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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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Paraskevis D, Nikolopoulos GK, Magiorkinis G, Hodges-Mameletzis I, Hatzakis A. The application of HIV molecular epidemiology to public health. INFECTION GENETICS AND EVOLUTION 2016; 46:159-168. [PMID: 27312102 DOI: 10.1016/j.meegid.2016.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 02/02/2023]
Abstract
HIV is responsible for one of the largest viral pandemics in human history. Despite a concerted global response for prevention and treatment, the virus persists. Thus, urgent public health action, utilizing novel interventions, is needed to prevent future transmission events, critical to eliminating HIV. For public health planning to prove effective and successful, we need to understand the dynamics of regional epidemics and to intervene appropriately. HIV molecular epidemiology tools as implemented in phylogenetic, phylodynamic and phylogeographic analyses have proven to be powerful tools in public health planning across many studies. Numerous applications with HIV suggest that molecular methods alone or in combination with mathematical modelling can provide inferences about the transmission dynamics, critical epidemiological parameters (prevalence, incidence, effective number of infections, Re, generation times, time between infection and diagnosis), or the spatiotemporal characteristics of epidemics. Molecular tools have been used to assess the impact of an intervention and outbreak investigation which are of great public health relevance. In some settings, molecular sequence data may be more readily available than HIV surveillance data, and can therefore allow for molecular analyses to be conducted more easily. Nonetheless, classic methods have an integral role in monitoring and evaluation of public health programmes, and should supplement emerging techniques from the field of molecular epidemiology. Importantly, molecular epidemiology remains a promising approach in responding to viral diseases.
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Affiliation(s)
- D Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| | - G K Nikolopoulos
- Hellenic Center for Diseases Control and Prevention, Maroussi, Greece
| | - G Magiorkinis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, United Kingdom
| | | | - A Hatzakis
- Hellenic Center for Diseases Control and Prevention, Maroussi, Greece
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Lu W, Chen S, Lai C, Lai M, Fang H, Dao H, Kang J, Fan J, Guo W, Fu L, Andrieu JM. Suppression of HIV Replication by CD8(+) Regulatory T-Cells in Elite Controllers. Front Immunol 2016; 7:134. [PMID: 27148256 PMCID: PMC4834299 DOI: 10.3389/fimmu.2016.00134] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 03/24/2016] [Indexed: 12/25/2022] Open
Abstract
We previously demonstrated in the Chinese macaque model that an oral vaccine made of inactivated SIV and Lactobacillus plantarum induced CD8(+) regulatory T-cells, which suppressed the activation of SIV(+)CD4(+) T-cells, prevented SIV replication, and protected macaques from SIV challenges. Here, we sought whether a similar population of CD8(+) T-regs would induce the suppression of HIV replication in elite controllers (ECs), a small population (3‰) of HIV-infected patients with undetectable HIV replication. For that purpose, we investigated the in vitro antiviral activity of fresh CD8(+) T-cells on HIV-infected CD4(+) T-cells taken from 10 ECs. The 10 ECs had a classical genomic profile: all of them carried the KIR3DL1 gene and 9 carried at least 1 allele of HLA-B:Bw4-80Ile (i.e., with an isoleucine residue at position 80). In the nine HLA-B:Bw4-80Ile-positive patients, we demonstrated a strong viral suppression by KIR3DL1-expressing CD8(+) T-cells that required cell-to-cell contact to switch off the activation signals in infected CD4(+) T-cells. KIR3DL1-expressing CD8(+) T-cells withdrawal and KIR3DL1 neutralization by a specific anti-killer cell immunoglobulin-like receptor (KIR) antibody inhibited the suppression of viral replication. Our findings provide the first evidence for an instrumental role of KIR-expressing CD8(+) regulatory T-cells in the natural control of HIV-1 infection.
