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Background: Transmitted drug resistance (TDR) is an increasingly prevalent problem worldwide, which will significantly compromise the effectiveness of HIV treatments. However, in Nanjing, China, there is still a dearth of research on the prevalence and transmission of TDR among ART-naïve HIV-1-infected individuals. This study aimed to understand the prevalence and transmission of TDR in Nanjing., Methods: A total of 1,393 participants who were newly diagnosed with HIV-1 and had not received ART between January 2019 and December 2021 were enrolled in this study. HIV-1 pol gene sequence was obtained by viral RNA extraction and nested PCR amplification. Genotypes, TDR and transmission cluster analyses were conducted using phylogenetic tree, Stanford HIV database algorithm and HIV-TRACE, respectively. Univariate and multivariate logistic regression analyses were performed to identify the factors associated with TDR., Results: A total of 1,161 sequences were successfully sequenced, of which CRF07_BC (40.6%), CRF01_AE (38.4%) and CRF105_0107 (6.3%) were the main HIV-1 genotypes. The overall prevalence of TDR was 7.8%, with 2.0% to PIs, 1.0% to NRTIs, and 4.8% to NNRTIs. No sequence showed double-class resistance. Multivariate logistic regression analysis revealed that compared with CRF01_AE, subtype B (OR = 2.869, 95%CI: 1.093-7.420) and female (OR = 2.359, 95%CI: 1.182-4.707) were risk factors for TDR. Q58E was the most prevalent detected protease inhibitor (PI) -associated mutation, and V179E was the most frequently detected non-nucleoside reverse transcriptase inhibitor (NNRTI) -associated mutation. A total of 613 (52.8%) sequences were segregated into 137 clusters, ranging from 2 to 74 sequences. Among 44 individuals with TDR (48.4%) within 21 clusters, K103N/KN was the most frequent TDR-associated mutation (31.8%), followed by Q58E/QE (20.5%) and G190A (15.9%). Individuals with the same TDR-associated mutations were usually cross-linked in transmission clusters. Moreover, we identified 9 clusters in which there was a transmission relationship between drug-resistant individuals, and 4 clusters in which drug-resistant cases increased during the study period., Conclusion: The overall prevalence of TDR in Nanjing was at a moderate level during the past 3 years. However, nearly half of TDR individuals were included in the transmission clusters, and some drug-resistant individuals have transmitted in the clusters. Therefore, HIV drug-resistance prevention, monitoring and response efforts should be sustained and expanded to reduce the prevalence and transmission of TDR in Nanjing., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Xu, Shi, Dong, Ding, Wu, Li, Zhang, Qiao, Li and Zhu.)

To understand the epidemiology, evolutionary and transmission characteristics of HIV-1 CRF07_BC in Nanjing, China. One hundred and fifty-nine patients with HIV-1 CRF07_BC were recruited. DNA sequencing, phylogenetic analysis, and molecular transmission cluster analysis were conducted to determine the molecular epidemiology and evolutionary characteristics. Of these HIV-1-infected patients, 95.6% were male, and men who sex with men (76.7%) were the main transmission route. Only 34.0% of these cases were born in Nanjing, and most of them (64.8%) reported having multiple sex partners in the last 6 months. The maximum likelihood phylogenetic analyses of HIV-1 CRF07_BC revealed two lineages. Overall, 67.3% of Nanjing sequences were connected to at least one other individual distributed in 11 clusters, and the average degree was 21.2 with range (1-178). The clustered patients were more likely to be male. The time to a most recent common ancestor for the early HIV-1 CRF07_BC circulating in Nanjing was estimated to be 1998.71[1997.36-2001.07]. The mean estimated evolutionary rate for the epidemic cluster was slightly lower at 2.38[2.12-2.65]  ×  10 -3 per site per year with the relaxed exponential clock model. HIV-1 CRF07_BC was transmitted into Nanjing more than 20 years ago from Yunnan and has become one of the most predominant subtypes with a higher evolutionary rate than before., (© 2020 Wiley Periodicals, Inc.)

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.

