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Pan W, Gao N, Hu B, Yin Y, Shen Y, Yang X, Wei W, Ni J, Dai S, Miao L, Qin Y, Jin L, Guo H, Wu J. The characteristics of HIV-1 subtype B on phylogenetic dynamic and molecular transmission network in Fuyang City, China, 2011 to 2019. Front Public Health 2023; 11:1092376. [PMID: 36935727 PMCID: PMC10015982 DOI: 10.3389/fpubh.2023.1092376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 03/08/2023] Open
Abstract
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.
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Affiliation(s)
- Wenting Pan
- Anhui No. 2 Provincial People's Hospital, Hefei, China
- Department of Health Inspection and Quarantine, School of Public Health, Anhui Medical University, Hefei, China
| | - Nannan Gao
- Department of Health Inspection and Quarantine, School of Public Health, Anhui Medical University, Hefei, China
| | - Bing Hu
- Department of AIDS Prevention and Control, Fuyang Center for Disease Control and Prevention, Fuyang, China
| | - Yueqi Yin
- School of Medicine, Ningbo University, Ningbo, China
| | - Yuelan Shen
- Department of AIDS Prevention and Control, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Xiaohui Yang
- Department of AIDS Prevention and Control, Fuyang Center for Disease Control and Prevention, Fuyang, China
| | - Wei Wei
- Department of AIDS Prevention and Control, Fuyang Center for Disease Control and Prevention, Fuyang, China
| | - Jie Ni
- Department of AIDS Prevention and Control, Fuyang Center for Disease Control and Prevention, Fuyang, China
| | - Seying Dai
- Department of AIDS Prevention and Control, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Lifeng Miao
- Department of AIDS Prevention and Control, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Yizu Qin
- Department of AIDS Prevention and Control, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Lin Jin
- Department of AIDS Prevention and Control, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Hongxiong Guo
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- *Correspondence: Hongxiong Guo
| | - Jianjun Wu
- Department of Health Inspection and Quarantine, School of Public Health, Anhui Medical University, Hefei, China
- Department of AIDS Prevention and Control, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Jianjun Wu
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Hu Z, Liu Y, Wang J, Meng Z, Leuba SI, Wei J, Duan X, Chu Z, Chen M, Shang H, Xu J. Frequently Transmission and Close Relationship Among Immigrants in the China-Myanmar Border Region Indicated by Molecular Transmission Analysis From a Cross-Sectional Data. Front Med (Lausanne) 2022; 8:693915. [PMID: 35572804 PMCID: PMC9094042 DOI: 10.3389/fmed.2021.693915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Zhili Hu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yingjie Liu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jibao Wang
- Department of STD/AIDS Prevention and Control, Dehong Prefecture Center for Disease Control and Prevention, Mangshi, China
| | - Zhefeng Meng
- Key Laboratory of Digestive Cancer Full Cycle Monitoring and Precise Intervention of Shanghai Municipal Health Commission, Minhang Hospital, Fudan University, Shanghai, China
| | - Sequoia I Leuba
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jie Wei
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xing Duan
- Department of STD/AIDS Prevention and Control, Dehong Prefecture Center for Disease Control and Prevention, Mangshi, China
| | - Zhenxing Chu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Min Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Hong Shang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Junjie Xu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, China.,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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3
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Zhang Y, Dai J, Li Z, Ma Y, Chen H, Dong L, Jin X, Yang M, Zeng Z, Sun P, Hu A, Chen M. Using molecular network analysis to explore the characteristics of HIV-1 transmission in a China-Myanmar border area. PLoS One 2022; 17:e0268143. [PMID: 35522692 PMCID: PMC9075624 DOI: 10.1371/journal.pone.0268143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/23/2022] [Indexed: 11/19/2022] Open
Abstract
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.
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Affiliation(s)
- Yuying Zhang
- School of Public Health, Kunming Medical University, Kunming, Yunnan, China
| | - Jie Dai
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Zhengxu Li
- Division for AIDS/STD Control and Prevention, Baoshan Center for Disease Control and Prevention, Baoshan, Yunnan, China
| | - Yanling Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Huichao Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Lijuan Dong
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Xiaomei Jin
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Min Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Zhijun Zeng
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Pengyan Sun
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Anyan Hu
- Division for AIDS/STD Control and Prevention, Baoshan Center for Disease Control and Prevention, Baoshan, Yunnan, China
- * E-mail: (MC); (AH)
| | - Min Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- * E-mail: (MC); (AH)
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4
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Chen M, Ma Y, Chen H, Dai J, Luo H, Yang C, Dong L, Jin X, Yang M, Yang L, Song L, Song Z, Jia M. Spatial clusters of HIV-1 genotypes in a recently infected population in Yunnan, China. BMC Infect Dis 2019; 19:669. [PMID: 31357947 PMCID: PMC6664787 DOI: 10.1186/s12879-019-4276-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 07/10/2019] [Indexed: 12/04/2022] Open
Abstract
Background As a gateway for HIV-1 in China, Yunnan has experienced dramatic changes in HIV-1 epidemics, during which HIV-1 genotypes have become complex. To track dynamic changes in HIV-1 genotypes, an HIV-1 molecular epidemiological study was implemented in the recently infected population in Yunnan. Methods From 6,357 HIV-1-positive samples diagnosed during the first half of 2015 in Yunnan, 586 samples were identified as recent infections with BED-capture enzyme immunoassay (CEIA) and were subjected to phylogenetic analyses. Spatial scanning analyses for the main HIV-1 genotypes were also performed. Results Among the 439 specimens successfully genotyped, more than ten genotypes were detected, including CRF08_BC (45.3%), CRF07_BC (19.4%), unique recombinant forms (URFs) (18.2%), CRF01_AE (11.4%), subtype C (2.1%), CRF85_BC (1.1%), CRF55_01B (0.9%), subtype B (0.5%), CRF64_BC (0.5%), CRF59_01B (0.2%), CRF83_cpx (0.2%) and CRF87_cpx (0.2%). Females, Chinese, heterosexual contact and intravenous drug injection were significantly associated with CRF08_BC infection; homosexual contact was significantly associated with CRF01_AE and CRF07_BC infection; males and non-Chinese had a higher risk of URF infection than females. Among all HIV-1 genotypes, the geographic coverage of CRF08_BC was the largest. For CRF08_BC, CRF07_BC, URFs and CRF01_AE, spatial clusters were detected. The two CRF08_BC clusters and one URF cluster were associated with heterosexual transmission, and two of CRF01_AE clusters were associated with homosexual transmission. Transmitted drug resistance (TDR)-associated mutations were detected in 2.4% of individuals. Conclusions The diversity of HIV-1 genotypes increased in recent infections because of a long-term HIV-1 epidemic in Yunnan. The predominant HIV-1 strains showed distinct demographic characteristics and formed spatial clusters. These findings improved our understanding of the evolution of HIV-1 in Yunnan and provided information for further HIV-1 control and prevention. Electronic supplementary material The online version of this article (10.1186/s12879-019-4276-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Yanling Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Huichao Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Jie Dai
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Hongbing Luo
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Chaojun Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Lijuan Dong
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Xiaomei Jin
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Min Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Li Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Lijun Song
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Zhizhong Song
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Manhong Jia
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China.
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Chen M, Ma Y, Chen H, Dai J, Luo H, Jia M, Song Z. Complete genome sequencing and evolutionary analysis of HCV subtype 6xg from IDUs in Yunnan, China. PLoS One 2019; 14:e0217010. [PMID: 31095618 PMCID: PMC6522032 DOI: 10.1371/journal.pone.0217010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/02/2019] [Indexed: 12/20/2022] Open
Abstract
Background HCV genotype 6 (HCV-6) typically circulates in Southeast Asia and exhibits the highest genetic diversity among the eight HCV genotypes. In our previous work, a group of HCV-6 sequences was not clearly classified. Here, we further characterized this HCV-6 variant and analyzed the evolutionary history of the enlarged HCV-6 family. Methods Blood samples from eight HCV seropositive samples collected from intravenous drug users (IDUs) in 2014 in Yunnan Province, China. The full-length HCV genome sequences were amplified by using reverse transcription PCR followed by DNA sequencing and phylogenetic analysis. Bayesian evolutionary analysis was performed with the complete coding region sequences of subtype 6a-6xh. Results The eight genomes had the same coding region of 9051 nucleotides. The complete coding region sequences of the eight HCV isolates formed a distinct phylogenetic group from the previously assigned HCV-6 subtypes (6a-6xf), however which clustered with 6xg reference sequences that were found in Kachin State, Myanmar, and recently assigned and released. The p-distances of the eight isolates to subtype 6a-6xf and 6xh ranged from 0.143 to 0.283. Based on the HCV-6 complete coding region sequences, we constructed a timescaled phylogenetic tree to reveal the HCV-6 evolutionary history, in which there were four HCV-6 phylogenetic subsets, whose median tMRCAs were 294.8, 388.5, 348.5 and 197.0 years ago, respectively. Subtype 6xg clustered into Subset I, and had the most recent common ancestor with subtype 6n, which dated back to 101.2 (95% HPD: 78.7, 125.8) years ago. The genetic evolutionary analysis further confirmed that subtype 6xg originated from Myanmar, and transmitted to Dehong through cross-border IDUs. Conclusion The HCV-6 variant characterized in this study belonged to newly assigned subtype 6xg. Our finding further confirmed the assignment of 6xg. HCV-6 family was highly divers and had a complicated evolutionary history in Southeast Asia. It is necessary to further characterize HCV-6 genetics in this region.
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Affiliation(s)
- Min Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yanling Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Huichao Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Jie Dai
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Hongbing Luo
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Manhong Jia
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- * E-mail: (ZS); (MJ)
| | - Zhizhong Song
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- * E-mail: (ZS); (MJ)
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6
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Nadai Y, Held K, Joseph S, Ahmed MIM, Hoffmann VS, Peterhoff D, Missanga M, Bauer A, Joachim A, Reimer U, Zerweck J, McCormack S, Cope AV, Tatoud R, Shattock RJ, Robb ML, Sandstroem EG, Hoelscher M, Maboko L, Bakari M, Kroidl A, Wagner R, Weber J, Pollakis G, Geldmacher C. Envelope-Specific Recognition Patterns of HIV Vaccine-Induced IgG Antibodies Are Linked to Immunogen Structure and Sequence. Front Immunol 2019; 10:717. [PMID: 31105688 PMCID: PMC6492543 DOI: 10.3389/fimmu.2019.00717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/18/2019] [Indexed: 11/13/2022] Open
Abstract
Background: A better understanding of the parameters influencing vaccine-induced IgG recognition of individual antigenic regions and their variants within the HIV Envelope protein (Env) can help to improve design of preventive HIV vaccines. Methods: Env-specific IgG responses were mapped in samples of the UKHVC003 Standard Group (UK003SG, n = 11 from UK) and TaMoVac01 (TMV01, n = 17 from Tanzania) HIV vaccine trials. Both trials consisted of three immunizations with DNA, followed by two boosts with recombinant Modified Vaccinia Virus Ankara (MVA), either mediating secretion of gp120 (UK003SG) or the presentation of cell membrane bound gp150 envelopes (TMV01) from infected cells, and an additional two boosts with 5 μg of CN54gp140 protein adjuvanted with glucopyranosyl lipid adjuvant (GLA). Env immunogen sequences in UK003SG were solely based on the clade C isolate CN54, whereas in TMV01 these were based on clades A, C, B, and CRF01AE. The peptide microarray included 8 globally representative Env sequences, CN54gp140 and the MVA-encoded Env immunogens from both trials, as well as additional peptide variants for hot spots of immune recognition. Results: After the second MVA boost, UK003SG vaccinees almost exclusively targeted linear, non-glycosylated antigenic regions located in the inter-gp120 interface. In contrast, TMV01 recipients most strongly targeted the V2 region and an immunodominant region in gp41. The V3 region was frequently targeted in both trials, with a higher recognition magnitude for diverse antigenic variants observed in the UK003SG (p < 0.0001). After boosting with CN54gp140/GLA, the overall response magnitude increased with a more comparable recognition pattern of antigenic regions and variants between the two trials. Recognition of most immunodominant regions within gp120 remained significantly stronger in UK003SG, whereas V2-region recognition was not boosted in either group. Conclusions: IgG recognition of linear antigenic Env regions differed between the two trials particularly after the second MVA boost. Structural features of the MVA-encoded immunogens, such as secreted, monomeric gp120 vs. membrane-anchored, functional gp150, and differences in prime-boost immunogen sequence variability most probably contributed to these differences. Prime-boosting with multivalent Env immunogens during TMV01 did not improve variant cross-recognition of immunodominant peptide variants in the V3 region.
