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Pang X, He Q, Tang K, Huang J, Fang N, Xie H, Ma J, Zhu Q, Lan G, Liang S. Drug resistance and influencing factors in HIV-1-infected individuals under antiretroviral therapy in Guangxi, China. J Antimicrob Chemother 2024; 79:1142-1152. [PMID: 38551451 DOI: 10.1093/jac/dkae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 03/06/2024] [Indexed: 05/03/2024] Open
Abstract
OBJECTIVES To assess the profiles and determinants of drug resistance in HIV-1-infected individuals undergoing ART in Guangxi. METHODS Samples and data were collected from HIV-1-infected individuals experiencing virological failure post-ART from 14 cities in Guangxi. Sequencing of the HIV-1 pol gene was conducted, followed by analysis for drug resistance mutations using the Stanford University HIV Drug Resistance Database. Logistic regression was employed to identify potential risk factors associated with both HIV drug resistance and mortality. RESULTS A total of 8963 individuals with pol sequences were included in this study. The overall prevalence of HIV-1 drug resistance (HIVDR) was 42.43% (3808/8963), showing a decrease from 59.62% to 41.40% from 2016 to 2023. Factors such as being aged ≥50 years, male, Han nationality, lower education levels, occupations including workers, peasants and children, AIDS, pre-treatment CD4 T cell counts <200 cells/mm3, infection with CRF01_AE and CRF55_01B subtypes, and ART regimen lamivudine/zidovudine/nevirapine were associated with higher susceptibility to HIVDR. The common mutations were M184V (17.38%) and K103N (22.14%). Additionally, the prevalence of M184V, S68G, M41L and G190A were different between the Han and Zhuang populations. Factors including age, gender, ethnicity, education level, occupation, infectious route, clinical stage, viral load, subtype, ART regimen and HIVDR showed significant associations with mortality. CONCLUSIONS The factors contributing to drug resistance in the HIV-1 ART individuals in Guangxi appear to be notably intricate. Continuous reinforcement of drug resistance surveillance is imperative, accompanied by the optimization of ART regimens to mitigate virological failures effectively.
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Affiliation(s)
- Xianwu Pang
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Qin He
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Kailing Tang
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Jinghua Huang
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Ningye Fang
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Haoming Xie
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Jie Ma
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Qiuying Zhu
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Guanghua Lan
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Shujia Liang
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi, China
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Shi P, Chen Z, Meng J, Su M, Yang X, Fan W, Shi H, Gao Y, Lu X. Molecular transmission networks and pre-treatment drug resistance among individuals with acute HIV-1 infection in Baoding, China. PLoS One 2021; 16:e0260670. [PMID: 34855860 PMCID: PMC8638862 DOI: 10.1371/journal.pone.0260670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 11/13/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) genetic diversity and pre-treatment drug resistance (PDR) are major barriers to successful antiretroviral therapy (ART). In China, sexual intercourse is the most frequent route of HIV-1 transmission. However, few studies have analyzed PDR and transmission networks in detail among individuals in China with acute HIV-1 infection and their sexual contacts. METHODS A cross-sectional study was conducted in Baoding City, Hebei Province, China from 2019-2020. CD4 T cell counts and viral loads were assessed and a HIV-1 genotypic PDR assay was developed in-house. Transmission networks were visualized using Cytoscape with a threshold genetic distance of 0.015 among HIV-1 subtypes. RESULTS From 139 newly diagnosed and drug-naïve individuals with HIV-1, 132 pol gene sequences were obtained and revealed eight HIV-1 subtypes. Circulating recombinant form (CRF)01_AE was the most frequent subtype (53.0%, 70/132) followed by CRF07_BC (26.5%, 35/132), B (13.6%, 18/132), unique recombinant forms (2.3%, 3/132), CRF55_01B (1.5%, 2/132), CRF103_01B (1.5%, 2/132), CRF65_cpx (0.8%, 1/132), and C (0.8%, 1/132). A total of 47 pol gene sequences were used to generate 10 molecular transmission networks. The overall prevalence of PDR was 7.6% and that of PDR to non-nucleotide reverse transcriptase inhibitors was 6.1%. Of three transmission networks for PDR, two were closely associated with Beijing and Tianjin, while another was restricted to sequences determined in this study. CONCLUSIONS These results demonstrate that during acute HIV-1 infection, PDR is transmitted in dynamic networks. This suggests that early detection, diagnosis, surveillance, and treatment are critical to effectively control HIV-1 spread.