Objective: This study aimed to investigate the epidemiological characteristics and HIV/AIDS-related knowledge, attitudes and practice (KAP) among HIV-positive college students., Design: A cross-sectional study., Setting: Five districts of Nanjing, China., Participants: A total of 156 college students with newly diagnosed HIV infection between September 2015 and July 2017., Main Outcome Measures: Social-demographic characteristics, mode of HIV acquisition, infection of sexually transmitted diseases, risky sexual behaviours and HIV/AIDS-related KAP were collected by a face-to-face questionnaire administered by trained interviewers., Results: About 98.7% (154/156) of HIV-positive college students in our study were men, and 96.1% (148/154) of them were infected by sexual intercourse with men. More than half (52.5%, 82/156) of participants were freshmen or sophomores. Nearly 30% (44/154) of male students did not realise the severe status of the HIV/AIDS epidemic among students who are men who have sex with men (MSM). More than four-fifths of male students did not know if their male regular (83.0%, 93/112) or casual (95.9%, 94/98) sexual partners were HIV-positive, while less than half of them had high-risk perceptions towards HIV infection from male regular and occasional sexual partners. Approximately one-half and four-fifths of male students had more than two regular (54.5%, 61/112) and occasional (79.6%, 78/98) partners during lifetime, respectively. However, only 62.5% (70/112) and 66.3% (65/98) of male students used condoms consistently during sexual intercourse with regular and casual partners, respectively. Geosocial networking apps have become the most dominant way for male students to seek sexual partners., Conclusions: This study reported a low level of HIV/AIDS-related knowledge, a high level of exposure to risky sexual behaviours and some valuable epidemiological characteristics among HIV-positive college students, which highlighted the importance of carrying out HIV/AIDS prevention education and risk warning education early and timely towards college students on campus., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Objective: To investigate the evolutionary dynamics and characteristic of the molecular transmission networks of HIV-1 CRF01_AE in Nanjing., Methods: Viral samples were collected from 580 newly diagnosed HIV-1-infected patients. HIV-1 pol sequences were obtained and used for for molecular evolutionary analyses. The ML trees were constructed by MEGA 6.0 using under GTR+ G + I model with 1000 bootstrap replicates. The emergence and estimation of tMRCA and the evolutionary rate of the different CRF01_AE clusters were inferred using Bayesian phylogenetic analysis approaches implemented in the BEAST package. Pairwise genetic distances were calculated under the Tamura-Nei 93 model, a genetic distance threshold of ≤1.2% was used to identify potential transmission clusters. Network diagrams were plotted using Cytoscape 3.3.0., Results: Of these HIV-1-infected patients, 551 (91.5%) were males. The largest number of infections were attributed to homosexual (462, 79.7%). A total of 518 full-length pol genes were successfully amplified, based on the phylogenetic analysis CRF01_AE was the most predominantly circulating strain (45.0%, 233/518). As shown in the ML tree, three distinct clusters were observed. The 'Nanjing lineage' 1, 2, 3 has an estimated tMRCA around1996.61, 1993.61, 1984.61 respectively. Of 233 Nanjing sequences, 123 (55.2%) distributed in 30 molecular clusters, average Links/node was 7.8 with range (1-33), most of Nanjing strains shared links with local strains., Conclusion: HIV-1 CRF01_AE was the most predominantly circulating strain, the epidemic of CRF01_AE in Nanjing was driven by multiple clusters of HIV-1 strains, and most CRF01_AE stains in our study were estimated to have originated in China in the 1990s., (Copyright © 2019 Elsevier B.V. All rights reserved.)

We aimed to investigate the molecular epidemic characteristics and viral transmission patterns of HIV-1 in a typical labor export area, Guangyuan city, China. Based on conducting phylogenetic trees and molecular transmission networks, a phylogenetic analysis was performed on HIV-1 pol sequences obtained from 211 migrant-history workers, 83 non-migrant-history individuals, and 21 migrant-history unknown individuals between January, 2012 and February, 2017 in Guangyuan city. Phylogenetic analysis revealed that CRF07_BC (48.3%, n = 152) and CRF01_AE (33.3%, n = 105) were the dominant strains in Guangyuan city, and circulated by multiple lineages with various epidemic characteristics. Geographic network analysis showed that Guangyuan city-related sequences with 20.3% CRF07_BC and 28.3% CRF01_AE were linked to that of other provinces, compared to that with 1.7% CRF07_BC and 5.0% CRF01_AE in cities of Sichuan. Molecular transmission network analysis further illustrated that migrant-history workers linked more sequences from other provinces than non-migrant-history individuals in both CRF07_BC (29.3% versus 0.0%, P = 0.013) and CRF01_AE (40.5% versus 10.0%, P = 0.001) networks. Our results highlighted that migrant-history workers in recent year played a vital role in fueling HIV-1 epidemic in Guangyuan city. Molecular transmission network analysis could be a useful approach for disclosing the transmission mechanism of HIV, which should be used in prevention and intervention efforts.