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Affiliation(s)
- Yuka Nadai
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Kathrin Held
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Sarah Joseph
- MRC Clinical Trials Unit at UCL, London, United Kingdom
| | - Mohamed I M Ahmed
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Verena S Hoffmann
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene, University Regensburg, Regensburg, Germany
| | | | - Asli Bauer
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,NIMR-Mbeya Medical Research Center, Mbeya, Tanzania
| | - Agricola Joachim
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Ulf Reimer
- JPT Peptide Technologies, Berlin, Germany
| | | | | | - Alethea V Cope
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Roger Tatoud
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Robin J Shattock
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Merlin Lee Robb
- US Military HIV Research Program, Silver Spring, MD, United States
| | - Eric G Sandstroem
- Department of Clinical Science and Education, Karolinska Institutet at Södersjukhuset, Stockholm, Sweden
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | | | - Muhammad Bakari
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Arne Kroidl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, University Regensburg, Regensburg, Germany.,Institute of Clinical Microbiology and Hygiene, University Hospital, Regensburg, Germany
| | - Jonathan Weber
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Georgios Pollakis
- Institute of Global Health (CIMI), University of Liverpool, Liverpool, United Kingdom
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
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7
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Chen M, Jia MH, Ma YL, Luo HB, Chen HC, Yang CJ, Dai J, Yang L, Dong LJ, Lu R, Song LJ, Han Y, Lu JY, Cheung AKL, Chen ZW, Lu L. The changing HIV-1 genetic characteristics and transmitted drug resistance among recently infected population in Yunnan, China. Epidemiol Infect 2018; 146:775-781. [PMID: 29534773 PMCID: PMC9134363 DOI: 10.1017/s0950268818000389] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/30/2017] [Accepted: 02/07/2018] [Indexed: 11/05/2022] Open
Abstract
Multiple human immunodeficiency virus (HIV)-1 genotypes in China were first discovered in Yunnan Province before disseminating throughout the country. As the HIV-1 epidemic continues to expand in Yunnan, genetic characteristics and transmitted drug resistance (TDR) should be further investigated among the recently infected population. Among 2828 HIV-positive samples newly reported in the first quarter of 2014, 347 were identified as recent infections with BED-captured enzyme immunoassay (CEIA). Of them, 291 were successfully genotyped and identified as circulating recombinant form (CRF)08_BC (47.4%), unique recombinant forms (URFs) (18.2%), CRF01_AE (15.8%), CRF07_BC (14.4%), subtype C (2.7%), CRF55_01B (0.7%), subtype B (0.3%) and CRF64_BC (0.3%). CRF08_BC and CRF01_AE were the predominant genotypes among heterosexual and homosexual infections, respectively. CRF08_BC, URFs, CRF01_AE and CRF07_BC expanded with higher prevalence in central and eastern Yunnan. The recent common ancestor of CRF01_AE, CRF07_BC and CRF08_BC dated back to 1983.1, 1992.1 and 1989.5, respectively. The effective population sizes (EPS) for CRF01_AE and CRF07_BC increased exponentially during 1991-1999 and 1994-1999, respectively. The EPS for CRF08_BC underwent two exponential growth phases in 1994-1998 and 2001-2002. Lastly, TDR-associated mutations were identified in 1.8% of individuals. These findings not only enhance our understanding of HIV-1 evolution in Yunnan but also have implications for vaccine design and patient management strategies.
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Affiliation(s)
- M. Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - M. H. Jia
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Y. L. Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - H. B. Luo
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - H. C. Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - C. J. Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - J. Dai
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - L. Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - L. J. Dong
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - R. Lu
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - L. J. Song
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Y. Han
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - J. Y. Lu
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - A. K. L. Cheung
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Z. W. Chen
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - L. Lu
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- College of Public Health, Kunming Medical University, Kunming, Yunnan, China
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8
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Ren L, Wang B, Gong K, Liu P, Zhou S, Zhang L, Xia X, Wang K. Epidemiology reveals Zhaotong City as the hub of human immunodeficiency virus type 1 transmission from the Yunnan province to other regions in China. J Gen Virol 2017; 98:3093-3100. [PMID: 29091580 DOI: 10.1099/jgv.0.000961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Yunnan province in China has a high incidence of human immunodeficiency virus-1 (HIV-1) infection. Zhaotong City is located in the Yunnan province, a neglected 'important region'. In this study, we evaluated the unique molecular epidemiological characteristics of HIV-1 infection in Zhaotong City. We collected 305 serum samples from HIV-infected patients in Zhaotong City between May 2015 and April 2016. A total of 122 samples were selected for HIV-1 gag-pol gene amplification, of which 88 were successfully amplified and sequenced for phylogenetic and phylogeographic analysis. Circulating recombinant forms 07_BC (CRF07_BC, 23 cases, 26.14 %) and CRF08_BC (49 cases, 55.68 %) were the predominant subtypes; the high proportions of these two subtypes differed from those elsewhere in the Yunnan province. The other subtypes were CRF01_AE (11 cases, 12.5 %), B (one case, 1.14 %) and unique recombinant forms (four cases, 4.55 %). Phylogeographic analysis of the CRF07_BC and CRF08_BC subtype strains revealed that Zhaotong was one of the regions in which CRF07_BC and CRF08_BC entered initially. The CRF08_BC strain originated from this region closer to the 'root' position of the phylogenetic tree. Thus, Zhaotong City may have been an important channel in the transmission route of HIV-1 from Yunnan to other parts of the country. Based on this unique distribution of HIV-1 subtypes in Zhaotong City, the epidemic outbreak in this area may have played an important role in the spread of CRF07_BC and CRF08_BC subtypes.
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Affiliation(s)
- Li Ren
- The First People's Hospital of Yunnan Province, Kunming 650031, Yunnan Province, PR China.,The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650031, Yunnan Province, PR China.,Medical Faculty of Kunming University of Science and Technology, Kunming 650093, Yunnan Province, PR China
| | - Bingbui Wang
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan province, Kunming University of Science and Technology, Kunming 650093, Yunnan Province, PR China
| | - Kunmei Gong
- The First People's Hospital of Yunnan Province, Kunming 650031, Yunnan Province, PR China
| | - Pan Liu
- Yan'an Hospital of Kunming Chenggong Hospital, Kunming 650501, Yunnan Province, PR China
| | - Shiyi Zhou
- Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, PR China
| | - Li Zhang
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan province, Kunming University of Science and Technology, Kunming 650093, Yunnan Province, PR China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan province, Kunming University of Science and Technology, Kunming 650093, Yunnan Province, PR China
| | - Kunhua Wang
- Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, PR China.,The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650031, Yunnan Province, PR China
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9
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Xiao P, Li J, Fu G, Zhou Y, Huan X, Yang H. Geographic Distribution and Temporal Trends of HIV-1 Subtypes through Heterosexual Transmission in China: A Systematic Review and Meta-Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:E830. [PMID: 28737729 PMCID: PMC5551268 DOI: 10.3390/ijerph14070830] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 07/09/2017] [Accepted: 07/21/2017] [Indexed: 11/17/2022]
Abstract
Background: Heterosexual transmission (HST) has become the current predominant transmission pathways of the HIV-1 epidemic in China. The aim of this study was to explore the geographic and dynamic change of HIV-1 subtypes through HST in China from published studies. Methods: Several electronic databases were searched to identify the studies, and the overall prevalence of HIV-1 subtypes was estimated by a meta-analysis method. Subgroup analysis was conducted by study region and time period. Publication bias was evaluated using Egger's test. The χ² test was used to evaluate the proportion differences among subgroups. Sensitivity analysis was carried out to assess the stability of the overall prevalence estimates. Results: 42 studies were included in our final analysis. The overall prevalence of CRF01_AE was 46.34% (95% CI: 40.56-52.17%), CRF07_BC was 19.16% (95% CI: 15.02-23.66%), B/B' was 13.25% (95% CI: 9.68-17.25%), CRF08_BC was 10.61% (95% CI: 7.08-14.70%), and C was 4.29% (95% CI: 1.85-7.48%). In subgroup analysis, the prevalence of CRF01_AE and CRF07_BC increased, while the prevalence of B/B' decreased over time, whereby the prevalence of CRF07_BC and CRF08_BC have exceeded that of B/B' since 2010. A significant higher prevalence of CRF01_AE was found in the South provinces, CRF07_BC in East provinces, CRF08_BC and C in Southwest provinces, and B/B' in North provinces. Conclusions: The HIV-1 prevalent strains have evolved into complicated and diverse subtypes, and the proportion of HIV-1 subtypes through HST has changed constantly in different regions and periods in China. This highlights the urgent need to vigorously strengthen the prevention and control of the HIV-1 epidemic.
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Affiliation(s)
- Peipei Xiao
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Jianjun Li
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210009, China.
| | - Gengfeng Fu
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210009, China.
| | - Ying Zhou
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210009, China.
| | - Xiping Huan
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210009, China.
| | - Haitao Yang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China.
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210009, China.
- Jiangsu Research Institute of Schistosomiasis Control, Wuxi 214064, China.
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10
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Nikolopoulos GK, Kostaki EG, Paraskevis D. Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia. INFECTION GENETICS AND EVOLUTION 2016; 46:256-268. [PMID: 27287560 DOI: 10.1016/j.meegid.2016.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 01/14/2023]
Abstract
HIV strains continuously evolve, tend to recombine, and new circulating variants are being discovered. Novel strains complicate efforts to develop a vaccine against HIV and may exhibit higher transmission efficiency and virulence, and elevated resistance to antiretroviral agents. The United Nations Joint Programme on HIV/AIDS (UNAIDS) set an ambitious goal to end HIV as a public health threat by 2030 through comprehensive strategies that include epidemiological input as the first step of the process. In this context, molecular epidemiology becomes invaluable as it captures trends in HIV evolution rates that shape epidemiological pictures across several geographical areas. This review briefly summarizes the molecular epidemiology of HIV among people who inject drugs (PWID) in Europe and Asia. Following high transmission rates of subtype G and CRF14_BG among PWID in Portugal and Spain, two European countries, Greece and Romania, experienced recent HIV outbreaks in PWID that consisted of multiple transmission clusters including subtypes B, A, F1, and recombinants CRF14_BG and CRF35_AD. The latter was first identified in Afghanistan. Russia, Ukraine, and other Former Soviet Union (FSU) states are still facing the devastating effects of epidemics in PWID produced by AFSU (also known as IDU-A), BFSU (known as IDU-B), and CRF03_AB. In Asia, CRF01_AE and subtype B (Western B and Thai B) travelled from PWID in Thailand to neighboring countries. Recombination hotspots in South China, Northern Myanmar, and Malaysia have been generating several intersubtype and inter-CRF recombinants (e.g. CRF07_BC, CRF08_BC, CRF33_01B etc.), increasing the complexity of HIV molecular patterns.