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Affiliation(s)
- Wei Lu
- Institut de Recherche sur les Vaccins et l'Immunothérapie des Cancers et du Sida, Université de Paris Descartes, Paris, France; Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Song Chen
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine , Guangzhou , China
| | - Chunhui Lai
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine , Guangzhou , China
| | - Mingyue Lai
- Xishuangbanna Center for Disease Control and Prevention , Jinghong , China
| | - Hua Fang
- Xishuangbanna Center for Disease Control and Prevention , Jinghong , China
| | - Hong Dao
- Xishuangbanna Center for Disease Control and Prevention , Jinghong , China
| | - Jun Kang
- Xishuangbanna Center for Disease Control and Prevention , Jinghong , China
| | - Jianhua Fan
- Xishuangbanna Center for Disease Control and Prevention , Jinghong , China
| | - Weizhong Guo
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine , Guangzhou , China
| | - Linchun Fu
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine , Guangzhou , China
| | - Jean-Marie Andrieu
- Institut de Recherche sur les Vaccins et l'Immunothérapie des Cancers et du Sida, Université de Paris Descartes , Paris , France
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Geographic origin and evolutionary history of China's two predominant HIV-1 circulating recombinant forms, CRF07_BC and CRF08_BC. Sci Rep 2016; 6:19279. [PMID: 26763952 PMCID: PMC4725877 DOI: 10.1038/srep19279] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/09/2015] [Indexed: 11/08/2022] Open
Abstract
To determine the origin and evolutionary history of two predominant and closely-related circulating recombinant forms (CRF07_BC and CRF08_BC), recombinant structures and phylogenies of 7 unique recombinant forms comprised of subtypes of B’ (Thai B linage) and C (designated URFs_BC) from archival specimens of injection drug users (IDUs) collected in 1996 to 1998 from western Yunnan and 4 circulating recombinant forms with B’/C recombinants recently identified (designated nCRFs_BC) in China were compared with those of CRF07_BC and CRF08_BC. The results showed that 5 of 7 URFs_BC and all the nCRFs_BC shared recombination breakpoints with CRF07_BC and/or CRF08_BC. Yunnan URFs_BC consistently occupied the basal branch positions compared with CRF07_BC, CRF08_BC, and nCRFs_BC in phylogenetic trees. The estimated most recent common ancestors (tMRCA) for Yunnan URFs_BC were from ~1987, approximately half a decade earlier than those for CRF07_BC (~1994) and CRF08_BC (~1992). Discrete phylogeographic and spatial diffusion analysis revealed that both CRF07_BC and CRF08 BC came from western Yunnan in the early 1990s. Our results provide compelling evidence for western Yunnan as the geographic origin of CRF07_BC and CRF08_BC, which emerged from a swarm of URFs_BC by a series of recombination events in western Yunnan in the early 1990s.
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The sexually driven epidemic in youths in China's southwestern border region was caused by dynamic emerging multiple recombinant HIV-1 strains. Sci Rep 2015; 5:11323. [PMID: 26133091 PMCID: PMC4489098 DOI: 10.1038/srep11323] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 05/01/2015] [Indexed: 11/25/2022] Open
Abstract
Dehong prefecture, Yunnan province on China’s southwestern border was the gateway of the country’s AIDS epidemic. Studies on HIV-1 molecular epidemiology will provide key information on virus transmission dynamics and help to inform HIV prevention strategies. HIV-1 infected youths (age 16–25 years) diagnosed in the continuous 3 months in 2009 to 2012 were enrolled. By means of phylogenetic and statistical analyses, It was showed that two thirds (133/205) of youths in Dehong, of which 74.1% were infected sexually, were infected by uncharacterized recombinant HIV-1 strains. Among them about 59.4% (79/131) were unique recombinant forms (URFs) and 40.6% (54/131) formed 11 transmission clusters, termed potential circulating recombinant forms (pCRFs). The emergence of recombinants was statistically significant related with people of low education, residents outside the capital city of Dehong and being Myanmar residents. It was the first report with ongoing HIV-1 recombinant strains in a sexually driven epidemic area in China. Great efforts should be put on reducing multiple risk exposures behavior in local young people, containing the spread of pCRFs to other regions, and preventing the URFs from evolving into future CRFs. Collaborative prevention across border is needed to better control the local AIDS epidemic.
