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Yabar CA, Vilcarino GF, Espetia S, Lujan F, Vásquez-Domínguez A, Yaya M, Acuña M, Santos D, Mamani E, Rodriguez-Bayona R, Salvatierra J, Obregon G, Romero S, Cardenas F, Lopez P, Rivera-Amill V. Social, Epidemiological, and Virological Characteristics from Peruvian Subjects Living with HIV-1/AIDS with Different Sexual Risk Behavior. AIDS Res Hum Retroviruses 2022; 38:288-299. [PMID: 34569275 DOI: 10.1089/aid.2021.0067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
HIV-1 genetic diversity and resistance profile might change according to the risky sexual behavior of the host. To show this, we recruited 134 individuals between the years 2015 and 2017 identified as transgender women sex workers (TWSW, n = 73) and Heterosexual Military Officers (HET-MO, n = 61). After obtaining informed consent, we collected a blood sample to perform the HIV genotyping, CD4 cell count, and viral load. We used bioinformatics approaches for detecting resistance mutations and recombination events. Epidemiological data showed that both groups reported sexually transmitted diseases and they were widespread among TWSW, especially syphilis and herpes virus (35.6%). Illegal drugs consumption was higher among TWSW (71.2%), whereas condom use was inconsistent for both HET-MO (57.4%) and TWSW (74.0%). TWSW showed the shortest time exposition to antiretroviral therapy (ART) (3.5 years) and the lowest access to ART (34.2%) that conducted treatment failure (>4 logs). HIV-1 sequences from TWSW and HET-MO were analyzed to determine the genetic diversity and antiretroviral drug resistance. Phylogeny analysis revealed 125 (93%) cases of subtype B, 01 subtype A (0.76%), 07 (5.30%) BF recombinants, and 01 (0.76%) AG recombinant. Also, TWSW showed a higher recombination index (9.5%, 7/73) than HET-MO (1.5%, 1/68). HET-MO only showed acquired resistance (26.23%, 16/61), whereas TWSW showed both acquired as transmitted resistance (9.59% for each). In conclusion, TWSW and HET-MO showed significant differences considering the epidemiological characteristics, genetic diversity, recombination events, and HIV resistance profile.
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Affiliation(s)
- Carlos Augusto Yabar
- Laboratorio de VTS/VIH-SIDA, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Chorrillos, Lima - Perú
- Facultad de Medicina Humana, Universidad de San Martín de Porres, La Molina, Lima - Perú
| | - Giovanny Francesco Vilcarino
- Laboratorio de VTS/VIH-SIDA, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Chorrillos, Lima - Perú
| | - Susan Espetia
- Laboratorio de VTS/VIH-SIDA, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Chorrillos, Lima - Perú
| | - Fiorela Lujan
- Laboratorio de VTS/VIH-SIDA, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Chorrillos, Lima - Perú
| | - Andres Vásquez-Domínguez
- Laboratorio de VTS/VIH-SIDA, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Chorrillos, Lima - Perú
| | - Mariela Yaya
- Laboratorio de VTS/VIH-SIDA, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Chorrillos, Lima - Perú
| | - Maribel Acuña
- Laboratorio de VTS/VIH-SIDA, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Chorrillos, Lima - Perú
| | - Daniel Santos
- Laboratorio de VTS/VIH-SIDA, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Chorrillos, Lima - Perú
| | - Edgardo Mamani
- Laboratorio de VTS/VIH-SIDA, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Chorrillos, Lima - Perú
| | | | - Javier Salvatierra
- Servicio de ITS VIH, Centro de Salud, “Alberto Barton,” Callao, Lima - Perú
| | - George Obregon
- Laboratorio de VTS/VIH-SIDA, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Chorrillos, Lima - Perú
| | - Soledad Romero
- Laboratorio de VTS/VIH-SIDA, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Chorrillos, Lima - Perú
| | - Fany Cardenas
- Laboratorio de VTS/VIH-SIDA, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Chorrillos, Lima - Perú
| | - Pablo Lopez
- Center for Research Resources, Ponce Health Sciences University-Ponce Research Institute, Ponce, Puerto Rico
| | - Vanessa Rivera-Amill
- Center for Research Resources, Ponce Health Sciences University-Ponce Research Institute, Ponce, Puerto Rico
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Recordon-Pinson P, Alves BM, Tumiotto C, Bellecave P, Bonnet F, Neau D, Soares EA, Soares MA, Fleury H. A New HIV-1 Circulating Recombinant Form (CRF98_cpx) Between CRF06_cpx and Subtype B Identified in Southwestern France. AIDS Res Hum Retroviruses 2018; 34:1005-1009. [PMID: 29947242 DOI: 10.1089/aid.2018.0122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
During a recent study on the sequencing data of our database between 2012 and 2016 in Southwestern France, we observed that eight patients harbored what seemed to be the same virus. Indeed, routine genotyping at the time of HIV diagnosis showed that protease and reverse transcriptase were related to CRF06_cpx and subtype B, respectively. The integrase sequences (available for three patients) were clustering with CRF06_cpx and envelope (Env) gp120 sequences (available for two patients) with subtype B. Since such a recombinant has not been recorded in the Los Alamos database, we decided to characterize the full-length genome of this virus. The data suggest the identification of a new circulating recombinant form (CRF) between CRF06_cpx and subtype B, the structure of which is very complex with multiple breakpoints. We will refer this CRF as CRF98_cpx.