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Affiliation(s)
- Georgios K Nikolopoulos
- Hellenic Centre for Diseases Control and Prevention, Amarousio, Greece; Hellenic Scientific Society for the Study of AIDS and Sexually Transmitted Diseases, Transmission Reduction Intervention Project-Athens site, Athens, Greece.
| | - Evangelia-Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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11
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Li J, Li L, Li H, Li J, Yang S, Zhang M, Ouyang H. Genomic Characterization of a Novel HIV-1 Second-Generation Recombinant Form Originated from CRF01_AE and CRF08_BC in Dali Prefecture of Yunnan Province, China. AIDS Res Hum Retroviruses 2016; 32:607-11. [PMID: 26885777 DOI: 10.1089/aid.2015.0383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Yunnan seems to be a "hot spot" region of HIV-1 recombination. CRF01_AE and subtype CRF08_BC are two main HIV-1 clades circulating in Yunnan. We report here a novel HIV-1 second-generation recombinant form originated from CRF01_AE and CRF08_BC. The strain (12YN10551) was isolated from a HIV-positive male infected through heterosexual contact in Dali prefecture of Yunnan province, China. This is the first report of HIV-1 near full-length genomic sequence in Dali. Recombinant analysis shows that 12YN10551 was composed of two well-established circulating recombinant forms (CRF01_AE and CRF08_BC). Two CRF01_AE recombinant fragments were inserted into the CRF08_BC backbone genome in the pol/vif/vpr/tat/rev and nef gene regions, respectively. The discovery and characterization of this new recombinant indicate that intersubtype recombination is continuously generating new forms of HIV-1. More work is needed to better monitor the genetic diversity of HIV-1 in this region.
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Affiliation(s)
- Jianjian Li
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Huiqin Li
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shaomin Yang
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Mi Zhang
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Hongmei Ouyang
- First People's Hospital of Yunnan Province, Kunming University of Science and Technology Affiliated Kun Hua Hospital, Kunming, China
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12
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Song Y, Feng Y, Miao Z, Wang B, Yang M, Zhang AM, Liu L, Xia X. Near-Full-Length Genome Sequences of a Novel HIV-1 Circulating Recombinant Form, CRF01_AE/B'/C (CRF78_cpx), in Yunnan, China. AIDS Res Hum Retroviruses 2016; 32:601-6. [PMID: 26885715 DOI: 10.1089/aid.2015.0351] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report a novel HIV circulating recombinant form (CRF78_cpx) composed mainly of CRF01_AE with inserts from subtypes B and C identified from three epidemiologically unlinked individuals in Yunnan province, China. Two of the subjects are heterosexual men and one is a male intravenous drug user. Sequencing and analyzing the near-full-length genome of these three isolates (YNTC88, YNTC19, and YNTC35) revealed identical recombination breakpoints in all three viruses, but considerable genetic diversity between them, across the genomes, indicating that this is not a newly created CRF, only newly detected. CRF78_cpx differs from previously documented CRF01-AE/B'/C forms in its distinct backbone, inserted fragment size, and breakpoints, and is not related to other described recombinants in the region such as CRF07_BC or CRF65_cpx (also composed of CRF01_AE, B', and C). Our present findings further enrich the diversity of the prevalent HIV-1 CRFs in Yunnan, which is considered as an epicenter of HIV-1 infections in China.
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Affiliation(s)
- Yindi Song
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Yue Feng
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Zhijiang Miao
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Binghui Wang
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Ming Yang
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - A-Mei Zhang
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Li Liu
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
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13
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Li J, Li L, Yang S, Li J, Zhang M, Yang C, Liu J, Li H. The Identification of a Novel HIV-1 CRF01_AE/B Recombinant Based on Near Full-Length Genomic Analysis in Yunnan Province, China. AIDS Res Hum Retroviruses 2016; 32:467-70. [PMID: 26678279 DOI: 10.1089/aid.2015.0245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recombination contributes substantially to the genetic diversity of HIV-1. Recently, many kinds of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were identified in China, especially in areas with multiple subtypes of HIV-1 circulating. Yunnan, which borders the "Golden triangle" region of South China, is an epicenter of HIV-1 infections in China. Multiple subtypes, including subtypes B, CRF01_AE, CRF07_BC, and CRF08_BC, were found epidemic in the area. Many URFs composed of subtypes B and C genomes were identified in Yunnan; however, CRF01_AE/B recombinant form is relatively rare. In this study, we identified a novel recombinant form of CRF01_AE/B, which was isolated from a heterosexual transmitted individual. The genomic structure of the strain is distinctly different from any previously reported URFs. Three CRF01_AE segments were inserted into the subtype B backbone genome. In the past few years, many kinds of URFs and CRFs have emerged and spread quickly in China, which implies that coinfection or super infection of more than one HIV-1 subtype might be common in China, especially in Yunnan. Therefore, more work is needed to monitor the appearance of URFs and survey the epidemiologic significance of the new recombination.
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Affiliation(s)
- Jianjian Li
- Department of HIV/AIDS Clinical Research, Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shaomin Yang
- Department of HIV/AIDS Clinical Research, Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Jingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Mi Zhang
- Department of HIV/AIDS Clinical Research, Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Cuixian Yang
- Department of HIV/AIDS Clinical Research, Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Jiafa Liu
- Department of HIV/AIDS Clinical Research, Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Huiqin Li
- Department of HIV/AIDS Clinical Research, Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
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14
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Li J, Li L, Yang S, Li J, Zhang M, Yang C, Liu J, Li H. Identification and characterization of two human immunodeficiency virus type 1 unique recombinant forms from Yunnan, China. Virol Sin 2016; 31:184-7. [PMID: 26847649 PMCID: PMC8193385 DOI: 10.1007/s12250-015-3671-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Jianjian Li
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, 650301, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Shaomin Yang
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, 650301, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Mi Zhang
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, 650301, China
| | - Cuixian Yang
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, 650301, China
| | - Jiafa Liu
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, 650301, China
| | - Huiqin Li
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, 650301, China.
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15
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Prevalence of different HIV-1 subtypes in sexual transmission in China: a systematic review and meta-analysis. Epidemiol Infect 2016; 144:2144-53. [PMID: 26892485 DOI: 10.1017/s0950268816000212] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sexual transmission has become the primary route of HIV transmission in China. Therefore, a comprehensive overview of HIV-1 subtype distribution is necessary for the prevention and control of the HIV epidemic. The present study aimed to provide a comprehensive prevalence estimate of different HIV-1 subtypes in sexual transmission in China. We conducted a systematic literature review for studies of HIV-1 subtypes in English and Chinese through several databases. Eligible articles were screened and selected by two authors independently. Random-effects model were applied to calculate the pooled prevalence of different HIV-1 subtypes, and subgroup analyses examined prevalence estimates across time, locations, and populations. A total of 130 eligible studies were identified, including 18 752 successfully genotyped samples. The pooled prevalence of CRF01_AE, subtype B, CRF07_BC, CRF08_BC, and subtype C were 44·54% (95% CI 40·81-48·30), 18·31% (95% CI 14·71-22·17), 16·45% (95% CI 13·82-19·25), 2·55% (95% CI 1·56-3·73), 0·37% (95% CI 0·11-0·72), respectively. The prevalence of subtype B in sexual transmission decreased, while the prevalence of CRF01_AE and CRF07_BC in sexual transmission, and CRF08_BC in heterosexual transmission increased. There is significant variation in HIV-1 subtype distribution between regions. The distribution of HIV-1 subtypes and circulating recombinant forms have changed significantly. The high genetic variability of HIV-1 poses a significant challenge for disease control and surveillance in China.
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16
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Liu Y, Gui T, Jia L, Li L, Bao Z, Li H, Wang X, Liu S, Zhuang D, Li T, Li J. Phylogenetic Analysis of HIV-1 CRF65_CPX Reveals Yunnan Province Is Still a Source Contributing to the Spread of HIV-1 in China. J Acquir Immune Defic Syndr 2015; 70:e120-2. [DOI: 10.1097/qai.0000000000000775] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Multilayered HIV-1 gag-specific T-cell responses contribute to slow progression in HLA-A*30-B*13-C*06-positive patients. AIDS 2015; 29:993-1002. [PMID: 25756195 PMCID: PMC4444423 DOI: 10.1097/qad.0000000000000652] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Objective: The HLA-A∗30-B∗13-C∗06 haplotype is reported to be associated with slow disease progression in the HIV-1-infected Northern Han Chinese population, but the mechanism remains unknown. Design: Gag-specific T-cell responses and gag sequencing were performed in nine B′ clade HIV-1-infected HLA-A∗30-B∗13-C∗06-positive slow progressors to understand HLA-associated viral control. Methods: Interferon-γ ELISPOT assays were performed to determine the Gag-specific T-cell responses and cross-reactivity to variant peptides. Longitudinal HIV-1 gag sequencing was performed at the clonal level. Results: The overlapping peptides (OLP)-48: RQANFLGKIWPSHKGRPGNF (RL42 Gag434-453); OLP-2: GQLDRWEKIRLRPGGKKKYR (RL42 Gag11-30); OLP-15: VQNLQGQMVHQPISPRTLNA (RL42 Gag135-154) and OLP-16: HQPISPRTLNAWVKVVEEKA (RL42 Gag144-163) were dominant in HLA-A∗30-B∗13-C∗06-positive patients. A new epitope [HQPISPRTL (Gag144-152, HL9)] within OLP-15 and OLP-16 was identified. Results showed that strong cross-reactive responses to multiple immunodominant peptides were associated with better clinical outcomes. In addition, efficient cross-recognition of HL9 autologous variants developed in patients was associated with high CD4+ T-cell counts. However, two patients who had developed mutations to their dominant responses during the follow-up experienced decrease in CD4+ T-cell counts. It appears that Gag-specific T-cell responses against one or more unmutated epitopes or cross-recognition of autologous epitope variants contribute to slow disease progression in HLA-A∗30-B∗13-C∗06-positive patients. Conclusion: We conclude that a single ‘appropriate’ Gag-specific T-cell response appears to be sufficient to protect patients from disease progression. HLA-A∗30-B∗13-C∗06-positive individuals benefited from having a choice of numerous immunodominant gag epitopes for T cells to react. The study offers new insight for future design of T-cell-based HIV-1 vaccine.
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Yang L, Chen M, Ma Y, Luo H, Yang C, Su Y, Chen H, Shi Y, Mei J, Jia M, Lu L. The changing trends of HIV-1 prevalence and incidence from sentinel surveillance of five sub-populations in Yunnan, China, 2001-2010. BMC Public Health 2015; 15:376. [PMID: 25886791 PMCID: PMC4409774 DOI: 10.1186/s12889-015-1722-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 03/30/2015] [Indexed: 11/10/2022] Open
Abstract
Background Yunnan is one of the provinces hardest-hit by HIV in China. To understand HIV epidemic dynamics and evaluate prevention effectiveness, we studied the changing trends in HIV-1 prevalence and incidence among five sub-populations in Yunnan. Methods Consecutive sentinel surveillances were conducted among people who inject drugs (PWID), male sexually transmitted diseases (STD) clinic attendees, and pregnant women for 2001–2010,female sex workers (FSWs) for 2007–2010, men who have sex with men (MSM) for 2008–2010. For the newly diagnosed HIV-seropositive samples, the recent infections were determined with BED-capture enzyme immunoassay (BED-CEIA), based on which HIV incidence was calculated for each sub-population using McDougal algorithm. Results From 231,117 individuals, 6,107 HIV-positive samples were tested with BED-CEIA, among which 964 samples were identified as recent infections. In PWID, HIV prevalence for 2001–2010 was between 27.16% and 18.35%, while the estimated incidence rate significantly decreased from 11.68% in 2001 to 1.70% in 2010. Among male STD clinic attendees, both the HIV prevalence (from 3.62% in 2001 to 1.73% in 2010) and incidence (from 1.10% in 2001 to 0.40% in 2010) showed a significant decreasing trend. In FSWs, the HIV prevalence for 2007–2010 kept stable (between 2.46% and 1.95%), while the HIV incidence significantly decreased (from 0.71% in 2007 to 0.31% in 2010). In MSM, the HIV prevalence (between 11.78% and 9.42%) and incidence (between 6.01% and 8.38%) remained stable at a relatively high level for 2008–2010. In pregnant women, the HIV prevalence (between 0.44% and 0.30%) and incidence (between 0.15% and 0.08%) remained stable for 2001–2010. Conclusion The HIV incidences in PWID, male STD clinic attendees and FSWs showed the decreasing trend, supporting a positive effect of prevention strategies for these sub-populations. MSM with the highest HIV incidence have become the sub-population most at risk. In most sub-populations, the HIV prevalence did not decline, suggesting the disease burden is still heavy. These findings are valuable for developing HIV prevention strategies in Yunnan.