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Transmission clustering among newly diagnosed HIV patients in Chicago, 2008 to 2011: using phylogenetics to expand knowledge of regional HIV transmission patterns. J Acquir Immune Defic Syndr 2015; 68:46-54. [PMID: 25321182 DOI: 10.1097/qai.0000000000000404] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION HIV transmission cluster analyses can inform HIV prevention efforts. We describe the first such assessment for transmission clustering among HIV patients in Chicago. METHODS We performed transmission cluster analyses using HIV pol sequences from newly diagnosed patients presenting to Chicago's largest HIV clinic between 2008 and 2011. We compared sequences through progressive pairwise alignment, using neighbor joining to construct an unrooted phylogenetic tree. We defined clusters as >2 sequences among which each sequence had at least 1 partner within a genetic distance of ≤1.5%. We used multivariable regression to examine factors associated with clustering and used geospatial analysis to assess geographic proximity of phylogenetically clustered patients. RESULTS We compared sequences from 920 patients, median age of 35 years, 75% male, 67% black, 23% Hispanic, and 8% had a rapid plasma reagin titer ≥1:16 concurrent with their HIV diagnosis. We had HIV transmission risk data for 54%; 43% identified as men who have sex with men (MSM). Phylogenetic analysis demonstrated 123 patients (13%) grouped into 26 clusters, the largest having 20 members. In multivariable regression, age <25, black race, MSM status, male gender, higher HIV viral load, and rapid plasma reagin ≥1:16 associated with clustering. We did not observe geographic grouping of genetically clustered patients. DISCUSSION Our results demonstrate high rates of HIV transmission clustering, without local geographic foci, among young black MSM in Chicago. Applied prospectively, phylogenetic analyses could guide prevention efforts and help break the cycle of transmission.
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Chen Y, Chen S, Kang J, Fang H, Dao H, Guo W, Lai C, Lai M, Fan J, Fu L, Andrieu JM, Lu W. Evolving molecular epidemiological profile of human immunodeficiency virus 1 in the southwest border of China. PLoS One 2014; 9:e107578. [PMID: 25207977 PMCID: PMC4160289 DOI: 10.1371/journal.pone.0107578] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 08/19/2014] [Indexed: 11/23/2022] Open
Abstract
Background We have previously reported in Xishuangbanna (Banna) Dai Autonomous Prefecture, a well-developed tourist destination in the southwest border of China, that HIV-1 transmitted dominantly through heterosexual contact with less divergent genotypes and few drug resistant mutations [1]. Due to the rapid increase of newly diagnosed HIV-1 cases per year in Banna in recent years, it’s important to evaluate the evolution of HIV-1 molecular epidemiology for the better understanding of ongoing HIV-1 outbreak in this region. Methodology/Principal Findings By sequencing of HIV-1 pol genes and phylogenetic analysis, we conducted a molecular epidemiologic study in 352 HIV-1-seropositive highly active antiretroviral treatment (HAART)-naïve individuals newly diagnosed at the Banna Center for Disease Control and Prevention between 2009 and 2011. Of 283 samples (84.1% taken from heterosexually acquired adults, 10.6% from needle-sharing drug users, 2.8% from men who have sex with men, 0.4% from children born from HIV-1-infected mothers, and 2.1% remained unknown) with successful sequencing for pol gene, we identified 108 (38.2%) HIV-1 subtype CRF08_BC, 101 (35.7%) CRF01_AE, 49 (17.3%) CRF07_BC, 5 (1.8%) C/CRF57_BC, 3 (1.1%) B’, 1 (0.4%) B/CRF51_01B, and 16 (5.7%) unique recombinants forms. Among these infected individuals, 104 (36.7%) cases showed drug resistant or resistance-relevant mutations, and 4 of them conferring high-level resistance to 3TC/FTC, EFV/NVP or NFV. Phylogenetic analysis revealed 21 clusters (2–7 sequences) with only 21.2% (60/283) sequences involved. Conclusion/Significance In contrast to our previous findings, CRF08_BC, replaced CRF01_AE, became the dominant genotype of HIV-1 in Banna prefecture. The viral strains with drug resistance mutations were detected frequently in newly diagnosed HIV-1-infected individuals in this region.
