Spatiotemporal Patterns of CRF07_BC in China: A Population-Based Study of the HIV Strain With the Highest Infection Rates

Divergent transmission dynamics and drug resistance evolution of HIV-1 CRF01_AE and CRF07_BC in Tianjin, China (2013-2022)

BACKGROUND

Tianjin, a major hub in northern China, faces rising HIV-1 infections dominated by CRF01_AE and CRF07_BC. This study elucidated their divergent transmission patterns and drug resistance dynamics to guide targeted interventions.

METHODS

This study included samples identified as CRF01_AE and CRF07_BC subtypes through various methods between 2013 and 2022. BEAST software was used to examine the spatiotemporal transmission patterns of these subtypes in Tianjin. By integrating HIV-TRACE, we constructed high-risk transmission clusters and identified drug resistance mutations (DRMs) based on the Stanford HIV Drug Resistance Database. Finally, the birth-death skyline serial (BDSKY) model was employed to dynamically assess the effective reproductive number (Re) of both subtypes to predict future transmission dynamics.

RESULTS

CRF01_AE might be introduced in 1988 from Henan and Zhejiang, forming multiple small clusters (< 10 nodes) and spreading through both heterosexual and men who have sex with men (MSM) in Tianjin, while CRF07_BC from Chongqing and Guizhou, et al. in 2004, experiencing explosive local transmission and forming a large cluster of 170 nodes primarily among MSM under 30 years old (P < 0.05). Phylogenetic analysis indicated that CRF01_AE has a significantly higher evolutionary rate (2.08 × 10⁻3 vs. 1.48 × 10⁻3 substitutions/site/year, P < 0.05), while CRF07_BC demonstrates a greater cluster formation capacity (56.6% vs. 37.1%, P < 0.05). CRF01_AE showed a higher mutation occurrence rate (5.18% vs. 2.49%, P < 0.05), particularly with non-nucleoside reverse transcriptase inhibitor (NNRTI) associated mutations (e.g., K101E). Although CRF07_BC had a lower resistance burden, the emergence of K103E mutations suggests a need for vigilance regarding potential decreases in sensitivity to newer NNRTIs. BDSKY modeling revealed that the Re for CRF01_AE dropped below 1 after 2016, whereas CRF07_BC's Re remains above 1, indicating that the risk of transmission still exists.

CONCLUSION

Subtype-specific strategies are critical: intensified resistance monitoring for CRF01_AE and cluster-focused interventions for CRF07_BC, particularly among young MSM.

Sequence Notes: Characterization of the Near-Full-Length Genome of Two Novel Unique Recombinant Genome (CRF01_AE/CRF79_0107, CRF01_AE/CRF07_BC) in Hebei, China

The global fight against human immunodeficiency virus (HIV) is complicated by its extensive genetic diversity, which arises from high mutation rates, rapid replication, and frequent recombination events. These factors lead to the emergence of numerous recombinant forms of HIV-1, contributing to the virus's adaptability and complicating prevention and treatment efforts. In this study, we identified two novel, unique recombinant forms (URFs) of HIV-1, CRF01_AE/CRF79_0107 and CRF01_AE/CRF07_BC, through near full-length genome sequence analysis. These URFs were detected in two individuals within the student men who have sex with men (MSM) population of Shijiazhuang, Hebei Province, China. Both utilized CRF01_AE as the underlying template, and PQ585802 represents a second-generation recombinant form comprising CRF01_AE and CRF79_0107. It is a novel recombinant form that was initially identified. PQ585803 represents a second-generation recombinant form, composed of CRF01_AE and CRF07_BC, and exhibits distinctive characteristics when compared to previously identified recombinant forms. This study underscores the urgent need for targeted public health measures focusing on high-risk populations, such as MSM and students, to curb the spread of HIV-1. Tailored education, enhanced access to prevention services, and strategies addressing risky behaviors are critical in reducing HIV-1 prevalence and mitigating the challenges posed by recombinant forms.