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Affiliation(s)
- Li Yang
- Institute for STD/AIDS Control and Prevention, Yunnan Center for Disease Control and Prevention, No 158, Dongsi Street, Xishan District, Kunming, 650022, , Yunnan Province, China.
| | - Min Chen
- Institute for STD/AIDS Control and Prevention, Yunnan Center for Disease Control and Prevention, No 158, Dongsi Street, Xishan District, Kunming, 650022, , Yunnan Province, China.
| | - Yanling Ma
- Institute for STD/AIDS Control and Prevention, Yunnan Center for Disease Control and Prevention, No 158, Dongsi Street, Xishan District, Kunming, 650022, , Yunnan Province, China.
| | - Hongbing Luo
- Institute for STD/AIDS Control and Prevention, Yunnan Center for Disease Control and Prevention, No 158, Dongsi Street, Xishan District, Kunming, 650022, , Yunnan Province, China.
| | - Chaojun Yang
- Institute for STD/AIDS Control and Prevention, Yunnan Center for Disease Control and Prevention, No 158, Dongsi Street, Xishan District, Kunming, 650022, , Yunnan Province, China.
| | - Yingzhen Su
- Institute for STD/AIDS Control and Prevention, Yunnan Center for Disease Control and Prevention, No 158, Dongsi Street, Xishan District, Kunming, 650022, , Yunnan Province, China.
| | - Huichao Chen
- Institute for STD/AIDS Control and Prevention, Yunnan Center for Disease Control and Prevention, No 158, Dongsi Street, Xishan District, Kunming, 650022, , Yunnan Province, China.
| | - Yuhua Shi
- Institute for STD/AIDS Control and Prevention, Yunnan Center for Disease Control and Prevention, No 158, Dongsi Street, Xishan District, Kunming, 650022, , Yunnan Province, China.
| | - Jingyuan Mei
- Institute for STD/AIDS Control and Prevention, Yunnan Center for Disease Control and Prevention, No 158, Dongsi Street, Xishan District, Kunming, 650022, , Yunnan Province, China.
| | - Manhong Jia
- Institute for STD/AIDS Control and Prevention, Yunnan Center for Disease Control and Prevention, No 158, Dongsi Street, Xishan District, Kunming, 650022, , Yunnan Province, China.
| | - Lin Lu
- Institute for STD/AIDS Control and Prevention, Yunnan Center for Disease Control and Prevention, No 158, Dongsi Street, Xishan District, Kunming, 650022, , Yunnan Province, China.
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Ye J, Lu H, Su X, Xin R, Bai L, Xu K, Yu S, Feng X, Yan H, He X, Zeng Y. Phylogenetic and temporal dynamics of human immunodeficiency virus type 1B in China: four types of B strains circulate in China. AIDS Res Hum Retroviruses 2014; 30:920-6. [PMID: 25050980 DOI: 10.1089/aid.2014.0074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To investigate the origin and evolutionary history of the spread of HIV-1 subtype B in China, a total of 409 sequences of pol gene sampled from 1994 to 2012 in 29 provinces across China was subjected to phylogenetic and Bayesian molecular clock analyses. The study reveals that subtype B strains in China are genetically diverse and can be classified into four distinct subgroups, namely B' (Thai-B), BJ-B (Beijing-B), Pan-B (Pandemic-B), and TW-B (Taiwan-B), according to the origin of the sequences. The BJ-B and TW-B are reported for the first time. Phylogeographic analysis reveals that B' exhibits a nationwide, transprovincial distribution, and is found in 21 provinces in China in this study, whereas the Pan-B, BJ-B, and TW-B lineages are restricted to particular regions. From the same common ancestor of B', there arise two subclusters in which sequences from Yunnan occupy the basal position. The times of the most recent common ancestors (tMRCAs) of B' and BJ-B are estimated to be 1983.6 (1975.9-1990.3) and 1995.3 (1989.6-2000.3), respectively. The skyline plot profile reveals an exponential decrease in median number of effective infections of subtype B in China from 1994 to 2009. The existence of four types of B clades also indicates distinct transmission networks of subtype B, originating from different introduction events at different time points. The data presented here offer a new perspective on the epidemic of HIV-1 subtype B in China.
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Affiliation(s)
- Jingrong Ye
- Beijing Center for Disease Prevention and Control, Beijing, China
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Viral Disease Control and Prevention, China Center for Disease Prevention and Control, Beijing, China
- College of Life Science and Bio-Engineering, Beijing University of Technology, Beijing, China
| | - Hongyan Lu
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Xueli Su
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Ruolei Xin
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Lishi Bai
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Ke Xu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Viral Disease Control and Prevention, China Center for Disease Prevention and Control, Beijing, China
| | - Shuangqing Yu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Viral Disease Control and Prevention, China Center for Disease Prevention and Control, Beijing, China
| | - Xia Feng
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Viral Disease Control and Prevention, China Center for Disease Prevention and Control, Beijing, China
| | - Hong Yan
- College of Life Science and Bio-Engineering, Beijing University of Technology, Beijing, China
| | - Xiong He
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yi Zeng
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Viral Disease Control and Prevention, China Center for Disease Prevention and Control, Beijing, China
- College of Life Science and Bio-Engineering, Beijing University of Technology, Beijing, China
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Promising antibody testing strategies for early infant HIV infection diagnosis in China. PLoS One 2014; 9:e99935. [PMID: 24971594 PMCID: PMC4074049 DOI: 10.1371/journal.pone.0099935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 05/20/2014] [Indexed: 01/12/2023] Open
Abstract
Background In China, 1.1% of people living with HIV were transmitted vertically, causing a heavy burden on families and society. Early infant diagnosis (EID) is critical for improving neonatal survival. The purpose of this study is to suggest improvement in antibody testing strategies with dried blood spots (DBSs) for EID in China through analysis of anti-HIV seroreversion of infants. Methods A total of 280 infants born to HIV infected mothers in four diverse provinces of China where multiple subtypes coexist were enrolled. The status of the infants' infection was determined by HIV antibody enzyme immunoassay and Western blot analysis at ≥18 months of age or by convincing clinical and epidemiologic data for deceased infants. A total of 1028 DBSs were collected during follow-up, which were tested to obtain anti-HIV signal to cut-off ratio (S/CO) data. Results For uninfected infants, anti-HIV S/CO decreased with age. Seropositivity percentage declined most rapidly at 6 months to 9 months of age and 98.7% children seroreverted by 12 months of age. For most infected infants, minimum S/CO values were obtained at ≤6 months of age. Antibody negative predictive value was 100% at ≥6 months of age. An S/CO increase ≥1.86 after three months follow-up can determine HIV infection. S/CO threshold of 3.17 can differentiate infected from uninfected infants for exposed kids at 9 months or older with sensitivity as 100% and specificity ≥94.2%. Significance Suggestions obtained through studying seroreversion data of Chinese HIV-exposed infants help improve antibody strategies for HIV EID in China. The infection can be determined as early as 3 months of age and excluded as early as 6 months of age.
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Wei H, His J, Feng Y, Xing H, He X, Liao L, Duan S, Ning C, Wang N, Takebe Y, Shao Y. Identification of a novel HIV-1 circulating recombinant form (CRF62_BC) in western Yunnan of China. AIDS Res Hum Retroviruses 2014; 30:380-3. [PMID: 24164474 DOI: 10.1089/aid.2013.0235] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We report here a novel HIV-1 circulating recombinant form (CRF62_BC) that was isolated from three epidemiologically unlinked individuals [one from an injecting drug user (IDU); two from heterosexuals] in Dehong prefecture of western Yunnan province. CRF62_BC harbored two subtype B segments in the pol and vpu-env regions in a subtype C backbone. Subregion tree analysis demonstrated that subtype B regions originated from a Thai-B (subtype B') lineage and the subtype C region was from an India C lineage. CRF62_BC is the fourth CRF composed of subtypes B' and C known to date after CRF07_BC, CRF08_BC, and CRF57_BC, which were originally found among IDUs in China. The emergence of CRF62_BC may indicate the continual generation of new recombinant strains in various high-risk populations in western Yunnan. This may complicate the development of effective vaccines to limit the HIV-1 epidemic and increase the difficulty of AIDS prevention and control in China.
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Affiliation(s)
- Huamian Wei
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Jenny His
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Xiang He
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
- Guangdong Provincial Institute of Public Health, Guangdong, People's Republic of China
| | - Lingjie Liao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Song Duan
- Dehong Center for Disease Control and Prevention, Dehong, People's Republic of China
| | - Chuanyi Ning
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Nidan Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yutaka Takebe
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
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Hsi J, Wei H, Xing H, Feng Y, He X, Liao L, Jia M, Wang N, Ning C, Shao Y. Genome sequence of a novel HIV-1 circulating recombinant form (CRF64_BC) identified from Yunnan, China. AIDS Res Hum Retroviruses 2014; 30:389-93. [PMID: 24205972 DOI: 10.1089/aid.2013.0234] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We report a novel HIV-1 circulating recombinant form (CRF64_BC) that was isolated from five epidemiologically unlinked HIV-infected persons in Yunnan province. CRF64_BC was composed of subtype B and subtype C, with five short subtype B segments inserted into the subtype C backbone. Phylogenetic analysis demonstrated that the C subregion was correlated with the India C lineage, which was transmitted into China in the early 1990s. The evolutionary history of the B subregion was not as clear as the C subregion, as the short length of this region yielded poor phylogenetic results. Dehong is considered the epicenter of HIV-1 in China, and recombinant strains such as CRF07_BC and CRF08_BC, which also originated from this region, have spread widely in China. The newly emerged CRF64_BC increases the complexity of the HIV epidemic in China and complicates the development of subtype-specific tools against HIV transmission.
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Affiliation(s)
- Jenny Hsi
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huamian Wei
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiang He
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Guangdong Provincial Institute of Public Health, Guangdong, China
| | - Lingjie Liao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Manhong Jia
- Yunnan Center for Disease Control and Prevention, Yunnan, China
| | - Nidan Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chuanyi Ning
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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Dang S, Wang Y, Budeus B, Verheyen J, Yang R, Hoffmann D. Differential selection in HIV-1 gp120 between subtype B and East Asian variant B'. Virol Sin 2014; 29:40-7. [PMID: 24452536 PMCID: PMC8206395 DOI: 10.1007/s12250-014-3389-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Accepted: 12/20/2013] [Indexed: 11/30/2022] Open
Abstract
HIV-1 evolves strongly and undergoes geographic differentiation as it spreads in diverse host populations around the world. For instance, distinct genomic backgrounds can be observed between the pandemic subtype B, prevalent in Europe and North-America, and its offspring clade B' in East Asia. Here we ask whether this differentiation affects the selection pressure experienced by the virus. To answer this question we evaluate selection pressure on the HIV-1 envelope protein gp120 at the level of individual codons using a simple and fast estimation method based on the ratio k a /k s of amino acid changes to synonymous changes. To validate the approach we compare results to those from a state-of-the-art mixed-effect method. The agreement is acceptable, but the analysis also demonstrates some limitations of the simpler approach. Further, we find similar distributions of codons under stabilizing and directional selection pressure in gp120 for subtypes B and B' with more directional selection pressure in variable loops and more stabilizing selection in the constant regions. Focusing on codons with increased k a /k s values in B', we show that these codons are scattered over the whole of gp120, with remarkable clusters of higher density in regions flanking the variable loops. We identify a significant statistical association of glycosylation sites and codons with increased k a /k s values.
