Spatial clusters of HIV-1 genotypes in a recently infected population in Yunnan, China

Prevalence of drug resistance mutations in low-level viremia patients under antiretroviral therapy in Southwestern China: a cross-sectional study

OBJECTIVES

This study aimed to evaluate the prevalence and characteristics of drug resistance mutations (DRMs) in patients with low-level viremia (LLV) in Southwestern China, as it has become a growing challenge in AIDS clinical practice.

METHODS

This cross-sectional study was performed in Yunnan Province, Southwestern China. LLV was defined as 50-999 copies/mL of plasma viral load with antiretroviral therapy (ART) for at least 6 months. HIV-1 DRM detection used validated in-house protocol.

RESULTS

A total of 470 sequences were obtained, and 13 HIV-1 genotypes were identified, among which CRF08_BC (47.5%), CRF07_BC (22.3%) and CRF01_AE (10.0%) subtypes were the most prevalent. The overall prevalence of DRMs was 45.7% (215/470), and the prevalence of DRMs to non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs) was 39.4% (185/470), 20.6% (97/470) and 5.3% (25/470), respectively. The most common NNRTI-associated mutations were K103N (16.0%), E138A (6.6%), V179D (6.6%) and P225H (4.9%), and those in NRTIs were M184V (17.0%), D67N (3.4%) and K65R (3.0%). PI-associated mutations were infrequent, occurring in less than 1.8% of cases. The prevalence of NNRTI-associated mutations (K101E and Y188C) was found to be statistically significant among various LLV groups. Additionally, significant variations were observed in the prevalence of NNRTI-associated mutations (V106I, V106M, E138A and P225H), NRTI-associated mutation (K65R) and PI-associated mutations (L33F and Q58E) across different subtypes.

CONCLUSIONS

The prevalence of DRMs in ART-experienced patients with LLV was high, and HIV-1 genotypes exhibited diversity in Yunnan Province. These findings indicate that regular DRM monitoring during LLV episodes was essential for effective clinical treatment and management in this region.

Interpreting the Epidemiological Characteristics of HIV-1 in Heterosexually Transmitted Population Based on Molecular Transmission Network in Kunming, Yunnan: A Retrospective Cohort Study

Heterosexuals have become the most prevalent group of HIV-1 in Kunming, Yunnan Province. Utilizing the principle of genetic similarity between their gene sequences, we built a molecular transmission network by gathering data from earlier molecular epidemiological studies. This allowed us to analyze the epidemiological features of this group and offer fresh concepts and approaches for the prevention and management of HIV-1 epidemics. Cytoscope was used to visualize and characterize the network following the processing of the sample gene sequences by BioEdit and HyPhy. The number of possible links and the size of the clusters were investigated as influencing factors using a zero-inflated Poisson model and a logistic regression model, respectively. A scikit-learn-based prediction model was developed to account for the dynamic changes in the HIV-1 molecular network. Six noteworthy modular clusters with network scores ranging from 4 to 9 were found from 150 clusters using Molecular Complex Detection analysis at a standard genetic distance threshold of 0.01. The size of the number of possible links and the network's clustering rate were significantly impacted by sampling time, marital status, and CD4+ T lymphocytes (all p < 0.05). The gradient boosting machine (GBM) model had the highest area under the curve value, 0.884 ± 0.051, according to scikit-learn. Though not all cluster subtypes grew equally, the network clusters were relatively specific and aggregated. The largest local transmission-risk group for HIV-1CRF08_BC is now the heterosexual transmission population. The most suitable model for constructing the HIV-1 molecular network dynamics prediction model was found to be the GBM model.

Using the Molecular Transmission Networks to Analyze the Epidemic Characteristics of HIV-1 CRF08_BC in Kunming, Yunnan

HIV-1CRF08_BC is the most prevalent epidemic subtype among heterosexual (HET) and intravenous drug users (IDUs) in Kunming, Yunnan. Using the pol region of gene sequences derived from molecular epidemiological surveys, we developed a molecular transmission network for the purpose of analyzing its epidemiological characteristics, assessing its epidemiological trends, identifying its potential transmission relationships, and developing targeted interventions. HyPhy 2.2.4 was used to calculate pairwise genetic distances between sequences; GraphPad-Prism 8.0 was employed to determine the standard genetic distance; and Cytoscope 3.7.2 was applied to visualize the network. We used the network analysis tools to investigate network characteristics and the Molecular Complex Detection (MCODE) tool to observe the growth of the network. We utilized a logistic regression model to examine the factors influencing clustering and a zero-inflated Poisson model to investigate the factors influencing potential transmission links. At the standard genetic distance threshold of 0.008, 406 out of 858 study participants were clustered in 132 dissemination networks with a total network linkage of 868, and the number of links per sequence ranged from 1 to 19. The MCODE analysis identified three significant modular clusters in the networks, with network scores ranging from 4.9 to 7. In models of logistic regression, HET, middle-aged and elderly individuals, and residents of northern and southeastern Kunming were more likely to enter the transmission network. According to the zero-inflated Poisson model, age, transmission category, sampling year, marital status, and CD4+ T level had a significant effect on the size of links. The molecular clusters in Kunming's molecular transmission network are specific and aggregate to a certain extent. HIV-1 molecular network analysis provided information on local transmission characteristics, and these findings helped to determine the priority of transmission-reduction interventions.

