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Li K, Chen H, Li J, Feng Y, Liang S, Rashid A, Liu M, Li S, Chu Q, Ruan Y, Xing H, Lan G, Qiao W, Shao Y. Distinct genetic clusters in HIV-1 CRF01_AE-infected patients induced variable degrees of CD4 + T-cell loss. mBio 2024; 15:e0334923. [PMID: 38385695 PMCID: PMC10936439 DOI: 10.1128/mbio.03349-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 02/23/2024] Open
Abstract
CRF01_AE strains have been shown to form multiple transmission clusters in China, and some clusters have disparate pathogenicity in Chinese men who have sex with men. This study focused on other CRF01_AE clusters prevalent in heterosexual populations. The CD4+ T-cell counts from both cross-section data in National HIV Molecular Epidemiology Survey and seropositive cohort data were used to evaluate the pathogenicity of the CRF01_AE clusters and other HIV-1 sub-types. Their mechanisms of pathogenicity were evaluated by co-receptor tropisms, predicted by genotyping and confirmed with virus isolate phenotyping, as well as inflammation parameters. Our research elucidated that individuals infected with CRF01_AE clusters 1 and 2 exhibited significantly lower baseline CD4+ T-cell counts and greater CD4+ T-cell loss in cohort follow-up, compared with other HIV-1 sub-types and CRF01_AE clusters. The increased pathogenesis of cluster 1 or 2 was associated with higher CXCR4 tropisms, higher inflammation/immune activation, and increased pyroptosis. The protein structure modeling analysis revealed that the envelope V3 loop of clusters 1 and 2 viruses is favorable for CXCR4 co-receptor usage. Imbedded with the most mutating reverse transcriptase, HIV-1 is one of the most variable viruses. CRF01_AE clusters 1 and 2 have been found to have evolved into more virulent strains in regions with predominant heterosexual infections. The virulent strains increased the pressure for early diagnosis and treatment in HIV patients. To save more lives, HIV-1 surveillance systems should be upgraded from serology and genotyping to phenotyping, which could support precision interventions for those infected by virulent viruses. IMPORTANCE Retroviruses swiftly adapt, employing error-prone enzymes for genetic and phenotypic evolution, optimizing survival strategies, and enhancing virulence levels. HIV-1 CRF01_AE has persistently undergone adaptive selection, and cluster 1 and 2 infections display lower counts and fast loss of CD4+ T cells than other HIV-1 sub-types and CRF01_AE clusters. Its mechanisms are associated with increased CXCR4 tropism due to an envelope structure change favoring a tropism shift from CCR5 to CXCR4, thereby shaping viral phenotype features and impacting pathogenicity. This underscores the significance of consistently monitoring HIV-1 genetic evolution and phenotypic transfer to see whether selection bias across risk groups alters the delicate balance of transmissible versus toxic trade-offs, since virulent strains such as CRF01_AE clusters 1 and 2 could seriously compromise the efficacy of antiviral treatment. Only through such early warning and diagnostic services can precise antiviral treatments be administered to those infected with more virulent HIV-1 strains.
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Affiliation(s)
- Kang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huanhuan Chen
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Jianjun Li
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Yi Feng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shujia Liang
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Abdur Rashid
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
| | - Meiliang Liu
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Sisi Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Qingfei Chu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuhua Ruan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Xing
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guanghua Lan
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Wentao Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yiming Shao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Medicine, Zhejiang University, Hangzhou, China
- Changping Laboratory, Beijing, China
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2
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Yu Y, Feng Y, Zhou Z, Li K, Hu X, Liao L, Xing H, Shao Y. Substitution of gp120 C4 region compensates for V3 loss-of-fitness mutations in HIV-1 CRF01_AE co-receptor switching. Emerg Microbes Infect 2023; 12:e2169196. [PMID: 36647730 PMCID: PMC9980400 DOI: 10.1080/22221751.2023.2169196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
HIV-1 infection is mediated by a viral envelope subsequently binding to CD4 receptor and two main coreceptors, CCR5 (R5) for primary infection and CXCR4 (X4) in chronic infection. Switching from R5 to X4 tropism in HIV-1 infection is associated with increased viral pathogenesis and disease progression. The coreceptor switching is mainly due to variations in the V3 loop, while the mechanism needs to be further elucidated. We systematically studied the determinant for HIV-1 coreceptor switching by substitution of the genes from one R5 and one X4 pseudoviruses. The study results in successfully constructing two panels of chimeric viruses of R5 to X4 forward and X4 to R5 reverse switching. The determinants for tropism switching are the combined substitution of the V3 loop and C4 region of the HIV-1 envelope. The possible mechanism of the tropism switching includes two components, the V3 loop to enable the viral envelope binding to the newly switched coreceptor and the C4 region, to compensate for the loss of fitness caused by deleterious V3 loop mutations to maintain the overall viral viability. The combined C4 and V3 substitution showed at least an eightfold increase in replication activity compared with the pseudovirus with only V3 loop substitution. The site-directed mutations of N425R and S440-I442 with charged amino acids could especially increase viral activity. This study could facilitate HIV-1 phenotype surveillance and select right entry inhibitor, CCR5 or CXCR4 antagonists, for antiviral therapy.
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Affiliation(s)
- Yueyang Yu
- School of Medicine, Nankai University, Tianjin, 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
| | - Zehua Zhou
- School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Kang Li
- School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Xiaoyan Hu
- School of Medicine, Nankai University, Tianjin, 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
| | - 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
| | - Yimig Shao
- School of Medicine, Nankai University, Tianjin, People’s Republic of China,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,Changping Laboratory, Beijing, People’s Republic of China, Yimig 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
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3
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Antonova A, Kazennova E, Lebedev A, Ozhmegova E, Kuznetsova A, Tumanov A, Bobkova M. Recombinant Forms of HIV-1 in the Last Decade of the Epidemic in the Russian Federation. Viruses 2023; 15:2312. [PMID: 38140553 PMCID: PMC10748268 DOI: 10.3390/v15122312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Currently, HIV-1 displays a substantial level of genetic diversity on a global scale, partly attributed to its recombinant variants. This study seeks to identify and analyze HIV-1 recombinants in Russia during the last decade of the epidemic. A comprehensive examination was conducted, encompassing 3178 partial pol sequences. Subtyping was achieved through various programs including COMET, the Stanford Database, REGA, jpHMM, RIP, and RDP4 for recombination analysis. The study also involved phylogenetic analysis to trace the origins of the identified recombinants. Primary resistance (PrimDR) prevalence and Drug Resistance Mutations (DRMs) were assessed. The study uncovered an overall proportion of recombinants at 8.7%, with a statistically significant increase in their frequency observed over time (p < 0.001). The Northwestern (18.5%) and Siberian (15.0%) Federal Districts exhibited a high prevalence of recombinants, while the Volga (1.9%) and Ural (2.8%) Federal Districts had a lower prevalence. Among HIV-1 recombinants, a PrimDR prevalence of 11.4% was identified. Notably, significant differences in DRMs were observed, with a higher prevalence of M184V in sub-subtype A6 (p = 0.018) and K103N in CRF63_02A6 (p = 0.002). These findings underscore the increasing HIV-1 genetic diversity and highlight a substantial prevalence of PrimDR among its recombinant forms, emphasizing the necessity for ongoing systematic monitoring.
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Affiliation(s)
- Anastasiia Antonova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Elena Kazennova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Aleksey Lebedev
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Ekaterina Ozhmegova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Anna Kuznetsova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Aleksandr Tumanov
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Marina Bobkova
- I. Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia;
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Zaongo SD, Chen Y. PSGL-1, a Strategic Biomarker for Pathological Conditions in HIV Infection: A Hypothesis Review. Viruses 2023; 15:2197. [PMID: 38005875 PMCID: PMC10674231 DOI: 10.3390/v15112197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
P-selectin glycoprotein ligand-1 (PSGL-1) has been established to be a cell adhesion molecule that is involved in the cellular rolling mechanism and the extravasation cascade, enabling the recruitment of immune cells to sites of inflammation. In recent years, researchers have established that PSGL-1 also functions as an HIV restriction factor. PSGL-1 has been shown to inhibit the HIV reverse transcription process and inhibit the infectivity of HIV virions produced by cells expressing PSGL-1. Cumulative evidence gleaned from contemporary literature suggests that PSGL-1 expression negatively affects the functions of immune cells, particularly T-cells, which are critical participants in the defense against HIV infection. Indeed, some researchers have observed that PSGL-1 expression and signaling provokes T-cell exhaustion. Additionally, it has been established that PSGL-1 may also mediate virus capture and subsequent transfer to permissive cells. We therefore believe that, in addition to its beneficial roles, such as its function as a proinflammatory molecule and an HIV restriction factor, PSGL-1 expression during HIV infection may be disadvantageous and may potentially predict HIV disease progression. In this hypothesis review, we provide substantial discussions with respect to the possibility of using PSGL-1 to predict the potential development of particular pathological conditions commonly seen during HIV infection. Specifically, we speculate that PSGL-1 may possibly be a reliable biomarker for immunological status, inflammation/translocation, cell exhaustion, and the development of HIV-related cancers. Future investigations directed towards our hypotheses may help to evolve innovative strategies for the monitoring and/or treatment of HIV-infected individuals.
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Affiliation(s)
| | - Yaokai Chen
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing 400036, China;
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5
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Ge Y, Zhou Y, Lu J, Qiu T, Shi LE, Zhang Z, Hu H, Wei P, Fu G. Immune reconstitution efficacy after combination antiretroviral therapy in male HIV-1 infected patients with homosexual and heterosexual transmission. Emerg Microbes Infect 2023:2214250. [PMID: 37216217 DOI: 10.1080/22221751.2023.2214250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We aimed to explore the impact of sexual transmission modes on immune reconstitution after combined antiretroviral therapy (cART). We have retrospectively analyzed longitudinal samples from 1557 treated male patients with virological suppression (HIV-1 RNA<50 copies/ml) for at least 2 years. Both heterosexuals (HET) and men who have sex with men (MSM) patients showed an increasing annual trend in CD4+ T cell counts after receiving cART (HET, β: 23.51 (cell/µl)/year, 95% CI: 16.70 to 30.31; MSM, β: 40.21 (cell/µl)/year, 95% CI: 35.82 to 44.61). However, the CD4+ T cell recovery rate was much lower in HET patients than MSM patients, determined by both the generalized additive mixed model (P < 0.001) and generalized estimating equations (P = 0.026). Besides HIV-1 subtypes, baseline CD4+ T cell counts and age at cART initiation, HET was an independent risk factor for immunological non-responders (adjusted OR: 1.73; 95% CI: 1.28 to 2.33). HET was also associated with lower probability of achieving conventional immune recovery (adjusted HR: 1.37; 95%CI: 1.22 to 1.67) and optimal immune recovery (adjusted HR: 1.48, 95%CI: 1.04-2.11). Male HET patients might have poorer immune reconstitution ability even after effective cART. Early initiation of cART after diagnosis and clinical monitoring for male HET patients should be highly emphasized.
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Affiliation(s)
- You Ge
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Ying Zhou
- Institute of HIV/AIDS/STI Prevention and Control, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu, China
| | - Jing Lu
- Institute of HIV/AIDS/STI Prevention and Control, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu, China
| | - Tao Qiu
- Institute of HIV/AIDS/STI Prevention and Control, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu, China
| | - Ling-En Shi
- Institute of HIV/AIDS/STI Prevention and Control, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu, China
| | - Zhi Zhang
- Institute of HIV/AIDS/STI Prevention and Control, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu, China
| | - Haiyang Hu
- Institute of HIV/AIDS/STI Prevention and Control, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu, China
| | - Pingmin Wei
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Gengfeng Fu
- Institute of HIV/AIDS/STI Prevention and Control, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu, China
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6
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A New HIV-1 K 28E 32-Reverse Transcriptase Variant Associated with the Rapid Expansion of CRF07_BC among Men Who Have Sex with Men. Microbiol Spectr 2022; 10:e0254522. [PMID: 36214682 PMCID: PMC9604004 DOI: 10.1128/spectrum.02545-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
HIV-1 CRF07_BC originated among injection drug users (IDUs) in China. After diffusing into men who have sex with men (MSM), CRF07_BC has shown a rapid expansion in this group; however, the mechanism remains unclear. Here, we identified a new K28E32 variant of CRF07_BC that was characterized by five specific mutations (E28K, K32E, E248V, K249Q, and T338S) in reverse transcriptase. This variant was mainly prevalent among MSM, and was overrepresented in transmission clusters, suggesting that it could have driven the rapid expansion of CRF07_BC in MSM, though founder effects cannot be ruled out. It was descended from an evolutionary intermediate accumulating four specific mutations and formed an independent phylogenetic node with an estimated origin time in 2003. The K28E32 variant was demonstrated to have significantly higher in vitro HIV-1 replication ability than the wild type. Mutations E28K and K32E play a critical role in the improvement of in vitro HIV-1 replication ability, reflected by improved reverse transcription activity. The results could allow public health officials to use this marker (especially E28K and K32E mutations in the reverse transcriptase (RT) coding region) to target prevention measures prioritizing MSM population and persons infected with this variant for test and treat initiatives. IMPORTANCE HIV-1 has very high mutation rate that is correlated with the survival and adaption of the virus. The variants with higher transmissibility may be more selective advantage than the strains with higher virulence. Several HIV-1 variants were previously demonstrated to be correlated with higher viral load and lower CD4 T cell count. Here, we first identified a new variant (the K28E32 variant) of HIV-1 CRF07_BC, described its origin and evolutionary dynamics, and demonstrated its higher in vitro HIV-1 replication ability than the wild type. We demonstrated that five RT mutations (especially E28K and K32E) significantly improve in vitro HIV-1 replication ability. The appearance of the new K28E32 variant was associated with the rapidly increasing prevalence of CRF07_BC among MSM.
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Renelt S, Schult-Dietrich P, Baldauf HM, Stein S, Kann G, Bickel M, Kielland-Kaisen U, Bonig H, Marschalek R, Rieger MA, Dietrich U, Duerr R. HIV-1 Infection of Long-Lived Hematopoietic Precursors In Vitro and In Vivo. Cells 2022; 11:cells11192968. [PMID: 36230931 PMCID: PMC9562211 DOI: 10.3390/cells11192968] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
Latent reservoirs in human-immunodeficiency-virus-1 (HIV-1)-infected individuals represent a major obstacle in finding a cure for HIV-1. Hematopoietic stem and progenitor cells (HSPCs) have been described as potential HIV-1 targets, but their roles as HIV-1 reservoirs remain controversial. Here we provide additional evidence for the susceptibility of several distinct HSPC subpopulations to HIV-1 infection in vitro and in vivo. In vitro infection experiments of HSPCs were performed with different HIV-1 Env-pseudotyped lentiviral particles and with replication-competent HIV-1. Low-level infection/transduction of HSPCs, including hematopoietic stem cells (HSCs) and multipotent progenitors (MPP), was observed, preferentially via CXCR4, but also via CCR5-mediated entry. Multi-lineage colony formation in methylcellulose assays and repetitive replating of transduced cells provided functional proof of susceptibility of primitive HSPCs to HIV-1 infection. Further, the access to bone marrow samples from HIV-positive individuals facilitated the detection of HIV-1 gag cDNA copies in CD34+ cells from eight (out of eleven) individuals, with at least six of them infected with CCR5-tropic HIV-1 strains. In summary, our data confirm that primitive HSPC subpopulations are susceptible to CXCR4- and CCR5-mediated HIV-1 infection in vitro and in vivo, which qualifies these cells to contribute to the HIV-1 reservoir in patients.