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Affiliation(s)
| | | | - Camille Tumiotto
- CNRS MFP-UMR 5234, Bordeaux, France
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
| | - Pantxika Bellecave
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
| | - Fabrice Bonnet
- Department of Internal Medicine, University Hospital of Bordeaux, Bordeaux, France
| | - Didier Neau
- Department of Infectious and Tropical Diseases, University Hospital of Bordeaux, Bordeaux, France
| | | | | | - Hervé Fleury
- CNRS MFP-UMR 5234, Bordeaux, France
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
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Zhang M, Jia D, Li H, Gui T, Jia L, Wang X, Li T, Liu Y, Bao Z, Liu S, Zhuang D, Li J, Li L. Phylodynamic Analysis Revealed That Epidemic of CRF07_BC Strain in Men Who Have Sex with Men Drove Its Second Spreading Wave in China. AIDS Res Hum Retroviruses 2017; 33:1065-1069. [PMID: 28569547 DOI: 10.1089/aid.2017.0091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
CRF07_BC was originally formed in Yunnan province of China in 1980s and spread quickly in injecting drug users (IDUs). In recent years, it has been introduced into men who have sex with men (MSM) and become the most dominant strain in China. In this study, we performed a comprehensively phylodynamic analysis of CRF07_BC sequences from China. All CRF07_BC sequences identified in China were retrieved from database. More sequences obtained in our laboratory were added to make the dataset more representative. A maximum-likelihood (ML) tree was constructed with PhyML3.0. Maximum clade credibility (MCC) tree and effective population size were predicted by using Markov Chains Monte Carlo sampling method with Beast software. A total of 610 CRF07_BC sequences coving 1,473 bp of the gag gene (from 817 to 2,289 according to HXB2 calculator) were included into the dataset. Three epidemic clusters were identified; two clusters comprised sequences from IDUs, while one cluster mainly contained sequences from MSMs. The time of the most recent common ancestor of clusters that composed of sequences from MSMs was estimated to be in 2000. Two rapid spreading waves of effective population size of CRF07_BC infections were identified in the skyline plot. The second wave coincided with the expanding of MSM cluster. The results indicated that the control of CRF07_BC infections in MSMs would help to decrease its epidemic in China.
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Affiliation(s)
- Min Zhang
- Anhui Medical University, Hefei, China
| | | | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tao Gui
- The 59th Hospital of PLA, Kaiyuan, Yunnan
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- Anhui Medical University, Hefei, China
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Vidyavijayan K, Hassan S, Precilla LK, Ashokkumar M, Chandrasekeran P, Swaminathan S, Hanna LE. Biased Nucleotide Composition and Differential Codon Usage Pattern in HIV-1 and HIV-2. AIDS Res Hum Retroviruses 2017; 33:298-307. [PMID: 27599904 DOI: 10.1089/aid.2015.0320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 and HIV-2 are closely related retroviruses with differences in pathogenicity and geographic distribution. HIV-2 infection is associated with slower disease progression and transmission, longer latency period, low or undetectable plasmatic viral loads, and reduced likelihood of progression to AIDS, compared to HIV-1. In this investigation, we analyzed HIV-2 genes and genomes and compared them with that of HIV-1 belonging to various subtypes. Comparative analysis of the effective number of codons (ENC) for each of the nine genes of the two viruses revealed that the tat gene of HIV-2 had a higher ENC value compared to HIV-1 tat, reflecting lower levels of expression of HIV-2 tat. Lower levels of tat protein particularly during the early stages of infection could result in a lower viral load, lower viral set point, and delayed progression of disease in HIV-2-infected individuals compared to HIV-1-infected subjects. Furthermore, the GC3 composition of the regulatory genes of HIV-2 was ≥50%, suggesting a firm effort by these viruses to adapt themselves to evolutionary survival. We hypothesize that differential codon usage could be one of the possible factors that could contribute to the diminished pathogenicity of HIV-2 in the host as compared to HIV-1.