Near-Full-Length Genomic Characterization of Two Novel HIV-1 Unique Recombinants (CRF01_AE/CRF07_BC) and (CRF01_AE/CRF68_01B) in Shijiazhuang, Hebei Province, China

Heterosexual transmission (HETE) represents the predominant method of transmission for the human immunodeficiency virus type 1 (HIV-1) in Shijiazhuang, Hebei Province, China. The number of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) continues to increase in this region. In the present study, two novel URFs (TFH010919 and TFH010944) were identified, both derived from HETEs in the Shijiazhuang area. The phylogenetic and recombination breakpoint analyses conducted on the near-full-length genomes of the two novel URFs revealed that the CRF01_AE strains serve as the predominant backbones for both TFH010919 and TFH010944. TFH010919 is a second-generation recombinant form composed of CRF01_AE and CRF07_BC, whereas TFH010944 is formed by the combination of CRF01_AE and CRF68_01B. This finding indicates that HIV-1 prevalence among HETEs remains a significant concern, driven by complex sexual networks that facilitate the spread of diverse recombinant strains, providing more opportunities for the recombination of viruses. The emergence of these new URFs revealed the ongoing evolution of HIV-1 and underscores the critical need for continuous monitoring of viral diversity in Hebei Province and surrounding regions to control HIV-1 transmission within the vulnerable population and beyond.

Mortality and immunological indicators of men who have sex with men living with HIV on antiretroviral therapy: a 10-year retrospective cohort study in Southern China

BACKGROUND

The proportion of people living with HIV (PLHIV) in Guangxi who are men who have sex with men (MSM) increased rapidly to nearly 10% in 2023; notably, over 95% of this particular population is currently receiving antiretroviral therapy (ART). This study aimed to describe the survival of MSM PLHIV, depict the characteristics and trends of changes in CD4+ T cell counts, CD4+/CD8+ T cell ratio, and viral load, and explore immunological indicators that may be related to mortality during different stages of treatment.

METHODS

Immunological indicators of MSM PLHIV receiving ART were extracted and categorized into baseline, mid-treatment, and last values. These were then incorporated into the Cox models in the form of repeated measurements to evaluate the associations (Adjusted-hazard ratios, aHRs) and 95% confidence intervals (95% CIs) of these immunological indicators with mortality at different stages.

RESULTS

A total of 5,642 patients who met the criteria were enrolled in the study, and 160 died, representing a mortality of 2.8%. The first, median, and last values of the CD4+ count and the CD4+/CD8+ ratio in surviving patients were significantly greater than the corresponding values in nonsurviving patients (P < 0.001). Except for the first viral load (P = 0.379), the median and last viral loads of the former were significantly lower than those of the latter (P < 0.001). In Cox model, with 2,144 cases, immunological indicators of increased mortality risk included a baseline CD4+ count below 200 cells/µL (aHR: 4.58, 95% CI: 2.28-9.19), a median (aHR: 8.46, 95% CI: 3.05-23.46), and a final (aHR: 4.43, 95% CI: 1.06-18.45) ratio below 0.7 and a median (aHR: 9.47, 95% CI: 4.02-22.35) and final (aHR: 14.46, 95% CI: 4.50-46.50) viral load 100,000 copies/mL and above.

CONCLUSIONS

Mortality among MSM PLHIV on ART in Guangxi is relatively low, and both high viral loads and low CD4+/CD8+ T cell ratios during treatment and at recent follow-up are strongly predictive of a serious prognosis and should be closely monitored.

Characterizing HIV-1 transmission by genetic cluster analysis among newly diagnosed patients in the China-Myanmar border region from 2020 to 2023

Cluster analysis of HIV sequence can provide insights into viral transmission patterns in border regions. This study aims to illuminate the HIV-1 subtype distribution and transmission dynamics among newly diagnosed individuals in Dehong prefecture, a region along the China-Myanmar border. Among 948 participants with pol gene sequences, 36 HIV-1 subtypes were identified, with URFs (18.8%, 178/948) being the dominant strain, followed by CRF01_AE (18.5%, 175/948) and CRF07_BC (10.9%, 103/948). Additionally, 287 sequences (30.3%, 287/948) were grouped into 91 clusters, 31 of which contained both Chinese and Burmese individuals. Multivariable logistic regression indicated that men who have sex with men (MSM), CD4 + cell count of 200∼499, and 500 cells/μl and above, and CRF01_AE were risk factors for entering the network. Through the Chord diagram, we found frequent transmission relationships among heterosexual China male group, especially those over 35 years of age. Additionally, the correlation between heterosexual Myanmar female group and heterosexual China male group among cross-risk groups deserved to be emphasized. Furthermore, the network exhibited a growing trend over time, with the largest active transmission cluster identified in Ruili county. In conclusion, the HIV-1 subtype landscape in Dehong has become increasingly complex, and the region has faced risks of transmission from both domestic and international sources. Targeted intervention strategies should be implemented for MSM, heterosexual Chinese middle-aged and elderly men, and heterosexual Burmese young adults to mitigate these risks. These findings provided evidence-based insights for local government to formulate coordinated transnational intervention approaches.