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Affiliation(s)
- Sebastian Renelt
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt, Germany
| | - Patrizia Schult-Dietrich
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt, Germany
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, 81377 Munich, Germany
- Institute of Medical Virology, Goethe University, 60596 Frankfurt, Germany
| | - Stefan Stein
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt, Germany
| | - Gerrit Kann
- Department of Medicine II/Infectious Diseases, Goethe University Hospital, 60596 Frankfurt, Germany
- Infektiologikum, Center for Infectious Diseases, 60596 Frankfurt, Germany
| | - Markus Bickel
- Infektiologikum, Center for Infectious Diseases, 60596 Frankfurt, Germany
| | | | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, German Red Cross Blood Donor Service Baden-Württemberg-Hessen, Goethe University, 60528 Frankfurt, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe University, 60438 Frankfurt, Germany
| | - Michael A. Rieger
- Department of Medicine, Hematology/Oncology, Goethe University Hospital, 60590 Frankfurt, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center, 69120 Heidelberg, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt, Germany
- Cardio-Pulmonary Institute, 60596 Frankfurt, Germany
| | - Ursula Dietrich
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt, Germany
| | - Ralf Duerr
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt, Germany
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Correspondence:
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Hu X, Feng Y, Li K, Yu Y, Rashid A, Xing H, Ruan Y, Lu L, Wei M, Shao Y. Unique profile of predominant CCR5-tropic in CRF07_BC HIV-1 infections and discovery of an unusual CXCR4-tropic strain. Front Immunol 2022; 13:911806. [PMID: 36211390 PMCID: PMC9540210 DOI: 10.3389/fimmu.2022.911806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 09/05/2022] [Indexed: 11/30/2022] Open
Abstract
CRF07_BC is one of the most prevalent HIV-1 strains in China, which contributes over one-third of the virus transmissions in the country. In general, CRF07_BC is associated with slower disease progression, while the underlying mechanisms remain unclear. Our study focused on envelope proteins (Env) and its V3 loop which determine viral binding to co-receptors during infection of cells. We studied a large dataset of 3,937 env sequences in China and found that CRF07_BC had a unique profile of predominantly single CCR5 tropism compared with CCR5 and CXCR4 dual tropisms in other HIV-1 subtypes. The percentages of the CXCR4-tropic virus in B (3.7%) and CRF01_AE (10.4%) infection are much higher than that of CRF07_BC (0.1%), which is supported by median false-positive rates (FPRs) of 69.8%, 25.5%, and 13.4% for CRF07_BC, B, and CRF01_AE respectively, with a cutoff FPR for CXCR4-tropic at 2%. In this study, we identified the first pure CXCR4-tropic virus from one CRF07_BC-infected patient with an extremely low CD4+T cell count (7 cells/mm3). Structural analysis found that the V3 region of this virus has the characteristic 7T and 25R and a substitution of conserved “GPGQ” crown motif for “GPGH”. This study provided compelling evidence that CRF07_BC has the ability to evolve into CXCR4 strains. Our study also lay down the groundwork for studies on tropism switch, which were commonly done for other HIV-1 subtypes, for the long-delayed CRF07_BC.
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Affiliation(s)
- Xiaoyan Hu
- School of Medicine, Nankai University, Tianjin, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for Acquired Immune Deficiency Syndrome/Sexually Transmitted Diseases (AIDS/STD) Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kang Li
- College of Life Sciences, Nankai University, Tianjin, China
| | - Yueyang Yu
- School of Medicine, Nankai University, Tianjin, China
| | - Abdur Rashid
- School of Medicine, Nankai University, Tianjin, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for Acquired Immune Deficiency Syndrome/Sexually Transmitted Diseases (AIDS/STD) Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuhua Ruan
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for Acquired Immune Deficiency Syndrome/Sexually Transmitted Diseases (AIDS/STD) Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lingling Lu
- School of Medicine, Nankai University, Tianjin, China
| | - Min Wei
- School of Medicine, Nankai University, Tianjin, China
- Nankai University Second People’s Hospital, Nankai University, Tianjin, China
- *Correspondence: Min Wei, ; Yiming Shao,
| | - Yiming Shao
- School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for Acquired Immune Deficiency Syndrome/Sexually Transmitted Diseases (AIDS/STD) Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- *Correspondence: Min Wei, ; Yiming Shao,
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9
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Ge Y, Liu Y, Fu G, Lu J, Li X, Du G, Fei G, Wang Z, Li H, Li W, Wei P. The Molecular Epidemiological and Immunological Characteristics of HIV-1 CRF01_AE/B Recombinants in Nanjing, China. Front Microbiol 2022; 13:936502. [PMID: 35910646 PMCID: PMC9335199 DOI: 10.3389/fmicb.2022.936502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus-type 1 (HIV-1) CRF01_AE/B recombinants are newly emerging strains that are spreading rapidly in Southern and Eastern China. This study aimed to elucidate the molecular epidemiological characteristics of HIV-1 CRF01_AE/B recombinants in Nanjing and to explore the impact of these novel strains on the immunological status. A total of 1,013 blood samples from newly diagnosed HIV-1-infected patients were collected in Nanjing from 2015 to 2019, among which 958 partial Pol sequences were sequenced successfully. We depicted the molecular epidemiological characteristics of CRF01_AE/B recombinants by the molecular evolutionary analysis, Bayesian system evolution analysis, and transmission network analysis. The generalized additive mixed model was applied to evaluate the CD4+ T-cell count change of CRF01_AE/B recombinants. The Kaplan–Meier analysis was performed to assess the time from combined antiretroviral therapy (cART) initiation to immune reconstruction. We have identified 102 CRF01_AE/B recombinants (102/958, 10.65%) in Nanjing, including CRF67_01B (45/102, 44.12%), CRF68_01B (35/102, 34.31%), and CRF55_01B (22/102, 12.57%). According to the Bayesian phylogenetic inference, CRF55_01B had a rapid decline stage during 2017–2019, while CRF67_01B and CRF68_01B have experienced a fast growth phase during 2014–2015 and then remained stable. We have constructed 83 transmission networks, in which three larger clusters were composed of CRF67_01B and CRF68_01B. CRF01_AE/B recombinants manifested a faster decrease rate of CD4+ T-cell count than CRF_07BC but similar to CRF01_AE. The probability of achieving immune reconstruction in CRF01_AE/B recombinants was lower than CRF07_BC in the subgroup of baseline CD4+ T-cell count at cART initiation <300 cells/μl. In summary, CRF67_01B and CRF68_01B were the major strains of CRF01_AE/B recombinants in Nanjing, which have formed large transmission clusters between Nanjing and other provinces. CRF01_AE/B recombinants might be associated with rapid disease progression and poor immune reconstruction. The continuous epidemiological monitoring of CRF01_AE/B recombinants should be highly emphasized.
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Affiliation(s)
- You Ge
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yangyang Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Gengfeng Fu
- Institute of HIV/AIDS/STI Prevention and Control, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, China
| | - Jing Lu
- Institute of HIV/AIDS/STI Prevention and Control, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, China
| | - Xiaoshan Li
- Department of Lung Transplant Center, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, China
| | - Guoping Du
- Department of Southeast University Hospital, Southeast University, Nanjing, China
| | - Gaoqiang Fei
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Zemin Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Han Li
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Wei Li
- Department of Quality Management, Children's Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Pingmin Wei
| | - Pingmin Wei
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
- Wei Li
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10
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Li K, Chen H, Li J, Feng Y, Lan G, Liang S, Liu M, Rashid A, Xing H, Shen Z, Shao Y. Immune reconstruction effectiveness of combination antiretroviral therapy for HIV-1 CRF01_AE cluster 1 and 2 infected individuals. Emerg Microbes Infect 2021; 11:158-167. [PMID: 34895083 PMCID: PMC8725829 DOI: 10.1080/22221751.2021.2017755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
There are great disparities of the results in immune reconstruction (IR) of the HIV-1 infected patients during combined antiretroviral therapy (cART), due to both host polymorphisms and viral genetic subtypes. Identifying these factors and elucidating their impact on the IR could help to improve the efficacy. To study the factors influencing the IR, we conducted a 15-year retrospective cohort study of HIV-1 infected individuals under cART. The trend of CD4+ count changes was evaluated by the generalized estimating equations. Cox proportional model and propensity score matching were used to identify variables that affect the possibility of achieving IR. The tropism characteristics of virus were compared using the coreceptor binding model. In addition to baseline CD4+ counts and age implications, CRF01_AE cluster 1 was associated with a poorer probability of achieving IR than infection with cluster 2 (aHR, 1.39; 95%CI, 1.02-1.90) and other subtypes (aHR, 1.83; 95%CI, 1.31-2.56). The mean time from cART initiation to achieve IR was much longer in patients infected by CRF01_AE cluster 1 than other subtypes/sub-clusters (P < 0.001). In-depth analysis indicated that a higher proportion of CXCR4 viruses were found in CRF01_AE clusters 1 and 2 (P < 0.05), and showed tendency to favour CXCR4 binding to V3 signatures. This study indicated the immune restoration impairment found in patients were associated with HIV-1 CRF01_AE cluster 1, which was attributed to the high proportion of CXCR4-tropic viruses. To improve the effectiveness of cART, more efforts should be made in the early identification of HIV-1 subtype/sub-cluster and monitoring of virus phenotypes.
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Affiliation(s)
- Kang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, People's Republic of China.,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
| | - Huanhuan Chen
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, People's Republic of China
| | - Jianjun Li
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, 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
| | - Guanghua Lan
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, People's Republic of China
| | - Shujia Liang
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, People's Republic of China
| | - Meiliang Liu
- School of Public Health, Guangxi Medical University, Nanning, People's Republic of China
| | - Abdur Rashid
- School of Medicine, Nankai University, Tianjin, 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
| | - Zhiyong Shen
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, People's Republic of China
| | - Yiming Shao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, People's Republic of China.,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.,Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, People's Republic of China
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11
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Zhang J, Huang XJ, Tang WM, Chu Z, Hu Q, Liu J, Ding H, Han X, Zhang Z, Jiang YJ, Geng W, Xia W, Xu J, Shang H. Rapid Clinical Progression and Its Correlates Among Acute HIV Infected Men Who Have Sex With Men in China: Findings From a 5-Year Multicenter Prospective Cohort Study. Front Immunol 2021; 12:712802. [PMID: 34367176 PMCID: PMC8339583 DOI: 10.3389/fimmu.2021.712802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/07/2021] [Indexed: 11/17/2022] Open
Abstract
Background In the “treat all” era, there are few data on the nature of HIV clinical progression in middle-income countries. The aim of the current study was to prospectively analyze the clinical progression of HIV and its indicators among men in China with acute HIV who have sex with men. Methods From 2009–2014 a total of 400 men with acute HIV infection (AHI) were identified among 7,893 men who have sex with men via periodic pooled nucleic acid amplification testing, and they were assigned to an AHI prospective cohort in Beijing and Shenyang, China. Rapid progression was defined as two consecutive CD4+ T cell counts < 350/µL within 3–24 months post-infection. Kaplan−Meier and Cox-regression analyses were conducted to identify predictors of rapid progression. Results Among 400 men with AHI 46.5% were rapid progressors, 35.1% reached rapid progressor status by 12 months post-infection, and 63.9% reached rapid progressor status by 24 months. Rapid progression was associated with herpes simplex-2 virus coinfection (adjusted hazard ratio [aHR] 1.7, 95% confidence interval [CI] 1.2–2.3], depression (aHR 1.9, 95% CI 1.5–2.6), baseline CD4+ T cell count < 500/μL (aHR 3.5, 95% CI 2.4–5.1), higher baseline HIV viral load (aHR 1.6, 95% CI 1.2–2.3), acute symptoms lasting ≥ 2 weeks (aHR 1.6, 95% CI 1.1–2.2), higher body mass index (aHR 0.9, 95% CI 0.9–1.0), higher HIV viral load (aHR 1.7, 95% CI 1.4–2.1), set point viral load at 3 months (aHR 2.0, 95% CI 1.6–2.5), each 100-cell/μL decrease in CD4+ T cell count at 3 months (aHR 2.2, 95% CI 1.9–2.5), and baseline routine blood tests including white blood cell count < 5.32, hemoglobin ≥ 151, mean corpuscular hemoglobin ≥ 30.5, hemoglobin concentration ≥ 342, mean platelet count ≥ 342, lymphocytes ≥ 1.98, and mixed cell count ≥ 0.4 (all p < 0.05). Conclusion Almost half of the patients underwent rapid clinical progression within 2 years after HIV infection. A treat-all policy is necessary and should be strengthened globally. Rapid progression was correlated with herpes simplex-2 virus coinfection, depression, low CD4+ T cell counts, and high set point viral load in acute infection stage. Rapid progression can be identified via simple indicators such as body mass index and routine blood test parameters in low and middle-income countries.
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Affiliation(s)
- Jing Zhang
- 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
| | - Xiao-Jie Huang
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Wei-Ming Tang
- Dermatology Hospital, Southern Medical University, Guangzhou, China.,University of North Carolina Project-China, Guangzhou, China.,School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - 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
| | - Qinghai 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
| | - Jing 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
| | - Haibo Ding
- 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
| | - Xiaoxu Han
- 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
| | - Zining Zhang
- 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
| | - Yong-Jun Jiang
- 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
| | - Wenqing Geng
- 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
| | - Wei Xia
- Beijing Youan Hospital, Capital Medical University, Beijing, 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
| | - 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
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12
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Ge Z, Feng Y, Li K, Lv B, Zaongo SD, Sun J, Liang Y, Liu D, Xing H, Wei M, Ma P, Shao Y. CRF01_AE and CRF01_AE Cluster 4 Are Associated With Poor Immune Recovery in Chinese Patients Under Combination Antiretroviral Therapy. Clin Infect Dis 2021; 72:1799-1809. [PMID: 32296820 DOI: 10.1093/cid/ciaa380] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 04/14/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) clades and clusters have different epidemic patterns and phenotypic profiles. It is unclear if they also affect patients' immune recovery (IR) in combination antiretroviral therapy (cART). METHODS We conducted a cohort study on 853 patients under cART for evaluating the impacts of viral factor on host IR. We used generalized estimating equations for factors affecting CD4 recovery, Kaplan-Meier curves for probability of achieving IR, and Cox hazards model for factors influencing IR capability. RESULTS Besides low baseline CD4 and old age, CRF01_AE and its cluster 4 were independently associated with lower CD4 cell level (P ≤ .003), slower IR (P ≤ .022), fewer patients (P < .001), and longer time achieving IR (P < .001), compared with CRF07_BC and CRF01_AE cluster 5. Higher percentage of CXCR4 (X4) viruses in the CRF01_AE and cluster 4-infected patients, compared with their respective counterparts (P < .001), accounted for the poor IR in infected patients (P < .001). Finally, we revealed that greater X4 receptor binding propensity of amino acids was exhibited in CRF01_AE clade (P < .001) and its cluster 4 (P ≤ .004). CONCLUSIONS Our study demonstrates that the CRF01_AE clade and cluster are associated with poor IR in patients under cART, which is ascribed to a high proportion of viruses with X4 tropism. HIV-1 genotyping and phenotyping should be used as a surveillance tool for patients initiating cART. CCR5 inhibitors should be used with caution in regions with high prevalence of X4 viruses.