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Affiliation(s)
- Penghui Shi
- Clinical Laboratory, The People’s Hospital of Baoding, Baoding, Hebei, China
| | - Zhixia Chen
- Infection Division, The People’s Hospital of Baoding, Baoding, Hebei, China
| | - Juan Meng
- Infection Division, The People’s Hospital of Baoding, Baoding, Hebei, China
| | - Miaomiao Su
- Infection Division, The People’s Hospital of Baoding, Baoding, Hebei, China
| | - Xuegang Yang
- Infection Division, The People’s Hospital of Baoding, Baoding, Hebei, China
| | - Weiguang Fan
- Clinical Laboratory, The People’s Hospital of Baoding, Baoding, Hebei, China
| | - Haoxi Shi
- Clinical Laboratory, The People’s Hospital of Baoding, Baoding, Hebei, China
| | - Ying Gao
- Clinical Laboratory, The People’s Hospital of Baoding, Baoding, Hebei, China
| | - Xinli Lu
- Department of AIDS Research, Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
- * E-mail:
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Li K, Liu M, Chen H, Li J, Liang Y, Feng Y, Xing H, Shao Y. Using molecular transmission networks to understand the epidemic characteristics of HIV-1 CRF08_BC across China. Emerg Microbes Infect 2021; 10:497-506. [PMID: 33657968 PMCID: PMC7993390 DOI: 10.1080/22221751.2021.189905 10.1080/22221751.2021.1899056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
HIV-1 CRF08_BC has become a major epidemic in heterosexuals and intravenous drug users (IDUs) in southern China. In order to evaluate the trends of its epidemic and facilitate targeted HIV prevention, we constructed the genetic transmission networks based on its pol sequences, derived from the National HIV Molecular Epidemiology Survey. Through retrospective network analysis, to study the epidemiological and demographic correlations with the transmission network. Of the 1,829 study subjects, 639 (34.9%) were clustered in 151 transmission networks. Factors associated with increased clustering include IDUs, heterosexual men, young adults and people with lower education (P < 0.05 for all). The IDUs, MSM, young adult and person with low education had more potential transmission links as well (P < 0.05 for all). The most crossover links were found between heterosexual women and IDUs, with 30.9% heterosexual women linked to IDUs. The crossover links heterosexual women were mainly those with middle age and single (P < 0.001). This study indicated that the HIV-1 CRF08_BC epidemic was still on going in China with more than one third of the infected people clustered in the transmission networks. Meanwhile, the study could help identify the active CRF08_BC spreader in the local community and greatly facilitate précising AIDS prevention with targeted intervention.