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Affiliation(s)
- Stefan Dang
- Research Group Bioinformatics, Center of Medical Biotechnology and Faculty of Biology, University of Duisburg-Essen, Essen, 45117 Germany
| | - Yan Wang
- AIDS and HIV Research Group, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071 China
| | - Bettina Budeus
- Research Group Bioinformatics, Center of Medical Biotechnology and Faculty of Biology, University of Duisburg-Essen, Essen, 45117 Germany
| | - Jens Verheyen
- Institute of Virology, University of Duisburg-Essen, Essen, 45117 Germany
| | - Rongge Yang
- AIDS and HIV Research Group, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071 China
| | - Daniel Hoffmann
- Research Group Bioinformatics, Center of Medical Biotechnology and Faculty of Biology, University of Duisburg-Essen, Essen, 45117 Germany
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Molecular evolution of the HIV-1 Thai epidemic between the time of RV144 immunogen selection to the execution of the vaccine efficacy trial. J Virol 2013; 87:7265-81. [PMID: 23576510 DOI: 10.1128/jvi.03070-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The RV144 HIV-1 vaccine trial (Thailand, 2003 to 2009), using immunogens genetically matched to the regional epidemic, demonstrated the first evidence of efficacy for an HIV-1 vaccine. Here we studied the molecular evolution of the HIV-1 epidemic from the time of immunogen selection to the execution of the efficacy trial. We studied HIV-1 genetic diversity among 390 volunteers who were deferred from enrollment in RV144 due to preexisting HIV-1 infection using a multiregion hybridization assay, full-genome sequencing, and phylogenetic analyses. The subtype distribution was 91.7% CRF01_AE, 3.5% subtype B, 4.3% B/CRF01_AE recombinants, and 0.5% dual infections. CRF01_AE strains were 31% more diverse than the ones from the 1990s Thai epidemic. Sixty-nine percent of subtype B strains clustered with the cosmopolitan Western B strains. Ninety-three percent of B/CRF01_AE recombinants were unique; recombination breakpoint analysis showed that these strains were highly embedded within the larger network that integrates recombinants from East/Southeast Asia. Compared to Thai sequences from the early 1990s, the distance to the RV144 immunogens increased 52% to 68% for CRF01_AE Env immunogens and 12% to 29% for subtype B immunogens. Forty-three percent to 48% of CRF01_AE sequences differed from the sequence of the vaccine insert in Env variable region 2 positions 169 and 181, which were implicated in vaccine sieve effects in RV144. In conclusion, compared to the molecular picture at the early stages of vaccine development, our results show an overall increase in the genetic complexity of viruses in the Thai epidemic and in the distance to vaccine immunogens, which should be considered at the time of the analysis of the trial results.
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Chen M, Yang L, Ma Y, Su Y, Yang C, Luo H, Chen H, Chen L, Yan W, Shi Y, Jia M, Lu L. Emerging variability in HIV-1 genetics among recently infected individuals in Yunnan, China. PLoS One 2013; 8:e60101. [PMID: 23555898 PMCID: PMC3608604 DOI: 10.1371/journal.pone.0060101] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 02/21/2013] [Indexed: 11/18/2022] Open
Abstract
Background Yunnan has the longest endured Human Immunodeficiency Virus-1 (HIV-1) epidemic in China, and the genetic diversity of HIV-1 constitutes an essential characteristic of molecular epidemiology in this region. To obtain a more comprehensive picture of the dynamic changes in Yunnan’s HIV-1 epidemic, a cross-sectional molecular epidemiological investigation was carried out among recently infected individuals. Methodology/Principal Findings We sequenced partial gag (HXB2∶781–1861) and env (HXB2∶7002–7541) genes from 308 plasma samples of recently infected patients. With phylogenetic analysis, 130 specimens generated interpretable genotyping data. We found that the circulating genotypes included: CRF08_BC (40.8%), unique recombinant forms (URFs, 27.7%), CRF01_AE (18.5%), CRF07_BC (9.2%), subtype B (2.3%) and C (1.5%). CRF08_BC was the most common genotype, and was predominant in both intravenous drug users (IDUs) and heterosexually transmitted populations. CRF08_BC and CRF07_BC still predominated in eastern Yunnan, but CRF08_BC showed increasing prevalence in western Yunnan. Strikingly, the URFs raised dramatically in most regions of Yunnan. Seven different types of URFs were detected from 12 prefectures, suggesting that complicated and frequent recombination is a salient feature of Yunnan’s HIV-1 epidemic. Among URFs, two BC clusters with distinctive recombination patterns might be potential new CRF_BCs. CRF01_AE was no longer confined to the prefectures bordering Myanmar, and had spread to the eastern part of Yunnan, especially the capital city of Kunming, with a large number of infections in the transient population. The ratios of the main genotypes showed no statistical differences between infected IDUs and heterosexually transmitted infections. Conclusions/Significance The changing patterns of the dominant HIV-1 genotypes in Yunnan indicate the complex evolving dynamic nature of the epidemic. Understanding new trends in molecular epidemiology of HIV-1 infection is critical for adjusting current prevention strategies and vaccine development in Yunnan.
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Affiliation(s)
- Min Chen
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Li Yang
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yanling Ma
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yingzhen Su
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Chaojun Yang
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Hongbing Luo
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Huichao Chen
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Ling Chen
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Wenyun Yan
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yuhua Shi
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Manhong Jia
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- * E-mail: (MJ); (LL)
| | - Lin Lu
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- College of Public Health, Kunming Medical University, Kunming, Yunnan, China
- * E-mail: (MJ); (LL)
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Lin H, He N, Zhou S, Ding Y, Qiu D, Zhang T, Wong FY. Behavioral and molecular tracing of risky sexual contacts in a sample of Chinese HIV-infected men who have sex with men. Am J Epidemiol 2013; 177:343-50. [PMID: 23348006 PMCID: PMC3566707 DOI: 10.1093/aje/kws256] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Contact tracing, coupled with molecular epidemiologic investigation, is especially useful for identifying an infection with few cases in the population, such as human immunodeficiency virus (HIV) infection in China. No such research is available on Chinese men who have sex with men (MSM). From 2008 to 2010 in Taizhou Prefecture in China, every newly diagnosed HIV-infected MSM was invited to participate as an “index case” in a contact tracing survey by providing contact information for up to 8 sexual contacts, who themselves were approached to receive voluntary HIV counseling and testing. Those who tested HIV-positive were then subjected to another contact tracing survey. This process was repeated until no more sexual contacts were reported or tested positive. A total of 100 HIV-infected MSM served as “index cases,” including the initial 49 cases identified through routine surveillance programs and 51 cases from the present survey. Traced MSM exhibited little willingness to receive voluntary counseling and testing. CRF01_AE (HIV type 1) was the dominant subtype. Seven of 49 independent sexual networks were deemed HIV transmission clusters. Fear of stigma or discrimination may deter Chinese MSM from receiving voluntary counseling and testing. Nonetheless, the integration of behavioral network analysis and HIV phylogenetic analysis provides enhanced evidence for developing tailored prevention strategies for HIV-infected MSM.
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Affiliation(s)
| | - Na He
- Correspondence to Dr. Na He, Department of Epidemiology, School of Public Health, Fudan University, Shanghai 200032, China (e-mail: )
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OuYang Y, Sun J, Huang Y, Lu L, Xu W, Hu X, Hong K, Jiang S, Shao Y, Ma L. Neutralization sensitivity of HIV-1 subtype B' clinical isolates from former plasma donors in China. Virol J 2013; 10:10. [PMID: 23289760 PMCID: PMC3599083 DOI: 10.1186/1743-422x-10-10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 12/27/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND HIV-1 subtype B' isolates have been predominantly circulating in China. Their intra- and inter-subtype neutralization sensitivity to autologous and heterologous plasmas has not been well studied. RESULTS Twelve HIV-1 B' clinical isolates obtained from patients were tested for their intra- and inter-subtype neutralization sensitivity to the neutralization antibodies in the plasmas from patients infected by HIV-1 B' and CRF07_BC subtypes, respectively. We found that the plasmas from the HIV-1 B'-infected patients could potently neutralize heterologous viruses of subtype B' with mean ID50 titer (1/x) of about 67, but they were not effective in neutralizing autologous viruses of subtype B' with mean ID50 titer (1/x) of about 8. The plasmas from HIV-1 CRF07_BC-infected patients exhibited weak inter-subtype neutralization activity against subtype B' viruses with ID50 titer (1/x) is about 22. The neutralization sensitivity of HIV-1 B' isolates was inversely correlated with the neutralizing activity of plasmas from HIV-1 B'-infected patients (Spearman's r = -0.657, P = 0.020), and with the number of potential N-glycosylation site (PNGS) in V1-V5 region (Spearman's r = -0.493, P = 0.034), but positively correlated with the viral load (Spearman's r = 0.629, P = 0.028). It had no correlation with the length of V1-V5 regions or the CD4+ T cell count. Virus AH259V has low intra-subtype neutralization sensitivity, it can be neutralized by 17b (IC50: 10μg/ml) and 447-52D (IC50: 1.6μg/ml), and the neutralizing antibodies (nAbs) in plasma AH259P are effective in neutralizing infection by the primary HIV-1 isolates with different subtypes with ID50 titers (1/x) in the range of 32-396. CONCLUSIONS These findings suggest that the HIV-1 subtype B' viruses may mutate under the immune pressure, thus becoming resistant to the autologous nAbs, possibly by changing the number of PNGS in the V1-V5 region of the viral gp120. Some of primary HIV-1 isolates are able to induce both intra- and inter-subtype cross-neutralizing antibody responses.
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Affiliation(s)
- Yabo OuYang
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China
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Chen M, Ma Y, Duan S, Xing H, Yao S, Su Y, Luo H, Yang L, Chen H, Fu L, Qu A, Ou CY, Jia M, Lu L. Genetic diversity and drug resistance among newly diagnosed and antiretroviral treatment-naive HIV-infected individuals in western Yunnan: a hot area of viral recombination in China. BMC Infect Dis 2012; 12:382. [PMID: 23270497 PMCID: PMC3552723 DOI: 10.1186/1471-2334-12-382] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Accepted: 12/21/2012] [Indexed: 11/10/2022] Open
Abstract
Background The emergence of an HIV-1 epidemic in China was first recognized in Dehong, western Yunnan. Due to its geographic location, Dehong contributed greatly in bridging HIV-1 epidemics in Southeast Asia and China through drug trafficking and injection drug use; and also extensively to the HIV genetic diversity in Yunnan and China. We attempt to monitor HIV-1 in this area by studying the HIV-1 genetic distribution and transmitted drug resistance (TDR) in various at-risk populations. Methods Blood samples from a total of 320 newly HIV-1 diagnosed individuals, who were antiretroviral therapy (ART)-naive, were collected from January 2009 to December 2010 in 2 counties in Dehong. HIV-1 subtypes and pol gene drug resistance (DR) mutations were genotyped. Results Among 299 pol sequences successfully genotyped (93.4%), subtype C accounted for 43.1% (n=129), unique recombinant forms (URFs) for 18.4% (n=55), CRF01_AE for 17.7% (n=54), B for 10.7% (n=32), CRF08_BC for 8.4% (n=25) and CRF07_BC for 1.7% (n=5). Subtype distribution in patients infected by different transmission routes varied. In contract to the previous finding of CRF01_AE predominance in 2002-2006, subtype C predominated in both injecting drug users (IDUs) and heterosexually transmitted populations in this study. Furthermore, we found a high level of BC, CRF01_AE/C and CRF01_AE/B/C recombinants suggesting the presence of active viral recombination in the area. TDR associated mutations were identified in 4.3% (n=13) individuals. A total of 1.3% of DR were related to protease inhibitors (PIs), including I85IV, M46I and L90M; 0.3% to nucleoside reverse transcriptase inhibitors (NRTIs), including M184I; and 2.7% to non-nucleoside reverse transcriptase inhibitors (NNRTIs), including K103N/S, Y181C, K101E and G190A. Conclusion Our work revealed diverse HIV-1 subtype distributions and intersubtype recombinations. We also identified a low but significant TDR mutation rate among ART-naive patients. These findings enhance our understanding of HIV-1 evolution and are valuable for the development and implementation of a comprehensive public health approach to HIV-1 DR prevention and treatment in the region.