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Affiliation(s)
- Zhangwen Ge
- School of Medicine, Nankai University, Tianjin, 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
| | - Kang Li
- 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
| | - Bowen Lv
- 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
| | | | - Jia Sun
- 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
| | - Yanling Liang
- 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
| | - Dan Liu
- Nankai University Second People's Hospital, Tianjin, 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
| | - Min Wei
- School of Medicine, Nankai University, Tianjin, China.,Nankai University Second People's Hospital, Tianjin, China
| | - Ping Ma
- Nankai University Second People's Hospital, Tianjin, China
| | - Yiming Shao
- School of Medicine, Nankai University, Tianjin, China.,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
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13
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Phylodynamic analysis reveals changing transmission dynamics of HIV-1 CRF01_AE in Japan from heterosexuals to men who have sex with men. Int J Infect Dis 2021; 108:397-405. [PMID: 34082091 DOI: 10.1016/j.ijid.2021.05.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND HIV-1 circulating recombinant form (CRF) 01_AE is the second major subtype in Japan. Our previous study indicated that CRF01_AE was predominantly circulating in heterosexuals/injecting drug users (IDUs). With implications of increased CRF01_AE infections among men who have sex with men (MSM), this study sought to investigate whether the transmission dynamics of CRF01_AE infections in Japan have changed. METHODS Sequences from 8032 newly diagnosed HIV-1-infected individuals were analysed. For 614 (7.6%) of CRF01_AE cases, clusters were identified and categorised by transmission risks. Median times to the most recent common ancestors (tMRCA) were estimated. RESULTS The individuals were predominantly Japanese (64%) and male (72%). MSM became the predominant transmission risk from 2014. Thirty transmission clusters (TCs) and 48 pairs, including 40% of individuals, were identified. MSM were approximately five times more likely to be in a TC compared to heterosexuals, and were the major contributors to TCs. tMRCA data suggest that MSM TCs emerged from 1996 and became predominant around 2000. CONCLUSIONS CRF01_AE has spread among MSM, with frequent and continuous cluster formations, and MSM has become the predominant transmission risk. Our study suggested that CRF01_AE transmission has shifted from heterosexuals/IDUs to MSM. Prevention measures targeting key populations should be considered for controlling CRF01_AE spread.
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14
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Marty N, Saeng-Aroon S, Heger E, Thielen A, Obermeier M, Pfeifer N, Kaiser R, Klimkait T. Adapting the geno2pheno[coreceptor] tool to HIV-1 subtype CRF01_AE by phenotypic validation using clinical isolates from South-East Asia. J Clin Virol 2021; 136:104755. [PMID: 33639408 DOI: 10.1016/j.jcv.2021.104755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/24/2020] [Accepted: 02/01/2021] [Indexed: 01/23/2023]
Abstract
OBJECTIVES Geno2pheno[coreceptor] is a widely used tool for the prediction of coreceptor usage (viral tropism) of HIV-1 samples. For HIV-1 CRF01_AE, a significant overcalling of X4-tropism is observed when using the standard settings of Geno2pheno[coreceptor]. The aim of this study was to provide the experimental backing for adaptations to the geno2pheno[coreceptor] algorithm in order to improve coreceptor usage predictions of clinical HIV-1 CRF01_AE isolates STUDY DESIGN: V3-sequences of 20 clinical HIV-1 subtype CRF01_AE samples were sequenced and analyzed by geno2pheno[coreceptor]. In parallel, coreceptor usage was determined for these samples by replicative phenotyping in human cells in the presence of specific X4- or R5-inhibitors. RESULTS The sole introduction of the CRF01_AE V3 region into a full-length otherwise subtype B provirus failed to produce replication-competent viral progeny. A successive genome-replacement strategy revealed that also CRF01_AE derived gag and pol sequences are necessary to generate HIV genomes with sufficient replication competence. Subsequent phenotypic analysis confirmed overcalling of X4-tropism for CRF01_AE viruses using the current version and the standard cut-off at 10% false positive rate (FPR) of geno2pheno[coreceptor]. Lowering the FPR cut-off to 2.5% reduced the X4-overcalling in our sample collection, while still allowing a safe administration of Maraviroc (MCV). CONCLUSION This study demonstrates the successful adjustment of geno2pheno[coreceptor] rules for subtype CRF01_AE. It also supports the unique strength of combining complementing methods, namely phenotyping and genotyping, for validating new bioinformatics tools prior to application in diagnostics.
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Affiliation(s)
- Nina Marty
- Molecular Virology, Department Biomedicine-Petersplatz, University of Basel, Petersplatz 10, 4055 Basel, Switzerland.
| | - Siriphan Saeng-Aroon
- Hazardous Pathogen Laboratory, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Eva Heger
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | | | | | - Nico Pfeifer
- Max Planck Institute for Informatics, Saarland Informatics Campus E1 4, Saarbruecken, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Thomas Klimkait
- Molecular Virology, Department Biomedicine-Petersplatz, University of Basel, Petersplatz 10, 4055 Basel, Switzerland
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15
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Zheng M, Yu M, Cheng S, Zhou N, Ning T, Li L, Zhao F, Zhao X, Zhu J, Jiang G. Characteristics of HIV-1 molecular transmission networks and drug resistance among men who have sex with men in Tianjin, China (2014-2018). Virol J 2020; 17:169. [PMID: 33143744 PMCID: PMC7640427 DOI: 10.1186/s12985-020-01441-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/27/2020] [Indexed: 11/25/2022] Open
Abstract
Background In Tianjin, China, there is a relatively high prevalence of HIV in men who have sex with men (MSM). The number of HIV cases in Tianjin is also increasing. We investigated the HIV molecular transmission network, genetic tropisms, and drug resistance mutations in Tianjin.
Methods Blood samples were collected from 510 newly diagnosed antiretroviral therapy (ART)-naïve HIV-1-infected subjects among MSM in Tianjin. Partial pol and env genes were sequenced and used for phylogenetic, genetic tropism, and genotypic drug resistance analyses. Molecular clusters were identified with 1.5% genetic distance and 90% bootstrap support. Results Among the 436 HIV-1 pol sequences obtained from the study participants, various genotypes were identified, including CRF01_AE (56.9%), CRF07_BC (27.8%), B (7.3%), CRF55_01B (4.1%), unique recombinant forms (URFs) (3.7%), and CRF59_01B (0.2%). A higher prevalence of X4 viruses was observed in individuals infected with CRF55_01B (56.3%) and CRF01_AE (46.2%) than with other subtypes. Of all 110 sequences in the 36 clusters, 62 (56.4%) were observed in 23 CRF01_AE clusters and 18 (16.4%) in four CRF07_BC clusters. Eight sequences clustered with at least one other shared the same drug resistance mutation (DRM). In different cluster sizes, the distributions of individuals by age, presence of sexually transmitted disease, and presence of DRMs, were significantly different. Conclusion We revealed the characteristics of HIV molecular transmission, tropism, and DRMs of ART-naïve HIV-infected individuals among the MSM population in Tianjin. Identifying infected persons at risk of transmission is necessary for proposing counseling and treating these patients to reduce the risk of HIV transmission.
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Affiliation(s)
- Minna Zheng
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Maohe Yu
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Shaohui Cheng
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Ning Zhou
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Tielin Ning
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Long Li
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Fangning Zhao
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Xuan Zhao
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Jingjin Zhu
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Guohong Jiang
- Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China.
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Existence of Replication-Competent Minor Variants with Different Coreceptor Usage in Plasma from HIV-1-Infected Individuals. J Virol 2020; 94:JVI.00193-20. [PMID: 32295903 DOI: 10.1128/jvi.00193-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/04/2020] [Indexed: 12/20/2022] Open
Abstract
Cell entry by HIV-1 is mediated by its principal receptor, CD4, and a coreceptor, either CCR5 or CXCR4, with viral envelope glycoprotein gp120. Generally, CCR5-using HIV-1 variants, called R5, predominate over most of the course of infection, while CXCR4-using HIV-1 variants (variants that utilize both CCR5 and CXCR4 [R5X4, or dual] or CXCR4 alone [X4]) emerge at late-stage infection in half of HIV-1-infected individuals and are associated with disease progression. Although X4 variants also appear during acute-phase infection in some cases, these variants apparently fall to undetectable levels thereafter. In this study, replication-competent X4 variants were isolated from plasma of drug treatment-naive individuals infected with HIV-1 strain CRF01_AE, which dominantly carries viral RNA (vRNA) of R5 variants. Next-generation sequencing (NGS) confirmed that sequences of X4 variants were indeed present in plasma vRNA from these individuals as a minor population. On the other hand, in one individual with a mixed infection in which X4 variants were dominant, only R5 replication-competent variants were isolated from plasma. These results indicate the existence of replication-competent variants with different coreceptor usage as minor populations.IMPORTANCE The coreceptor switch of HIV-1 from R5 to CXCR4-using variants (R5X4 or X4) has been observed in about half of HIV-1-infected individuals at late-stage infection with loss of CD4 cell count and disease progression. However, the mechanisms that underlie the emergence of CXCR4-using variants at this stage are unclear. In the present study, CXCR4-using X4 variants were isolated from plasma samples of HIV-1-infected individuals that dominantly carried vRNA of R5 variants. The sequences of the X4 variants were detected as a minor population using next-generation sequencing. Taken together, CXCR4-using variants at late-stage infection are likely to emerge when replication-competent CXCR4-using variants are maintained as a minor population during the course of infection. The present study may support the hypothesis that R5-to-X4 switching is mediated by the expansion of preexisting X4 variants in some cases.
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The prevalence, temporal trends, and geographical distribution of HIV-1 subtypes among men who have sex with men in China: A systematic review and meta-analysis. Epidemiol Infect 2020; 147:e83. [PMID: 30869019 PMCID: PMC6518548 DOI: 10.1017/s0950268818003400] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The aim of this meta-analysis was to provide a comprehensive overview of human immunodeficiency virus (HIV)-1 subtypes and to investigate temporal and geographical trends of the HIV-1 epidemic among men who have sex with men (MSM) in China. Chinese and English articles published between January 2007 and December 2017 were systematically searched. Pooled HIV-1 prevalence was calculated, and its stability was analysed using sensitivity analysis. Subgroups were based on study time period, sampling area and prevalence. Publication bias was measured using Funnel plot and Egger's test. A total of 68 independent studies that included HIV-1 molecular investigations were eligible for meta-analysis. Circulating recombinant form (CRF) 01_AE (57.36%, 95% confidence interval (CI) 53.76–60.92) was confirmed as the most prevalent HIV-1 subtype among MSM in China. Subgroup analysis for time period found that CRF01_AE steadily increased prior to 2012 but decreased during 2012–2016. Further whereas CRF07_BC increased over time, B/B′ decreased over time. CRF55_01B has increased in recent years, with higher pooled estimated rate in Guangdong (12.22%, 95% CI 10.34–13.17) and Fujian (8.65%, 95% CI 4.98–13.17) provinces. The distribution of HIV-1 subtypes among MSM in China has changed across different regions and periods. HIV-1 strains in MSM are becoming more complex. Long-term molecular monitoring in this population remains necessary for HIV-1 epidemic control and prevention.
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Liang Y, Han Z, Shui J, Cheng W, Zhong F, Cai Q, Wang H, Wu H, Xu H, Tang S. HIV-1 genotype is independently associated with immunodeficiency progression among Chinese men who have sex with men: an observational cohort study. HIV Med 2019; 21:279-288. [PMID: 31863622 DOI: 10.1111/hiv.12823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVES HIV-1 genetic diversity is increasing among men who have sex with men (MSM) in China, but the association of HIV-1 genotype with disease progression remains to be elucidated. METHODS We collected data in an observational longitudinal cohort study of 860 HIV-1-infected MSM in Guangzhou, China between January 2008 and March 2017. Kaplan-Meier analysis and Cox proportional hazard model were used to predict the time from HIV-1 diagnosis to immunodeficiency progression (CD4 cell count < 200 cells/μl) as well as adjusted hazard ratio (aHR). RESULTS CRF01_AE and HIV-1 subtype B infection were associated with higher percentage of patients progressed to immunodeficiency and higher incidence of immunodeficiency than infection with CRF07_BC or CRF55_01B. Compared with CRF07_BC, the time from HIV-1 diagnosis to immunodeficiency were different among the major HIV-1 genotypes, which ranked as follows, in descending order: CRF07_BC (7.03 years) > CRF55_01B (5.71 years, P = 0.014; aHR 3.752, P = 0.0923) > CRF01_AE (5.18 years, P < 0.001; aHR 4.733, P = 0.0152). HIV-1 genotype, viral load and baseline CD4 T-cell count were three independent variables associated with disease progression. CONCLUSIONS Our results confirm differential rates of immunodeficiency progression as a function of HIV-1 genotype. The impact of HIV-1 genotype on HIV epidemics, patient management and prevention should be further investigated.
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Affiliation(s)
- Y Liang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangzhou, China
| | - Z Han
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - J Shui
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangzhou, China
| | - W Cheng
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - F Zhong
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Q Cai
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangzhou, China
| | - H Wang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangzhou, China
| | - H Wu
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - H Xu
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - S Tang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,Dermatology Hospital, Southern Medical University, Guangzhou, China
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19
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Infrequent HIV Infection of Circulating Monocytes during Antiretroviral Therapy. J Virol 2019; 94:JVI.01174-19. [PMID: 31597764 DOI: 10.1128/jvi.01174-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/27/2019] [Indexed: 12/18/2022] Open
Abstract
Whereas human immunodeficiency virus (HIV) persists in tissue macrophages during antiretroviral therapy (ART), the role of circulating monocytes as HIV reservoirs remains controversial. Three magnetic bead selection methods and flow cytometry cell sorting were compared for their capacity to yield pure CD14+ monocyte populations. Cell sorting by flow cytometry provided the purest population of monocytes (median CD4+ T-cell contamination, 0.06%), and the levels of CD4+ T-cell contamination were positively correlated with the levels of integrated HIV DNA in the monocyte populations. Using cell sorting by flow cytometry, we assessed longitudinally the infection of monocytes and other cell subsets in a cohort of 29 Thai HIV-infected individuals. Low levels of HIV DNA were detected in a minority of monocyte fractions obtained before and after 1 year of ART (27% and 33%, respectively), whereas HIV DNA was readily detected in CD4+ T cells from all samples. Additional samples (2 to 5 years of ART) were obtained from 5 individuals in whom monocyte infection was previously detected. Whereas CD4+ T cells were infected at high levels at all time points, monocyte infection was inconsistent and absent in at least one longitudinal sample from 4/5 individuals. Our results indicate that infection of monocytes is infrequent and highlight the importance of using flow cytometry cell sorting to minimize contamination by CD4+ T cells.IMPORTANCE The role of circulating monocytes as persistent HIV reservoirs during ART is still controversial. Several studies have reported persistent infection of monocytes in virally suppressed individuals; however, others failed to detect HIV in this subset. These discrepancies are likely explained by the diversity of the methods used to isolate monocytes and to detect HIV infection. In this study, we show that only flow cytometry cell sorting yields a highly pure population of monocytes largely devoid of CD4 contaminants. Using this approach in a longitudinal cohort of HIV-infected individuals before and during ART, we demonstrate that HIV is rarely found in monocytes from untreated and treated HIV-infected individuals. This study highlights the importance of using methods that yield highly pure populations of cells as flow cytometry cell sorting to minimize and control for CD4+ T-cell contamination.