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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, China CDC, Beijing, People’s Republic of China
| | - Meiliang Liu
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, People’s Republic of China
| | - Huanhuan Chen
- Guangxi Center for Disease Prevention and Control, Nanning, People’s Republic of China
| | - Jianjun Li
- Guangxi Center for Disease Prevention and Control, Nanning, People’s Republic of 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, China CDC, Beijing, People’s Republic of China
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, 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, China CDC, 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, China CDC, Beijing, 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, China CDC, Beijing, People’s Republic of China
- Guangxi Center for Disease Prevention and Control, Nanning, People’s Republic of China
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Scriven YA, Mulinge MM, Saleri N, Luvai EA, Nyachieo A, Maina EN, Mwau M. Prevalence and factors associated with HIV-1 drug resistance mutations in treatment-experienced patients in Nairobi, Kenya: A cross-sectional study. Medicine (Baltimore) 2021; 100:e27460. [PMID: 34622871 PMCID: PMC8500620 DOI: 10.1097/md.0000000000027460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/20/2021] [Indexed: 01/05/2023] Open
Abstract
ABSTRACT An estimated 1.5 million Kenyans are HIV-seropositive, with 1.1 million on antiretroviral therapy (ART), with the majority of them unaware of their drug resistance status. In this study, we assessed the prevalence of drug resistance to nucleoside reverse transcriptase inhibitors (NRTIs), nucleoside reverse transcriptase inhibitors (NNRTIs), and protease inhibitors, and the variables associated with drug resistance in patients failing treatment in Nairobi, Kenya.This cross-sectional study utilized 128 HIV-positive plasma samples obtained from patients enrolled for routine viral monitoring in Nairobi clinics between 2015 and 2017. The primary outcome was human immunodeficiency virus type 1 (HIV-1) drug resistance mutation counts determined by Sanger sequencing of the polymerase (pol) gene followed by interpretation using Stanford's HIV Drug Resistance Database. Poisson regression was used to determine the effects of sex, viral load, age, HIV-subtype, treatment duration, and ART-regimen on the primary outcome.HIV-1 drug resistance mutations were found in 82.3% of the subjects, with 15.3% of subjects having triple-class ART resistance and 45.2% having dual-class resistance. NRTI primary mutations M184 V/I and K65R/E/N were found in 28.8% and 8.9% of subjects respectively, while NNRTI primary mutations K103N/S, G190A, and Y181C were found in 21.0%, 14.6%, and 10.9% of subjects. We found statistically significant evidence (P = .013) that the association between treatment duration and drug resistance mutations differed by sex. An increase of one natural-log transformed viral load unit was associated with 11% increase in drug resistance mutation counts (incidence rate ratio [IRR] 1.11; 95% CI 1.06-1.16; P < .001) after adjusting for age, HIV-1 subtype, and the sex-treatment duration interaction. Subjects who had been on treatment for 31 to 60 months had 63% higher resistance mutation counts (IRR 1.63; 95% CI 1.12-2.43; P = .013) compared to the reference group (<30 months). Similarly, patients on ART for 61 to 90 months were associated with 133% higher mutation counts than the reference group (IRR 2.33; 95% CI 1.59-3.49; P < .001). HIV-1 subtype, age, or ART-regimen were not associated with resistance mutation counts.Drug resistance mutations were found in alarmingly high numbers, and they were associated with viral load and treatment time. This finding emphasizes the importance of targeted resistance monitoring as a tool for addressing the problem.
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Affiliation(s)
- Yvonne A Scriven
- Centre for Infectious and Parasitic Diseases Control Research, Kenya Medical Research Institute, Busia, Kenya
| | - Martin M Mulinge
- Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya
- Kenya AIDS Vaccine Initiative - Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Norah Saleri
- Centre for Infectious and Parasitic Diseases Control Research, Kenya Medical Research Institute, Busia, Kenya
| | - Elizabeth A Luvai
- Centre for Infectious and Parasitic Diseases Control Research, Kenya Medical Research Institute, Busia, Kenya
| | - Atunga Nyachieo
- Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Esther N Maina
- Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Matilu Mwau
- Centre for Infectious and Parasitic Diseases Control Research, Kenya Medical Research Institute, Busia, Kenya