Using molecular network analysis to understand current HIV-1 transmission characteristics in an inland area of Yunnan, China

HIV-1 molecular surveillance provides a new approach to explore transmission risks and targeted interventions. From January to June 2021, 663 newly reported HIV-1 cases were recruited in Zhaotong City, Yunnan Province, China. The distribution characteristics of HIV-1 subtypes and HIV-1 molecular network were analysed. Of 542 successfully subtyped samples, 12 HIV-1 strains were identified. The main strains were CRF08_BC (47.0%, 255/542), CRF01_AE (17.0%, 92/542), CRF07_BC (17.0%, 92/542), URFs (8.7%, 47/542), and CRF85_BC (6.5%, 35/542). CRF08_BC was commonly detected among Zhaotong natives, illiterates, and non-farmers and was mostly detected in Zhaoyang County. CRF01_AE was frequently detected among married and homosexual individuals and mostly detected in Weixin and Zhenxiong counties. Among the 516 pol sequences, 187 (36.2%) were clustered. Zhaotong natives, individuals aged ≥60 years, and illiterate individuals were more likely to be found in the network. Assortativity analysis showed that individuals were more likely to be genetically associated when stratified by age, education level, occupation, and reporting area. The genetic diversity of HIV-1 reflects the complexity of local HIV epidemics. Molecular network analyses revealed the subpopulations to focus on and the characteristics of the risk networks. The results will help optimise local prevention and control strategies.

Molecular networks reveal complex interactions with MSM in heterosexual women living with HIV-1 who play peripheral roles in Guangzhou, China

BACKGROUND

With the number of newly diagnosed HIV-positive heterosexual women increasing yearly, it is urgent to understand HIV-1 transmission among heterosexual women in Guangzhou, China.

METHODS

HIV-1 pol sequences were obtained from people living with HIV-1 during 2008 to 2017 in Guangzhou, China. A molecular network was constructed using HIV-1 TRAnsmission Cluster Engine with 1.5% genetic distance. Potential linkage and centrality metric were measured with Cytoscape. Transmission pathways between heterosexual women and men who have sex with men (MSM) were determined using Bayesian phylogenetic analysis.

RESULTS

In the network, 1799 (62.6%) MSM, 692 (24.1%) heterosexual men and 141 (4.9%) heterosexual women formed 259 clusters. Molecular clusters including MSM and heterosexuals were more likely to form larger networks (P<0.001). Nearly half of the heterosexual women (45.4%) were linked to heterosexual men and 17.7% to MSM, but only 0.9% of MSM were linked to heterosexual women. Thirty-three (23.4%) heterosexual women linked to at least one MSM node and were in peripheral role. Compared to general heterosexual women, the proportion of heterosexual women linked to MSM infected with CRF55_01B (P<0.001) and CRF07_BC (P<0.001) was higher than that of other subtypes, and the proportion diagnosed between 2012-2017 (P=0.001) was higher than that in 2008-2012. In MCC trees, 63.6% (21/33) of the heterosexual women differentiated from the heterosexual evolutionary branch, while 36.4% (12/33) differentiated from the MSM evolutionary branch.

CONCLUSION

Heterosexual women living with HIV-1 were mainly linked to heterosexual men and were in peripheral positions in the molecular network. The role of heterosexual women in HIV-1 transmission was limited, but the interaction between MSM and heterosexual women were complex. Awareness of the HIV-1 infection status of sexual partners and active HIV-1 detection are needed for women.

Identification of two novel HIV-1 circulating recombinant forms of CRF111_01C and CRF116_0108 in southwestern Yunnan, China

