Characteristics of HIV-1 molecular transmission networks and drug resistance among men who have sex with men in Tianjin, China (2014-2018)

Evolving molecular HIV clusters revealed genotype-specific dynamics in Guangzhou, China (2008-2020)

OBJECTIVES

This study investigated the genotype-specific dynamics of molecular HIV clusters (MHCs) in Guangzhou, China, aiming to enhance HIV control.

METHODS

HIV pol sequences from people with HIV (PWH) in Guangzhou (2008-2020) were obtained for genotyping and molecular network creation. MHCs were identified and categorized into three types: emerging, growing, or stable. Clustering rates, proportions of cluster types and members within each type were calculated and their trends were assessed using joinpoint regression.

RESULTS

Among 8,395 PWH, the most prevalent HIV-1 genotypes were CRF07_BC (39.7%) and CRF01_AE (32.6%). The genotype composition has been stable since 2012 (Ps>0.05). The overall clustering rate was 43.3%, with significant variations across genotypes (P<0.001), indicating genotype-specific transmission fitness. Significant declines in overall and genotype-specific clustering rates towards the end of 2020 (Ps<0.05), potentially offer support for HIV control efforts in reducing local infections. The continuously increasing proportions of stable clusters and the gradually decreasing proportions of emerging and growing clusters (either Ps<0.05 or Ps>0.05) suggests a trend towards stable molecular network structure. However, growing clusters exhibited CRF55_01B, CRF07_BC and CRF59_01B dominance that indicate their priority for interventions.

CONCLUSIONS

The evolving molecular HIV clusters highlight the genotype-specific cluster dynamics, providing fresh insights for enhanced prevention and control strategies.

Application of molecular epidemiology in revealing HIV-1 transmission network and recombination patterns in Tianjin, China

Using a comprehensive molecular epidemiological approach, we characterized the transmission dynamics of HIV-1 among the MSM population in Tianjin, China. Our findings revealed that 38.56% (386/1001) of individuals clustered across 109 molecular transmission clusters (TCs), with MSM aged 50 and below being the group most commonly transmitting HIV-1. Among the identified TCs, CRF01_AE predominated, followed by CRF07_BC. Notably, CRF07_BC demonstrated a higher propensity for forming large clusters compared to CRF01_AE. Birth-death skyline analyses of the two largest clusters indicated that the HIV/AIDS transmission may be at a critical point, nearly all had Re approximately 1 by now. A retrospective analysis revealed that the rapid expansion of these large clusters was primarily driven by the introduction of viruses in 2021, highlighting the crucial importance of continuous molecular surveillance in identifying newly emerging high-risk transmission chains and adapting measures to address evolving epidemic dynamics. Furthermore, we detected the transmission of drug-resistant mutations (DRMs) within the TCs, particularly in the CRF07_BC clusters (K103N, Y181C, and K101E) and CRF01_AE clusters (P225H and K219R), emphasizing the importance of monitoring to support the continued efficacy of first-line therapies and pre-exposure prophylaxis (PrEP). Recombination analyses indicated that complex recombinant patterns, associated with increased amino acid variability, could confer adaptive traits to the viruses, potentially providing a competitive advantage in certain host populations or regions. Our study highlights the potential of integrating molecular epidemiological and phylodynamic approaches to inform targeted interventions.

The origin and spread of HIV-1 CRF59_01B epidemic in China: A molecular network and phylogeographic analysis