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Widiyanti M, Hadi MI. Viral and Host Factors are Related to the Progression of HIV Diseases in Mimika, Papua. Open Access Maced J Med Sci 2019; 7:3429-3432. [PMID: 32002067 PMCID: PMC6980796 DOI: 10.3889/oamjms.2019.437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Papua has a high cumulative number of HIV, which has expanded epidemic status with the most risk factors are heterosexuals. AIM This study aims to determine factors associated with HIV disease progression include host and viral factors. METHODS Eighty-four subjects recruited in Rumah Sakit Mitra Masyarakat (RSMM) VCT's laboratory, interviewed with questionnaires and also did laboratory examinations. HIV-1 subtypes were identified using RT-PCR, nested PCR and sequencing. Then, CD4+ data is checked using PIMA Analyzer. Demographic and clinical data obtained from the patient's medical record. After collected, data were analysed using Fisher's exact test. RESULTS The results showed two factors that influence the progression of HIV disease were HIV subtypes (p = 0.002) and Body Mass Index (p = 0.033). The HIV-1 subtype also correlated with CD4+ levels with a value of p = 0.04. CONCLUSION HIV-1 subtype correlates with HIV progression, so it is necessary to develop HIV/AIDS management strategies and clinical counselling.
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Affiliation(s)
- Mirna Widiyanti
- Balai Penelitian dan Pengembangan Kesehatan Papua, Indonesia
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21
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Li K, Liu M, Li J, Dong A, Zhou Y, Ding Y, Liang Y, Shao Y. Genomic Characterization of a Novel HIV-1 Second-Generation Recombinant Form (CRF01_AE/B) from Men Who Have Sex with Men in Guangxi Zhuang Autonomous Region, China. AIDS Res Hum Retroviruses 2019; 35:972-977. [PMID: 31187643 DOI: 10.1089/aid.2019.0149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report here a novel HIV-1 recombinant form (18GXD4705) composed of CRF01_AE and subtype B, acquired from an unmarried HIV-positive young man subject infected through homosexual contact in Guangxi Province of eastern China. The phylogenetic analysis of the near full-length genome of 18GXD4705 indicated that one subtype B segment was inserted into the CRF01_AE backbone, with one recombinant breakpoint demonstrated in the pol region. The CRF01_AE region (I and III) of recombinant correlated with a previously reported subcluster 4 lineage. The B subregions (II) are greatly clustered together, with B strain references. The continued generation of this novel recombinant increases the genetic complexity and diversity of the HIV epidemic in Guangxi. In addition, further molecular epidemiological investigations should be conducted to continuously monitor the dynamic transmission of HIV-1 in the region.
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Affiliation(s)
- Kang Li
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- 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
| | - Meiliang Liu
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Jianjun Li
- Guangxi Center for Disease Prevention and Control, Nanning, China
| | - Aaobo Dong
- 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
| | - Yuxi Zhou
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yibo Ding
- 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
| | - Yanling Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- 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
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- 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
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22
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Critical amino acid residues and potential N-linked glycosylation sites contribute to circulating recombinant form 01_AE pathogenesis in Northeast China. AIDS 2019; 33:1431-1439. [PMID: 30889014 PMCID: PMC6635051 DOI: 10.1097/qad.0000000000002197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Supplemental Digital Content is available in the text Objective: The current study aimed to understand epidemiological feature and critical factors associated with pathogenesis of circulating recombinant form (CRF) 01_AE strains in Northeast China. Design: Compared analysis was made between CRF01_AE and non-CRF01_AE samples to understand the pathogenicity features of CRF01_AE. Further analyses between CRF01_AE samples with high or low CD4+ cell counts and between samples with different coreceptor usages were done to explore the possible factors correlating to the pathogenesis of CRF01_AE viruses. Methods: The genotypes of newly identified strains were determined by phylogenetic analyses using Mega 6.06. Coreceptor usage was predicted by Geno2Pheno algorithm. Potential N-linked glycosylation site (PNGS) number was calculated using the online N-glycosite software. The properties of amino acid sequences were analyzed by the online ProtParam tool. Results: CRF01_AE become the main HIV-1 genotype since 2010. Compared with non-CRF01_AE group, the CRF01_AE group showed a higher proportion of samples with CD4+ cell count less than 200 cells/μl. Shorter amino acid length, fewer PNGSs and the presence of a basic motif R/KNXT or NR/KT in V4 correlated to a lower CD4+ cell count, and existence or coexistence of Thr12, Arg13, Val21 and Lys33, presence of more than 4 of net charges and lack of the PNGS within V3 favored to the X4/R5X4 coreceptor usage of CRF01_AE viruses. Conclusion: CRF01_AE has dominated HIV-1 genotype in Northeast China. Infection with CRF01_AE exhibited a fast disease progression, which may be associated with specific amino acid residues and PNGSs in V3 and V4 regions as well as amino acid length of V4 region.
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23
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Chung YS, Choi JY, Yoo MS, Seong JH, Choi BS, Kang C. Phylogenetic transmission clusters among newly diagnosed antiretroviral drug-naïve patients with human immunodeficiency virus-1 in Korea: A study from 1999 to 2012. PLoS One 2019; 14:e0217817. [PMID: 31166970 PMCID: PMC6550428 DOI: 10.1371/journal.pone.0217817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 05/21/2019] [Indexed: 11/29/2022] Open
Abstract
Population-level phylogenetic patterns reflect both transmission dynamics and genetic changes, which accumulate because of selection or drift. In this study, we determined whether a longitudinally sampled dataset derived from human immunodeficiency virus (HIV)-1-infected individuals over a 14-year period (1999–2012) could shed light on the transmission processes involved in the initiation of the HIV-1 epidemic in Korea. In total, 927 sequences were acquired from 1999 to 2012; each sequence was acquired from an individual patient who had not received treatment. Sequences were used for drug resistance and phylogenetic analyses. Phylogenetic and other analyses were conducted using MEGA version 6.06 based on the GTR G+I parameter model and SAS. Of the 927 samples, 863 (93.1%) were classified as subtype B and 64 were classified as other subtypes. Phylogenetic analysis demonstrated that 104 of 927 patient samples (11.2%) were grouped into 37 clusters. Being part of a transmission cluster was significantly associated with subtype-B viruses, infection via sexual contact, and the infection of young males. Of all clusters, three (~8.1%) that comprised 10 individual samples (22.2% of 45 individuals) included at least one member with total transmitted drug resistance (TDR). In summary, HIV transmission cluster analyses can integrate laboratory data with behavioral data to enable the identification of key transmission patterns to develop tailored interventions aimed at interrupting transmission chains.
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Affiliation(s)
- Yoon-Seok Chung
- Division of Viral Diseases, Center for Laboratory Control and Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Ju-Yeon Choi
- Division of Viral Diseases, Center for Laboratory Control and Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Myoung-Su Yoo
- Division of Viral Diseases Research, Center for Research of Infectious Diseases, National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Jae Hyun Seong
- Division of Viral Diseases Research, Center for Research of Infectious Diseases, National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Byeong-Sun Choi
- Division of Viral Diseases Research, Center for Research of Infectious Diseases, National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Chun Kang
- Division of Viral Diseases, Center for Laboratory Control and Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
- * E-mail:
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Co-receptor tropism and genetic characteristics of the V3 regions in variants of antiretroviral-naive HIV-1 infected subjects. Epidemiol Infect 2019; 147:e181. [PMID: 31063103 PMCID: PMC6518647 DOI: 10.1017/s0950268819000700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Co-receptor tropism has been identified to correlate with HIV-1 transmission and the disease progression in patients. A molecular epidemiology investigation of co-receptor tropism is important for clinical practice and effective control of HIV-1. In this study, we investigated the co-receptor tropism on HIV-1 variants of 85 antiretroviral-naive patients with Geno2pheno algorithm at a false-positive rate of 10%. Our data showed that a majority of the subjects harboured the CCR5-tropic virus (81.2%, 69/85). No significant differences in gender, age, baseline CD4+ T-cell counts and transmission routes were observed between subjects infected with CXCR4-tropic or CCR5-tropic virus. The co-receptor tropism appeared to be associated with the virus genotype; a significantly more CXCR4-use was predicted in CRF01_AE infections whereas all CRF07_BC and CRF08_BC were predicted to use CCR5 co-receptor. Sequences analysis of V3 revealed a higher median net charge in the CXCR4 viruses over CCR5 viruses (4.0 vs. 3.0, P < 0.05). The predicted N-linked glycosylation site between amino acids 6 and 8 in the V3 region was conserved in CCR5 viruses, but not in CXCR4 viruses. Besides, variable crown motifs were observed in both CCR5 and CXCR4 viruses, of which the most prevalent motif GPGQ existed in both viral tropism and almost all genotypes identified in this study except subtype B. These findings may offer important implications for clinical practice and enhance our understanding of HIV-1 biology.
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25
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Xiao P, Zhou Y, Lu J, Yan L, Xu X, Hu H, Li J, Ding P, Qiu T, Fu G, Huan X, Yang H. HIV-1 genotype diversity and distribution characteristics among heterosexually transmitted population in Jiangsu province, China. Virol J 2019; 16:51. [PMID: 31023323 PMCID: PMC6485170 DOI: 10.1186/s12985-019-1162-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/10/2019] [Indexed: 01/17/2023] Open
Abstract
Background Heterosexual transmission has contributed greatly to the current HIV-1 epidemic in China. However, the HIV-1 genetic characteristics in the heterosexually transmitted population in Jiangsu province remained unclear. Methods A molecular epidemiological investigation on heterosexual transmission of HIV-1 was conducted across Jiangsu province. 301 HIV-1 patients infected through heterosexual transmission were involved in this study. The epidemiological information was investigated by trained staff via face-to-face interviews. Blood samples were taken from each patient, HIV-1 RNA was extracted from the plasma, and used for amplifying the gag and env genes followed by further products sequencing. The genotypes of HIV-1 were determined using phylogenetic tree analyses in the neighbor-joining method. Results A total of 262 samples were successfully taken for genotyping. The main subtypes which accounted for 90.5% of all HIV-1 strains are CRF01_AE (45.4%), CRF07_BC (21.4%), subtype B (12.6%), CRF08_BC (11.1%). Minor subtypes were also detected, such as CRF68_01B, subtype C, CRF55_01B, CRF02_AG and subtype A. Time trend analysis suggested the prevalence of subtype B and CRF08_BC decreased gradually, but the prevalence of CRF01_AE increased over time. A relatively higher prevalence of CRF07_BC in Central Jiangsu and subtype B were detected in South Jiangsu, while a relatively lower prevalence of subtype B and CRF08_BC were detected in Central Jiangsu. Conclusion Complex and unbalanced HIV distribution characteristics suggest that heterosexual transmission of HIV needs to be taken seriously. It is necessary to implement more effective and comprehensive intervention strategies for further control of HIV-1 dissemination.
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Affiliation(s)
- Peipei Xiao
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University
- , No.87 Dingjiaqiao, Nanjing, 210009, China
| | - Ying Zhou
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Jing Lu
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Li Yan
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University
- , No.87 Dingjiaqiao, Nanjing, 210009, China
| | - Xiaoqin Xu
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Haiyang Hu
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Jianjun Li
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Ping Ding
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Tao Qiu
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Gengfeng Fu
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Xiping Huan
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Haitao Yang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University
- , No.87 Dingjiaqiao, Nanjing, 210009, China. .,Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China. .,Jiangsu Research Institute of Schistosomiasis Control, No.117 Meiyuan Yangxiang, Wuxi, 214064, China.
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Ou W, Li K, Feng Y, Huang Q, Ge Z, Sun J, Zhou Z, Liang Y, Xing H, Liang H, Shao Y. Characterization of a New HIV-1 CRF01_AE/B Recombinant Virus Form Among Men Who Have Sex with Men in Shanghai, China. AIDS Res Hum Retroviruses 2019; 35:414-418. [PMID: 30229664 DOI: 10.1089/aid.2018.0197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To date, there are 16 types of CRF01_AE/B circulating recombinant forms identified, and most of them are distributed in Asian countries such as China, Malaysia, and Singapore. Previous HIV molecular epidemiological surveys showed that CRF01_AE (27.6%) and B (9.6%) subtypes are predominant strains in mainland of China. At the same time, the HIV-1 virus spreads faster in the men who have sex with men (MSM) population than in other risk groups. In Shanghai district, ∼66.0% of newly reported cases were infected through homosexual transmission. In this study, we report a novel recombinant strain of CRF01_AE/B. The near full-length genome phylogenetic tree showed that the strain clustered with the CRF01_AE reference sequence and placed in the peripheral position within the branch of the CRF01_AE strain. Subregional evolutionary results indicated that the CRF01_AE subtype was derived from cluster 4 of CRF01_AE, which is mainly distributed in northern China. The subtype B was correlated with the U.S./Europe B, which are widely prevalent in the Chinese MSM population. In recent years, a large number of recombinant forms between CRF01_AE and B strains are continuously emerging in China. Therefore, understanding the current epidemic recombinant forms will have significant implications for prevention and treatment of HIV/AIDS.