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Mendes Da Silva RK, Monteiro de Pina Araujo II, Venegas Maciera K, Gonçalves Morgado M, Lindenmeyer Guimarães M. Genetic Characterization of a New HIV-1 Sub-Subtype A in Cabo Verde, Denominated A8. Viruses 2021; 13:v13061093. [PMID: 34201179 PMCID: PMC8230070 DOI: 10.3390/v13061093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 12/16/2022] Open
Abstract
Previous molecular characterization of Human immunodeficiency virus (HIV-1) samples from Cabo Verde pointed out a vast HIV-1 pol diversity, with several subtypes and recombinant forms, being 5.2% classified as AU-pol. Thus, the aim of the present study was to improve the characterization of these AU sequences. The genomic DNA of seven HIV-1 AU pol-infected individuals were submitted to four overlapping nested-PCR fragments aiming to compose the full-length HIV-1 genome. The final classification was based on phylogenetic trees that were generated using the maximum likelihood and bootscan analysis. The genetic distances were calculated using Mega 7.0 software. Complete genome amplification was possible for two samples, and partial genomes were obtained for the other five. These two samples grouped together with a high support value, in a separate branch from the other sub-subtypes A and CRF26_A5U. No recombination was verified at bootscan, leading to the classification of a new sub-subtype A. The intragroup genetic distance from the new sub-subtype A at a complete genome was 5.2%, and the intergroup genetic varied from 8.1% to 19.0% in the analyzed fragments. Our study describes a new HIV-1 sub-subtype A and highlights the importance of continued molecular surveillance studies, mainly in countries with high HIV molecular diversity.
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Affiliation(s)
- Rayana Katylin Mendes Da Silva
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil; (R.K.M.D.S.); (K.V.M.); (M.G.M.)
| | | | - Karine Venegas Maciera
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil; (R.K.M.D.S.); (K.V.M.); (M.G.M.)
| | - Mariza Gonçalves Morgado
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil; (R.K.M.D.S.); (K.V.M.); (M.G.M.)
| | - Monick Lindenmeyer Guimarães
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil; (R.K.M.D.S.); (K.V.M.); (M.G.M.)
- Correspondence: ; Tel.: +55-21-3865-8154
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Park H, Brenner B, Ibanescu RI, Cox J, Weiss K, Klein MB, Hardy I, Narasiah L, Roger M, Kronfli N. Phylogenetic Clustering among Asylum Seekers with New HIV-1 Diagnoses in Montreal, QC, Canada. Viruses 2021; 13:v13040601. [PMID: 33915869 PMCID: PMC8066823 DOI: 10.3390/v13040601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/22/2021] [Accepted: 03/30/2021] [Indexed: 01/08/2023] Open
Abstract
Migrants are at an increased risk of HIV acquisition. We aimed to use phylogenetics to characterize transmission clusters among newly-diagnosed asylum seekers and to understand the role of networks in local HIV transmission. Retrospective chart reviews of asylum seekers linked to HIV care between 1 June 2017 and 31 December 2018 at the McGill University Health Centre and the Jewish General Hospital in Montreal were performed. HIV-1 partial pol sequences were analyzed among study participants and individuals in the provincial genotyping database. Trees were reconstructed using MEGA10 neighbor-joining analysis. Clustering of linked viral sequences was based on a strong bootstrap support (>97%) and a short genetic distance (<0.01). Overall, 10,645 provincial sequences and 105 asylum seekers were included. A total of 13/105 participant sequences (12%; n = 7 males) formed part of eight clusters. Four clusters (two to three people) included only study participants (n = 9) and four clusters (two to three people) included four study participants clustered with six individuals from the provincial genotyping database. Six (75%) clusters were HIV subtype B. We identified the presence of HIV-1 phylogenetic clusters among asylum seekers and at a population-level. Our findings highlight the complementary role of cohort data and population-level genotypic surveillance to better characterize transmission clusters in Quebec.
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Affiliation(s)
- Hyejin Park
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (H.P.); (J.C.); (M.B.K.)
| | - Bluma Brenner
- McGill AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (B.B.); (R.-I.I.)
| | - Ruxandra-Ilinca Ibanescu
- McGill AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (B.B.); (R.-I.I.)
| | - Joseph Cox
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (H.P.); (J.C.); (M.B.K.)