Human immunodeficiency virus type 1 CRF59_01B, identified in China in 2013, has been detected nationwide, exhibiting notably high prevalence in Guangzhou and its vicinity. This study aimed to unravel its origin and migration. A data set was established, incorporating all available CRF59_01B pol gene sequences and their metadata from Guangzhou and the public database. Bayesian phylogeographic analysis demonstrated that CRF59_01B originated in Shenzhen, the neighboring city of Guangzhou, around 1998 with posterior probability of 0.937. Molecular network analysis detected 1131 transmission links and showed a remarkably high clustering rate (78.9%). Substantial inter-city transmissions (26.5%, 300/1131) were observed between Shenzhen and Guangzhou while inter-region transmissions linked Guangzhou with South (46) and Southwest (64) China. The centre of Guangzhou was the hub of CRF59_01B transmission, including the inflow from Shenzhen (3.57 events/year) and outflow to the outskirts of Guangzhou (>2 events/year). The large-scale analysis revealed significant migration from Shenzhen to Guangzhou (5.08 events/year) and North China (0.59 events/year), and spread from Guangzhou to Central (0.47 events/year), East (0.42 events/year), South (0.76 events/year), Southwest China (0.76 events/year) and Shenzhen (1.89 events/year). Shenzhen and Guangzhou served as the origin and the hub of CRF59_01B circulation, emphasizing inter-city cooperation and data sharing to confine its nationwide diffusion.

Distinct Rates and Transmission Patterns of Major HIV-1 Subtypes among Men who Have Sex with Men in Guangxi, China

The diversity and transmission patterns of major HIV-1 subtypes among MSM population in Guangxi remains unknown. Understanding the characteristics is crucial for effective intervention strategies. Between 2016 and 2021, we recruited individuals newly diagnosed with HIV-1 from MSM population in Guangxi. HIV-1 pol region was amplified and sequenced, and constructed molecular network, assessed clustering rate, cluster growth rate, spatial clustering, and calculating the basic reproductive number (R0) based on sequences data. We identified 16 prevalent HIV-1 subtypes among Guangxi MSM, with CRF07_BC (53.1%), CRF01_AE (26.23%), and CRF55_01B (12.96%) predominating. In the network, 618 individuals (66.17%) formed 59 clusters. Factors contributing to clustering included age < 30 years (AOR = 1.35), unmarried status (AOR = 1.67), CRF07_BC subtype (AOR = 3.21), and high viral load (AOR = 1.43). CRF07_BC had a higher likelihood of forming larger clusters and having higher degree than CRF01_AE and CRF55_01B. Notably, CRF07_BC has higher cluster growth rate and higher basic reproductive number than CRF01_AE and CRF55_01B. Our findings underscore CRF07_BC as a prominent driver of HIV-1 spread among Guangxi's MSM population, highlighting the viability of targeted interventions directed at specific subtypes and super clusters to control HIV-1 transmission within this population.

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.

Characteristics of genotype, drug resistance, and molecular transmission network among newly diagnosed HIV-1 infections in Shenzhen, China

The HIV-1 pandemic has persisted for four decades, and poses a major challenge to global public health. Shenzhen, a city with large number of migrant populations in China, is suffering HIV-1 epidemic. It is necessary to continuously conduct the molecular surveillance among newly diagnosed HIV-1 patients in these migrant population. In this study, plasma samples of newly diagnosed and ART-naive HIV-1 infections were collected from Shenzhen city in China. The partial genes of HIV-1 gag and pol were amplified and sequenced for the analysis of genotype, drug resistance, and molecular transmission network. Ninety-one sequences of pol gene were obtained from newly diagnosed HIV-1 infections in Shenzhen, and seven HIV-1 subtypes were revealed in this investigation. Among them, the circulating recombinant form (CRF) 07_BC was the mostly frequent subtype (53.8%, 49/91), followed by CRF01_AE (20.9%, 19/91), CRF55_01B (9.9%, 9/91), unique recombinant forms (URFs) (8.8%, 8/91), B (3.3%, 3/91), CRF59_01B (2.2%, 2/91), and CRF08_BC (1.1%, 1/91). The overall prevalence of pretreatment drug resistance (PDR) was 23.1% (21/91), and 52.38% (11/21) of the PDR was specific for the nonnucleotide reverse transcriptase inhibitors (NNRTIs). Furthermore, a total of 3091 pol gene sequences were used to generate 19 molecular transmission clusters, and then one growing cluster, a new cluster, and a cluster with growth reactivation were identified. The result revealed that more sexual partner, CRF_07BC subtype, and seven amino acid deletions in gag p6 region might be the influencing factors associated with the high risk of transmission behavior. Compared with CRF01_AE subtype, CRF07_BC subtype strains were more likely to form clusters in molecular transmission network. This suggests that long-term surveillance of the HIV-1 molecular transmission should be a critical measure to achieve a precise intervention for controlling the spread of HIV-1 in China.