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Affiliation(s)
- K.K. Vidyavijayan
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (ICMR), Chennai, India
| | - Sameer Hassan
- Division of Biomedical Informatics, Department of Clinic Research, National Institute for Research in Tuberculosis (ICMR), Chennai, India
| | - Lucia K. Precilla
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (ICMR), Chennai, India
| | - Manickam Ashokkumar
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (ICMR), Chennai, India
| | | | - Soumya Swaminathan
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (ICMR), Chennai, India
| | - Luke Elizabeth Hanna
- Department of HIV/AIDS, National Institute for Research in Tuberculosis (ICMR), Chennai, India
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Zhang J, Guo Z, Yang J, Pan X, Jiang J, Ding X, Zhang W, Xia Y, Xu Y, Huang J. Genetic diversity of HIV-1 and transmitted drug resistance among newly diagnosed individuals with HIV infection in Hangzhou, China. J Med Virol 2015; 87:1668-76. [PMID: 25899877 DOI: 10.1002/jmv.24223] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2015] [Indexed: 11/06/2022]
Abstract
HIV transmitted drug resistance (TDR) can compromise antiretroviral therapy (ART) in resource-limited countries like China where ART has been scaled up and thus leads to an important public health concern. The aim of the study was to elucidate the HIV-1 genetic characteristics and TDR in Hangzhou, China. Two-hundred eleven ART-naive, newly diagnosed individuals were enrolled during January and August 2013. Specimens were classified as recent or chronic infections using the BED capture enzyme immunoassay (BED-CEIA). The pol fragment covering the entire protease and the first 300 codons of the reverse transcriptase gene was amplified by RT-PCR and nested PCR. Genotypic drug resistance (DR) and phylogenetic analysis were performed on the 200 obtained sequences. Multiple genotypes were identified, including CRF01_AE (62.0%), CRF07_BC (31.0%), subtype B (2.0%), CRF08_BC (1.5%), CRF55_01B (1.0%), CRF18_cpx (0.5%), and unique recombinant forms (URFs, 2.0%). All the four URFs were found in men who have sex with men, consisting of a recombination of CRF01_AE with subtype B or CRF07_BC. The prevalence of primary DR in newly diagnosed individuals in Hangzhou was low (4.0%). The proportion of DR mutation to protease inhibitors (PIs), nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs) was 1.5%, 1.5%, and 1.0%, respectively. BED-CEIA revealed that 21.8% (45/211) of the specimens were associated with recent infections. The prevalence of TDR in recent infections was moderate (6.5%). High HIV diversity and relatively high prevalence of TDR in new infections has been found in Hangzhou, indicating an increasing challenge for future HIV prevention and treatment.
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Affiliation(s)
- Jiafeng Zhang
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Zhihong Guo
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jiezhe Yang
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Xiaohong Pan
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jun Jiang
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Xiaobei Ding
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Wenjun Zhang
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yan Xia
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yun Xu
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jingjing Huang
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
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Ong LY, Razak SNH, Lee YM, Sri La Sri Ponnampalavanar S, Syed Omar SF, Azwa RI, Tee KK, Kamarulzaman A. Molecular diversity of HIV-1 and surveillance of transmitted drug resistance variants among treatment Naïve patients, 5 years after active introduction of HAART in Kuala Lumpur, Malaysia. J Med Virol 2013; 86:38-44. [PMID: 24127302 DOI: 10.1002/jmv.23772] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2013] [Indexed: 12/14/2022]
Abstract
Expansion of antiretroviral treatment programs have led to the growing concern for the development of antiretroviral drug resistance. The aims were to assess the prevalence of drug resistant HIV-1 variants and to identify circulating subtypes among HAART-naïve patients. Plasma specimens from N = 100 HIV+ HAART-naïve adult were collected between March 2008 and August 2010 and viral RNA were extracted for nested PCR and sequenced. PR-RT sequences were protein aligned and checked for transmitted drug resistance mutations. Phylogenetic reconstruction and recombination analysis were performed to determine the genotypes. Based on the WHO consensus guidelines, none of the recruited patients had any transmitted drug resistance mutations. When analyzed against the Stanford guidelines, 35% of patients had at least one reported mutation that may reduce drug susceptibility to PI (24%), NRTI (5%), and NNRTI (14%). The commonly detected mutation that may affect current first line therapy was V179D (3%), which may lead to reduced susceptibility to NNRTI. The predominant circulating HIV-1 genotypes were CRF01_AE (51%) and CRF33_01B (17%). The prevalence of unique recombinant forms (URF) was 7%; five distinct recombinant structures involving CRF01_AE and subtype B' were observed, among them a cluster of three isolates that could form a novel circulating recombinant form (CRF) candidate. Transmitted drug resistance prevalence among HAART-naïve patients was low in this cohort of patients in Kuala Lumpur despite introduction of HAART 5 years ago. Owing to the high genetic diversity, continued molecular surveillance can identify the persistent emergence of HIV-1 URF and novel CRF with significant epidemiological impact.
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Affiliation(s)
- Lai Yee Ong
- Faculty of Medicine, Centre of Excellence for Research in AIDS (CERiA), University of Malaya, Kuala Lumpur, Malaysia
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