- Department of Medicine, Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC H3A 0G4, Canada
| | - Karl Weiss
- Department of Medicine, Division of Infectious Diseases and Medical Microbiology, Jewish General Hospital, Montreal, QC H3T 1E2, Canada;
| | - Marina B. Klein
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (H.P.); (J.C.); (M.B.K.)
- Department of Medicine, Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Isabelle Hardy
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC H3T 1J4, Canada; (I.H.); (M.R.)
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, QC H2X 0A9, Canada
| | - Lavanya Narasiah
- Direction Régionale de Santé Publique, CIUSSS Centre-Sud-de-l’Île-de-Montréal, Montréal, QC H2L 1M3, Canada;
- Clinique des Réfugiés, CISSS Montérégie Centre, Brossard, QC J4Z 1A5, Canada
| | - Michel Roger
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC H3T 1J4, Canada; (I.H.); (M.R.)
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, QC H2X 0A9, Canada
| | - Nadine Kronfli
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (H.P.); (J.C.); (M.B.K.)
- Department of Medicine, Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Correspondence: ; Tel.: +1-514-934-1934; Fax: +1-514-843-2092
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Kapaata A, Balinda SN, Xu R, Salazar MG, Herard K, Brooks K, Laban K, Hare J, Dilernia D, Kamali A, Ruzagira E, Mukasa F, Gilmour J, Salazar-Gonzalez JF, Yue L, Cotten M, Hunter E, Kaleebu P. HIV-1 Gag-Pol Sequences from Ugandan Early Infections Reveal Sequence Variants Associated with Elevated Replication Capacity. Viruses 2021; 13:v13020171. [PMID: 33498793 PMCID: PMC7912664 DOI: 10.3390/v13020171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 01/05/2023] Open
Abstract
The ability to efficiently establish a new infection is a critical property for human immunodeficiency virus type 1 (HIV-1). Although the envelope protein of the virus plays an essential role in receptor binding and internalization of the infecting virus, the structural proteins, the polymerase and the assembly of new virions may also play a role in establishing and spreading viral infection in a new host. We examined Ugandan viruses from newly infected patients and focused on the contribution of the Gag-Pol genes to replication capacity. A panel of Gag-Pol sequences generated using single genome amplification from incident HIV-1 infections were cloned into a common HIV-1 NL4.3 pol/env backbone and the influence of Gag-Pol changes on replication capacity was monitored. Using a novel protein domain approach, we then documented diversity in the functional protein domains across the Gag-Pol region and identified differences in the Gag-p6 domain that were frequently associated with higher in vitro replication.
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Affiliation(s)
- Anne Kapaata
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Sheila N. Balinda
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Rui Xu
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Maria G. Salazar
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Kimberly Herard
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Kelsie Brooks
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Kato Laban
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Jonathan Hare
- Imperial College London, London SW7 2AZ, UK; (J.H.); (J.G.)
- International AIDS Vaccine Initiative (IAVI), New York, NY 10004, USA
| | - Dario Dilernia
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | | | - Eugene Ruzagira
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Freddie Mukasa
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Jill Gilmour
- Imperial College London, London SW7 2AZ, UK; (J.H.); (J.G.)