Objectives: The epidemic of HIV-1 CRF01_AE has become a major public health issue in China. This study aimed to characterise the transmission patterns of genetic networks for CRF01_AE nationwide and elucidate possible opportunities for prevention., Methods: We isolated and conducted genetic transmission network analysis of all available CRF01_AE pol sequences (n=4704) from China in the Los Alamos HIV sequence database., Results: A total of 1391 (29.6%) sequences were identified as belonging to 400 separate networks. Of men who have sex with men (MSM) in the networks, 93.8% were linked to other MSM and only 2.4% were linked to heterosexual women. However, 11.8% heterosexual women in the networks were linked to MSM. Lineages composed mainly of MSM had higher transmission than those that were mostly heterosexuals. Of the 1391 individuals in networks, 513 (36.9%) were linked to cases diagnosed in different provinces. The proportion of individuals involved in inter-province links was interrelated with the number of migrant people (Spearman's r =0.738, p =0.001)., Conclusions: The outcome of this study could help improve our ability to understand HIV transmission among various regions and risk groups in China, and highlighted the importance of targeting MSM and migrants by prevention and intervention efforts., Competing Interests: Competing interests: None declared., (© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)

Objective: To investigate the viral genetic evolution, spatial origins and patterns of transmission of HIV-1 subtype B in Shanghai, China., Methods: A total of 242 Shanghai subtype B and 1519 reference pol sequences were subjected to phylogenetic inference and genetic transmission network analyses., Results: Phylogenetic analysis revealed that subtype B strains circulating in Shanghai were genetically diverse and closely associated with viral sequence lineages in Beijing (76 of 242 [31.4%]), Central China (Henan/Hebei/Hunan/Hubei) (43 of 242 [17.8%]), Chinese Taiwan (20 of 242 [8.3%]), Japan (6 of 242 [2.5%]), and Korea (7 of 242 [2.9%]), suggesting multiple introductions into Shanghai from mainland China and Taiwan, Japan, and Korea. Interestingly, a monophyletic Shanghai lineage (SH-L) (36 of 242 [14.9%]) of HIV-1 subtype B most likely originated from an Argentine strain, transferred through Liaoning infected individuals. In-depth analyses of 195 Shanghai subtype B sequences revealed that a total of 37.9% (n = 74) sequences contributed to 35 transmission networks, whereof 33.8% (n = 25) of the sequences associated with infected individuals from other provinces., Conclusions: Our new findings reflect the evolution complexity and transmission dynamics of HIV-1 subtype B in Shanghai, which would provide critical information for the design of effective prevention measures against HIV transmission., (Copyright © 2017 The British Infection Association. Published by Elsevier Ltd. All rights reserved.)

To explore the evolutionary dynamics and molecular transmission patterns of HIV-1 CRF01&#95;AE in depth among men who have sex with men (MSM) in Shanghai, we constructed phylogenetic tree and genetic transmission networks based on 1, 152 pol sequences from MSM, 282 from other risk groups and 795 references. Phylogenetic analyses identified two distinct major CRF01&#95;AE lineages and a Shanghai-based sub-lineage. The estimated tMRCAs for lineage 1 and 2 were 1996.0 (1992.9-1999.2) and 1997.8 (1994.3-2001.4), respectively. Of the 1, 152 MSM, 681 (59.1%) were identified as belonging to 241 separate networks. Of these 681 individuals in networks, 74.2% were linked to cases diagnosed in different years, 4.3% were linked to heterosexual women, and 0.7% were linked to persons who inject drugs. A total of 71 networks including 180 individuals diagnosed in Shanghai with the same domicile were found. Recent infection (P = 0.022) and sampling year after 2011 (P < 0.001) were significantly associated with potential transmission links among the networks. Besides, a significant transmission of viruses with drug resistant mutations at V179D/E were found in the networks. Given these findings, we propose that genetic transmission analysis is a useful tool in HIV intervention strategies to curb the spread of virus and promoting public health.