Yunnan, the region hardest hit by HIV/AIDS in China, is also an area with the most abundant HIV-1 genetic diversity. A large number of novel HIV-1 circulating recombinant forms (CRFs) and unique recombinants were identified among injection drug users in Yunnan; however, few were found among sexual contacts. Here, we obtained 15 near full-length genome sequences (NFLGs) from HIV-1 seropositive heterosexual contacts in Yunnan who received antiretroviral therapy during the period from 2014 to 2016. Phylogenetic analysis showed that six NFLGs belonged to CRF01_AE (n = 3) and CRF106_cpx (n = 3), and the other nine sequences were novel inter-subtype recombinants. Of the recombinants, two novel CRFs (CRF111_01 C (n = 4) and CRF116_0108 (n = 4)) and one CRF106_cpx variant (n = 1) were identified. CRF111_01 C had a CRF01_AE backbone with seven subtype C fragments inserted into the gag, pol, vif, env, nef and 3'LTR regions. CRF116_0108 had a CRF08_BC backbone with a CRF01_AE fragment inserted into the pol, tat, rev, vif, vpr, vpu and env regions. Phylogeographic analyses estimated that CRF111_01 C and CRF116_0108 originated approximately 1995.7-1998.6 and 1991.7-1993.7, respectively. These identifications of two novel HIV-1 CRFs highlighted the importance of continuous surveillance in heterosexual contacts and other high-risk groups in this region and the surrounding regions.

Young MSM changed temporal HIV-1 epidemic pattern in Heilongjiang Province, China

Background

Human immunodeficiency virus type 1 (HIV-1) epidemic in China is featured by geographical diversity of epidemic patterns. Understanding the characteristics of regional HIV-1 epidemic allows carrying out targeted prevention and controlling measures. This seven-year cross-sectional study was conducted in Heilongjiang, one province of Northeast China, where newly diagnosed infection is fast increasing yearly, but temporal HIV-1 epidemic trend is largely unknown.

Methods

Information of 1,006 newly diagnosed HIV-1-infected participants were collected before antiretroviral therapy during 2010-2016 in Heilongjiang province. HIV-1 genotype was identified based on the viral gag and env gene sequences. Recent infection was determined by Limiting-Antigen Avidity assays. Comparison analyses on the median ages, CD4 counts, proportions of stratified age groups and CD4 count groups, and rates of recent HIV-1 infection among different population and sampling times were performed to understand temporal HIV-1 epidemic features.

Results

Homosexual contact among men who have sex with men (MSM) was the main transmission route and CRF01_AE was the most dominant HIV-1 genotype. During 2010-2016, the HIV-1 epidemic showed three new changes: the median age continued to decline, the cases with a CD4 count more than 500 cells/μl (CD4hi cases) disproportionally expanded, and the recent HIV-1 infection rate steadily increased. MSM cases determined the temporal trend of HIV-1 epidemic here. Increase of young MSM cases (aged <30 years) made the main contribution to the younger age trend of MSM cases. These young MSM exhibited a higher median CD4 count, a higher proportion of CD4hi cases, and a higher rate of recent HIV-1 infection than cases aged 30 years and more. MSM infected by CRF01_AE virus mostly affected HIV-1 epidemic patterns among MSM population.

Conclusion

Young MSM have become a new hotspot and vulnerable group for HIV-1 transmission in Heilongjiang Province, Northeast China. The rapid increase in the number of young MSM cases, mainly those with CRF01_AE infection, changed temporal HIV-1 epidemic pattern here. Measures for prevention and control of HIV-1 infection among this population are urgently needed in the future.

HIV-1 pretreatment drug resistance and genetic transmission network in the southwest border region of China

BACKGROUND

HIV drug resistance increased with the widespread use of antiretroviral drugs, and posed great threat to antiretroviral therapy (ART). Pu'er Prefecture, lying in the southwest of Yunnan Province, China, borders Myanmar, Laos and Vietnam, is also the area where AIDS was discovered earlier, however, in which there has been no information on HIV drug resistance.

METHODS

A cross-sectional survey of pretreatment drug resistance (PDR) was conducted in Pu'er Prefecture in 2021. Partial pol gene sequences were obtained to analyze drug resistance and construct genetic transmission network. HIV drug resistance was analyzed using the Stanford University HIVdb algorithm.

RESULTS

A total of 295 sequences were obtained, among which 11 HIV-1 strain types were detected and CRF08_BC (62.0%, 183/295) was the predominant one. Drug resistance mutations (DRMs) were detected in 42.4% (125/295) of the sequences. The prevalence of PDR to any antiretroviral drugs, nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs) were 10.8% (32/295), 9.5% (28/295), 1.0% (3/295) and 0.3% (1/295), respectively. The risk of PDR occurrence was higher among individuals with CRF01_AE strain types. HIV-1 molecular network was constructed, in which 56.0% (42/75) of links were transregional, and 54.7% (41/75) of links were associated with Lancang County. Among the sequences in the network, 36.8% (35/95) harbored DRMs, and 9.5% (9/95) were drug resistance strains. Furthermore, 8 clusters had shared DRM.

CONCLUSION

The overall prevalence of PDR in this study was in a moderate level, but NNRTIs resistance was very approaching to the threshold of public response initiation. PDR was identified in the transmission network, and DRMs transmission was observed. These findings suggested that the consecutive PDR surveillance should be conducted in this region.