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Affiliation(s)
- Yingyu Chen
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Song Chen
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
- Institut de Recherche sur les Vaccins et l’Immunologie des Cancers et du Sida, Université Paris Descartes/Institut de Recherche pour le Développement, Paris, France
| | - Jun Kang
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Hua Fang
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Hong Dao
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Weizhong Guo
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chunhui Lai
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Mingyue Lai
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Jianhua Fan
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Linchun Fu
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jean-Marie Andrieu
- Institut de Recherche sur les Vaccins et l’Immunologie des Cancers et du Sida, Université Paris Descartes/Institut de Recherche pour le Développement, Paris, France
| | - Wei Lu
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
- Institut de Recherche sur les Vaccins et l’Immunologie des Cancers et du Sida, Université Paris Descartes/Institut de Recherche pour le Développement, Paris, France
- * E-mail:
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Yan M, Zhao K, Du J, Li L, Wu D, Xu S, Zeng X, Wang G, Yu XF. HIV-1 diversity and drug-resistant mutations in infected individuals in Changchun, China. PLoS One 2014; 9:e100540. [PMID: 24945273 PMCID: PMC4063969 DOI: 10.1371/journal.pone.0100540] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 05/25/2014] [Indexed: 11/30/2022] Open
Abstract
Objectives Human immunodeficiency virus type 1 (HIV-1) infection has been detected in all provinces of China. Although epidemiological and phylogenetic studies have been conducted in many regions, such analyses are lacking from Jilin province in northeastern China. Method Epidemiological and phylogenetic analyses, as well as detection of drug-resistant mutations, were conducted on 57 HIV-1 infected patients from Changchun city identified and confirmed through annual surveillance by local Centers for Disease Control in Jilin province of northeastern China in 2012. Results Sexual contact was determined to be the major pathway for HIV-1 transmission in Jilin, where hetero- and homosexual activities contributed almost equally. Phylogenetic analyses detected multiple subtypes of HIV-1 including subtype G circulating in Jilin, with multiple origins for each of them. Both subtype B and CRF01_AE were dominant, and evidence of subtype B transmitting between different high-risk groups was observed. Mutations in the viral protease at position 71 indicated the presence of a selective pressure. Several drug-resistant mutations were detected, although they were predicted with low-level resistance to antiviral treatments. Conclusions Information from this study fills the gap in knowledge of HIV-1 transmission in Changchun city, Jilin province, China. By revealing the origin and evolutionary status of local HIV-1 strains, this work contributes to ongoing efforts in the control and prevention of AIDS.
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Affiliation(s)
- Ming Yan
- First Hospital of Jilin University, Changchun, Jilin, China
| | - Ke Zhao
- First Hospital of Jilin University, Changchun, Jilin, China
| | - Juan Du
- First Hospital of Jilin University, Changchun, Jilin, China
| | - Linzhang Li
- First Hospital of Jilin University, Changchun, Jilin, China
| | - Donglin Wu
- Jilin Provincial Center for Disease Control and Prevention, Changchun, Jilin, China
| | - Shengming Xu
- First Hospital of Jilin University, Changchun, Jilin, China
| | - Xiangchao Zeng
- First Hospital of Jilin University, Changchun, Jilin, China
| | - Guanjun Wang
- First Hospital of Jilin University, Changchun, Jilin, China
- * E-mail: (XFY); (GW)
| | - Xiao-Fang Yu
- First Hospital of Jilin University, Changchun, Jilin, China
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail: (XFY); (GW)
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Li L, Chen L, Liang S, Liu W, Li T, Liu Y, Li H, Bao Z, Wang X, Li J. Subtype CRF01_AE dominate the sexually transmitted human immunodeficiency virus type 1 epidemic in Guangxi, China. J Med Virol 2013; 85:388-95. [PMID: 23341369 DOI: 10.1002/jmv.23360] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2012] [Indexed: 11/07/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection by sexual transmission in Guangxi, China had increased dramatically. However, limited information is available on the genetic characterization of the HIV-1 epidemic. In this study, HIV-1 seropositive drug-naïve patients infected by heterosexual transmission were enrolled. The full length gag and pol genes were sequenced followed by phylogenetic analysis, recombinant analysis and drug resistant analysis. Multiple subtypes were identified, including CRF01_AE (80.1%), CRF07_BC (6.4%), CRF08_BC (10.2%), subtype B (1.7%), and URFs (1.7%). In the phylogenetic tree, two large CRF01_AE clusters were identified. One cluster is originating from Vietnam strains as being reported previously in intravenous drug users. One novel cluster was identified and showed close relationship to strains from Fujian province. Inter-subtype recombination among CRF01_AE, subtype B and C was identified. Low level drug-resistance in drug-naïve heterosexually transmitted infections was found. The results suggested that multiple originating CRF01_AE strains dominated the HIV-1 epidemic in heterosexual transmission in Guangxi province.