To estimate the nationwide and regional distribution of HIV-1 genotypes in China in the past three decades, province-specific HIV-1 molecular epidemiology data were derived from 260 independent studies of HIV molecular prevalence through searching PubMed, VIP Chinese Journal Database (VIP), China National Knowledge Infrastructure, and Wanfang Data from January 1981 to December 2015. The nationwide and regional distribution of HIV-1 genotypes was estimated by weighting the genotype distribution from each province- and risk-specific subpopulation with the number of reported cases in the corresponding subgroups in the relevant periods. A sharp transition of HIV-1 subtypes and recombinant distribution was observed in various risk groups and regions over time. CRF01&#95;AE has rapidly surged among almost all risk groups and in all areas, and it has become dominant among men who have sex with men and heterosexuals. A wide variety of new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were rapidly appearing in several risk groups and regions. After 2007, CRF01&#95;AE was the most prevalent strain, accounting for 42.5% of all national infections, followed by CRF07&#95;BC (28.9%), subtype B'/B (10.9%), CRF08&#95;BC (10.0%), and subtype C (2.8%). URFs and other CRFs were responsible for 2.6% and fewer than 1% of infections nationwide, respectively. The nationwide and regional distributions of HIV-1 subtypes and recombinants were sharply shifting in China. CRF01&#95;AE and new CRFs played an increasing role in the nationwide or regional HIV pandemic. The nationwide diversity of HIV-1 poses a formidable challenge to HIV vaccine development and disease prevention.

To characterize the current frequency of HIV-1 coreceptor usage in China and assess the candidacy of CCR5 antagonists for treatment of HIV infections. In addition, we aimed to evaluate the potential of X4/DM virus transmission in recently infected men who have sex with men (MSM) individuals.Viral tropism testing was performed on samples from 399 MSM individuals and on 2408 available Chinese HIV-1 V3 sequences downloaded from the Los Alamos database using Geno2pheno and WebPSSM in combination. The transmission clusters were evaluated using pol sequences from 291 recently infected MSM with a maximum likelihood, maximum pairwise distance, and Bayesian inference.A higher prevalence of X4/DM viruses was observed in individuals infected with CRF01&#95;AE strains than with subtype B (27.8% vs 12.2%, P < 0.001) and CRF07&#95;BC/CRF08&#95;BC/C (27.8% vs 1.0%, P < 0.001). Seven clusters containing only X4/DM viruses were detected in 40 transmission clusters. No significant difference in proportions between clustered X4/DM viruses and R5 viruses was found (P = 0.683).The high proportion of CXCR4 usage for CRF01&#95;AE strains may result in the loss of susceptibility to maraviroc since CRF01&#95;AE has become the most prevalent strains in China. The high prevalence of X4/DM viruses among recently CRF01&#95;AE-infected individuals may be attributed to the stochasticity of HIV transmission, which implied that the early viral tropism screening and treatment would be the key for controlling the epidemic of CRF01&#95;AE strains in China., Competing Interests: The authors have no conflicts of interest to disclose.

The HIV-1 epidemic among men who have sex with men (MSM) has been spreading throughout China. Shanghai, a central gathering place for MSM, is facing a continuously increasing incidence of HIV-1 infection. In order to better understand the dynamics of HIV-1 diversity and its influence on patient's immune status at baseline on diagnosis, 1265 newly HIV-1-infected MSM collected from January 2009 to December 2013 in Shanghai were retrospectively analyzed for genetic subtyping, CD4+T cell counts, and viral loads. HIV-1 phylogenetic analysis revealed a broad viral diversity including CRF01&#95;AE (62.13%), CRF07&#95;BC (24.51%), subtype B (8.06%), CRF55&#95;01B (3.24%), CER67&#95;01B (0.95%), CRF68&#95;01B (0.4%), CRF08&#95;BC (0.08%) and CRF59&#95;01B (0.08%). Twenty-four unique recombination forms (URFs) (1.98%) were identified as well. Bayesian inference analysis indicated that the introduction of CRF01&#95;AE strain (1997) was earlier than CRF07&#95;BC strain (2001) into MSM population in Shanghai based on the time of the most recent common ancestor (tMRCA). Three epidemic clusters and five sub-clusters were found in CRF01&#95;AE. Significantly lower CD4+T cell count was found in individuals infected with CRF01&#95;AE than in those infected with CRF07&#95;BC infection (P<0.01), whereas viral load was significantly higher those infected with CRF01&#95;AE than with CRF07&#95;BC (P<0.01). In addition, the patients with >45 years of age were found to have lower CD4+T cell counts and higher viral loads than the patients with <25 years of age (P<0.05). This study reveals the presence of HIV-1 subtype diversity in Shanghai and its remarkable influence on clinical outcome. A real-time surveillance of HIV-1 viral diversity and phylodynamics of epidemic cluster, patient's baseline CD4+T cell count and viral load would be of great value to monitoring of disease progression, intervention for transmission, improvement of antiretroviral therapy strategy and design of vaccines.