The Temporal and Spatial Epidemiology Employed in the Elimination of the HIV Epidemic in the Largest Capital of the Brazilian Rainforest

BACKGROUND

The main goal of this study was to analyze the human immunodeficiency virus (HIV) epidemic temporally and spatially in Belém from 2007 to 2018.

METHODS

The incidence rates were analyzed according to time using autoregressive integrated moving-average models, as well as spatially using spatial autocorrelation, Kernel density, scan statistics, and regression techniques.

RESULTS

During the study period, 6007 notifications of new cases of HIV/AIDS were reported. The time series analysis revealed a stabilized trend of incidence from 2007 to October 2016, followed by irregular fluctuations until the end of December 2018. Seasonal behavior was observed from 2019 to 2022. The high-high incidence clusters were found in the central and transition areas. An expansion of the number of new reported cases was observed in the central area. Three spatial risk zones were observed. The higher relative risk zone was concentrated in the transition area. The spatial regression showed that the incidence rates were positively correlated with the Family Health Strategy (FHS) coverage.

CONCLUSIONS

To eliminate HIV in Belém, it will be necessary to decentralize testing and ART and expand the coverage of FHS to ensure universal access to healthcare for citizens.

The Impact of Low-Level Viraemia on Virological Failure—Results From a Multicenter HIV Antiretroviral Therapy Cohort Study in Yunnan, China

Background

HIV viral load (VL) is an important indicator to monitor treatment response in antiretroviral therapy (ART). Patients on ART may experience viral blips, with low-level elevations of VL between 50 and 999 copies/mL known as low-level viraemia (LLV), but not reaching the threshold for virological failure (≥1,000 copies/mL) defined by WHO guidelines. The objective was to investigate the long-term impact of LLV on virological failure.

Methods

We analyzed adults who were ART naïve at baseline. LLV was defined as having an VL of 51–999 copies/mL at least once. The subjects with LLV were grouped into three categories: 51–199, 200–399, and 400–999 copies/mL. Patients with multiple episodes of LLV were classified based on the highest VL result. The subjects with LLV were also grouped by the frequency of LLV, i.e., a single episode, two consecutive episodes, two intermittent episodes, more than two consecutive episodes, and more than two intermittent episodes. Multivariable Cox models were used to predict the association of LLV with virological failure.

Results

A total of 93,944 subjects were included. The median number of VL tests performed was 3. There were 21,203 LLV cases, with an overall incidence of 22.6%. Most of the LLV cases were found in subjects with LVs of 50–199 copies/mL, followed by 400–999 and 200–399 copies/mL. Most of the LLV cases experienced single episodes, and the numbers of LLV with two consecutive episodes, two intermittent episodes, more than two consecutive episodes and more than two intermittent episodes were decreased successively. The risk factors associated with virological failure include: intermediate-level (200–399 copies/mL) and high-level (400–999 copies/mL) LLV, single episodes of LLV and two or more than two consecutive episodes of LLV, which may put the subjects at a 1.28–2.26-fold higher risk for virological failure.

Conclusion

Strengthened immediate medical attention should be placed on patients with VL of 200–999 copies/mL. The patients having experienced LLV once should be targeted for case management and repeat VL testing within 24 weeks to determine persistent LLV and monitor virological failure.

Transmission and Drug Resistance Characteristics of Human Immunodeficiency Virus-1 Strain Using Medical Information Data Retrieval System

This study was aimed at exploring the transmission and drug resistance characteristics of acquired immunodeficiency syndrome (AIDS) caused by human immunodeficiency virus-1 (HIV-1). The query expansion algorithm based on Candecomp Parafac (CP) decomposition was adopted to construct a data information retrieval system for semantic web and tensor decomposition. In the latent variable model based on tensor decomposition, the three elements in the triples generated feature vectors to calculate the training samples. The HIV patient data set was selected to evaluate the performance of the system, and then, the HIV gene resistance of 213 patients was retrospectively analyzed based on the electronic medical records. 43 cases showed failure of ribonucleic acid drug resistance, the ART virological failure rate was 24.43% (43/213), and one case was not reported. There was 1 case of RNA hemolysis that could not be detected. There were 50 resistant cases of nonnucleotide reverse transcriptase inhibitors (NNRTI), accounting for 29.94% (50/167), and there were 17 resistant cases of nucleotide reverse transcriptase inhibitors (NRTI), accounting for 10.18% (17/167) of all mutation cases. Among the HIV-1 strains, 19 cases failed the detection of drug resistance sites in the integrase region, and mutations in the integrase region were significantly more than those in the protease region. There were 12 types of HIV-1 strains with drug-resistant mutations. The fusion technical scheme constructed in this study showed excellent performance in medical information retrieval. In this study, the characteristics of HIV-1 of AIDS patients were analyzed from different directions, and effective treatment was performed for patients, so as to provide reference for clinical diagnosis of AIDS patients.