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Affiliation(s)
- Min Chen
- Yunnan Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan 650022, China
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Zhang M, Zhang L, Zhang C, Hong K, Shao Y, Huang Z, Wang S, Lu S. DNA prime-protein boost using subtype consensus Env was effective in eliciting neutralizing antibody responses against subtype BC HIV-1 viruses circulating in China. Hum Vaccin Immunother 2012; 8:1630-7. [PMID: 23111170 DOI: 10.4161/hv.21648] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Previously, we have shown that DNA prime-protein boost is effective in eliciting neutralizing antibodies (NAb) against randomly selected HIV-1 isolates. Given the genetic diversity of HIV-1 viruses and the unique predominant subtypes in different geographic regions, it is critical to test the DNA prime-protein boost approach against circulating viral isolates in key HIV endemic areas. In the current study, the same DNA prime-protein boost vaccine was used as in previous studies to investigate the induction of NAb responses against HIV-1 clade BC, a major subtype circulating in China. A codon optimized gp120-BC DNA vaccine, based on the consensus envelope (Env) antigen sequence of clade BC, was constructed and a stable CHO cell line expressing the same consensus BC gp120 protein was produced. The immunogenicity of this consensus gp120-BC was examined in New Zealand White rabbits by either DNA prime-protein boost or protein alone vaccination approaches. High levels of Env-specific antibody responses were elicited by both approaches. However, DNA prime-protein boost but not the protein alone immune sera contained significant levels of NAb against pseudotyped viruses expressing HIV-1 BC Env antigens. Furthermore, high frequencies of CD4 binding site-targeted antibodies were found in the DNA prime- protein boost rabbit sera indicating that the positive NAb may be the result of antibodies against conformationally sensitive epitopes on HIV-1 Env. The findings support that DNA prime-protein boost was effective in eliciting NAb against a key HIV-1 virus subtype in China. This result may lead to the development of regional HIV vaccines through this approach.
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Affiliation(s)
- Mingshun Zhang
- Jiangsu Province Key Laboratory in Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University; Nanjing, China
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Li L, Chen L, Yang S, Li T, Li J, Liu Y, Jia L, Yang B, Bao Z, Li H, Wang X, Zhuang D, Liu S, Li J. Recombination form and epidemiology of HIV-1 unique recombinant strains identified in Yunnan, China. PLoS One 2012; 7:e46777. [PMID: 23056447 PMCID: PMC3467292 DOI: 10.1371/journal.pone.0046777] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 09/05/2012] [Indexed: 11/18/2022] Open
Abstract
Several studies identified HIV-1 recombination in some distinct areas in Yunnan, China. However, no comprehensive studies had been fulfilled in the whole province up to now. To illustrate the epidemiology and recombination form of Unique Recombinant Forms (URFs) circulating in Yunnan, 788 HIV-1 positive individuals residing in 15 prefectures of Yunnan were randomly enrolled into the study. Full-length gag and pol genes were amplified and sequenced. Maximum likelihood tree was constructed for phylogenetic analysis. Recombinant breakpoints and genomic schematics were identified with online software jpHMM. 63 (10.2%) unique recombinant strains were identified from 617 strains with subtypes. The URFs distributed significantly differently among prefectures (Pearson chi-square test, P<0.05). IDUs contained more URFs than sexual transmitted population (Pearson chi-square test, P<0.05). Two main recombinant forms were identified by considering the presence of CRF01_AE segments in full length gag-pol genes, which were B′/C and B′/C/CRF01-AE recombinants. Three clusters were identified in the ML tree which contained more than three sequences and supported by high bootstrap values. One CRF was identified. Many of URFs contained identical breakpoints. The results will contribute to our understanding on HIV recombination and provide clues to the identification of potential CRFs in China.
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Affiliation(s)
- Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lili Chen
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Urumqi General Hospital of Lanzhou Military Area Command, Urumqi, Xinjiang, China
| | - Shaomin Yang
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jianjian Li
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bihui Yang
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- * E-mail:
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Extensive and complex HIV-1 recombination between B', C and CRF01_AE among IDUs in south-east Asia. AIDS 2012; 26:1121-9. [PMID: 22333750 DOI: 10.1097/qad.0b013e3283522c97] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
OBJECTIVE To investigate the subtype characterization of HIV-1 among IDUs in northern Myanmar. DESIGN A molecular epidemiological investigation was conducted among IDUs in Laza and Maizayang cities of northern Myanmar. METHODS A total of 83 HIV-1-positive serums were collected from consenting IDUs during June to August 2009. HIV-1 p17, pol, vif-env, C2V3 fragments were amplified and sequenced. Phylogenetic and bootscanning analyses were performed. RESULTS A very high proportion (86.1%) of HIV-1 intersubtype recombinants and very low proportion of subtypes B' (3.8%), C (7.6%) and CRF01_AE (1.3%) were found in this HIV-infected IDUs cohort. These recombinants cover all four kinds of recombination forms formed among CRF01_AE, B and C. The B/C and CRF01_AE/B/C recombinants are the two most dominant recombinants, accounting for 54.4 and 42.6% of all cases, respectively, and indicating the ongoing generation of extensive and complex HIV-1 recombination among CRF01_AE, B' and C in northern Myanmar. Intriguingly, most recombinants have different chimeric patterns from each other, forming 64 unique recombination forms (URFs) that are quite distinct from any previously identified circulating recombinant forms (CRFs) and URFs in Asia. CONCLUSION The extremely high proportion of intersubtype recombinants, especially CRF01_AE/B'/C recombinants (42.6%), strongly suggests that northern Myanmar is a big forge for HIV-1 recombination among CRF01_AE, B' and C.
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Tee KK, Kamarulzaman A, Matano T, Takebe Y. Phylodynamic inference of infectious diseases caused by HIV, enterovirus 71 and the 2009 swine-origin human influenza virus. Future Virol 2012. [DOI: 10.2217/fvl.12.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rapidly evolving nature of viruses, particularly RNA viruses, exhibit complex phylodynamic behaviors, accumulating mutations across the genome on a timescale observable by humans. Phylodynamic investigations provide unique and quantitative evolutionary data on the origin, progression in terms of time and space, and epidemic and transmission history of pathogens. This review describes recent phylodynamic conjectures on three distinct categories of human viruses, including HIV, enterovirus 71 and the swine-origin pandemic influenza virus H1N1, which are of enormous importance to public health.
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Affiliation(s)
- Kok Keng Tee
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Adeeba Kamarulzaman
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yutaka Takebe
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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Xu S, Zhong P, Li J, Song A, Li H, Nie J, Li X, Wang Y. Comparative evaluation of the ViroSeq™ HIV-1 genotyping system and an in-house method for analysis of HIV-1 drug-resistance mutations in China. Mol Diagn Ther 2011; 15:41-52. [PMID: 21469769 DOI: 10.1007/bf03257192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND AND OBJECTIVE With the introduction of the ViroSeq™ HIV-1 Genotyping System (ViroSeq™ assay) into China, it is important to evaluate the impact of the diversity of HIV-1 genotypes found in China on the performance of the ViroSeq™ assay compared with an in-house method. MATERIALS AND METHODS A total of 318 plasma samples, collected from 206 HIV-1-infected patients receiving antiretroviral therapy and 112 treatment-naïve HIV-1-infected patients, were used for evaluating the concordance of genotypes, genotypic resistance mutations, and phenotypic resistance between the ViroSeq™ assay and an in-house method for analyzing HIV-1 drug resistance in China. RESULTS A concordance of genotypes between the ViroSeq™ assay and the in-house method was observed for the 313 samples (98.4%), using the Stanford University HIV Drug Resistance Database (Version 6.0.5). The overall concordances of drug-resistance-related mutations (DRRMs) in the HIV-1 protease (PR) and reverse transcriptase (RT) coding sequences within the HIV-1 pol gene, scored by the ViroSeq™ assay and the in-house method, were 99.5% and 98.1%, respectively. Discrepancies between the two methods were found in 38 samples assayed for protease inhibitor (PI) DRRMs, 36 samples assayed for nucleoside reverse transcriptase inhibitor (NRTI) DRRMs, and 72 samples assayed for non-nucleoside reverse transcriptase inhibitor (NNRTI) DRRMs, and 100%, 88.9%, and 87.5% of the samples with discrepancies for PI, NRTI, and NNRTI DRRMs, respectively, were genotyped as subtype B. One NNRTI mutation (the RT mutation Y318F) was reported only by the ViroSeq™ assay, and this discrepancy resulted from the difference in the pol gene lengths generated by the two systems. Furthermore, the overall concordance of phenotypic resistance was 94.7% (301/318) between the two methods. CONCLUSION The ViroSeq™ assay will be a useful tool for monitoring clinical drug resistance and for better management of HIV-1 patients receiving antiretroviral therapy in China.
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Affiliation(s)
- Sihong Xu
- Department of Cell Biology, National Institute for the Control of Pharmaceutical and Biological Products, Beijing, PR China
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Phylogeographic analyses reveal a crucial role of Xinjiang in HIV-1 CRF07_BC and HCV 3a transmissions in Asia. PLoS One 2011; 6:e23347. [PMID: 21858079 PMCID: PMC3155551 DOI: 10.1371/journal.pone.0023347] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 07/13/2011] [Indexed: 01/20/2023] Open
Abstract
Background China faces an increasing prevalence of two HIV-1 circulating recombinant forms (CRFs) 07_BC and 08_BC. Both CRFs_BC were previously demonstrated to originate in Yunnan and spread to Liaoning from Yunnan via injection drug use (IDU) in China. Supposing it is true, we are unable to answer why only CRF07_BC, rather than both CRFs_BC together, was transmitted to Xinjiang. Methodology/Principal Findings We investigated the phylogeography of CRF07_BC and CRF08_BC using multiple HIV-1 genomic regions with Bayesian phylogeography method. Phylogenetic reconstructions showed that all CRF07_BC sequences were divided into two clades, Yunnan and Xinjiang, and all strains from other regions of mainland China clustered within the Xinjiang clade. Significant geographic diffusion links of Xinjiang with other regions (including Liaoning, Beijing, Jiangsu and Guangdong) were supported by Bayes factor tests. The temporal dynamics analyses showed that CRF07_BC spread from Xinjiang to Liaoning in 1996.10, and to Jiangsu in 2000.9. The analyses of CRF08_BC not only confirmed the previous conclusion on temporal and spatial dynamics of CRF08_BC, but also indicated that the CRF08_BC strains from Guangdong and Shanghai originated from Yunnan. The analyses of HCV 3a showed that it was introduced into Xinjiang in the early 1980s, and spread from Xinjiang to Yunnan in 1990.10 and to Jiangsu in 1999.2, and further from Yunnan to Guangxi in 1995.3. The temporal and spatial dynamics of HCV 3a were similar to some extent to that of HIV-1 CRF07_BC and/or CRF08_BC, suggesting a possible association in migration patterns between HCV and HIV-1 through IDU. In addition, HCV 3a spread from Xinjiang to Pakistan, implying a drug trafficking route linking them. Conclusions/Significance Xinjiang, as the most important transfer station for drug trafficking from Golden Crescent to other regions of China, plays a very crucial role in the transmission of viruses (e.g., HIV-1 and HCV) through IDU in Asia.
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Chen L, Yang S, Li J, Li J, Liu Y, Wang Z, Yang B, Li T, Li H, Bao Z, Zhuang D, Liu S, Li L. Near full-length genomic characterization of a novel HIV type 1 CRF07_ BC/CRF08_ BC recombinant strain from Yunnan, China. AIDS Res Hum Retroviruses 2011; 27:693-9. [PMID: 21083434 DOI: 10.1089/aid.2010.0264] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Yunnan province was considered the HIV-1 epicenter of China, where many subtypes and CRFs of HIV-1 were circulating. CRF07_BC and CRF08_BC were two of the main circulating subtypes that caused more than 90% of the HIV-1 infections in intravenous drug users (IDUs) in this district. The cocirculation of these two CRFs in the same area and population predicted the emergence of new second-generation recombinants. This study presented a near full-length genomic analysis of a novel HIV-1 recombination (09YN072) involving CRF07_BC and CRF08_BC. The analyses of the sequence of 09YN072 showed that two CRF07_BC segments were inserted into the CRF08_BC backbone. The discovery of the novel recombinant strain complicates the HIV-1 epidemic in Yunnan, China, as well as the development of effective vaccines to limit the spread of HIV-1 in China.