National and Regional Molecular Epidemiology of HIV-1 - China, 2004-2023

Introduction

The genetic diversity of human immunodeficiency virus (HIV)-1 subtypes significantly influences the effectiveness of diagnostic tools, antiretroviral therapy (ART), and vaccine development. This study aimed to assess the regional and national prevalence of HIV-1 subtypes and recombinants in China between 2004 and 2023 using pol gene segment analysis.

Methods

We analyzed annual HIV/AIDS reports and pol gene segment sequences from all Chinese provinces between 2004 and 2023. The distribution of HIV-1 subtypes and recombinants across China and within its regions was estimated by multiplying the proportion of each subtype, circulating recombinant form (CRF), and unique recombinant form (URF) in each province by the corresponding number of reported HIV infections.

Results

Analysis of 94,476 pol gene segments from 31 provinces revealed that CRF01_AE strain accounted for 32.1% of HIV-1 infections during 2004-2023, while CRF07_BC lineage represented 39.1%. CRF08_BC strain contributed 9.2%, followed by subtype B (8.7%) and CRF55_01B (2.4%). Other CRFs collectively comprised 6.0% of infections, while URFs and other subtypes accounted for 1.3% and 1.1%, respectively.

Conclusions

The study revealed significant regional variations and temporal changes in the proportions of HIV-1 CRFs, subtypes, and URFs across China, emphasizing the importance of continued surveillance of strain distribution patterns.

Men with a history of commercial heterosexual contact play essential roles in the transmission of HIV-1 CRF55_01B from men who have sex with men to the general population in Guangxi, China

Background

There is increasing focus on HIV-1 CRF55_01B in China. However, there is limited information regarding the dissemination of CRF55_01B across different regions and populations in Guangxi. This study was performed to elucidate the evolutionary history of the introduction and dissemination of CRF55_01B in Guangxi.

Methods

Molecular network and phylogenetic analyses were used to investigate the transmission characteristics of CRF55_01B in China. The analyses particularly focused on the cross-provincial spatial and temporal transmission patterns between Guangdong Province and Guangxi, as well as the transmission dynamics among different regions and populations within Guangxi.

Results

In total, 2226 partial pol sequences of CRF55_01B strains sampled from 2007 to 2022 were collected, including 1895 (85.09%) sequences from Guangdong, 199 (8.94%) sequences from Guangxi, and 172 (7.59%) sequences from other provinces of China. Most people living with HIV in Guangxi were infected with HIV-1 through heterosexuals (52.76%). Among these, 19.10% had a history of commercial heterosexual contact (CHC) and 15.58% had a history of non-marital non-commercial heterosexual contact (NMNCHC). Overall, 1418 sequences were identified in the molecular network. Notably, the sequences from Guangdong Province were most closely linked to those from Guangxi. Phylogenetic analysis showed that CRF55_01B was first introduced from Shenzhen City to Nanning City around 2007. Subsequently, CRF55_01B established local transmission within Guangxi, with Nanning City serving as the transmission center from 2008 to 2017. After 2017, the CRF55_01B strain spread to other regions of Guangxi. Men who have sex with men (MSM) and men with a history of CHC have played a significant role in the transmission of CRF55_01B among different populations in Guangxi.

Conclusions

This study provides evidence on the transmission trajectory of CRF55_01B among different regions and populations in Guangxi. Given the bridging role of men with a history of CHC in the dissemination of CRF55_01B from MSM to the general population, it is imperative to enhance surveillance among key populations to mitigate the secondary transmission of HIV-1.