Frequently Transmission and Close Relationship Among Immigrants in the China-Myanmar Border Region Indicated by Molecular Transmission Analysis From a Cross-Sectional Data

Background

Accurate identification of molecular transmission clusters (MTCs) and understanding the dynamics of human immunodeficiency virus (HIV) transmission are necessary to develop targeted interventions to prevent HIV transmission. We evaluated the characteristics of antiretroviral therapy-naïve individuals who belonged to HIV-1 MTCs in the China-Myanmar border region to inform targeted effective HIV intervention.

Methods

Phylogenetic analyses were undertaken on HIV-1 pol sequences to characterize subtypes or circulating recombinant forms and identify MTCs. MTCs were defined as those with 2 or more sequences having bootstrap support > 80% and a pairwise gene distance less than or equal to 0.03. Factors correlated with MTCs were evaluated using logistic regression analysis. The chi-square test was used to compare differences between Chinese and Burmese participants belonging to MTCs.

Results

A total of 900 people had their pol gene successfully sequenced. Twenty-one MTCs were identified and included 110 individuals (12.2%). Individuals in MTCs were more likely to be Burmese [aOR = 2.24 (95% CI: 1.33, 3.79), P = 0.003], be younger [aOR = 0.34 (95% CI: 0.20, 0.58), P < 0.001 for age 26-50 vs. 25 years or younger], have a lower CD4 T cell count [aOR = 2.86 (95% CI: 1.34, 6.11), P = 0.007 for < 200 vs. 350 or greater], and have subtypes CRF07_BC or C [CRF07_BC: aOR = 7.88 (95% CI: 3.55, 17.52), P < 0.001; C: aOR = 2.38 (95% CI: 1.23, 4.62), P = 0.010 compared to CRF01_AE]. In MTCs, Burmese were younger (89.7 vs. 57.7% for age 25 years or younger), had a lower education level (41.0 vs. 8.5% for illiterate), were more likely to be infected through injection drug use (35.9 vs. 12.7%), and had a higher proportion of subtype BC (33.3 vs. 15.5%) and CRF01_AE (20.5 vs. 8.5%) compared to Chinese (P < 0.05 for all).

Conclusion

Burmese participants were more likely to belong to MTCs, and most MTCs had both Burmese and Chinese participants. These data highlight the bidirectional transmission of HIV-1 frequently transmission and close relationship among immigrants in the China-Myanmar border region. Local health departments should pay more attention to HIV screening and intervention to immigrants Burmese with the characteristics of younger age, having lower CD4 T cell count and infected with HIV subtypes CRF07_ BC or C.

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.

Using molecular network analysis to explore the characteristics of HIV-1 transmission in a China-Myanmar border area

Background

The China-Myanmar border area is considered a hot spot of active HIV-1 recombination in Southeast Asia. To better understand the characteristics of HIV-1 transmission in this area, a cross-sectional HIV-1 molecular epidemiological survey was conducted in Baoshan Prefecture of Yunnan Province.

Methods

In total, 708 newly reported HIV-1 cases in Baoshan Prefecture from 2019 to 2020 were included in this study. HIV-1 gag, pol and env genes were sequenced, and the spatial and demographic distributions of HIV-1 genotypes were analyzed. The characteristics of HIV-1 transmission were investigated using the HIV-1 molecular network method.

Results

In the 497 samples with genotyping results, 19 HIV-1 genotypes were found, with URFs being the predominant strains (30.2%, 150/497). The main circulating HIV-1 strains were mostly distributed in the northern area of Baoshan. URFs were more likely identified in Burmese individuals, intravenous drug users and those younger than 50 years old. CRF08_BC was more likely detected in farmers and those of Han ethnicity, CRF01_AE in the young and those of Han ethnicity, and CRF07_BC in the subpopulation with junior middle school education and higher. Moreover, CRF118_BC and CRF64_BC were more likely found in the subpopulation aged ≥40 years and ≥50 years, respectively. Among 480 individuals with pol sequence detection, 179 (37.3%) were grouped into 78 clusters, with Baoshan natives being more likely to be in the network. The proportion of the linked individuals showed significant differences when stratified by the regional origin, marital status, age and county of case reporting. In the molecular network, recent infections were more likely to occur among nonfarmers and individuals aged below 30 years.

Conclusions

HIV-1 genetics has become complex in Baoshan. HIV-1 molecular network analysis provided transmission characteristics in the local area, and these findings provided information to prioritize transmission-reduction interventions.