The characteristics of HIV-1 subtype B on phylogenetic dynamic and molecular transmission network in Fuyang City, China, 2011 to 2019

Introduction

HIV-1 subtype B, as once one of the earliest strains introduced into mainland China rapidly spread in commercial plasma donors and heterosexuals in 1990s. Here, we aim to investigate the origin and evolutionary history of HIV-1 subtype B in Fuyang city, China.

Methods

We collected sequences tested from Fuyang in the east of China where higher prevalence of HIV-1 among commercial plasma donors and heterosexuals to construct a phylogenetic tree using the Markov chain Monte Carlo (MCMC) algorithm, infer molecular transmission network using TN93 model and visualize it with Cytoscape software.

Results and discussion

Our results showed that >99% of subtype B sequences belonged to Thai B. The sequences from Fuyang often cluster closer to those from other its adjacent cities, which clustered together and formed a monophyletic cluster. HIV-1 B circulating in Fuyang dates back to approximately 1990. Among the 1,437 sequences, 166 clustered at a genetic distance of ≤1.2%, resulting in 73 clusters. The degree of clustering with at least one other person was 11.55%. Among the transmission clusters, 50 (80.65%) comprised two individuals. Most clusters consisted of both heterosexual transmission routes and men who have sex with men. Phylogenetic and molecular network analyses revealed a common origin with neighboring regions in mainland China, local onwards transmission after its introduction, and a limited clustering degree. However, at least two co-existing transmission routes in most transmission clusters imply a greater challenge in controlling the spread of HIV-1. Our findings highlight the value on tailoring prevention interventions by combination of molecular surveillance and epidemiology.

The Molecular Epidemiological and Immunological Characteristics of HIV-1 CRF01_AE/B Recombinants in Nanjing, China

Human immunodeficiency virus-type 1 (HIV-1) CRF01_AE/B recombinants are newly emerging strains that are spreading rapidly in Southern and Eastern China. This study aimed to elucidate the molecular epidemiological characteristics of HIV-1 CRF01_AE/B recombinants in Nanjing and to explore the impact of these novel strains on the immunological status. A total of 1,013 blood samples from newly diagnosed HIV-1-infected patients were collected in Nanjing from 2015 to 2019, among which 958 partial Pol sequences were sequenced successfully. We depicted the molecular epidemiological characteristics of CRF01_AE/B recombinants by the molecular evolutionary analysis, Bayesian system evolution analysis, and transmission network analysis. The generalized additive mixed model was applied to evaluate the CD4+ T-cell count change of CRF01_AE/B recombinants. The Kaplan–Meier analysis was performed to assess the time from combined antiretroviral therapy (cART) initiation to immune reconstruction. We have identified 102 CRF01_AE/B recombinants (102/958, 10.65%) in Nanjing, including CRF67_01B (45/102, 44.12%), CRF68_01B (35/102, 34.31%), and CRF55_01B (22/102, 12.57%). According to the Bayesian phylogenetic inference, CRF55_01B had a rapid decline stage during 2017–2019, while CRF67_01B and CRF68_01B have experienced a fast growth phase during 2014–2015 and then remained stable. We have constructed 83 transmission networks, in which three larger clusters were composed of CRF67_01B and CRF68_01B. CRF01_AE/B recombinants manifested a faster decrease rate of CD4+ T-cell count than CRF_07BC but similar to CRF01_AE. The probability of achieving immune reconstruction in CRF01_AE/B recombinants was lower than CRF07_BC in the subgroup of baseline CD4+ T-cell count at cART initiation &lt;300 cells/μl. In summary, CRF67_01B and CRF68_01B were the major strains of CRF01_AE/B recombinants in Nanjing, which have formed large transmission clusters between Nanjing and other provinces. CRF01_AE/B recombinants might be associated with rapid disease progression and poor immune reconstruction. The continuous epidemiological monitoring of CRF01_AE/B recombinants should be highly emphasized.