Men who have sex with men (MSM) have recently accounted for an alarmingly increasing proportion of HIV-1 transmission in China. In order to investigate the immune status as a result of CRF01&#95;AE infection and CXCR4 co-receptor usage in a young Shanghai-based HIV-1-infected MSM population in Shanghai, 364 HIV-1-infected MSM with average age of 22.7 years old, newly diagnosed between Jan 2009 and Jul 2013 were analyzed for CD4+T cell count, subtyping using phylogenetic analysis, and viral co-receptor tropism using Geno2pheno and webPSSM in combination. A total of 276 individuals were identified as recently infected. Subtype assignment were as follows: 176 (63.8%) CRF01&#95;AE, 77 (27.9%) CRF07&#95;BC, and 23 (8.3%) subtype B. Besides, 24 second-generation recombinant strains were identified. A lower CD4+T cell count at baseline survey was observed among CRF01&#95;AE strain-infected individuals, compared to those who were infected with CRF07&#95;BC (P<0.01). The frequency of baseline CD4+T cell count <200 was higher and the frequency of CD4 T counts >500 lower in CRF01&#95;AE infection than CRF07&#95;BC infection. It is worth noting that 32.4%-40.9% of CRF01&#95;AE strain-infected individuals were predicted to carry CXCR4-tropic viruses whereas none of CRF07&#95;BC and subtype B were found to be as CXCR4-tropic viruses (P<0.001). As could be expected CXCR4 tropism was associated with lower CD4 T counts. This study revealed that CRF01&#95;AE strains with high frequency of CXCR4 tropism are prevailing in the young MSM population in China and could potentially cause a severe loss of CD4+T cell count and rapid disease progression. A regular surveillance of HIV-1 subtypes, CD4+T cell count and viral co-receptor usage would be greatly beneficial for effectively monitoring disease progression, improvement of antiretroviral therapy strategy and prompt intervention of transmission.

Background: Asian HIV epidemics are concentrated among particular behavioural groups, but large variations exist in epidemic types, timing, and geographical spread between countries and within countries, especially in China. We aimed to understand the complexity of HIV epidemics in China by systematically analysing prevalence trends by data source, region, population group, and time period., Methods: We collected HIV prevalence data from official national sentinel surveillance sites at the provincial level from Jan 1, 1995, to Dec 31, 2010. We also searched PubMed, VIP Chinese Journal Database (VIP), China National Knowledge Infrastructure, and Wanfang Data from Jan 1, 1990, to Dec 31, 2012, for independent studies of HIV prevalence. We integrated both sets of data, and used an intraclass correlation coefficient test to assess the similarity of geographical pattern of HIV disease burden across 31 Chinese provinces in 2010. We investigated prevalence trends (and 95% CIs) to infer corresponding incidence by region, population group, and year., Findings: Of 6850 articles identified by the search strategy, 821 studies (384,583 drug users, 52,356 injecting drug users, 186,288 female sex workers, and 87,834 men who have sex with men) met the inclusion criteria. Official surveillance data and findings from independent studies showed a very similar geographical distribution and magnitude of HIV epidemics across China. We noted that HIV epidemics among injecting drug users are decreasing in all regions outside southwest China and have stabilised at a high level in northwest China. Compared with injecting drug users, HIV prevalence in female sex workers is much lower and has stabilised at low levels in all regions except in the southwest. In 2010, national HIV prevalence was 9·08% (95% CI 8·04-10·52) in injecting drug users and 0·36% (0·12-0·71) in female sex workers, whereas incidence in both populations stabilised at rates of 0·57 (0·43-0·72) and 0·02 (0·01-0·04) per 100 person-years, respectively. By comparison, HIV prevalence in men who have sex with men increased from 1·77% (1·26-2·57) in 2000, to 5·98% (4·43-8·18) in 2010, with a national incidence of 0·98 (0·70-1·25) per 100 person-years in 2010. We recorded strong associations between HIV prevalence among at-risk populations in each province, supporting the existence of overlap in risk behaviours and mixing among these populations., Interpretation: HIV epidemics in China remain concentrated in injecting drug users, female sex workers, and men who have sex with men. HIV prevalence is especially high in southwest China. Sex between men has clearly become the main route of HIV transmission., (Copyright © 2013 Elsevier Ltd. All rights reserved.)