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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
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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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Chen S, Cai W, He J, Vidal N, Lai C, Guo W, He H, Chen X, Fu L, Peeters M, Delaporte E, Andrieu JM, Lu W. Molecular epidemiology of human immunodeficiency virus type 1 in Guangdong province of southern China. PLoS One 2012; 7:e48747. [PMID: 23144953 PMCID: PMC3492446 DOI: 10.1371/journal.pone.0048747] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 10/01/2012] [Indexed: 11/29/2022] Open
Abstract
Background Although the outbreak of human immunodeficiency virus type 1 (HIV-1) in Guangdong has been documented for more than a decade, the molecular characteristics of such a regional HIV-1 epidemic remained unknown. Methodology/Principal Findings By sequencing of HIV-1 pol/env genes and phylogenetic analysis, we performed a molecular epidemiologic study in a representative subset (n = 200) of the 508 HIV-1-seropositive individuals followed up at the center for HIV/AIDS care and treatment of Guangzhou Hospital of Infectious Diseases. Of 157 samples (54.1% heterosexual acquired adults, 20.4% needle-sharing drug users, 5.7% receivers of blood transfusion, 1.3% men who have sex with men, and 18.5% remained unknown) with successful sequencing for both pol and env genes, 105 (66.9%) HIV-1 subtype CRF01_AE and 24 (15.3%) CRF07_BC, 9 (5.7%) B’, 5 (3.2%) CRF08_BC, 5 (3.2%) B, 1 (0.6%) C, 3 (1.9%) CRF02_AG, and 5 (3.2%) inter-region recombinants were identified within pol/env sequences. Thirteen (8.3%) samples (3 naïves, 6 and 5 received with antiretroviral treatment [ART] 1–21 weeks and ≥24 weeks respectively) showed mutations conferring resistance to nucleoside/nonnucleoside reverse transcriptase inhibitors or protease inhibitors. Among 63 ART-naïve patients, 3 (4.8%) showed single or multiple drug resistant mutations. Phylogenetic analysis showed 8 small clusters (2–3 sequences/cluster) with only 17 (10.8%) sequences involved. Conclusion/Significance This study confirms that sexual transmission with dominant CRF01_AE strain is a major risk for current HIV-1 outbreak in the Guangdong’s general population. The transmission with drug-resistant variants is starting to emerge in this region.
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Affiliation(s)
- Song Chen
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
- Laboratoire d’Oncologie et Virologie Moléculaire, Université Paris Descartes, Paris, France
| | - Weiping Cai
- Guangzhou Hospital of Infectious Diseases, Guangzhou, China
| | - Jingyang He
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Nicole Vidal
- UMI 233, Institut de Recherche pour le Développement and Université de Monpellier 1, Monpellier, France
| | - Chunhui Lai
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weizhong Guo
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haolan He
- Guangzhou Hospital of Infectious Diseases, Guangzhou, China
| | - Xiejie Chen
- Guangzhou Hospital of Infectious Diseases, Guangzhou, China
| | - Linsheng Fu
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Martine Peeters
- UMI 233, Institut de Recherche pour le Développement and Université de Monpellier 1, Monpellier, France
| | - Eric Delaporte
- UMI 233, Institut de Recherche pour le Développement and Université de Monpellier 1, Monpellier, France
| | - Jean-Marie Andrieu
- Laboratoire d’Oncologie et Virologie Moléculaire, Université Paris Descartes, Paris, France
| | - Wei Lu
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
- UMI 233, Institut de Recherche pour le Développement and Université de Monpellier 1, Monpellier, France
- * E-mail:
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Aldous JL, Pond SK, Poon A, Jain S, Qin H, Kahn JS, Kitahata M, Rodriguez B, Dennis AM, Boswell SL, Haubrich R, Smith DM. Characterizing HIV transmission networks across the United States. Clin Infect Dis 2012; 55:1135-43. [PMID: 22784872 PMCID: PMC3529609 DOI: 10.1093/cid/cis612] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 06/29/2012] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Clinically, human immunodeficiency virus type 1 (HIV-1) pol sequences are used to evaluate for drug resistance. These data can also be used to evaluate transmission networks and help describe factors associated with transmission risk. METHODS HIV-1 pol sequences from participants at 5 sites in the CFAR Network of Integrated Clinical Systems (CNICS) cohort from 2000-2009 were analyzed for genetic relatedness. Only the first available sequence per participant was included. Inferred transmission networks ("clusters") were defined as ≥2 sequences with ≤1.5% genetic distance. Clusters including ≥3 patients ("networks") were evaluated for clinical and demographic associations. RESULTS Of 3697 sequences, 24% fell into inferred clusters: 155 clusters of 2 individuals ("dyads"), 54 clusters that included 3-14 individuals ("networks"), and 1 large cluster that included 336 individuals across all study sites. In multivariable analyses, factors associated with being in a cluster included not using antiretroviral (ARV) drugs at time of sampling (P < .001), sequence collected after 2004 (P < .001), CD4 cell count >350 cells/mL (P < .01), and viral load 10,000-100,000 copies/mL (P < .001) or >100,000 copies/mL (P < .001). In networks, women were more likely to cluster with other women (P < .001), and African Americans with other African Americans (P < .001). CONCLUSIONS Molecular epidemiology can be applied to study HIV transmission networks in geographically and demographically diverse cohorts. Clustering was associated with lack of ARV use and higher viral load, implying transmission may be interrupted by earlier diagnosis and treatment. Observed female and African American networks reinforce the importance of diagnosis and prevention efforts targeted by sex and race.
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Affiliation(s)
- Jeannette L Aldous
- Division of Infectious Diseases, University of California, San Diego, 200 W Arbor Dr, MC 8208, San Diego, CA 92103, USA.
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Zeng P, Wang J, Huang Y, Guo X, Li J, Wen G, Yang T, Yun Z, He M, Liu Y, Yuan Y, Schulmann J, Glynn S, Ness P, Jackson JB, Shan H. The human immunodeficiency virus-1 genotype diversity and drug resistance mutations profile of volunteer blood donors from Chinese blood centers. Transfusion 2011; 52:1041-9. [PMID: 22044422 DOI: 10.1111/j.1537-2995.2011.03415.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND The global human immunodeficiency virus (HIV)-1 epidemic is becoming increasingly diverse and complex. Molecular epidemiologic characteristics were studied for HIV-1-infected blood donors from five Chinese regions to determine genotype diversity and drug resistance mutations (DRMs) profile. STUDY DESIGN AND METHODS HIV-1 confirmed-reactive serum samples were collected from 172 blood donors from five blood centers during 2007 to 2010. HIV-1 Pol including whole protease and partial reverse transcriptase genes was amplified, sequenced, and analyzed for the subtype determination and drug resistance profile description. RESULT A total of 113 amplified sequences including 82 from Kunming blood center and 31 from four other blood centers had the following genotype characteristics: G (0.9%), B (2.7%), circulating recombinant form (CRF) 01_AE (32.7%), CRF07_BC (22.1%), and CRF08_BC (41.6%). Female donors represent 45.1% of all cases and 63.9% cases with DRMs. The prevalence of samples with potential low or higher resistance among Chinese blood donors is 4.4%. CONCLUSION HIV-1 infection in Chinese blood donors is genetically diverse and the subtype distribution reflects that from the high-risk populations. Our results support continuous molecular epidemiologic surveillance for HIV-1 in blood donors as a part of a comprehensive HIV control program.