Pre-treatment and acquired antiretroviral drug resistance among people living with HIV in Tianjin, China

OBJECTIVES

This study investigated the prevalence and patterns of pre-treatment and acquired HIV drug resistance mutations among people living with HIV (PLWH) on antiretroviral therapy (ART) for 12 (±3) months in Tianjin, China.

METHODS

From Jan 2018 to Dec 2020, PLWH with HIV-1 RNA greater than 1000 copies/mL visiting the ART clinic in the Tianjin Second People's Hospital were enrolled. Viral RNA isolated from blood samples were taken for genotypic resistance testing using an in-house method. Major drug resistance mutations were analyzed for reverse transcriptase and protease Sanger sequences using the Stanford University HIV Drug Resistance Database. Multivariable Poisson regressions were used to evaluate the factors associated with drug resistance mutations.

RESULTS

HIV drug resistance testing was successfully performed on 584 ART-naive and 71 ART-experienced participants. Pre-treatment drug resistance mutation prevalence was 13.5% (79/584) to any antiretroviral drug, 12.5% (73/584) to non-nucleoside reverse transcriptase inhibitors (NNRTIs), 1.5% (9/584) to nucleoside reverse-transcriptase inhibitors (NRTIs), and 0.3% (2/584) to protease inhibitors (PIs). Acquired drug resistance to any antiretroviral drug among PLWH on ART with viral load >1000 copies/mL was 88.7% (63/71). The prevalence of mutation for NNRTIs, NRTIs, and PIs were 93.7% (59/63), 82.5% (52/63), and 3.2% (2/63), respectively.

CONCLUSIONS

Pre-treatment and acquired drug resistance mutations were highly prevalent among PLWH in Tianjin; therefore, routine baseline genotypic resistance testing and adequate intervals of viral load surveillance are urgently needed for the long-term treatment success. Our findings provide important evidence for first- and second-line regimen drugs for PLWH, especially in China.

Risk Factors of Drug Resistance and the Potential Risk of HIV-1 Transmission of Patients with ART Virological Failure: A Population-Based Study in Sichuan, China

Background

Sichuan Province, in the interior of Southwest China, is the most severe HIV-affected area in China. Few data are currently available for people living with HIV/AIDS (PLWH) with virological failure of antiretroviral therapy (ART). Estimating the HIV-1 drug-resistant spread influencing factors and transmission patterns of the HIV-1 epidemic of PLWH with ART virological failure are critical in Sichuan.

Methods

We evaluated the drug-resistant transmission patterns on 5790 PLWH in 2018 with identified pol sequences of the five main HIV-1 subtypes (ie, subtype B, CRF08_BC, CRF85_BC, CRF07_BC, and CRF01_AE) in Sichuan Province, China. The multivariate logistic regression model was used to explore potential influencing factors of the spread of drug resistance (DR) clustering in the genetic transmission network. Spatial analyses were applied to demonstrate drug-resistant spatial clustering patterns of spatial connections of HIV-1 intercity transmission. Genetic transmission networks were performed by comparing sequences, calculating the pairwise distance, and visualizing the network.

Results

There were identified 452 transmission clusters containing 2159 of 5790 patients (37.29%) in the HIV-1 genetic transmission networks. Some clinical and demographic factors (eg, route of transmission, subtype) determined the DR clustering in the genetic transmission networks. The high drug-resistant clustering rates were mainly distributed in the Southern and Northeast of Sichuan Province (eg, Deyang, Neijiang), especially for CRF85_BC, which showed the highest clustering rate. Some cities had with strong intracity links (eg, Yibin, Neijiang), some cities had with strong transmission links with another city (eg, Ziyang and Guangyuan), 12 of 37 drug resistance mutation sites had a significant difference in the five subtypes (P < 0.001).

Conclusion

Our findings revealed the HIV-1 drug-resistant spread influencing factors and transmission patterns of PLWH with ART virological failure, which showed regions with high drug-resistant transmission of PLWH may not be a match for regions with severe epidemics in Sichuan, and it provided evidence-based to drug-resistant transmission targeting interventions.