- International AIDS Vaccine Initiative (IAVI), New York, NY 10004, USA
| | - Jesus F. Salazar-Gonzalez
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Ling Yue
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Matthew Cotten
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK
- Correspondence: ; Tel.: +25-6701-509-685
| | - Eric Hunter
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Pontiano Kaleebu
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
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Dennis AM, Hué S, Billock R, Levintow S, Sebastian J, Miller WC, Eron JJ. Human Immunodeficiency Virus Type 1 Phylodynamics to Detect and Characterize Active Transmission Clusters in North Carolina. J Infect Dis 2021; 221:1321-1330. [PMID: 31028702 DOI: 10.1093/infdis/jiz176] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/11/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) phylodynamics can be used to monitor epidemic trends and help target prevention through identification and characterization of transmission clusters. METHODS We analyzed HIV-1 pol sequences sampled in North Carolina from 1997 to 2014. Putative clusters were identified using maximum-likelihood trees and dated using Bayesian Markov Chain Monte Carlo inference. Active clusters were defined as clusters including internal nodes from 2009 to 2014. Effective reproductive numbers (Re) were estimated using birth-death models for large clusters that expanded ≥2-fold from 2009 to 2014. RESULTS Of 14 921 persons, 7508 (50%) sequences were identified in 2264 clusters. Only 288 (13%) clusters were active from 2009 to 2014; 37 were large (10-36 members). Compared to smaller clusters, large clusters were increasingly populated by men and younger persons; however, nearly 60% included ≥1 women. Clusters with ≥3 members demonstrated assortative mixing by sex, age, and sample region. Of 15 large clusters with ≥2-fold expansion, nearly all had Re approximately 1 by 2014. CONCLUSIONS Phylodynamics revealed transmission cluster expansion in this densely sampled region and allowed estimates of Re to monitor active clusters, showing the propensity for steady, onward propagation. Associations with clustering and cluster characteristics vary by cluster size. Harnessing sequence-derived epidemiologic parameters within routine surveillance could allow refined monitoring of local subepidemics.
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Affiliation(s)
- Ann M Dennis
- Division of Infectious Diseases, University of North Carolina at Chapel Hill
| | - Stéphane Hué
- London School of Hygiene and Tropical Medicine, United Kingdom
| | - Rachael Billock
- Department of Epidemiology, University of North Carolina at Chapel Hill
| | - Sara Levintow
- Department of Epidemiology, University of North Carolina at Chapel Hill
| | - Joseph Sebastian
- Campbell University School of Osteopathic Medicine, South Lillington, North Carolina
| | | | - Joseph J Eron
- Division of Infectious Diseases, University of North Carolina at Chapel Hill
- Department of Epidemiology, University of North Carolina at Chapel Hill
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Sacks-Davis R, Chibo D, Peach E, Aleksic E, Crowe SM, El Hayek C, Marukutira T, Higgins N, Stoove M, Hellard M. Phylogenetic clustering networks among heterosexual migrants with new HIV diagnoses post-migration in Australia. PLoS One 2020; 15:e0237469. [PMID: 32870911 PMCID: PMC7462279 DOI: 10.1371/journal.pone.0237469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/27/2020] [Indexed: 01/28/2023] Open
Abstract
Background It is estimated that approximately half of new HIV diagnoses among heterosexual migrants in Victoria, Australia, were acquired post-migration. We investigated the characteristics of phylogenetic clusters in notified cases of HIV among heterosexual migrants. Methods Partial HIV pol sequences obtained from routine clinical genotype tests were linked to Victorian HIV notifications with the following exposures listed on the notification form: heterosexual sexual contact, injecting drug use, bisexual sexual contact, male-to male sexual contact or heterosexual sexual contact in combination with injecting drug use, unknown exposure. Those with heterosexual sexual contact as the only exposure were the focus of this study, with the other exposures included to better understand transmission networks. Additional reference sequences were extracted from the Los Alamos database. Maximum likelihood methods were used to infer the phylogeny and the robustness of the resulting tree was assessed using bootstrap analysis. Phylogenetic clusters were defined on the basis of bootstrap and genetic distance. Results HIV pol sequences were available for 332 of 445 HIV notifications attributed to only heterosexual sexual contact in Victoria from 2005–2014. Forty-three phylogenetic clusters containing at least one heterosexual migrant were detected, 30 (70%) of which were pairs. The characteristics of these phylogenetic clusters varied considerably by cluster size. Pairs were more likely to be composed of people living with HIV from a single country of birth (p = 0.032). Larger clusters (n≥3) were more likely to contain people born in Australian/New Zealand (p = 0.002), migrants from more than one country of birth (p = 0.013) and viral subtype-B, the most common subtype in Australia (p = 0.006). Pairs were significantly more likely to contain females (p = 0.037) and less likely to include HIV diagnoses with male-to-male sexual contact reported as a possible exposure (p<0.001) compared to larger clusters (n≥3). Conclusion Migrants appear to be at elevated risk of HIV acquisition, in part due to intimate relationships between migrants from the same country of origin, and in part due to risks associated with the broader Australian HIV epidemic. However, there was no evidence of large transmission clusters driven by heterosexual transmission between migrants. A multipronged approach to prevention of HIV among migrants is warranted.