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Affiliation(s)
- Weidong Ou
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- Division of Research on Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kang Li
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- Division of Research on Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Feng
- Division of Research on Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qiao Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Zhangwen Ge
- Division of Research on Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jia Sun
- Division of Research on Virology and Immunology, 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
| | - Zhehua Zhou
- Division of Research on Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanling Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Hui Xing
- Division of Research on Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yiming Shao
- Guangxi Key Laboratory of AIDS Prevention and Treatment and Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- Division of Research on Virology and Immunology, 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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Rapid CD4+ T-cell decline is associated with coreceptor switch among MSM primarily infected with HIV-1 CRF01_AE in Northeast China. AIDS 2019; 33:13-22. [PMID: 30102662 DOI: 10.1097/qad.0000000000001981] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE CRF01_AE is the most prevalent HIV-1 subtype among MSM in China. However, the characteristics and underlying mechanism of the accelerated CD4 T-cell decline in CRF01_AE-infected MSM remain incompletely understood. DESIGN A long-term prospective follow-up study was conducted with 1388 MSM at risk of HIV-1 infection in Northeast China. MSM with primary HIV-1 CRF01_AE infection were identified and followed for 3-6 years to explore the determinants of rapid CD4 T-cell decline. METHODS Tropism was determined in primary infection by both single genome amplification-based genotypic prediction using four different algorithms and phenotypic determination using clinical isolates. Serial isolates were used to determine phenotype of coreceptor switch. Human leukocyte antigen genotypes and T-cell activation markers were determined. RESULTS Fifty-nine MSM primarily infected with HIV-1 CRF01_AE were discovered and recruited for the follow-up study. CCR5-utilizing (R5) viruses accounted for up to 98% of HIV-1 CRF01_AE infections in Northeast China. Survival analysis indicated 39.5% of the patients underwent coreceptor switch within 3 years after infection. After adjustment for other potential risk factors, linear mixed-effect models demonstrated patients experienced R5 to CXCR4-utilizing/dual-tropic (X4/DM) coreceptor switch within 3 years after infection underwent a faster CD4 T-cell decline compared to those without coreceptor switch. CONCLUSIONS Primary HIV-1 CRF01_AE infection among MSM in Northeast China is characterized by R5 viral infection and early R5 to X4/DM coreceptor switch, which is associated with rapid CD4 T-cell decline. The findings highlight the importance of immediate treatment among the CRF01_AE-infected MSM.
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Disparate impact on CD4 T cell count by two distinct HIV-1 phylogenetic clusters from the same clade. Proc Natl Acad Sci U S A 2018; 116:239-244. [PMID: 30559208 PMCID: PMC6320496 DOI: 10.1073/pnas.1814714116] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Past studies on HIV-1 evolution were mainly at the genetic level. This study provides well-matched genotype and phenotype data and demonstrates the disparate pathogenicity of two major CRF01_AE clusters. While CRF01_AE cluster 4 and cluster 5 are associated with the men-who-have-sex-with-men (MSM) route of transmission, cluster 4 but not cluster 5 causes a low CD4 count, which is associated with the higher prevalence CXCR4 viruses in cluster 4. The higher CXCR4 use tendency in cluster 4 is derived from its unique V3 loop favoring CXCR4 binding. This study demonstrates disparate HIV-1 phenotypes between different phylogenetic clusters. It is important to monitor HIV-1 evolution at both the genotype and phenotype level to identify and control more pathogenic HIV-1 strains. HIV-1 evolved into various genetic subtypes and circulating recombinant forms (CRFs) in the global epidemic. The same subtype or CRF is usually considered to have similar phenotype. Being one of the world’s major CRFs, CRF01_AE infection was reported to associate with higher prevalence of CXCR4 (X4) viruses and faster CD4 decline. However, the underlying mechanisms remain unclear. We identified eight phylogenetic clusters of CRF01_AE in China and hypothesized that they may have different phenotypes. In the National HIV Molecular Epidemiology Survey, we discovered that people infected by CRF01_AE cluster 4 had significantly lower CD4 counts (391 vs. 470, P < 0.0001) and higher prevalence of X4-using viruses (17.1% vs. 4.4%, P < 0.0001) compared with those infected by cluster 5. In an MSM cohort, X4-using viruses were only isolated from seroconvertors in cluster 4, which was associated with low a CD4 count within the first year of infection (141 vs. 440, P = 0.003). Using a coreceptor binding model, we identified unique V3 signatures in cluster 4 that favor CXCR4 use. We demonstrate that the HIV-1 phenotype and pathogenicity can be determined at the phylogenetic cluster level in the same subtype. Since its initial spread to humans from chimpanzees, estimated to be the first half of the 20th century, HIV-1 continues to undergo rapid evolution in larger and more diverse populations. The divergent phenotype evolution of two major CRF01_AE clusters highlights the importance of monitoring the genetic evolution and phenotypic shift of HIV-1 to provide early warning of the appearance of more pathogenic strains.
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Leelawiwat W, Pattanasin S, Sriporn A, Wasinrapee P, Kongpechsatit O, Mueanpai F, Tongtoyai J, Holtz TH, Curlin ME. Association between HIV genotype, viral load and disease progression in a cohort of Thai men who have sex with men with estimated dates of HIV infection. PLoS One 2018; 13:e0201386. [PMID: 30063722 PMCID: PMC6067726 DOI: 10.1371/journal.pone.0201386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/13/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Differences between HIV genotypes may affect HIV disease progression. We examined infecting HIV genotypes and their association with disease progression in a cohort of men who have sex with men with incident HIV infection in Bangkok, Thailand. METHODS We characterized the viral genotype of 189 new HIV infections among MSM identified between 2006-2014 using hybridization and sequencing. Plasma viral load (PVL) was determined by PCR, and CD4+ T-cell counts were measured by flow cytometry. We used Generalized Estimating Equations to examine factors associated with changes in CD4+ T-cell counts. Factors associated with immunologic failure were analyzed using Cox proportional hazard models. RESULTS Among 189 MSM, 84% were infected with CRF01_AE, 11% with recombinant B/CRF01_AE and 5% with subtype B. CD4+ T-cell decline rates were 68, 65, and 46 cells/μL/year for CRF01_AE, recombinants, and subtype B, respectively, and were not significantly different between HIV subtypes. CD4+ T-cell decline rate was significantly associated with baseline PVL and CD4+ T-cell counts (p <0.001). Progression to immunologic failure was associated with baseline CD4+ T-cell ≤ 500 cells/μL (AHR 1.97; 95% CI 1.14-3.40, p = 0.015) and PVL > 50,000 copies/ml (AHR 2.03; 1.14-3.63, p = 0.017). There was no difference in time to immunologic failure between HIV subtypes. CONCLUSION Among HIV-infected Thai MSM, low baseline CD4+ T-cell and high PVL are associated with rapid progression. In this cohort, no significant difference in CD4+ T-cell decline rate or time to immunologic failure was seen between CRF01_AE and other infecting HIV subtypes.
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Affiliation(s)
- Wanna Leelawiwat
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- * E-mail:
| | - Sarika Pattanasin
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Anuwat Sriporn
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Punneeporn Wasinrapee
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Oranuch Kongpechsatit
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Famui Mueanpai
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Jaray Tongtoyai
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Timothy H. Holtz
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Marcel E. Curlin
- Thailand Ministry of Public Health–U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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Lu Z, Jiao Y, Li J, Lan G, Lu C, Li X, Tang Z, Wang N. After 18 months of antiretroviral therapy, total HIV DNA decreases more pronouncedly in patients infected by CRF01_AE than in those infected by subtype B and CRF07_BC. Microbiol Immunol 2018; 62:248-254. [PMID: 29377267 DOI: 10.1111/1348-0421.12578] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 12/19/2022]
Abstract
Whether the amount of HIV DNA is associated with the subtype of HIV-1 after antiretroviral therapy (ART) has not been reported. In the present study, the amount of HIV DNA and RNA and CD4+T counts in blood and semen prior to and after 18 months of ART were compared in 48 patients infected by CRF01_AE, subtype B or CRF07_BC of HIV-1. Viral RNA was suppressed and CD4 cell count recovery achieved in all patients. The level of HIV DNA were similar before ART; however, patients with CRF01_AE had less HIV DNA after ART than those with subtype B and CRF07_BC infection. According to prediction of co-receptor usage by Geno2Pheno and PSSM in combination, more than 35.6% of clones for CRF01_AE were predicted as CXCR4-using before ART, whereas less than 6% of those for subtype B and CRF07_BC were predicted as CXCR4-using. After 18 months of ART, no CXCR4-using clones were predicted in any of the subtypes. Despite more HIV RNA and fewer CD4 + T cells in patients with CRF01_AE before therapy, no significant differences (P > 0.05) in viral RNA or CD4 cell counts were observed between the subtypes after 18 months of ART. Thus, 18 months of antiretroviral therapy was more efficient in patients with CRF01_AE. Considering that successful ART dramatically reduces the viral load in both blood and semen, risks of sexual transmission of HIV were reduced, contributing to prevention of rapid spread of HIV among men who have sex with men in the region.
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Affiliation(s)
- Zhenzhen Lu
- Institute of HIV/AIDS Prevention and Control, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China.,Department of Infectious Diseases, Beijing 302 Hospital, Beijing 100069, China
| | - Yanmei Jiao
- AIDS Antiviral Treatment Clinic, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Jianjun Li
- Institute of HIV/AIDS Prevention and Control, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Guanghua Lan
- Institute of HIV/AIDS Prevention and Control, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Chunyan Lu
- AIDS Research Center, Ruikang Hospital affiliated to Guangxi University of Chinese Medicine, Nanning, 530011, China
| | - Xuan Li
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Zhenzhu Tang
- Institute of HIV/AIDS Prevention and Control, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Ning Wang
- Department of Infectious Diseases, Beijing 302 Hospital, Beijing 100069, China
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Yang Y, Zhao XP, Zou HC, Chu MJ, Zhong P, Li XS, Li XY, Yu YH, Zhu KX, Chen YJ, Xia F, Zhu BW, Ruan LQ, Bao YN, Zhuang X. Phylogenetic and temporal dynamics of human immunodeficiency virus type 1 CRF01_AE and CRF07_BC among recently infected antiretroviral therapy-naïve men who have sex with men in Jiangsu province, China, 2012 to 2015: A molecular epidemiology-based study. Medicine (Baltimore) 2018; 97:e9826. [PMID: 29419684 PMCID: PMC5944696 DOI: 10.1097/md.0000000000009826] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 12/31/2017] [Accepted: 01/17/2018] [Indexed: 11/25/2022] Open
Abstract
The prevalence and incidence of human immunodeficiency virus type 1 (HIV-1) among men who have sex with men (MSM) are on the rise throughout China. With a large population of MSM, Jiangsu Province is facing an escalating HIV-1 epidemic.The aim of this study was to explore the phylogenetic and temporal dynamics of HIV-1 CRF01_AE and CRF07_BC among antiretroviral therapy (ART)-naïve MSM recently infected with HIV-1 in Jiangsu Province.We recruited MSM in Jiangsu Province (Suzhou, Wuxi, Nantong, Taizhou and Yancheng) 2012 to 2015. We collected information on demographics and sexual behaviors and a blood sample for HIV genome RNA extraction, RT-PCR amplification, and DNA sequencing. Multiple alignments were made using Gene Cutter, with the selected reference sequences of various subtypes/recombinants from the Los Alamos HIV-1 database. Phylogenetic and Bayesian evolutionary analysis was performed by MEGA version 6.0, Fasttree v2.1.7. and BEAST v1.6.2. Categorical variables were analyzed using χ test (or Fisher exact test where necessary). χ test with trend was used to assess the evolution of HIV-1 subtype distribution over time. All data were analyzed using SPSS20.0 software package (IBM Company, New York, NY).HIV-1 phylogenetic analysis revealed a broad viral diversity including CRF01_AE (60.06%), CRF07_BC (22.29%), subtype B (5.88%), CRF67_01B (5.26%), CRF68_01B (2.79%), CRF55_01B (1.55%), CRF59_01B (0.93%), and CRF08_BC (0.62%). Two unique recombination forms (URFs) (0.62%) were also detected. Four epidemic clusters and 1 major cluster in CRF01_AE and CRF07_BC were identified. The introduction of CRF01_AE strain (2001) was earlier than CRF07_BC strain (2004) into MSM resided in Jiangsu based on the time of the most recent common ancestor.Our study demonstrated HIV-1 subtype diversity among ART-naïve MSM recently infected with HIV-1 in Jiangsu. We first depicted the spatiotemporal dynamics, traced the dates of origin for the HIV-1 CRF01_AE/07_BC strains and made inference for the effective population size among newly infected ART-naïve MSM in Jiangsu from 2012 to 2015. A real-time surveillance of HIV-1 viral diversity and phylodynamics of epidemic cluster would be of great value to the monitoring of the epidemic and control of transmission, improvement of antiretroviral therapy strategies, and design of vaccines.
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Affiliation(s)
- Yue Yang
- Department of Epidemiology and Health Statistics, School of
Public Health, Nantong University, Nantong
- Department of Infection Management Office, the First
Affiliated Hospital with Nanjing Medical University, Jiangsu Province Hospital, Nanjing,
Jiangsu Province
- Department of AIDS and STD, Shanghai Municipal Center for
Disease Control and Prevention; Shanghai Municipal Institute for Preventive Medicine,
Shanghai
| | - Xiu-Ping Zhao
- Department of AIDS and STD, Suzhou Center for Disease
Prevention and Control, Suzhou, Jiangsu Province
| | - Hua-Chun Zou
- School of Public Health, Sun Yat-sen University, Guangzhou,
Guangdong Province, China
- Kirby Institute, University of New South Wales, Sydney,
Australia
| | - Min-Jie Chu
- Department of Epidemiology and Health Statistics, School of
Public Health, Nantong University, Nantong
| | - Ping Zhong
- Department of AIDS and STD, Shanghai Municipal Center for
Disease Control and Prevention; Shanghai Municipal Institute for Preventive Medicine,
Shanghai
| | - Xiao-Shan Li
- Teaching and Research Office of Epidemiology and Health
Statistics, School of Public Health, Southeast University, Nanjing, Jiangsu
Province
| | - Xiao-Yan Li
- Ningbo Medical Center Lihuili Eastern Hospital; Taipei
Medical University Ningbo Medical Center, Ningbo, Zhejiang Province, China
| | - Yu-Hui Yu
- Department of Epidemiology and Health Statistics, School of
Public Health, Nantong University, Nantong
| | - Ke-Xin Zhu
- Department of Epidemiology and Health Statistics, School of
Public Health, Nantong University, Nantong
| | - Yu-Jia Chen
- Department of Epidemiology and Health Statistics, School of
Public Health, Nantong University, Nantong
| | - Fei Xia
- Department of Epidemiology and Health Statistics, School of
Public Health, Nantong University, Nantong
| | - Bo-Wen Zhu
- Department of Epidemiology and Health Statistics, School of
Public Health, Nantong University, Nantong
| | - Luan-Qi Ruan
- Department of Epidemiology and Health Statistics, School of
Public Health, Nantong University, Nantong
| | - Yi-Ning Bao
- Department of Epidemiology and Health Statistics, School of
Public Health, Nantong University, Nantong
| | - Xun Zhuang
- Department of Epidemiology and Health Statistics, School of
Public Health, Nantong University, Nantong
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Soulie C, Morand-Joubert L, Cottalorda J, Charpentier C, Bellecave P, Le Guen L, Yerly S, Montes B, Fafi-Kremer S, Dina J, Avettand-Fenoel V, Amiel C, Roussel C, Pallier C, Zafilaza K, Sayon S, Signori-Schmuck A, Mirand A, Trabaud MA, Berger S, Calvez V, Marcelin AG. Performance of genotypic algorithms for predicting tropism for HIV-1 CRF01_AE recombinant. J Clin Virol 2018; 99-100:57-60. [PMID: 29331843 DOI: 10.1016/j.jcv.2017.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/04/2017] [Accepted: 12/28/2017] [Indexed: 11/19/2022]
Abstract
OBJECTIVES There is no consensus about the performances of genotypic rules for predicting HIV-1 non-B subtype tropism. Three genotypic methods were compared for CRF01_AE HIV-1 tropism determination. METHODS The V3 env region of 207 HIV-1 CRF01_AE and 178 B subtypes from 17 centers in France and 1 center in Switzerland was sequenced. Tropism was determined by Geno2Pheno algorithm with false positive rate (FPR) 5% or 10%, the 11/25 rule or the combined criteria of the 11/25, net charge rule and NXT/S mutations. RESULTS Overall, 72.5%, 59.4%, 86.0%, 90.8% of the 207 HIV-1 CRF01_AE were R5-tropic viruses determined by Geno2pheno FPR5%, Geno2pheno FPR10%, the combined criteria and the 11/25 rule, respectively. A concordance of 82.6% was observed between Geno2pheno FPR5% and the combined criteria for CRF01_AE. The results were nearly similar for the comparison between Geno2pheno FPR5% and the 11/25 rule. More mismatches were observed when Geno2pheno was used with the FPR10%. Neither HIV viral load, nor current or nadir CD4 was associated with the discordance rate between the different algorithms. CONCLUSION Geno2pheno predicted more X4-tropic viruses for this set of CRF01_AE sequences than the combined criteria or the 11/25 rule alone. For a conservative approach, Geno2pheno FPR5% seems to be a good compromise to predict CRF01_AE tropism.