Epidemiological profile and molecular genetic characterization of HIV-1 among female sex workers and elderly male clients in Guangxi, China

The HIV/AIDS prevalence in female sex workers (FSWs) and elderly male clients is increasing in Guangxi, China, but the transmission relationship between them remains unclear. This study aims to illuminate the transmission network between FSWs and elderly male clients using molecular epidemiological analyses. Phylogenetic analysis indicated that CRF01_AE was the dominant strain, followed by CRF07_BC and CRF08_BC in both groups. Multivariate logistic regression analysis indicated that viral loads of 50 to 1000 copies/mL, immunological treatment failure and CRF07_BC were risk factors for entering the transmission network. Transmission network analysis showed that CRF07_BC tended to form large clusters, whereas CRF01_AE tended to form multiple but small clusters. Two groups of 11 FSWs and 169 clients were intricately intertwined. Spatial analysis demonstrated the formation of hotspots and clusters of transmission sharing regional differences. In conclusion, our study provides direct genetic evidence of transmission linkages between FSWs and elderly male clients. Although the CRF01_AE subtype was still the predominant subtype in the region, the higher degree and larger clusters found in CRF07_BC illustrate a rapid and intensive uptrend, which is expected to increase its prevalence in the region in the future.

Genetic Characteristics of Three Unique Recombinant Forms of HIV-1 in Yunnan, China

To explore the molecular epidemiological status of human immunodeficiency virus type 1 (HIV-1) in Yunnan, China, three HIV-1 near full-length genomes were amplified and sequenced from plasma samples that were collected from Burmese patients newly diagnosed with HIV-1 in Dehong Prefecture in Yunnan Province in 2017. Phylogenetic and bootscanning analyses revealed that all the sequences might be HIV-1 second-generation recombinant forms of circulating recombinant forms (CRF07_BC and CRF83_cpx) and unique recombinant forms. One of the sequences contained six CRF01_AE fragments, five subtype C fragments, and two subtype B fragments, which were separated by 12 breakpoints. These results revealed that the second-generation recombination of HIV-1 within different strains is still ongoing in Dehong, China. Systematic surveys and immediate interventions are urgently needed to prevent the formation of increasingly complex HIV-1 recombinant forms.

Characteristics of drug resistance in HIV-1 CRF55_01B from ART-experienced patients in Guangdong, China

BACKGROUND

HIV-1 acquired drug resistance (ADR) has become a critical clinical and public health issue. Recently, HIV-1 CRF55_01B has been found more frequently in the MSM population.

OBJECTIVE

To investigate the characteristics of HIV-1 drug resistance mutations (DRMs) and the extent of changes in drug susceptibility among ART-experienced CRF55_01B-infected adults of Guangdong.

METHODS

ADR was tested for immediately in CRF55_01B-infected patients with virological failure. Demographic and epidemiological information was collected. DRMs and antiretroviral susceptibility were interpreted using the Stanford University HIV Drug Resistance Database HIVdb program.

RESULTS

Overall, 162 (4.78%) CRF55_01B isolates were identified from 2013 to 2018. Among DRMs, M184V (43.83%) was the most frequent NRTI DRM, followed by K65R (23.46%), and V179E (98.77%) was the most frequent NNRTI DRM, followed by K103N (47.53%) and Y181C (14.81%). According to the HIVdb program, 79.01% of the CRF55_01B-infected patients carried mutations conferring low-level or higher drug resistance to any of the three classes of ART drugs. Among PI DRMs, only one mutation affording low-level resistance to nelfinavir was found (0.62%). Among NRTI DRMs, a high proportion of high-level resistance to lamivudine (58.64%) and emtricitabine (58.02%) was found. As regards NNRTIs, more than 75% of patients carried efavirenz and nevirapine DRMs. The percentages of high-level resistance were 70.99%, 63.58%, 22.22%, 17.90% and 4.32% for nevirapine, efavirenz, rilpivirine, doravirine and etravirine, respectively.

CONCLUSIONS

High frequencies of DRMs and resistance were observed among CRF55_01B-infected patients failing ART in Guangdong, and interventions may be considered to minimize ecological contributions to ART.

The Identification of A Novel HIV-1 Second-Generation Recombinant form (CRF01_AE/CRF07_BC) Among Men Who Have Sex with Men in Jiangsu, China

BACKGROUND

CRF01_AE and CRF07_BC are the two major HIV-1 virus strains circulating in China. The proportion of dominant subtypes (CRF01_AE and CRF07_BC) among MSM in Jiangsu province was over 80%. A large number of URFs have been found in China in recent years.

OBJECTIVE

This study aimed to report on novel HIV-1 recombinants.

METHODS

We constructed Phylogenetic trees using the maximum likelihood (ML) method with 1000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination breakpoints using SimPlot 3.5.1.

RESULTS

We identified a novel, second-generation HIV-1 recombinant (JS020202) between CRF01_ AE and CRF07_BC. The analysis of near full-length genome (NFLG) showed there were at least 8 breakpoints in the virus, which differed from any previously identified CRF and URF around the world.