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Affiliation(s)
- Lili Chen
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Urumqi General Hospital of Lanzhou Military Area Command, Urumqi, China
| | - Shaomin Yang
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jianjian Li
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zheng Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bihui Yang
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Liu Y, Li L, Yang S, Bao Z, Li H, Wang Z, Zhuang D, Liu S, Chen L, Fan Y, Zhong M, Gao L, Wang X, Li J. Identification and characterization of two new HIV type 1 Unique (B/C) recombinant forms in China. AIDS Res Hum Retroviruses 2011; 27:445-51. [PMID: 20977352 DOI: 10.1089/aid.2010.0212] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recombination was most important in the generation of new viral strains and in the increase of HIV diversity. There were more and more new HIV-1 strains. Not only circulating recombinant forms (CRFs) but also unique recombinant forms (URFs) have been reported around the world. CRF07_BC and CRF08_BC were the two predominant CRFs circulated in Yunnan Province, southwest China. In the present study, we identified two new HIV Type 1 unique (B/C) recombinant gorms in Yunnan Province by nucleotide sequencing in two halves of HIV genome. Although the genomic structures of the two B/C recombinants were different from previously identified CRFs (CRF07_BC and CRF08_BC) and URFs in Yunnan Pprovince, they have several common recombination sites with CRF07_BC and CRF08_BC.
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Affiliation(s)
- Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shaomin Yang
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zheng Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lili Chen
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yishan Fan
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Min Zhong
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Li Gao
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Performance of NucliSens HIV-1 EasyQ Version 2.0 compared with six commercially available quantitative nucleic acid assays for detection of HIV-1 in China. Mol Diagn Ther 2011; 14:305-16. [PMID: 21053996 DOI: 10.1007/bf03256386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
BACKGROUND AND OBJECTIVES Six HIV-1 viral load assays have been widely used in China. These include the Cobas Amplicor HIV-1 Monitor Version 1.5 ('Amplicor'), Cobas AmpliPrep/Cobas TaqMan HIV-1 test Version 1.0 ('CAP/CTM'), Versant HIV-1 RNA Version 3.0 (branched DNA [bDNA]-based assay; 'Versant bDNA'), Abbott RealTime HIV-1 assay ('Abbott RealTime'), NucliSens HIV-1 QT (nucleic acid sequence-based amplification assay; 'NucliSens NASBA'), and NucliSens EasyQ HIV-1 Version 1.1 ('EasyQ V1.1'). Recently, an updated version of EasyQ V1.1, NucliSens EasyQ HIV-1 Version 2.0 ('EasyQ V2.0') was introduced into China. It is important to evaluate the impact of HIV-1 genotypes on the updated assay compared with the other commercial available assays in China. METHODS A total of 175 plasma samples with different HIV-1 clades prevalent in China were collected from treatment-naïve patients. The viral loads of those samples were determined with the seven HIV-1 viral load assays, and the quantitative differences between them were evaluated. RESULTS Overall, EasyQ V2.0 exhibited a significant correlation (R = 0.769-0.850, p ≤ 0.001) and high agreement (94.77-97.13%, using the Bland-Altman model) with the other six assays. Although no significant differences between EasyQ V2.0 and the other six assays were observed when quantifying clade B' samples, there were statistically significant differences between EasyQ V2.0 and the Amplicor, Versant bDNA, and Abbott RealTime assays when quantifying clade BC samples, and between EasyQ V2.0 and the Versant bDNA and Abbott RealTime assays when quantifying clade AE samples. For clade BC samples, the quantitative differences between EasyQ V2.0 and the Amplicor, Versant bDNA, and Abbott RealTime assays exceeded 0.5 log(10) IU/mL in approximately 50% of samples and exceeded 1 log(10) IU/mL in approximately 15% of samples. For clade AE samples, the quantitative differences between EasyQ V2.0 and the CAP/CTM, Versant bDNA, and Abbott RealTime assays exceeded 0.5 log(10) IU/mL in approximately 50% of samples, and the differences between EasyQ V2.0 and CAP/CTM exceeded 1 log(10) IU/mL in approximately 15% of samples. CONCLUSION Genotypes may affect the quantification of HIV-1 RNA, especially in clade BC samples with respect to EasyQ V2.0 and the Amplicor, Versant bDNA, or Abbott RealTime assays, and in clade AE samples with respect to EasyQ V2.0 and the Versant bDNA or Abbott RealTime assays. It is therefore strongly suggested that, where possible, the HIV-1 viral load in infected patients be quantified at follow-up by the same version of the same assay that was used initially.
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Takebe Y, Liao H, Hase S, Uenishi R, Li Y, Li XJ, Han X, Shang H, Kamarulzaman A, Yamamoto N, Pybus OG, Tee KK. Reconstructing the epidemic history of HIV-1 circulating recombinant forms CRF07_BC and CRF08_BC in East Asia: the relevance of genetic diversity and phylodynamics for vaccine strategies. Vaccine 2010; 28 Suppl 2:B39-44. [PMID: 20510742 DOI: 10.1016/j.vaccine.2009.07.101] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 07/21/2009] [Accepted: 07/24/2009] [Indexed: 11/18/2022]
Abstract
HIV-1 CRF07_BC and CRF08_BC are closely related circulating recombinant forms (CRFs) with serious public health consequences in China. The temporal and spatial dynamics of these CRFs were determined by estimating their times of divergence, using phylogenetic and Bayesian coalescent methods. Studies of the timelines of CRF07_BC and CRF08_BC trace the expansion of these strains back their origins to Yunnan province. The present study highlights the relevance of incorporating evolutionary and molecular epidemiological analyses into an in-depth understanding of the genesis of HIV epidemic, providing information for determining regional and global public health policies, including future vaccine strategies.
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Affiliation(s)
- Yutaka Takebe
- Laboratory of Molecular Virology and Epidemiology, AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
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Shang H, Zhong P, Liu J, Han X, Dai D, Zhang M, Zhao K, Xu R, Yu XF. High prevalence and genetic diversity of HCV among HIV-1 infected people from various high-risk groups in China. PLoS One 2010; 5:e10631. [PMID: 20523729 PMCID: PMC2877711 DOI: 10.1371/journal.pone.0010631] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 04/22/2010] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Co-infection with HIV-1 and HCV is a significant global public health problem and a major consideration for anti-HIV-1 treatment. HCV infection among HIV-1 positive people who are eligible for the newly launched nationwide anti-HIV-1 treatment program in China has not been well characterized. METHODOLOGY A nationwide survey of HIV-1 positive injection drug uses (IDU), former paid blood donors (FBD), and sexually transmitted cases from multiple provinces including the four most affected provinces in China was conducted. HCV prevalence and genetic diversity were determined. We found that IDU and FBD have extremely high rates of HCV infection (97% and 93%, respectively). Surprisingly, people who acquired HIV-1 through sexual contact also had a higher rate of HCV infection (20%) than the general population. HIV-1 subtype and HCV genotypes were amazingly similar among FBD from multiple provinces stretching from Central to Northeast China. However, although patterns of overland trafficking of heroin and distinct HIV-1 subtypes could be detected among IDU, HCV genotypes of IDU were more diverse and exhibited significant regional differences. CONCLUSION Emerging HIV-1 and HCV co-infection and possible sexual transmission of HCV in China require urgent prevention measures and should be taken into consideration in the nationwide antiretroviral treatment program.
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Affiliation(s)
- Hong Shang
- Key Laboratory of AIDS Immunology of Ministry of Health, No 1 Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ping Zhong
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Jing Liu
- Key Laboratory of AIDS Immunology of Ministry of Health, No 1 Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaoxu Han
- Key Laboratory of AIDS Immunology of Ministry of Health, No 1 Hospital of China Medical University, Shenyang, Liaoning, China
| | - Di Dai
- Key Laboratory of AIDS Immunology of Ministry of Health, No 1 Hospital of China Medical University, Shenyang, Liaoning, China
| | - Min Zhang
- Key Laboratory of AIDS Immunology of Ministry of Health, No 1 Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ke Zhao
- Center for Virus and AIDS Research, Jilin University First Hospital, Changchun, Jilin, China
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Rongzhen Xu
- Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiao-Fang Yu
- Center for Virus and AIDS Research, Jilin University First Hospital, Changchun, Jilin, China
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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Abstract
PURPOSE OF REVIEW Drug abuse has resulted in a huge public health and economic burden in China, especially the rapid spread of HIV/AIDS and hepatitis C virus (HCV) infection. Multiple HIV and HCV subtypes were detected among drug users in China, this study reviews the molecular distribution of HIV and HCV among injection drug users (IDUs) and explores new epidemiologic trends of HIV and HCV among drug users in China. RECENT FINDINGS The 2009 National Narcotic Control Commission report showed that the percentage of users of 'new-type drugs', including amphetamine-type stimulants (ATS: methamphetamine and MDMA/ecstasy) and ketamine, was about 27% of total drug users. The pooled data from published papers showed that CRF07BC was the predominant HIV-1 subtype, which accounted for 38.8%, and it was followed by AE, which accounted for 22.7% among HIV-positive IDUs. Following these, the CRF08BC, B' and C subtypes accounted for about 10.8%, 9.9% and 9.2%, respectively. Subtype 6a was the predominant HCV subtype, accounting for 36.7%, and subtypes 3b, 1a, 3a and 1b were the next most predominant subtypes. SUMMARY With the increase of 'new-type drugs' use and AE HIV-1 subtype infection among IDUs, the situation regarding HIV/AIDS and HCV infection has become complicated. More comprehensive prevention and intervention strategies should be instigated for the extensive high-risk populations in China.
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Acute Infection of Chinese Macaques by a CCR5-Tropic SHIV Carrying a Primary HIV-1 Subtype B' Envelope. J Acquir Immune Defic Syndr 2010; 53:285-91. [DOI: 10.1097/qai.0b013e3181cc4f4a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Genetic and epidemiologic characterization of HIV-1 infection In Liaoning Province, China. J Acquir Immune Defic Syndr 2010; 53 Suppl 1:S27-33. [PMID: 20104106 DOI: 10.1097/qai.0b013e3181c7d5bf] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Although many studies of HIV-1 in China have focused on high-risk injecting drug users and former blood donors in high prevalence regions, little is known about HIV-1 in relatively low prevalence provinces. Here, we compare the epidemiologic and genetic profile of HIV-1 in Liaoning-a low prevalence province-with those identified in China's most severely affected provinces. MATERIALS AND METHODS Two hundred eight HIV-1-positive subjects from all major cities in Liaoning province were recruited between 2000 and 2008. 2.6 kilobase gag-pol sequences were amplified from plasma viral RNA and sequenced directly. The HIV-1 sequences obtained were analyzed using phylogenetic and recombinant approaches. RESULTS We have shown that in recent years, although HIV-1 prevalence in Liaoning has remained low, the rate of new infection has increased rapidly, particularly among men who have sex with men and heterosexual risk individuals (together comprising >54% of infected individuals in 2007). Furthermore, phylogenetic analysis has identified all major subtypes/circulating recombinant forms of HIV-1 in Liaoning previously identified in high prevalence provinces. Our study also shows close relationships between HIV-1 subtype/circulating recombinant form and certain risk behaviors. Notably, men who have sex with men and heterosexual risk individuals harbor most divergent strains of HIV-1 from multiple high-risk groups. CONCLUSIONS Our study suggested that HIV-1 continues to spread to the general population through sexual contact; Liaoning, therefore, serves as the critical base for the introduction and spread of HIV-1 in northeast China. We believe the transmission patterns suggested herein will help guide public health workers in reducing further spread of HIV-1 within China.