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Affiliation(s)
- C Soulie
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France.
| | - L Morand-Joubert
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Saint Antoine, Service de Virologie, Paris, France
| | | | - C Charpentier
- IAME, UMR 1137-Université Paris Diderot, Sorbonne Paris Cité, INSERM, AP-HP, Hôpital Bichat, Laboratoire de Virologie, Paris, France
| | - P Bellecave
- CHU de Bordeaux, Laboratoire de Virologie, Univ. Bordeaux, CNRS UMR 5234, Bordeaux, France
| | - L Le Guen
- Laboratoire de virologie, CHU, Nantes, France
| | - S Yerly
- Laboratory of Virology, Geneva University Hospitals, Switzerland
| | - B Montes
- Laboratoire de Virologie, CHU, Montpellier, France
| | | | - J Dina
- Laboratoire de virologie, CHU, Caen, France
| | - V Avettand-Fenoel
- AP-HP, Laboratoire de Virologie, Hôpital Necker, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, EA7327, France
| | - C Amiel
- AP-HP, Laboratoire de Virologie, Hôpital Tenon, Paris, France
| | | | | | - K Zafilaza
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | - S Sayon
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | | | | | - M A Trabaud
- Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - S Berger
- Laboratoire de Virologie, CHU de Nancy Brabois, EA 7300, Université de Lorraine, Faculté de Médecine, Vandoeuvre les Nancy, France
| | - V Calvez
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | - A G Marcelin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
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Jiao YM, Chen GL, Zhu WJ, Huang HH, Fu JL, Chen WW, Shi M, Zhang T, Wu H, Wang FS. Higher viral load and genetic diversity of HIV-1 in seminal compartments than in blood of seven Chinese men who have sex with men and have early HIV-1 infection. Microbiol Immunol 2017; 61:239-246. [PMID: 28500746 DOI: 10.1111/1348-0421.12488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/03/2017] [Accepted: 05/08/2017] [Indexed: 02/01/2023]
Abstract
To date, there have been no reports characterizing HIV-1 in the semen of Chinese men who have sex with men (MSM) with early infection. In this study, genetic diversity and viral load of HIV-1 in the seminal compartments and blood of Chinese MSM with early HIV-1 infection were examined. Viral load and genetic diversity of HIV-1 in paired samples of semen and blood were analyzed in seven MSM with early HIV-1 infection. HIV-1 RNA and DNA were quantitated by real-time PCR assays. Through sequencing the C2-V5 region of the HIV-1 env gene, the HIV-1 genotype and genetic diversity based on V3 loop amino acid sequences were determined by using Geno2pheno and PSSM programs co-receptor usage. It was found that there was more HIV-1 RNA in seminal plasma than in blood plasma and total, and more 2-LTR circular and integrated HIV-1 DNA in seminal cells than in peripheral blood mononuclear cells from all seven patients with early HIV-infection. There was also greater HIV-1 genetic diversity in seminal than in blood compartments. HIV-1 in plasma displayed higher genetic diversity than in cells from the blood and semen. In addition, V3 loop central motifs, which present some key neutralizing antibody epitopes, varied between blood and semen. Thus, virological characteristics in semen may be more representative when evaluating risk of transmission in persons with early HIV infection.
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Affiliation(s)
- Yan-Mei Jiao
- Treatment and Research Center for Infectious Diseases, 302 Military Hospital of China, Beijing 100039, China
| | - Guang-Lei Chen
- Beijing You'an Hospital, Capital Medical University, Beijing 10069, China
| | - Wei-Jun Zhu
- MOH Key Laboratory of Systems Biology of Pathogens and AIDS Research Center, Institute of Pathogen Biology, Beijing, 100730, China
| | - Hui-Huang Huang
- Treatment and Research Center for Infectious Diseases, 302 Military Hospital of China, Beijing 100039, China
| | - Jun-Liang Fu
- Treatment and Research Center for Infectious Diseases, 302 Military Hospital of China, Beijing 100039, China
| | - Wei-Wei Chen
- Treatment and Research Center for Infectious Diseases, 302 Military Hospital of China, Beijing 100039, China
| | - Ming Shi
- Treatment and Research Center for Infectious Diseases, 302 Military Hospital of China, Beijing 100039, China
| | - Tong Zhang
- Beijing You'an Hospital, Capital Medical University, Beijing 10069, China
| | - Hao Wu
- Beijing You'an Hospital, Capital Medical University, Beijing 10069, China
| | - Fu-Sheng Wang
- Treatment and Research Center for Infectious Diseases, 302 Military Hospital of China, Beijing 100039, China
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Li X, Gao R, Zhu K, Wei F, Fang K, Li W, Song Y, Ge Y, Ji Y, Zhong P, Wei P. Genetic transmission networks reveal the transmission patterns of HIV-1 CRF01_AE in China. Sex Transm Infect 2017; 94:111-116. [PMID: 28784618 DOI: 10.1136/sextrans-2016-053085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 05/10/2017] [Accepted: 06/10/2017] [Indexed: 01/31/2023] Open
Abstract
OBJECTIVES The epidemic of HIV-1 CRF01_AE has become a major public health issue in China. This study aimed to characterise the transmission patterns of genetic networks for CRF01_AE nationwide and elucidate possible opportunities for prevention. METHODS We isolated and conducted genetic transmission network analysis of all available CRF01_AE pol sequences (n=4704) from China in the Los Alamos HIV sequence database. RESULTS A total of 1391 (29.6%) sequences were identified as belonging to 400 separate networks. Of men who have sex with men (MSM) in the networks, 93.8% were linked to other MSM and only 2.4% were linked to heterosexual women. However, 11.8% heterosexual women in the networks were linked to MSM. Lineages composed mainly of MSM had higher transmission than those that were mostly heterosexuals. Of the 1391 individuals in networks, 513 (36.9%) were linked to cases diagnosed in different provinces. The proportion of individuals involved in inter-province links was interrelated with the number of migrant people (Spearman's r=0.738, p=0.001). CONCLUSIONS The outcome of this study could help improve our ability to understand HIV transmission among various regions and risk groups in China, and highlighted the importance of targeting MSM and migrants by prevention and intervention efforts.
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Affiliation(s)
- Xiaoshan Li
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China.,Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Rong Gao
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, China
| | - Kexin Zhu
- School of Public Health, Nantong University, Nantong, China
| | - Feiran Wei
- Department of Oncology, Medical School of Southeast University, Nanjing, China
| | - Kun Fang
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Wei Li
- Department of Infectious Disease Prevention and School Health, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Yue Song
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - You Ge
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yu Ji
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Ping Zhong
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Pingmin Wei
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
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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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Kuang WD, Zhou YH, Zhong P, Zhang C, Wang JH. Amino acids at positions 3, 168, and 169 are associated with the ability of Nef proteins from HIV-1 CRF01_AE to downmodulate CD4. J Med Virol 2017; 89:1788-1795. [PMID: 28500742 DOI: 10.1002/jmv.24851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/24/2017] [Indexed: 11/08/2022]
Abstract
Several HIV-1 subtypes are co-circulating among various high-risk groups in China, and an increasing prevalence of CRF01_AE was observed among MSM (men who have sex with men) within recent years. Patients infected with CRF01_AE may experience a more rapid disease progression than patients infected with non-CRF01_AE; however, the underlying mechanisms remains elusive. HIV-1 Nef is a multifunctional protein and plays critical roles in viral pathogenesis. Nef downregulates CD4 and human leukocyte antigen (HLA) to promote viral transmission and escape from the host immune response. In this study, we investigated the CD4 downmodulation activity of Nef proteins isolated from HIV-1 CRF01_AE and analyzed a potential relationship of Nef's capacity to downregulate CD4 with disease progression. We found that the majority of these Nefs from HIV-1 CRF01_AE efficiently downregulated CD4; Nefs with weaker CD4 downmodulation activity tended to be associated with higher CD4 levels and lower viral loads. Further elucidation revealed that amino acid residues at positions 3, 168, and 169 of CRF01_AE Nefs were associated with the capacity to downregulate CD4. Our data suggest that the capacity of Nef-mediated CD4 downregulation is not the only determinant for controlling disease progression, and other host and viral factors should be considered to explain the rapid disease progression of patients infected with HIV-1 CRF01_AE.
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Affiliation(s)
- Wen-Dong Kuang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yan-Heng Zhou
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Ping Zhong
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Chiyu Zhang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Hua Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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Li X, Zhu K, Xue Y, Wei F, Gao R, Duerr R, Fang K, Li W, Song Y, Du G, Yan W, Musa TH, Ge Y, Ji Y, Zhong P, Wei P. Multiple introductions and onward transmission of HIV-1 subtype B strains in Shanghai, China. J Infect 2017; 75:160-168. [PMID: 28551370 DOI: 10.1016/j.jinf.2017.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/29/2017] [Accepted: 05/11/2017] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To investigate the viral genetic evolution, spatial origins and patterns of transmission of HIV-1 subtype B in Shanghai, China. METHODS A total of 242 Shanghai subtype B and 1519 reference pol sequences were subjected to phylogenetic inference and genetic transmission network analyses. RESULTS Phylogenetic analysis revealed that subtype B strains circulating in Shanghai were genetically diverse and closely associated with viral sequence lineages in Beijing (76 of 242 [31.4%]), Central China (Henan/Hebei/Hunan/Hubei) (43 of 242 [17.8%]), Chinese Taiwan (20 of 242 [8.3%]), Japan (6 of 242 [2.5%]), and Korea (7 of 242 [2.9%]), suggesting multiple introductions into Shanghai from mainland China and Taiwan, Japan, and Korea. Interestingly, a monophyletic Shanghai lineage (SH-L) (36 of 242 [14.9%]) of HIV-1 subtype B most likely originated from an Argentine strain, transferred through Liaoning infected individuals. In-depth analyses of 195 Shanghai subtype B sequences revealed that a total of 37.9% (n = 74) sequences contributed to 35 transmission networks, whereof 33.8% (n = 25) of the sequences associated with infected individuals from other provinces. CONCLUSIONS Our new findings reflect the evolution complexity and transmission dynamics of HIV-1 subtype B in Shanghai, which would provide critical information for the design of effective prevention measures against HIV transmission.
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Affiliation(s)
- Xiaoshan Li
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Kexin Zhu
- School of Public Health, Nantong University, Nantong, China
| | - Yile Xue
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Feiran Wei
- Department of Oncology, Medical School of Southeast University, Nanjing, China
| | - Rong Gao
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, China
| | - Ralf Duerr
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Kun Fang
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Wei Li
- Department of Infectious Disease Prevention and School Health, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Yue Song
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Guoping Du
- Hospital Office, Southeast University Hospital, Nanjing, China
| | - Wenjuan Yan
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Taha Hussein Musa
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - You Ge
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yu Ji
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Ping Zhong
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China.
| | - Pingmin Wei
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China.
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Lu X, Kang X, Liu Y, Cui Z, Guo W, Zhao C, Li Y, Chen S, Li J, Zhang Y, Zhao H. HIV-1 molecular epidemiology among newly diagnosed HIV-1 individuals in Hebei, a low HIV prevalence province in China. PLoS One 2017; 12:e0171481. [PMID: 28178737 PMCID: PMC5298910 DOI: 10.1371/journal.pone.0171481] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/21/2017] [Indexed: 11/23/2022] Open
Abstract
New human immunodeficiency virus type 1 (HIV-1) diagnoses are increasing rapidly in Hebei. The aim of this study presents the most extensive HIV-1 molecular epidemiology investigation in Hebei province in China thus far. We have carried out the most extensive systematic cross-sectional study based on newly diagnosed HIV-1 positive individuals in 2013, and characterized the molecular epidemiology of HIV-1 based on full length gag-partial pol gene sequences in the whole of Hebei. Nine HIV-1 genotypes based on full length gag-partial pol gene sequence were identified among 610 newly diagnosed naïve individuals. The four main genotypes were circulating recombinant form (CRF)01_AE (53.4%), CRF07_BC (23.4%), subtype B (15.9%), and unique recombinant forms URFs (4.9%). Within 1 year, three new genotypes (subtype A1, CRF55_01B, CRF65_cpx), unknown before in Hebei, were first found among men who have sex with men (MSM). All nine genotypes were identified in the sexually contracted HIV-1 population. Among 30 URFs, six recombinant patterns were revealed, including CRF01_AE/BC (40.0%), CRF01_AE/B (23.3%), B/C (16.7%), CRF01_AE/C (13.3%), CRF01_AE/B/A2 (3.3%) and CRF01_AE/BC/A2 (3.3%), plus two potential CRFs. This study elucidated the complicated characteristics of HIV-1 molecular epidemiology in a low HIV-1 prevalence northern province of China and revealed the high level of HIV-1 genetic diversity. All nine HIV-1 genotypes circulating in Hebei have spread out of their initial risk groups into the general population through sexual contact, especially through MSM. This highlights the urgency of HIV prevention and control in China.