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Affiliation(s)
- Peibin Zeng
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, Sichuan, China
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Chan PA, Tashima K, Cartwright CP, Gillani FS, Mintz O, Zeller K, Kantor R. Short communication: Transmitted drug resistance and molecular epidemiology in antiretroviral naive HIV type 1-infected patients in Rhode Island. AIDS Res Hum Retroviruses 2011; 27:275-81. [PMID: 20954831 DOI: 10.1089/aid.2010.0198] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transmission of HIV-1 drug resistance has important clinical and epidemiological consequences including earlier treatment failure and forward transmission of resistance strains in high-risk groups. To evaluate the prevalence and molecular epidemiology of transmitted drug resistance in Rhode Island, we collected genotypic, demographic, clinical, and laboratory data from treatment-naive individuals presenting to the largest outpatient HIV clinic in the state from January 2007 to November 2007. Sequences from 35 treatment-naive individuals were available, 83% of whom were men who had sex with men (MSM). All sequences were HIV-1 subtype B. Drug resistance mutations were identified in 7/35 [20%; 95% confidence interval (CI), 0.08-0.37] patients, six of whom had K103N. Two phylogenetic transmission clusters were found, involving 17% (6/35) of individuals, three in each cluster. We did not find an association between belonging to a cluster and age, gender, AIDS-defining illness, CD4 cell count, or viral load. Drug resistance mutations were more commonly observed in transmission clusters (p = 0.08). Individuals in one cluster all had K103N and were MSM who had attended local bathhouses. Individuals forming clusters were significantly more likely to have visited a bathhouse compared to nonclusters (p = 0.02). The prevalence of transmitted drug resistance in Rhode Island is high, further justifying genotypic testing on presentation to care and prior to treatment initiation. Molecular epidemiological analysis and association of resistance with phylogenetic networks using data obtained for clinical purposes may serve as useful tools for the prevention of drug resistance transmission and for contact tracing.
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Affiliation(s)
- Philip A. Chan
- Division of Infectious Disease, The Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Karen Tashima
- Division of Infectious Disease, The Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | | | - Fizza S. Gillani
- Division of Infectious Disease, The Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Orli Mintz
- Division of Infectious Disease, The Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Kimberly Zeller
- Division of Family Medicine, The Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Rami Kantor
- Division of Infectious Disease, The Warren Alpert Medical School of Brown University, Providence, Rhode Island
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Shanmugasundaram U, Solomon S, Murugavel KG, Nagalingeswaran K, Solomon SS, Mayer KH, Pachamuthu B. Short communication: Nucleotide variation and positively selected sites in HIV type 1 reverse transcriptase among heterosexual transmission pairs. AIDS Res Hum Retroviruses 2010; 26:895-9. [PMID: 20672974 DOI: 10.1089/aid.2010.0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mutations in the env gene of HIV-1 have been the primary focus in most epidemiologically related cohort studies of virus evolution and very limited studies have focused on the reverse transcriptase (RT) region, the primary target of antiretroviral therapy (ART). Hence, we measured the selection pressure and searched for the positively selected sites in the RT sequences amplified from HIV-1-infected heterosexual transmission pairs. Married couples (n = 10) who were ART naive were included in this study. Phylogenetic analysis, the measurement of synonymous and nonsynonymous ratio (dN/dS) and the interpatient nucleotide variation, was done. Phylogenetic analysis demonstrated distinct subclusters of the RT sequences from heterosexual transmission pairs and the median (IQR) nucleotide variation between the epidemiologically related transmission pairs was significantly (p < 0.001) lower [0.01% (0.01-0.02%)] compared to the epidemiologically unrelated transmission pairs [0.04% (0.03-0.04%)]. The ratio of dN/dS was <1 and codons 135, 162, 166, 207, and 211 were positively selected in >50% of the donor and recipient RT sequences. Purifying selection pressure and low nucleotide variation in the RT sequences between epidemiologically related transmission pairs highlight its essential role in HIV-1 replication. The effect of the RT positively selected mutations that persist over time following transmission between individuals needs to be studied to determine the fitness cost of the mutations in vivo, which may possibly represent good targets for inclusion in HIV-1 vaccines.