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Wild J, Bieler K, Köstler J, Frachette MJ, Jeffs S, Vieira S, Esteban M, Liljeström P, Pantaleo G, Wolf H, Wagner R. Preclinical evaluation of the immunogenicity of C-type HIV-1-based DNA and NYVAC vaccines in the Balb/C mouse model. Viral Immunol 2009; 22:309-19. [PMID: 19811088 DOI: 10.1089/vim.2009.0038] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As part of a European initiative (EuroVacc), we report the design, construction, and immunogenicity of two HIV-1 vaccine candidates based on a clade C virus strain (CN54) representing the current major epidemic in Asia and parts of Africa. Open reading frames encoding an artificial 160-kDa GagPolNef (GPN) polyprotein and the external glycoprotein gp120 were fully RNA and codon optimized. A DNA vaccine (DNA-GPN and DNA-gp120, referred to as DNA-C), and a replication-deficient vaccinia virus encoding both reading frames (NYVAC-C), were assessed regarding immunogenicity in Balb/C mice. The intramuscular administration of both plasmid DNA constructs, followed by two booster DNA immunizations, induced substantial T-cell responses against both antigens as well as Env-specific antibodies. Whereas low doses of NYVAC-C failed to induce specific CTL or antibodies, high doses generated cellular as well as humoral immune responses, but these did not reach the levels seen following DNA vaccination. The most potent immune responses were detectable using prime:boost protocols, regardless of whether DNA-C or NYVAC-C was used as the priming or boosting agent. These preclinical findings revealed the immunogenic response triggered by DNA-C and its enhancement by combining it with NYVAC-C, thus complementing the macaque preclinical and human phase I clinical studies of EuroVacc.
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Affiliation(s)
- Jens Wild
- Institute of Medical Microbiology, University of Regensburg, Regensburg, Germany
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Zhao F, Wang Z, Li WJ. Human immunodeficiency virus type 1 subtypes prevalence in central China. Yonsei Med J 2009; 50:644-9. [PMID: 19881967 PMCID: PMC2768238 DOI: 10.3349/ymj.2009.50.5.644] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 12/26/2008] [Accepted: 01/07/2009] [Indexed: 11/27/2022] Open
Abstract
PURPOSE To study the epidemic characteristics, transmission sources and routes of various subtypes of human immunodeficiency virus type 1 (HIV-1) and sequence variations in Henan, central China. To provide theoretical foundation for Acquired Immune Deficiency Syndrome (AIDS) prevention strategy in this region where the primary HIV transmission route was through former paid blood donation. MATERIALS AND METHODS HIV-1 gene env and gag were amplified by nested polymerase chain reaction (PCR) from uncultured peripheral blood mononuclear cells (PBMCs) obtained from 1,287 HIV-1 confirmed samples in Henan. RESULTS Among 1,287 samples, 5 HIV-1 strains were found including subtypes B' (95.9%), C (0.47%) and recombinant subtypes CRF 07_BC (1.09%), CRF 08_BC (1.79%) and CRF 01_AE (0.78%). Phylogenetic tree analysis found that 1,234 Henan subtype B' were closely related to those commonly found in Thailand, and were distantly related to other international subtypes. The dominant strain in former blood plasma donors (FPDs) was subtype B', and the dominant strains in sexual transmission were subtype B' and BC. Among HIV patients who were most likely infected through routes other than paid blood donation, the percentage of non-B' subtypes was much higher than those of FPD. CONCLUSION These findings suggest that the prevailing strain of HIV-1 in Henan is subtype B', similar to the B' subtype found in Thailand. In addition, for the first time we found subtypes C and recombinant subtypes CRF07_BC, CRF08_BC and CRF01_AE in this region. Indicating that the subtype feature of HIV-1 became more complicated than before in central China.
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Affiliation(s)
- Fei Zhao
- School of Public Health, Zhengzhou University, Zhengzhou, China.
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Ma L, Guo Y, Yuan L, Huang Y, Sun J, Qu S, Yu X, Meng Z, He X, Jiang S, Shao Y. Phenotypic and genotypic characterization of human immunodeficiency virus type 1 CRF07_BC strains circulating in the Xinjiang Province of China. Retrovirology 2009; 6:45. [PMID: 19442296 PMCID: PMC2693499 DOI: 10.1186/1742-4690-6-45] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2008] [Accepted: 05/14/2009] [Indexed: 12/01/2022] Open
Abstract
Background HIV-1 CRF07_BC recombinant previously circulated mainly among the intravenous drug users (IDUs) in Xinjiang province of China and is currently spreading in the entire country. The aim of this study is to characterize the genotypic and phenotypic properties of HIV-1 CRF07_BC isolates in comparison with those of the subtype B' (Thailand B) which is prevalent in the former plasma donors (FPDs) in China. Results Twelve HIV-1 CRF07_BC variants were isolated from the blood of the HIV-1-infected IDUs in Xinjiang province, and 20 subtype B' isolates were obtained from the FPDs in Anhui and Shanxi provinces of China. All the CRF07_BC viruses utilized CCR5 co-receptor, whereas 12 subtype B' viruses were R5-tropic, and the remaining B' isolates were dual (R5X4) tropic. CRF07_BC viruses had lower net charge value in the V3 loop and exhibited slower replication kinetics than subtype B' viruses. The number and location of the potential N-linked glycosylation sites in V1/V2 and the C2 region of the CRF07_BC viruses were significantly different from those of the subtype B' viruses. Conclusion The HIV-1 CRF07_BC recombinant strains with relatively lower net charges in the V3 loop exclusively utilize CCR5 co-receptor for infection and exhibit slow replication kinetics in the primary target cells, suggesting that CRF07_BC may be superior over B' and other HIV-1 subtypes in initiating infection in high-risk population. These findings have molecular implications for the adaptive evolution of HIV-1 circulating in China and the design of tailored therapeutic strategy for treatment of HIV-1 CRF07_BC infection.
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Affiliation(s)
- Liying Ma
- State Key Laboratory for Infectious Disease Control and Prevention, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China.
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Rapidly Increasing Prevalence of HIV and Syphilis and HIV-1 Subtype Characterization Among Men Who Have Sex With Men in Jiangsu, China. Sex Transm Dis 2009; 36:120-5. [DOI: 10.1097/olq.0b013e31818d3fa0] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
HIV has advanced from high-risk groups such as intravenous drug users to some in the general population, according to comprehensive new data from the south of China. What needs to be done to halt its spread?
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Xu S, Song A, Nie J, Li X, Li J, Bao Z, Wang Y. Comparative evaluation of the COBAS AmpliPrep/COBAS TaqMan HIV type 1 test (CAP/CTM) and VERSANT HIV type 1 RNA 3.0 assay (bDNA) for quantifying HIV type 1 viral loads in China. AIDS Res Hum Retroviruses 2008; 24:1365-73. [PMID: 18928395 DOI: 10.1089/aid.2008.0005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In the present study, 277 clinical samples from untreated and treated HIV-1-infected patients with different clades were used to assess the agreement between the COBAS AmpliPrep/COBAS TaqMan HIV-1 test (CAP/CTM) and VERSANT HIV-1 RNA 3.0 Assay (bDNA). A qualitative comparison of the results of the two assays showed concordance for 255 positive and 15 negative samples (94.95%, kappa = 0.798). However, seven samples with viral loads close to the lower limit of detection for CAP/CTM were negative by bDNA. A significant correlation (r = 0.881, p < 0.001) was observed for 253 samples with viral loads within the dynamic ranges of the two assays, and Bland-Altman analysis showed good agreement (96.05%) between the two assays for these 253 samples [mean (+/-2 SD), 0.389(-0.385, 1.163)]. Furthermore, ART drugs had no impact on the performances of the two assays. For samples with different clades predominant in China, the fitted regression line differed significantly from the line of equality, although significant correlations (r = 0.850-0.891, p < 0.001) and good agreements (92.86-97.25%) were found for the two assays. The mean differences for clade B' and BC samples were significant (p < 0.01). Good precision for clade B' samples was achieved for the CAP/CTM (CV: 20.73%) and bDNA (CV: 12.19%) assays. Furthermore, for clades B', BC, and AE, both assays exhibited good linearities (r = 0.9773-0.9998). Thus, the CAP/CTM and bDNA assays could be useful for quantifying HIV-1 RNA in routine clinical samples and monitoring viral loads in treated and untreated HIV-infected patients in China.
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Affiliation(s)
- Sihong Xu
- Department of Cell Biology, National Institute for the Control of Pharmaceutical and Biological Products, Beijing 100050, P.R. China
| | - Aijing Song
- Department of Cell Biology, National Institute for the Control of Pharmaceutical and Biological Products, Beijing 100050, P.R. China
| | - Jianhui Nie
- Department of Cell Biology, National Institute for the Control of Pharmaceutical and Biological Products, Beijing 100050, P.R. China
| | - Xiuhua Li
- Department of Cell Biology, National Institute for the Control of Pharmaceutical and Biological Products, Beijing 100050, P.R. China
| | - Jingyun Li
- Center of AIDS, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing 100071, P.R. China
| | - Zuoyi Bao
- Center of AIDS, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing 100071, P.R. China
| | - Youchun Wang
- Department of Cell Biology, National Institute for the Control of Pharmaceutical and Biological Products, Beijing 100050, P.R. China
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The epidemic origin and molecular properties of B': a founder strain of the HIV-1 transmission in Asia. AIDS 2008; 22:1851-8. [PMID: 18753865 DOI: 10.1097/qad.0b013e32830f4c62] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To clarify the epidemic origin and molecular properties of the B' subtype that is an important strain in the HIV-1 epidemic in Asia. DESIGN The genealogical relationship between the B' and B subtype was investigated with two globally representative datasets covering the gag and env regions. B' sequences were identified, from which the epidemic origin, population genetics and the signature mutation sites of the B' subtype were inferred. METHODS Two globally representative datasets were compiled, using phylogenetic methods. Through coalescent-based analysis, the genealogical relationship between the B' and B subtypes was investigated. The divergence times and population genetic parameters of B' were estimated in a Bayesian framework using Markov Chains Monte Carlo sampling under a relaxed molecular clock method. Additionally, molecular properties of the B' were identified by performing comparative sequence analysis with the HIV-1 M group. RESULTS About 15 years later after the B subtype began to spread, the B' diverged from the B subtype. The demographic history of B' was reconstructed, and the epidemic of B' was estimated to originate around 1985. Eight and nine distinct signature mutation sites, unique to B', were found around the p17 and V3 regions, respectively. CONCLUSION Our research is the first large-scale investigation on HIV-1 B' at a global level and provides a deep insight into one of the founder strains of HIV-1 epidemic in Asia. Our results provide an important reference for HIV scientists, public health officials and HIV vaccine designers.
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Temporal and spatial dynamics of human immunodeficiency virus type 1 circulating recombinant forms 08_BC and 07_BC in Asia. J Virol 2008; 82:9206-15. [PMID: 18596096 DOI: 10.1128/jvi.00399-08] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) CRF08_BC and CRF07_BC are two major recombinants descended from subtypes B' and C. Despite their massive epidemic impact in China, their migration patterns and divergence times remain unknown. Phylogenetic and population genetic analyses were performed on 228 HIV-1 sequences representing CRF08_BC, CRF07_BC, and subtype C strains from different locations across China, India, and Myanmar. Genome-specific rates of evolution and divergence times were estimated using a Bayesian Markov chain Monte Carlo framework under various evolutionary models. CRF08_BC originated in 1990.3 (95% credible region [CR], 1988.6 to 1991.9) in Yunnan province before spreading to Guangxi (south) and Liaoning (northeast) around 1995. Inside Guangxi region, the eastward expansion of CRF08_BC continued from Baise city (west) to Binyang (central) between 1997 and 1998 and later spread into Pingxiang around 1999 in the south, mainly through injecting drug users. Additionally, CRF07_BC diverged from its common ancestor in 1993.3 (95% CR, 1991.2 to 1995.2) before crossing the border into southern Taiwan in late 1990s. Phylogenetic analysis indicates that both CRF08_BC and CRF07_BC can trace their origins to Yunnan. The parental Indian subtype C lineage likely entered China around 1981.2 (95% CR, 1976.7 to 1985.9). Using a multiple unlinked locus model, we also showed that the dates of divergence calculated in this study may not be significantly affected by intrasubtype recombination among different lineages. This is the first phylodynamic study depicting the spatiotemporal dynamics of HIV/AIDS in East Asia.
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