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Affiliation(s)
- Xinli Lu
- College of Life Science, Hebei University, Baoding, Hebei, China
- Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
| | - Xianjiang Kang
- College of Life Science, Hebei University, Baoding, Hebei, China
- * E-mail: (SC); (XK)
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ze Cui
- Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
| | - Wei Guo
- NO. 201 hospital of the People’s Liberation Army of China, Liaoyang, Liaoning, China
| | - Cuiying Zhao
- Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
| | - Yan Li
- Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
| | - Suliang Chen
- Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
- * E-mail: (SC); (XK)
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuqi Zhang
- Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
| | - Hongru Zhao
- Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
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Li X, Xue Y, Lin Y, Gai J, Zhang L, Cheng H, Ning Z, Zhou L, Zhu K, Vanham G, Kang L, Wang Y, Zhuang M, Pan Q, Zhong P. Evolutionary Dynamics and Complicated Genetic Transmission Network Patterns of HIV-1 CRF01_AE among MSM in Shanghai, China. Sci Rep 2016; 6:34729. [PMID: 27698457 PMCID: PMC5048130 DOI: 10.1038/srep34729] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 09/20/2016] [Indexed: 11/25/2022] Open
Abstract
To explore the evolutionary dynamics and molecular transmission patterns of HIV-1 CRF01_AE in depth among men who have sex with men (MSM) in Shanghai, we constructed phylogenetic tree and genetic transmission networks based on 1, 152 pol sequences from MSM, 282 from other risk groups and 795 references. Phylogenetic analyses identified two distinct major CRF01_AE lineages and a Shanghai-based sub-lineage. The estimated tMRCAs for lineage 1 and 2 were 1996.0 (1992.9–1999.2) and 1997.8 (1994.3–2001.4), respectively. Of the 1, 152 MSM, 681 (59.1%) were identified as belonging to 241 separate networks. Of these 681 individuals in networks, 74.2% were linked to cases diagnosed in different years, 4.3% were linked to heterosexual women, and 0.7% were linked to persons who inject drugs. A total of 71 networks including 180 individuals diagnosed in Shanghai with the same domicile were found. Recent infection (P = 0.022) and sampling year after 2011 (P < 0.001) were significantly associated with potential transmission links among the networks. Besides, a significant transmission of viruses with drug resistant mutations at V179D/E were found in the networks. Given these findings, we propose that genetic transmission analysis is a useful tool in HIV intervention strategies to curb the spread of virus and promoting public health.
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Affiliation(s)
- Xiaoshan Li
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China.,School of Public Health, Southeast University, Nanjing, China
| | - Yile Xue
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Yi Lin
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Jing Gai
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Lei Zhang
- Research Center for Public Health, School of Medicine, Tsinghua University, Beijing, China
| | - Hua Cheng
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Zhen Ning
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Leiming Zhou
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Kexin Zhu
- School of Public Health, Nantong University, Nantong, China
| | - Guido Vanham
- Biomedical Sciences Department, Institute of Tropical Medicine of Antwerp, Belgium
| | - Laiyi Kang
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Ying Wang
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Minghua Zhuang
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Qichao Pan
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Ping Zhong
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
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Li X, Li W, Zhong P, Fang K, Zhu K, Musa TH, Song Y, Du G, Gao R, Guo Y, Yan W, Xuan Y, Wei P. Nationwide Trends in Molecular Epidemiology of HIV-1 in China. AIDS Res Hum Retroviruses 2016; 32:851-9. [PMID: 27080587 DOI: 10.1089/aid.2016.0029] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To estimate the nationwide and regional distribution of HIV-1 genotypes in China in the past three decades, province-specific HIV-1 molecular epidemiology data were derived from 260 independent studies of HIV molecular prevalence through searching PubMed, VIP Chinese Journal Database (VIP), China National Knowledge Infrastructure, and Wanfang Data from January 1981 to December 2015. The nationwide and regional distribution of HIV-1 genotypes was estimated by weighting the genotype distribution from each province- and risk-specific subpopulation with the number of reported cases in the corresponding subgroups in the relevant periods. A sharp transition of HIV-1 subtypes and recombinant distribution was observed in various risk groups and regions over time. CRF01_AE has rapidly surged among almost all risk groups and in all areas, and it has become dominant among men who have sex with men and heterosexuals. A wide variety of new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were rapidly appearing in several risk groups and regions. After 2007, CRF01_AE was the most prevalent strain, accounting for 42.5% of all national infections, followed by CRF07_BC (28.9%), subtype B'/B (10.9%), CRF08_BC (10.0%), and subtype C (2.8%). URFs and other CRFs were responsible for 2.6% and fewer than 1% of infections nationwide, respectively. The nationwide and regional distributions of HIV-1 subtypes and recombinants were sharply shifting in China. CRF01_AE and new CRFs played an increasing role in the nationwide or regional HIV pandemic. The nationwide diversity of HIV-1 poses a formidable challenge to HIV vaccine development and disease prevention.
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Affiliation(s)
- Xiaoshan Li
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Wei Li
- Department of Infectious Disease Prevention and School Health, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Ping Zhong
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Kun Fang
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Kexin Zhu
- School of Public Health, Nantong University, Nantong, China
| | - Taha Hussein Musa
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yue Song
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Guoping Du
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Rong Gao
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yan Guo
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Wenjuan Yan
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yang Xuan
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Pingmin Wei
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
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Li X, Zhu K, Li W, Fang K, Musa TH, Song Y, Du G, Gao R, Guo Y, Yan W, Xuan Y, Zhong P, Wei P. Coreceptor usage of Chinese HIV-1 and impact of X4/DM transmission clusters among recently infected men who have sex with men. Medicine (Baltimore) 2016; 95:e5017. [PMID: 27684870 PMCID: PMC5265963 DOI: 10.1097/md.0000000000005017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To characterize the current frequency of HIV-1 coreceptor usage in China and assess the candidacy of CCR5 antagonists for treatment of HIV infections. In addition, we aimed to evaluate the potential of X4/DM virus transmission in recently infected men who have sex with men (MSM) individuals.Viral tropism testing was performed on samples from 399 MSM individuals and on 2408 available Chinese HIV-1 V3 sequences downloaded from the Los Alamos database using Geno2pheno and WebPSSM in combination. The transmission clusters were evaluated using pol sequences from 291 recently infected MSM with a maximum likelihood, maximum pairwise distance, and Bayesian inference.A higher prevalence of X4/DM viruses was observed in individuals infected with CRF01_AE strains than with subtype B (27.8% vs 12.2%, P < 0.001) and CRF07_BC/CRF08_BC/C (27.8% vs 1.0%, P < 0.001). Seven clusters containing only X4/DM viruses were detected in 40 transmission clusters. No significant difference in proportions between clustered X4/DM viruses and R5 viruses was found (P = 0.683).The high proportion of CXCR4 usage for CRF01_AE strains may result in the loss of susceptibility to maraviroc since CRF01_AE has become the most prevalent strains in China. The high prevalence of X4/DM viruses among recently CRF01_AE-infected individuals may be attributed to the stochasticity of HIV transmission, which implied that the early viral tropism screening and treatment would be the key for controlling the epidemic of CRF01_AE strains in China.
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Affiliation(s)
- Xiaoshan Li
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing
| | - Kexin Zhu
- School of Public Health, Nantong University, Nantong
| | - Wei Li
- Department of Infectious Disease Prevention and School Health, Nanjing Municipal Center for Disease Control and Prevention, Nanjing
| | - Kun Fang
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing
| | - Taha Hussein Musa
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing
| | - Yue Song
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing
| | - Guoping Du
- Hospital Office, Southeast University Hospital, Nanjing
| | - Rong Gao
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing
| | - Yan Guo
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing
| | - Wenjuan Yan
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing
| | - Yang Xuan
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing
| | - Ping Zhong
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
- Correspondence: Pingmin Wei, Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, 87 Dingjiaqiao Road (W), Nanjing 210009, China (e-mail: ); Ping Zhong, Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, 1380 Zhongshan Road (W), Shanghai 200336, China, (e-mail: )
| | - Pingmin Wei
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing
- Correspondence: Pingmin Wei, Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, 87 Dingjiaqiao Road (W), Nanjing 210009, China (e-mail: ); Ping Zhong, Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, 1380 Zhongshan Road (W), Shanghai 200336, China, (e-mail: )
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Non-R5-tropic HIV-1 in subtype A1 and D infections were associated with lower pretherapy CD4+ cell count but not with PI/(N)NRTI therapy outcomes in Mbarara, Uganda. AIDS 2016; 30:1781-8. [PMID: 27124899 DOI: 10.1097/qad.0000000000001128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Previous studies suggest that infection with non-R5-tropic subtype B HIV-1, compared with R5, is associated with a more rapid decline in CD4 cell count, but does not affect PI/(N)NRTI therapy outcome. Here, we explored clinical correlates associated with viral tropism in subtype A1 and D infections. METHODS HIV-1 subtype A1 (n = 196) and D (n = 143) pretherapy plasma samples and up to 7.5 years of posttherapy virologic and CD4 data were collected from a cross-sectional cohort in Mbarara, Uganda. Tropism and subtype were inferred using env V3 (geno2pheno) and gp41 (RIP) Sanger sequences. For each subtype, R5 infection was compared with non-R5 in terms of: pretherapy viral load and CD4 cell count (Mann-Whitney tests), and therapy outcomes, including time to virologic suppression, postsuppression virologic rebound, CD4 decline and CD4 recovery (log-rank tests). RESULTS A 94% of all patients in this study achieved virologic suppression within median 3 months posttherapy. In both subtypes, non-R5 infection was associated with lower pretherapy CD4 cell count (non-R5 vs. R5; A: median 57 vs. 147 cells/μl P = 0.005; D: 80 vs. 128 cells/μl P = 0.006). Multivariable linear regression confirmed that tropism, not subtype nor the interaction between subtype and tropism, was a significant predictor of pretherapy CD4 cell count (P < 0.0001). None of pretherapy viral load, time to virologic suppression, virologic rebound, CD4 decline nor CD4 recovery was significantly different (all P > 0.09). CONCLUSION Regardless of HIV-1 subtype or tropism, the majority of patients in this Ugandan cohort responded to therapy, even though non-R5 infection was associated with lower pretherapy CD4 cell count.
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Lima K, de Souza Leal É, Cavalcanti AMS, Salustiano DM, de Medeiros LB, da Silva SP, Lacerda HR. Epidemiological, Clinical and Antiretroviral Susceptibility Characterization of Human Immunodeficiency Virus Subtypes B and Non-B in Pernambuco, Northeast Brazil. PLoS One 2016; 11:e0155854. [PMID: 27218259 PMCID: PMC4878750 DOI: 10.1371/journal.pone.0155854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/05/2016] [Indexed: 01/15/2023] Open
Abstract
Background HIV-1 diversity causes important differences in the virus’ biological properties and their interactions with hosts, such as cell tropism, responses to antiretroviral therapy, drug-resistance, and disease progression. Objectives We evaluated the interrelationship of phylogenetic inference with epidemiological and laboratory data for HIV-1 isolates circulating in Pernambuco, Northeast Region—Brazil. Study design A total of 168 HIV-1 pol sequences were analysed, 64 were obtained from 2002–2003, and 104, from 2007–2009. Socio-demographic, clinical, and behavioural data were obtained from medical records. Laboratory testing enabled the determination of recent HIV-1 infections and co-infections with HBV, HCV, HTLV, or syphilis. Surveillance drug-resistance mutation analysis and antiretroviral susceptibility profiling were performed using HIV Drug-Resistance Database. Results HIV-1 non-B was associated with female, lower education, lower viral loads, and higher T cell counts mean. Frequencies of co-infection HIV-HBV, HIV-HCV, and HIV-syphilis were 27.8% (95% CI: 19.8–37.7), 1.04% (95% CI: 0.05–5.00) and 14.7% (95% CI: 8.6–23.0), respectively. Drug-resistant mutations rate was 2.98% (95% CI: 1.10–6.47). HIV-HBV subtype B co-infection was associated with men who have sex with men (MSM), higher education, higher viral loads and males. HIV-syphilis subtype non-B co-infection was associated with MSM status, lower T cell counts and males. Conclusions Data showed the importance of molecular characterisations of the HIV-1 epidemic and its relation with epidemiological and clinical characteristics of the population, as well as its association with other infectious diseases, so they can effort to improve preventive measures for health services and more information about the progress and effects of the epidemic in Northeastern–Brazil.
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Affiliation(s)
- Kledoaldo Lima
- Postgraduate at Department of Tropical Medicine, Federal University of Pernambuco, Recife, Pernambuco, Brazil
- * E-mail:
| | | | | | | | | | | | - Heloísa Ramos Lacerda
- Postgraduate at Department of Tropical Medicine, Federal University of Pernambuco, Recife, Pernambuco, Brazil
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Yang Z, Huang Z, Dong Z, Zhang S, Han J, Jin M. Prevalence of high-risky behaviors in transmission of HIV among high school and college student MSM in China: a meta-analysis. BMC Public Health 2015; 15:1272. [PMID: 26690367 PMCID: PMC4687281 DOI: 10.1186/s12889-015-2614-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/15/2015] [Indexed: 11/24/2022] Open
Abstract
Background The aim of this study was to investigate the prevalence of high-risky behaviors, such as unprotected anal intercourse (UAI) in the last 6 months, condom using in their last homosexual anal intercourse, No. of male partners in the last 6 months among high school and college male students who have sex with men (MSM) in China. Methods The relevant trials were retrieved up to June 2015 from several public databases, and a meta-analysis was conducted according to the published studies. The estimated rate and its 95 % confidence intervals (CI) of the relevant indexes among high school and college student MSM were collected and calculated using a fixed-effects model (the Mantel-Haenszel method) or a random-effects model (the DerSimonian and Laird method) when appropriate. Results A total of 15 studies (18 research data), including 3297 student MSM, were performed in this meta-analysis. The overall results showed that the rate of student MSM who reported having had UAI in the last 6 months was 65.2 % (95 % CI = 60.2 % to 70.1 %), the prevalence of student MSM having more than one male partner in the last 6 months was 58.2 % (95 % CI = 51.1 % to 65.4 %), the rate of student MSM who reported using a condom in their last homosexual anal intercourse experience was 57.5 % (95 % CI = 49.8 % to 65.1 %), the prevalence of student MSM who were infected with HIV was 3.8 % (95 % CI = 2.5 % to 5.1 %), and the rate of student MSM who were infected with syphilis was 4.6 % (95 % CI = 3.8 % to 5.4 %). Conclusions There are high UAI prevalence and low condom using rate in the last homosexual anal intercourse experience among high school and college student MSM in China, and corresponding control measures for this group and more effective health education of student MSM are required to prevent HIV or sexually transmitted diseases from spreading to the general population.
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Affiliation(s)
- Zhongrong Yang
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, Zhejiang Province, China.
| | - Zhaohui Huang
- Anhui Provincial Family Planning Institute of Science and Technology, Hefei, 230000, Anhui Province, China.
| | - Zhengquan Dong
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, Zhejiang Province, China.
| | - Sichao Zhang
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, Zhejiang Province, China.
| | - Jiankang Han
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, Zhejiang Province, China.
| | - Meihua Jin
- Huzhou Center for Disease Control and Prevention, Huzhou, 313000, Zhejiang Province, China.