The distinct spatiotemporal evolutionary landscape of HBV and HDV largely determines the unique epidemic features of HDV globally

Chronic infection of hepatitis B virus (HBV) and hepatitis D virus (HDV) causes the most severe form of viral hepatitis. Due to the dependence on HBV, HDV was deemed to co-evolve and co-migrate with HBV. However, we previously found that the naturally occurred HDV/HBV combinations do not always reflect the most efficient virological adaptation (Wang et al., 2021). Moreover, regions with heavy HBV burden do not always correlate with high HDV prevalence (e.g., East Asia), and vice versa (e.g., Central Asia). Herein, we systematically elucidated the spatiotemporal evolutionary landscape of HDV to understand the unique epidemic features of HDV. We found that the MRCA of HDV was from South America around the late 13th century, was globally dispersed mainly via Central Asia, and evolved into eight genotypes from the 19th to 20th century. In contrast, the MRCA of HBV was from Europe ∼23.7 thousand years ago (Kya), globally dispersed mainly via Africa and East Asia, and evolved into eight genotypes ∼1100 years ago. When HDV stepped in, all present-day HBV genotypes had already formed and its global genotypic distribution had stayed stable geographically. Nevertheless, regionalized HDV adapted to local HBV genotypes and human lineages, contributing to the global geographical separation of HDV genotypes. Additionally, a sharp increase in HDV infections was observed after the 20th century. In conclusion, HDV exhibited a distinct spatiotemporal distribution path compared with HBV. This unique evolutionary relationship largely fostered the unique epidemic features we observe nowadays. Moreover, HDV infections may continue to ramp up globally, thus more efforts are urgently needed to combat this disease.

Molecular network characteristics and drug resistance analysis of 392 newly reported MSM HIV/AIDS cases in Chongqing, China

To comprehensively investigate the molecular transmission patterns of HIV-1 genotypes among men who have sex with men (MSM) in Chongqing, we employed 392 pol sequences of MSM to construct a phylogenetic tree and gene transmission network. Among the viral subtypes, CRF07_BC accounted for 73.2% (287/392) and CRF01_AE accounted for 20.7% (81/392), emerging as the predominant subtypes in this investigation. Additionally, we observed the presence of CRF55_01B, subtype B, CRF08_BC and other circulating recombinant forms. The HIV-1 molecular network was constructed with a gene distance threshold of 1.5%, resulting in an entry rate of 61.4% (241/392). Within the network, we identified a total of 23 molecular clusters, with the largest cluster being the CRF07_BC molecular cluster comprising 148 node values. Transmitted drug-resistance (TDR) mutations were found in 4.34% of the cases, with 1.79% associated with protease inhibitors (PIs), 0.51% with nucleoside reverse transcriptase inhibitors (NRTIs), and 2.55% with non-nucleoside reverse transcriptase inhibitors (NNRTIs). Statistical analysis indicated a higher enrollment rate in the HIV-1 molecular network among infected individuals with the CRF07_BC subtype, those identifying with same-sex sexual roles as "vers," and individuals with higher education levels. This suggests the need for strengthened investigation and intervention in this population to prevent the formation of larger transmission clusters. Furthermore, continuous monitoring of the HIV-1 molecular dynamics network is necessary to promptly and accurately track changes in molecular epidemic characteristics.

Near-full-length genome analysis of two novel HIV second recombinant forms in Hebei, China

The number of individuals infected with HIV-1 among men who have sex with men (MSM) has risen rapidly in recent years in China, and the subtypes CRF01_AE, CRF07_BC, and B, as well as many novel unique recombinant forms (URFs) are prevalent among them. Co-circulation of strains among MSM populations allows the generation of circulating recombinant forms (CRFs) and URFs. In this study, we identified two new URFs from two HIV-1-positive subjects who were infected through homosexual contact in Hebei, China. Analysis of near-full-length genome sequences, using phylogenetic and recombination analysis showed that the two URFs originated from CRF01_AE, CRF07_BC, and B, and CRF01_AE segments in the backbone of the URFs were derived from cluster 4 of CRF01_AE. The CRF07_BC segments of two URFs were clustered with 07BC_N in a phylogenetic tree. The identification of novel URFs with complex genomic structures shows that it is necessary to strengthen surveillance of HIV-1 variants in MSM populations in this region.

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.

