and provides a molecular epidemiology framework for understanding how HIV-1 epidemics can change in large cities with diverse risk groups.

The application of HIV molecular epidemiology to public health

HIV is responsible for one of the largest viral pandemics in human history. Despite a concerted global response for prevention and treatment, the virus persists. Thus, urgent public health action, utilizing novel interventions, is needed to prevent future transmission events, critical to eliminating HIV. For public health planning to prove effective and successful, we need to understand the dynamics of regional epidemics and to intervene appropriately. HIV molecular epidemiology tools as implemented in phylogenetic, phylodynamic and phylogeographic analyses have proven to be powerful tools in public health planning across many studies. Numerous applications with HIV suggest that molecular methods alone or in combination with mathematical modelling can provide inferences about the transmission dynamics, critical epidemiological parameters (prevalence, incidence, effective number of infections, Re, generation times, time between infection and diagnosis), or the spatiotemporal characteristics of epidemics. Molecular tools have been used to assess the impact of an intervention and outbreak investigation which are of great public health relevance. In some settings, molecular sequence data may be more readily available than HIV surveillance data, and can therefore allow for molecular analyses to be conducted more easily. Nonetheless, classic methods have an integral role in monitoring and evaluation of public health programmes, and should supplement emerging techniques from the field of molecular epidemiology. Importantly, molecular epidemiology remains a promising approach in responding to viral diseases.

Characterization of the Near Full-Length Genome of a Novel HIV-1 CRF01_AE/CRF07_BC Recombinant in an Injection Drug User from Southern Taiwan

HIV-1 CRF07_BC became prevalent in Taiwan after the epidemic among injection drug users (IDUs). We describe a unique recombinant form (URF) consisting of CRF01_AE and CRF07_BC (named URF_0107-H8) genes detected from an IDU. The 8.8 kb near full-length genome of URF_0107-H8 had a CRF01_AE backbone with two CRF07_BC fragments in the reverse transcriptase and integrase region [RT-Int; HXB2 nucleotide (nt) positions 2942-4709] and within the envelop (nt 8467-8722) gene. Phylogenetic analyses revealed that its 1.8 kb RT-Int sequence clustered with those of CRF07_BC strains from Taiwan, while sequences of CRF01_AE portions were more similar to those of Central African origin than contemporaneous CRF01_AE isolates in Taiwan or prevalent in East or Southeast Asia. Recombination breakpoints and phylogenetic relationships of URF_0107-H8 were different from those of CRF01_AE/CRF07_BC URFs previously reported from China. This highlighted the importance of continual monitoring of genetic evolution of HIV strains and the emergence of new recombinants.

A Large-scale Survey of CRF55_01B from Men-Who-Have-Sex-with-Men in China: implying the Evolutionary History and Public Health Impact

The HIV-1 epidemic among men-who-have-sex-with-men (MSM) continues to expand in China, involving the co-circulation of several different lineages of HIV-1 strains, including subtype B and CRF01_AE. This expansion has created conditions that facilitate the generation of new recombinant strains. A molecular epidemiologic survey among MSM in 11 provinces/cities around China was conducted from 2008 to 2013. Based on pol nucleotide sequences, a total of 19 strains (1.95%) belonged to the CRF55_01B were identified from 975 MSM in 7 provinces, with the prevalence range from 1.5% to 12.5%. Near full length genome (NFLG) sequences from six epidemiologically-unlinked MSM were amplified for analyzing evolutionary history, an identical genome structure composed of CRF01_AE and subtype B with four unique recombination breakpoints in the pol region were identified. Bayesian molecular clock analyses for both CRF01_AE and B segments indicated that the estimated time of the most recent common ancestors of CRF55_01B was around the year 2000. Our study found CRF55_01B has spread throughout the most provinces with high HIV-1 prevalence and highlights the importance of continual surveillance of dynamic changes in HIV-1 strains, the emergence of new recombinants, and the need for implementing effective prevention measures specifically targeting the MSM population in China.

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

Introduction

The HIV epidemic in men who have sex with men (MSM) continues to grow in most countries. However, the phylodynamic and virological differences among HIV-1 strains circulating in MSM and other populations are not well characterized.

Methods

Nearly full-length genomes (NFLGs) of the HIV-1 CRF01_AE were obtained from the Los Alamos HIV database. Phylogenetic analyses were conducted using the NFLG, gag, pol and env genes, using the maximum likelihood method. Selection pressure analyses at the codon level were performed for each gene in the phylogenetic clusters using PAML.

Results

Sequences isolated from MSM in China clustered in Clusters 1 (92.5%) and 2 (85.71%). The major risk factor for Cluster 3 was heterosexual transmission (62.16%). The ratio of non-synonymous to synonymous substitutions in the env gene (0.7–0.75) was higher than the gag (0.26–0.34) or pol (0.21–0.26) genes. In env gene, Cluster 1 (4.56×10^-3subs/site/year) and 2 (6.01×10^-3subs/site/year) had higher evolutionary rates than Cluster 3 (1.14×10^-3subs/site/year). Positive selection affected 4.2–6.58% of the amino acid sites in the env gene. Two sites (HXB2:136 and 316) evolved similarly in Clusters 1 and 2, but not Cluster 3.

Conclusion

The HIV-1 CRF01_AE in MSM is evolving differently than in other populations.

Phylogeny and Phylogeography of a Recent HIV-1 Subtype F Outbreak among Men Who Have Sex with Men in Spain Deriving from a Cluster with a Wide Geographic Circulation in Western Europe

We recently reported the rapid expansion of an HIV-1 subtype F cluster among men who have sex with men (MSM) in the region of Galicia, Northwest Spain. Here we update this outbreak, analyze near full-length genomes, determine phylogenetic relationships, and estimate its origin. For this study, we used sequences of HIV-1 protease-reverse transcriptase and env V3 region, and for 17 samples, near full-length genome sequences were obtained. Phylogenetic analyses were performed via maximum likelihood. Locations and times of most recent common ancestors were estimated using Bayesian inference. Among samples analyzed by us, 100 HIV-1 F1 subsubtype infections of monophyletic origin were diagnosed in Spain, including 88 in Galicia and 12 in four other regions. Most viruses (n = 90) grouped in a subcluster (Galician subcluster), while 7 from Valladolid (Central Spain) grouped in another subcluster. At least 94 individuals were sexually-infected males and at least 71 were MSM. Seventeen near full-length genomes were uniformly of F1 subsubtype. Through similarity searches and phylogenetic analyses, we identified 18 viruses from four other Western European countries [Switzerland (n = 8), Belgium (n = 5), France (n = 3), and United Kingdom (n = 2)] and one from Brazil, from samples collected in 2005–2011, which branched within the subtype F cluster, outside of both Spanish subclusters, most of them corresponding to recently infected individuals. The most probable geographic origin and age of the Galician subcluster was Ferrol, Northwest Galicia, around 2007, while the Western European cluster probably emerged in Switzerland around 2002. In conclusion, a recently expanded HIV-1 subtype F cluster, the largest non-subtype B cluster reported in Western Europe, continues to spread among MSM in Spain; this cluster is part of a larger cluster with a wide geographic circulation in diverse Western European countries.