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Dauwe K, Mortier V, Schauvliege M, Van Den Heuvel A, Fransen K, Servais JY, Bercoff DP, Seguin-Devaux C, Verhofstede C. Characteristics and spread to the native population of HIV-1 non-B subtypes in two European countries with high migration rate. BMC Infect Dis 2015; 15:524. [PMID: 26572861 PMCID: PMC4647655 DOI: 10.1186/s12879-015-1217-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/14/2015] [Indexed: 12/13/2022] Open
Abstract
Background Non-B subtypes account for at least 50 % of HIV-1 infections diagnosed in Belgium and Luxembourg. They are considered to be acquired through heterosexual contacts and infect primarily individuals of foreign origin. Information on the extent to which non-B subtypes spread to the local population is incomplete. Methods Pol and env gene sequences were collected from 410 non-subtype B infections. Profound subtyping was performed using 5 subtyping tools and sequences of both pol and env. Demographic information, disease markers (viral load, CD4 count) and viral characteristics (co-receptor tropism) were compared between subtypes. Maximum likelihood phylogenetic trees were constructed and examined for clustering. Results The majority of non-B infections were diagnosed in patients originating from Africa (55.8 %), individuals born in Western Europe represented 30.5 %. Heterosexual transmission was the most frequently reported transmission route (79.9 %), MSM transmission accounted for 12.2 % and was significantly more frequently reported for Western Europeans (25.7 % versus 4.3 % for individuals originating from other regions; p < 0.001). Subtypes A and C and the circulating recombinant forms CRF01_AE and CRF02_AG were the most represented and were included in the comparative analysis. Native Western Europeans were underrepresented for subtype A (14.5 %) and overrepresented for CRF01_AE (38.6 %). The frequency of MSM transmission was the highest for CRF01_AE (18.2 %) and the lowest for subtype A (0 %). No differences in age, gender, viral load or CD4 count were observed. Prevalence of CXCR4-use differed between subtypes but largely depended on the tropism prediction algorithm applied. Indications for novel intersubtype recombinants were found in 20 patients (6.3 %). Phylogenetic analysis revealed only few and small clusters of local transmission but could document one cluster of CRF02_AG transmission among Belgian MSM. Conclusions The extent to which non-B subtypes spread in the native Belgian-Luxembourg population is higher than expected, with 30.5 % of the non-B infections diagnosed in native Western Europeans. These infections resulted from hetero- as well as homosexual transmission. Introduction of non-B variants in the local high at risk population of MSM may lead to new sub-epidemics and/or increased genetic variability and is an evolution that needs to be closely monitored.
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Affiliation(s)
- Kenny Dauwe
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Annelies Van Den Heuvel
- Aids Reference laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Nationalestraat 155, B-2000, Antwerp, Belgium.
| | - Katrien Fransen
- Aids Reference laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Nationalestraat 155, B-2000, Antwerp, Belgium.
| | - Jean-Yves Servais
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Danielle Perez Bercoff
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Carole Seguin-Devaux
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
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Li X, Xue Y, Cheng H, Lin Y, Zhou L, Ning Z, Wang X, Yu X, Zhang W, Shen F, Zheng X, Gai J, Li X, Kang L, Nyambi P, Wang Y, Zhuang M, Pan Q, Zhuang X, Zhong P. HIV-1 Genetic Diversity and Its Impact on Baseline CD4+T Cells and Viral Loads among Recently Infected Men Who Have Sex with Men in Shanghai, China. PLoS One 2015; 10:e0129559. [PMID: 26121491 PMCID: PMC4486722 DOI: 10.1371/journal.pone.0129559] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/10/2015] [Indexed: 11/20/2022] Open
Abstract
The HIV-1 epidemic among men who have sex with men (MSM) has been spreading throughout China. Shanghai, a central gathering place for MSM, is facing a continuously increasing incidence of HIV-1 infection. In order to better understand the dynamics of HIV-1 diversity and its influence on patient's immune status at baseline on diagnosis, 1265 newly HIV-1-infected MSM collected from January 2009 to December 2013 in Shanghai were retrospectively analyzed for genetic subtyping, CD4+T cell counts, and viral loads. HIV-1 phylogenetic analysis revealed a broad viral diversity including CRF01_AE (62.13%), CRF07_BC (24.51%), subtype B (8.06%), CRF55_01B (3.24%), CER67_01B (0.95%), CRF68_01B (0.4%), CRF08_BC (0.08%) and CRF59_01B (0.08%). Twenty-four unique recombination forms (URFs) (1.98%) were identified as well. Bayesian inference analysis indicated that the introduction of CRF01_AE strain (1997) was earlier than CRF07_BC strain (2001) into MSM population in Shanghai based on the time of the most recent common ancestor (tMRCA). Three epidemic clusters and five sub-clusters were found in CRF01_AE. Significantly lower CD4+T cell count was found in individuals infected with CRF01_AE than in those infected with CRF07_BC infection (P<0.01), whereas viral load was significantly higher those infected with CRF01_AE than with CRF07_BC (P<0.01). In addition, the patients with >45 years of age were found to have lower CD4+T cell counts and higher viral loads than the patients with <25 years of age (P<0.05). This study reveals the presence of HIV-1 subtype diversity in Shanghai and its remarkable influence on clinical outcome. A real-time surveillance of HIV-1 viral diversity and phylodynamics of epidemic cluster, patient's baseline CD4+T cell count and viral load would be of great value to monitoring of disease progression, intervention for transmission, improvement of antiretroviral therapy strategy and design of vaccines.
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Affiliation(s)
- Xiaoyan Li
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
- Public Health College, Nantong University, Nantong, Jiangsu Province, China
| | - Yile Xue
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Hua Cheng
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Yi Lin
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Leiming Zhou
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Zhen Ning
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Xuqin Wang
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Xiaolei Yu
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Wei Zhang
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Fangwei Shen
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Xiaohong Zheng
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Jing Gai
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Xiaoshan Li
- Public Health College, Nantong University, Nantong, Jiangsu Province, China
| | - Laiyi Kang
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Phillipe Nyambi
- Department of Pathology, New York University School of Medicine, New York, United States of America
| | - Ying Wang
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Minghua Zhuang
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Qichao Pan
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Xun Zhuang
- Public Health College, Nantong University, Nantong, Jiangsu Province, China
| | - Ping Zhong
- Department AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
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HIV-1 subtype B/B' and baseline drug resistance mutation are associated with virologic failure: a multicenter cohort study in China. J Acquir Immune Defic Syndr 2015; 68:289-97. [PMID: 25501612 DOI: 10.1097/qai.0000000000000473] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Distribution of HIV-1 subtypes, transmitted drug resistance (TDR)/drug resistance mutation (DRM), and their impact on response to combination antiretroviral therapy remain poorly understood in China. METHODS We analyzed data from our multicenter cohort study with 444 antiretroviral-naive participants recruited between 2008 and 2010. HIV-1 subtype and tropism were determined by V3 sequencing, and TDR/DRM was determined by Pol sequencing. Virologic and immunologic responses were monitored over 96 weeks of follow-up. The initial combination antiretroviral therapy regimen for all patients was nevirapine + lamivudine + zidovudine or stavudine. Analysis 1 included patients who finished 96 weeks of follow-up (n = 379), and analysis 2 included all 444 patients. RESULTS Subtype B/B' was associated with higher prevalence of TDR/DRM to nucleoside reverse transcriptase inhibitors and nonnucleoside reverse transcriptase inhibitors. Median time to HIV-1 suppression was 18 weeks in all 3 subtype groups. In Cox proportional models for viral suppression, neither viral tropism nor HIV-1 subtypes had any impact on viral suppression; however, subtypes CRF01_AE and C/CRF07_BC/CRF08_BC were associated with lower risk of virologic failure compared with subtype B/B', with adjusted hazard ratio of 0.11 (P = 0.032) and 0.06 (P = 0.036), respectively in analysis 1, 0.42 (P = 0.047) and 0.22 (P = 0.008), respectively in analysis 2. This association was attenuated by adding DRM profiles to multivariate regression models. Neither subtype nor HIV-1 tropism affected immunologic response. CONCLUSIONS HIV-1 subtype tended to be associated with virologic but not immunologic response; this effect could be ascribed to baseline DRM.
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Kouri V, Khouri R, Alemán Y, Abrahantes Y, Vercauteren J, Pineda-Peña AC, Theys K, Megens S, Moutschen M, Pfeifer N, Van Weyenbergh J, Pérez AB, Pérez J, Pérez L, Van Laethem K, Vandamme AM. CRF19_cpx is an Evolutionary fit HIV-1 Variant Strongly Associated With Rapid Progression to AIDS in Cuba. EBioMedicine 2015; 2:244-54. [PMID: 26137563 PMCID: PMC4484819 DOI: 10.1016/j.ebiom.2015.01.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 01/22/2015] [Accepted: 01/26/2015] [Indexed: 12/12/2022] Open
Abstract
Background Clinicians reported an increasing trend of rapid progression (RP) (AIDS within 3 years of infection) in Cuba. Methods Recently infected patients were prospectively sampled, 52 RP at AIDS diagnosis (AIDS-RP) and 21 without AIDS in the same time frame (non-AIDS). 22 patients were sampled at AIDS diagnosis (chronic-AIDS) retrospectively assessed as > 3 years infected. Clinical, demographic, virological, epidemiological and immunological data were collected. Pol and env sequences were used for subtyping, transmission cluster analysis, and prediction of resistance, co-receptor use and evolutionary fitness. Host, immunological and viral predictors of RP were explored through data mining. Findings Subtyping revealed 26 subtype B strains, 6 C, 6 CRF18_cpx, 9 CRF19_cpx, 29 BG-recombinants and other subtypes/URFs. All patients infected with CRF19 belonged to the AIDS-RP group. Data mining identified CRF19, oral candidiasis and RANTES levels as the strongest predictors of AIDS-RP. CRF19 was more frequently predicted to use the CXCR4 co-receptor, had higher fitness scores in the protease region, and patients had higher viral load at diagnosis. Interpretation CRF19 is a recombinant of subtype D (C-part of Gag, PR, RT and nef), subtype A (N-part of Gag, Integrase, Env) and subtype G (Vif, Vpr, Vpu and C-part of Env). Since subtypes D and A have been associated with respectively faster and slower disease progression, our findings might indicate a fit PR driving high viral load, which in combination with co-infections may boost RANTES levels and thus CXCR4 use, potentially explaining the fast progression. We propose that CRF19 is evolutionary very fit and causing rapid progression to AIDS in many newly infected patients in Cuba. We propose that CRF19 is evolutionary very fit, causing rapid progression to AIDS in many newly infected patients in Cuba. CRF19 is a recombinant of subtype D, subtype A and subtype G, with a subtype D protease estimated to be particularly fit. A fit protease with high viral load and co-infections, may boost RANTES levels and thus CXCR4 use, hence fast progression.
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Affiliation(s)
- Vivian Kouri
- Virology Department, Institute of Tropical Medicine Pedro Kourí, Autopista Novia del Mediodía Km 6, Marianao 13, Havana City, Cuba
| | - Ricardo Khouri
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium ; LIMI-LIP, Centro de Pesquisa Gonçalo Moniz, FIOCRUZ, Salvador-Bahia, Brazil
| | - Yoan Alemán
- Virology Department, Institute of Tropical Medicine Pedro Kourí, Autopista Novia del Mediodía Km 6, Marianao 13, Havana City, Cuba
| | - Yeissel Abrahantes
- Virology Department, Institute of Tropical Medicine Pedro Kourí, Autopista Novia del Mediodía Km 6, Marianao 13, Havana City, Cuba
| | - Jurgen Vercauteren
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium
| | - Andrea-Clemencia Pineda-Peña
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium ; Clinical and Molecular Infectious Diseases Group, Faculty of Sciences and Mathematics, Universidad del Rosario, Bogotá, Colombia
| | - Kristof Theys
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium
| | - Sarah Megens
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium
| | - Michel Moutschen
- AIDS Reference Center, Centre Hospitalier Universitaire de Liège, Liège, Belgium
| | - Nico Pfeifer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany
| | - Johan Van Weyenbergh
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium
| | - Ana B Pérez
- Virology Department, Institute of Tropical Medicine Pedro Kourí, Autopista Novia del Mediodía Km 6, Marianao 13, Havana City, Cuba
| | - Jorge Pérez
- Virology Department, Institute of Tropical Medicine Pedro Kourí, Autopista Novia del Mediodía Km 6, Marianao 13, Havana City, Cuba
| | - Lissette Pérez
- Virology Department, Institute of Tropical Medicine Pedro Kourí, Autopista Novia del Mediodía Km 6, Marianao 13, Havana City, Cuba
| | - Kristel Van Laethem
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, B-3000 Leuven, Belgium ; Centro de Malária e outras Doenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
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Zhao K, Kang W, Liu Q, Li Y, Liu Q, Jiang W, Zhuang Y, Guo Z, Yu Z, Li X, Wang C, Yao N, Sun Y. Genotypes and transmitted drug resistance among treatment-naive HIV-1-infected patients in a northwestern province, China: trends from 2003 to 2013. PLoS One 2014; 9:e109821. [PMID: 25333965 PMCID: PMC4198111 DOI: 10.1371/journal.pone.0109821] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 09/07/2014] [Indexed: 01/30/2023] Open
Abstract
Background Transmitted drug resistance (TDR) reduces the efficacy of initial antiretroviral treatment and has become a public health concern. Little information is available regarding the genetic diversity of HIV-1 and the prevalence of TDR among treatment-naïve patients in a northwestern province of China since the implementation of national free antiretroviral therapy (ART). Methods Blood samples from 372 HIV-1 treatment-naive patients were collected between 2003 and 2013 in Shaanxi province. Viral RNA was extracted for nested PCR, and phylogenetic reconstruction and recombination analyses were performed to characterize patterns of the HIV-1 subtypes. Genotypic drug resistance testing was performed using an in-house assay to determine trends in the prevalence of HIV-1 transmitted drug resistance. Results Multiple genotypes were identified among the patients in Shaanxi, including B (25.0%), C (0.3%), G (0.3%), and CRF01_AE (39.2%), CRF07_BC (32.7%), CRF08_BC (0.8%), CRF55_01B (1.1%), and URFs (0.6%). The subtypes were associated with the transmission routes (χ2 = 77.113, p<0.01). In this study, a low baseline CD4+ T cell count and a high viral load were found among CRF01_AE-infected patients compared with patients who were infected with non-CRF01_AE (p<0.01) through sexual transmission; however, the CRF01_AE subtype was not associated with a low baseline CD4+ T cell count or a high viral load in Chinese patients infected through blood transmission (p = 0.249). The overall TDR rate in this population was 4.4% between 2003 and 2013. A univariate logistic regression model revealed that a low CD4 T cell count (≤100 cells/µL) was associated with the development of drug-resistant strains. Conclusion Our work revealed diverse HIV-1 subtype distributions in Shaanxi province. We identified a low and stable TDR time trend among ART-naive patients. These findings enhance our understanding of HIV-1 genetic diversity and provide some guidelines for the improvement and implementation of a comprehensive public health strategy of HIV-1 TDR prevention.
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Affiliation(s)
- Ke Zhao
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Wenzhen Kang
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Qingquan Liu
- Department of Endocrinology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Yuan Li
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Qing Liu
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Wei Jiang
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Yan Zhuang
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Zisheng Guo
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Zhuoran Yu
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Xinhong Li
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Chunfu Wang
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Na Yao
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Yongtao Sun
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- * E-mail:
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