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Affiliation(s)
| | - Suniti Solomon
- Y.R. Gaitonde Centre for AIDS Research and Education, Chennai, India
| | | | | | - Sunil S. Solomon
- Y.R. Gaitonde Centre for AIDS Research and Education, Chennai, India
| | - Kenneth H. Mayer
- Warren Alpert School of Medicine, Brown University/Miriam Hospital, Providence, Rhode Island
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Broughton-Neiswanger LE, White SN, Knowles DP, Mousel MR, Lewis GS, Herndon DR, Herrmann-Hoesing LM. Non-maternal transmission is the major mode of ovine lentivirus transmission in a ewe flock: a molecular epidemiology study. INFECTION GENETICS AND EVOLUTION 2010; 10:998-1007. [PMID: 20601169 DOI: 10.1016/j.meegid.2010.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 06/03/2010] [Accepted: 06/07/2010] [Indexed: 11/29/2022]
Abstract
Transmission of ovine progressive pneumonia virus (OPPV), a lentivirus of sheep, occurs through both maternal and non-maternal means. Currently, the contribution of each route to the overall flock OPPV prevalence is poorly understood since previous serological epidemiologic studies lacked the ability to accurately track routes of transmission within an infected flock. In this study, the amount of maternal OPP transmission was assessed in a naturally infected ewe flock by applying molecular analyses to proviral sequences derived from peripheral blood leukocytes of OPP positive dam-daughter pairs (N=40). Both proviral envelope (env) and long terminal repeat (LTR) sequences, separately and combined, were utilized in the following 2 sequence analysis methods: phylogenetic analysis and pairwise distance calculations. True maternal transmission events were defined as agreement in 2 out of the 2 sequence analysis methods. Using this criterion, proviral env sequences resulted in a 14.3% maternal transmission frequency, and proviral LTR sequences resulted in a 10% maternal transmission frequency. Both proportions of maternal transmission varied significantly from equality (P<0.0001). This indicates that the remaining 85.7-90% of daughters are infected via non-maternal transmission. This is also the first study to calculate the OPP proviral rate of change for the env gene and LTR promoter. Accurately defining the routes of OPPV transmission provides critical epidemiological data supporting management intended to reduce flock transmission and viral dose.
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Affiliation(s)
- Liam E Broughton-Neiswanger
- Washington State University, Department of Veterinary Microbiology and Pathology, Pullman, WA 99164-7040, USA
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Surprisingly High Prevalence of Subtype C and Specific HIV-1 Subtype/CRF Distribution in Men Having Sex With Men in Senegal. J Acquir Immune Defic Syndr 2009; 52:249-52. [DOI: 10.1097/qai.0b013e3181af70a4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Molecular Epidemiological Study of HIV-1 CRF01_AE Transmission in Hong Kong. J Acquir Immune Defic Syndr 2009; 51:530-5. [DOI: 10.1097/qai.0b013e3181aac516] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
OBJECTIVES To determine the prevalence of HIV in Hainan island and the molecular epidemiological linkages related to risk factors of viral transmission. METHODS A governmental HIV/AIDS surveillance program, HIV serological study was conducted in volunteers from several high-risk groups between 1991 and 2006 in Hainan province. By phylogenetic reconstruction, we performed a molecular epidemiological tracing in a representative subset of the HIV-1-seropositive individuals diagnosed during this survey. RESULTS Of 499 752 volunteers, 523 (0.1%) accumulated cases of HIV-1 infection (69.2% needle-sharing drug users, 19.3% heterosexually acquired adults, 3.3% receivers of blood transfusion, 0.8% children born from HIV-1-infected mothers, and 7.7% remained unknown) were diagnosed. Among 83 patient samples examined (70 were infected with HIV-1 subtypes CRF01_AE and eight, two, one, one, and one were B', C, CRF08_BC, B, and a new CRF01_AE/B' recombinant, respectively), 66 (79.5%) were segregated into one large cluster (59 sequences) (founder effect) and one small cluster (three sequences) of CRF01_AE, one small cluster (two sequences) of B', and one small cluster (two sequences) of C. Phylogenetic and epidemiological linkages confirmed four heterosexual transmission events and rejected two potential heterosexual transmission suggested by contact tracing. Only two cases of CRF01_AE showed mutations conferring resistance to nucleoside and nonnucleoside reverse transcriptase inhibitors. CONCLUSION The reconstruction of current HIV-1 outbreaks by molecular epidemiological tracing is helpful for identifying epidemic sources and for defining prevention strategies.
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