CONCLUSION

Novel diverse CRF01_AE/07_BC suggested the complexity trends of HIV-1 genetics. The emergency situation of diverse recombinant strains should be monitored continuously.

A thematic analysis of experiences of HIV risks among female sex workers in the Yunnan-Vietnam Chinese border region

Background

The Yunnan province is located near the “Golden Triangle” border region between China, Myanmar and Thailand, which has the highest HIV/AIDS prevalence in China. Female sex workers (FSWs) in the Yunnan province are highly vulnerable to HIV infection. The objective of this study was to examine the experiences of FSWs in the Yunnan to better understand the risk of infection and the potential for transmission of HIV.

Methods

Semi-structured interviews were conducted between May 2018 and June 2018 with 20 FSWs recruited in Hekou County, Yunnan Province, China. Thematic analysis was conducted to identify themes that highlighted increased exposure of FSWs to the risk of HIV infection and transmission.

Results

The findings showed that FSWs’ primary source for HIV information was gynecologists, with few visiting the local HIV charity Red Ribbon. FSWs reported infrequent visits for check-ups with some seeing a gynecologist once a year. FSWs felt that the onus was on them to prevent STI/HIV infection by using a condom during sex, regardless of their ability to negotiate use. FSWs were also reluctant to see a gynecologists for treatment. Instead, they resorted to douching as a way of preventing HIV/STIs and treating vaginal health problems, such as leucorrhea. Most FSWs worked without the influence of alcohol and drugs. A small number of FSWs reported heroin addiction and injecting drug use.

Conclusion

The findings suggest a need for innovative HIV prevention strategies among FSWs and their clients in the Chinese border region. Governmental agencies should continue to implement practical strategies in terms of HIV prevention education and condom use through tailored interventions that are localized. Such strategies should include localized tailored interventions that dispel myths about douching as a method of HIV/STI prevention and incorporate a mobile outreach approach, similar to the ‘roadside restaurant’ outreach that has been successful in rural China.

Complicated genotypes circulating among treatment naïve HIV-1 patients in Guangzhou, China

Guangzhou city is the political, economic, and cultural center of the Guangdong Province, China. The molecular epidemiological characteristics of HIV-1 in Guangzhou are not widely known. The aim of this study was to explore the characteristics of HIV-1 genotypes among treatment naïve HIV/AIDS patients living in Guangzhou. HIV-1 RNA was extracted from serum specimens. The partial pol gene of the HIV-1 genome was amplified and sequenced. The genotypes were screened using the subtyping tool COMET and further confirmed by phylogenetic analysis, with the exception of the URFs that were analyzed by jpHMM and RIP. The distributions of HIV genotypes in different risk populations were analyzed. Subsequently, pol sequences were used to construct transmission networks and analyze drug resistance. Twelve HIV-1 genotypes including 3 subtypes and 9 CRFs, with several URFs were identified from 1388 HIV-1 sequences, which were derived from 1490 patients. The main genotypes circulating in Guangzhou were CRF07_BC (38.3%), CRF01_AE (32.3%), and CRF55_01B (10.7%). CRF01_AE was the secondary dominant strain and multiple lineages of CRF01_AE had been identified in Guangzhou. The 01B recombinant forms, including CRF55_01B, CRF59_01B and CRF68_01B, have circulated widely in Guangzhou. 42.22% (586/1388) of the study sequences fell into 143 transmission networks, and the three main clusters revealed that sequences from MSM and HET populations were intermixed. 5.40% (75/1388) of patients had pre-treatment drug resistance. The HIV-1 strains that were present in Guangzhou have demonstrated complex genotypes. Particular attention should be given on these genotypes for the further strategy of prevention and intervention of HIV transmission.

The origin and spread of CRF85_BC, driven by heterosexual transmission among older people in Sichuan, China

BACKGROUND

CRF_BC recombinants, including CRF07_BC and CRF08_BC, were considered the predominant subtypes in China. Since the discovery of HIV-1 circulating recombinant form CRF 85_BC in Southwest China in 2016, this BC recombinant forms had been reported in different regions of China. However, the history and magnitude of CRF85_BC transmission were still to be investigated.

METHOD

We conducted the most recent molecular epidemiology of HIV-1 among newly reported HIV-1 infected patients in Sichuan in 2019 by sequencing and phylogenetic analysis of 1291 pol sequences. Then, we used maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of pol sequences to reconstruct the phylogeographic and demographic dynamics of the CRF85_BC.