Criteria for classification, nomenclature, and reference sequence selection for HIV sub-subtypes of CRF01_AE and CRF07_BC strains in China

The available knowledge regarding classification, nomenclature, and reference sequence selection for the various sub-subtypes of circulating recombinant forms (CRFs) is inadequate to fulfill the growing demands of research focused on HIV prevention. We analyzed the spread of CRF01_AE and CRF07_BC strains, mainly in China, to complement and update the existing nomenclature and to propose a reference sequence selection criteria for sub-subtypes of CRFs.

Genomic Characteristics of the New HIV-1 CRF07_BC K28E32 Variant

Accompanied with the appearance and prevalence of the new K28E32 variant among men who have sex with men, HIV-1 circulating recombinant form 07_BC (CRF07_BC) was becoming the most predominant subtype circulating in China. The K28E32 variant with five specific mutations in reverse transcriptase coding region appears to have significantly higher in vitro HIV-1 replication ability than the wild-type strain. In this study, we characterized the special mutations/substitutions in the K28E32 variant at the genomic level. Ten specific mutations that rarely appeared in other six main HIV-1 subtypes/CRFs (A-D, CRF01_AE, and CRF02_AG) were identified in the coding genes/regions of the K28E32 variant, including S77L and a novel seven-amino acid detection (32DKELYPL38) (p6Δ7) in p6, I135L in integrase, T189S in Vif, H/Y15L/F in Vpr, I264V/A and LV/LI328-329VG in gp41, and H82C and S97P in Rev. The special locations of the novel p6Δ7, and gp41 mutations I264V/A and LV/LI328-329VG in crucial protein functional domains suggest that these mutations might be functionally important to the K28E32 variant. Furthermore, eight specific substitutions were identified in Rev responsive element (RRE) of the K28E32 variant, and were revealed to increase the stability of RRE structure with a lower minimum free energy. Whether these mutations/substitutions contribute to improved transmissibility of the CRF07_BC K28E32 variant needs to be further confirmed.

Genetic Diversity and Characteristics of Drug Resistance Among Treatment-Naive People Living with HIV in Xi'an, China

Purpose

The genetic diversity and genetic predisposition for drug resistance mutations are the primary features of human immunodeficiency virus type 1 (HIV-1), which could cause the incidence of failure of antiretroviral therapy (ART). This study investigates the distribution of various HIV-1 genotypes and the incidence of pretreatment drug resistance (PDR) in the antiretroviral-naive HIV-1 infected participants in Xi'an, China.

Patients and Methods

In this study, a cross-sectional analysis was carried out at the Xi'an Eighth Hospital between January 2020 and December 2021 among newly-diagnosed ART-naive HIV-1 infected participants. A nested PCR technique was used for amplifying the target segment of 1.3 kb present in the pol gene that spanned the reverse transcriptase and the protease regions. HIV-1 genotypes and the PDR-associated mutations were identified using the Stanford HIV Drug Resistance Database.

Results

A total of 317 pol gene sequences were retrieved, amplified, and sequenced. The circulating recombinant form (CRF), CRF07_BC (51.7%) was seen to be the most prevalent HIV-1 genotype, followed by other genotypes like CRF01_AE (25.9%), B (14.2%), and CRF55_01B (4.7%). PDR was found in 18.3% of the population. The PDR mutation frequency in the non-nucleoside reverse transcriptase inhibitor (NNRTI) (16.1%) was significantly higher compared to that of the nucleoside reverse transcriptase inhibitor (NRTI) (4.4%) and the protease inhibitor (0.9%). V179D/E (both were 4.4%) was seen to be the most predominant type of NNRTI mutation. K65R and M184V (1.3%) were the most frequent NRTI-associated mutations. About half (48.3%) of the sequenced HIV-1 strains that had mutations could show a potential low-level NNRTI resistance owing to V179D/E. Multivariate regression analysis revealed one PDR mutation associated with subtype CRF01_AE (p=0.002) and CRF55_01B (p<0.001) as a higher risk mutation.

Conclusion

Diverse and complex HIV-1 genotypes are distributed in Xi'an, China. Considering new evidence, it is necessary to screen for baseline HIV-1 drug resistance among the newly-diagnosed HIV-1 individuals.

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.