Mining relationships between transmission clusters from contact tracing data: An application for investigating COVID-19 outbreak

OBJECTIVE

Contact tracing of reported infections could enable close contacts to be identified, tested, and quarantined for controlling further spread. This strategy has been well demonstrated in the surveillance and control of COVID-19 (coronavirus disease 2019) epidemics. This study aims to leverage contact tracing data to investigate the degree of spread and the formation of transmission cascades composing of multiple clusters.

MATERIALS AND METHODS

An algorithm on mining relationships between clusters for network analysis is proposed with 3 steps: horizontal edge creation, vertical edge consolidation, and graph reduction. The constructed network was then analyzed with information diffusion metrics and exponential-family random graph modeling. With categorization of clusters by exposure setting, the metrics were compared among cascades to identify associations between exposure settings and their network positions within the cascade using Mann-Whitney U test.

RESULTS

Experimental results illustrated that transmission cascades containing or seeded by daily activity clusters spread faster while those containing social activity clusters propagated farther. Cascades involving work or study environments consisted of more clusters, which had a higher transmission range and scale. Social activity clusters were more likely to be connected, whereas both residence and healthcare clusters did not preferentially link to clusters belonging to the same exposure setting.

CONCLUSIONS

The proposed algorithm could contribute to in-depth epidemiologic investigation of infectious disease transmission to support targeted nonpharmaceutical intervention policies for COVID-19 epidemic control.

Distribution characteristics of drug resistance mutations of HIV CRF01_AE, CRF07_BC and CRF08_BC from patients under ART in Ganzhou, China

BACKGROUND

Drug resistance mutation (DRM)-associated virological failure has become a critical issue for ART and the elimination of HIV.

OBJECTIVES

To investigate the distribution characteristics of DRMs of HIV CRF01_AE, CRF07_BC and CRF08_BC, the predominant subtypes in China.

METHODS

Patients receiving ART up to 31 August 2020 in Ganzhou in China were recruited. Full-length sequences of the HIV pol gene were amplified from patients with virological failure. DRMs and antiretroviral susceptibility were explored using the Stanford University HIV Drug Resistance Database HIVdb Program.

RESULTS

Overall, 279 of 2204 patients under ART were found to have virological failure. Nine HIV subtypes were identified among 211 sequences that were amplified successfully and CRF08_BC (37.0%), CRF01_AE (26.1%) and CRF07_BC (25.6%) were the most prevalent, with mutation frequencies of 44.9% (35/78), 52.7% (29/55) and 35.2% (19/54), respectively. The most common DRMs of these three subtypes were K103N and M184V, while the mutation frequencies of M41L, D67N, K70R, K101E, V106M, Y181C, K219E, H221Y and N348I were obviously different among subtypes. The resistance levels and frequencies for antiretroviral drugs for these three subtypes were similar and resistances to nevirapine, efavirenz, lamivudine and emtricitabine were the most frequently observed. Compared with CRF01_AE and CRF07_BC, CRF08_BC had higher proportions of DRMs for NRTIs and lower frequencies of resistance to NRTIs and NNRTIs.

CONCLUSIONS

The distribution characteristics of DRMs of HIV CRF01_AE, CRF07_BC and CRF08_BC were inconsistent and should be considered when selecting antiretroviral strategies, developing new drugs and controlling HIV strains containing DRMs.

Spatial Analysis of People Living with HIV/AIDS Transmitted Through Commercial Heterosexual Contact or Non-Marital Non-Commercial Heterosexual Contact - China, 2018

What is already known about this topic?

Significant changes in human immunodeficiency virus (HIV) transmission modes have occurred in China, and the proportion of heterosexual transmission increased in recent years.

What is added by this report?

The proportions of diverse transmission routes and subgroups of heterosexual transmission were analyzed by provincial-level administrative divisions (PLADs), and nationwide spatial clustering of HIV transmission through commercial heterosexual contact (CHC) and non-marital non-commercial heterosexual contact (NMNCHC) was explored.

What are the implications for public health practice?

This report provides evidence for geographic clustering of HIV transmission through CHC and NMNCHC in China and identifies priority regions where specified research and targeted HIV prevention and control strategies should be implemented.