RESULTS

HIV-1 CRF85_BC (68/1291, 5.27%) became the fourth most prevalent strain revealing a significant increase in local population. CRF85_BC were only found in heterosexually infected individuals and the majority of CRF85_BC (95.45%) were circulating among the people living with HIV aged 50 years and over (PLHIV50+), suggesting a unique prevalent pattern. The founder lineages of CRF85_BC were likely to have first emerged in Yunnan, a province of Southwest China bordering Sichuan, in the early 2000s. It then spread exponentially to various places (including Guangxi, Sichuan, et al) and became endemic around 2008.6 (2006.7-2010.2) in Sichuan.

CONCLUSION

Taken together, our findings on HIV-1 subtype CRF85_BC infections provided new insights into the spread of this virus and extended the understanding of the HIV epidemic in China.

Genotypic Methods for HIV Drug Resistance Monitoring: The Opportunities and Challenges Faced by China

AIDS is a globalized infectious disease. In 2014, UNAIDS launched a global project of "90-90-90" to end the HIV epidemic by 2030. The second and third 90 require 90% of HIV-1 infected individuals receiving antiretroviral therapy (ART) and durable virological suppression. However, wide use of ART will greatly increase the emergence and spreading of HIV drug resistance and current HIV drug resistance test (DRT) assays in China are seriously lagging behind, hindering to achieve virological suppression. Therefore, recommending an appropriate HIV DRT method is critical for HIV routine surveillance and prevention in China. In this review, we summarized the current existing HIV drug resistance genotypic testing methods around the world and discussed the advantages and disadvantages of these methods.

Multiple HIV-1 Genotypes Circulating Among College Students in Nanjing, China

College students are disproportionately affected by HIV-1 in China. However, little is known about the genetic characteristics of HIV-1 among this population. A molecular epidemiological investigation was conducted among the newly diagnosed antiretroviral therapy-naïve HIV-1-infected individuals during 2015-2019 in Nanjing city, China. The pol fragment (HXB2: 2,253-3,311) was obtained by HIV-1 RNA extraction and gene amplification, and subjected to genotyping, recombination analysis, and phylogenetic inference. A total of 945 pol sequences from 226 students and 719 nonstudents were successfully amplified. Multiple genotypes were identified in students, including CRF01_AE (37.66%), CRF07_BC (32.90%), CRF55_01B (5.63%), CRF68_01B (3.46%), CRF67_01B (3.03%), subtype B (1.73%), and CRF58_01B (1.30%) and unique recombinant forms (URFs) of 01C_like (7.08%), 0107_like (3.98%), 01BC_like (2.21%), and 01B_like (1.33%). The distribution of genotypes among students was similar to that among nonstudents. The estimated mean evolutionary rate of URFs was 2.89 × 10^-3 [95% Bayesian credible interval: 1.89-3.90] nucleotide substitutions/site/year. Approximately 64% (21/33) of URFs among students were located in three major clusters (0107_like, 01C_like 1, and 01C_like 2 clusters), which had recent time to the most recent common ancestors and low mean genetic distance, and presumably originated from Nanjing (posterior probability ≥0.99, state probability ≥0.9). Among 226 students with pol segments, the prevalence of primary and transmitted drug resistance mutations was 15.93% and 3.98%, respectively. The rapid evolution of multiple HIV-1 genotypes and high prevalence of URFs circulating among students in Nanjing emphasized the necessity of comprehensive surveillance for HIV-1 transmission among this population.

The characteristics of pretreatment HIV-1 drug resistance in western Yunnan, China

HIV-1 drug resistance can compromise the effectiveness of antiretroviral therapy (ART). A survey of pretreatment HIV-1 drug resistance (PDR) was conducted in Lincang Prefecture of Yunnan Province. From 372 people living with HIV/AIDS initiating ART for the first time during 2017-2018, 322 pol sequences were obtained, of which 11 HIV-1 strain types were detected. CRF08_BC (70.2%, 226/322) was the predominant strain, followed by URF strains (10.6%, 34/322). Drug resistance mutations (DRMs) were detected among 34.2% (110/322) of the participants. E138A/G/K/R (14.3%, 46/322) and V179E/D/T (13.7%, 47/322) were the predominant DRMs. Specifically, E138 mutations commonly occurred in CRF08_BC (19.9%, 45/226). Among the DRMs detected, some independently conferred resistance, such as K65R (1.6%, 5/322), Y188C/F/L (0.9%, 3/322), K103N (0.6%, 2/322) and G190A (0.3%, 1/322), which conferred high-level resistance. The prevalence of PDR was 7.5% (95% CI: 4.6-10.3%) and the prevalence of non-nucleotide reverse transcriptase inhibitor (NNRTI) resistance was 5.0% (95% CI: 2.6-7.4%), which is below the threshold (⩾10%) of initiating a public health response. In conclusion, HIV-1 genetic diversity and an overall moderate level of PDR prevalence were found in western Yunnan. PDR surveillance should be continually performed to decide whether a public health response to NNRTI resistance should be initiated.