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Affiliation(s)
- Rachel Sacks-Davis
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- * E-mail:
| | - Doris Chibo
- Victorian Infectious Disease Reference Laboratory, Peter Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Eman Aleksic
- Burnet Institute, Melbourne, Victoria, Australia
| | - Suzanne M. Crowe
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Carol El Hayek
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Tafireyi Marukutira
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Nasra Higgins
- Department of Health and Human Services, Melbourne, Victoria, Australia
| | - Mark Stoove
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Margaret Hellard
- Burnet Institute, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Hepatitis Services, Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
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Bonny TS, Kirby C, Martens C, Rose R, Desai N, Seisa M, Petropoulos C, Florman S, Friedman-Moraco RJ, Turgeon NA, Brown D, Segev DL, Durand CM, Tobian AAR, Redd AD. Outcomes of donor-derived superinfection screening in HIV-positive to HIV-positive kidney and liver transplantation: a multicentre, prospective, observational study. Lancet HIV 2020; 7:e611-e619. [PMID: 32730756 PMCID: PMC8073978 DOI: 10.1016/s2352-3018(20)30200-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/23/2020] [Accepted: 05/04/2020] [Indexed: 01/23/2023]
Abstract
BACKGROUND One of the primary risks of HIV-positive to HIV-positive organ transplantation is loss of virological control because of donor-derived HIV superinfection, which occurs when an HIV-positive individual becomes infected with a new distinct HIV strain. In this study, as part of the larger HIV Organ Policy Equity pilot study, HIV-positive to HIV-positive kidney and liver transplant recipients in the USA were examined for evidence of sustained donor-derived HIV superinfection. METHODS In this multicentre, prospective, observational study, HIV-positive to HIV-positive kidney and liver transplant recipients were followed in three hospitals in the USA. Candidates with well controlled HIV infection on ART, no active opportunistic infections, and minimum CD4 T-cell counts (>100 cells per μL for liver and >200 cells per μL for kidney per federal guidelines) were eligible to receive a kidney or liver from deceased HIV-positive donors without active infections or neoplasm. Peripheral blood mononuclear cells were collected from donor-recipient pairs at the time of transplantation, and from recipients at several timepoints up to 3 years after transplantation. Donor samples were assessed for HIV RNA viral load, CD4 cell count, and antiretroviral drug-resistant mutations. Donor and recipient HIV proviral DNA, and viral RNA from the viraemic timepoint were sequenced using a site-directed next-generation sequencing assay for the reverse transcriptase and gp41 genes. Neighbour-joining phylogenetic trees and direct sequence comparison were used to detect the presence of HIV superinfection. This study is registered with ClinicalTrials.gov, NCT02602262. FINDINGS 14 HIV-positive to HIV-positive kidney and eight liver transplant recipients were followed from March, 2016, to July, 2019. 17 recipients had adequate viral sequences allowing for HIV superinfection assessment. Eight donors were suppressed (viral load <400 copies per mL), and none had multiclass drug-resistant mutations detected. None of the recipients examined had evidence of HIV superinfection. One recipient had a viraemic episode (viral load of 2 080 000 copies per mL) 3 years after transplantation as a result of non-adherence to ART. Only recipient viral sequences were detected during the viraemic episode, suggesting that the donor virus, if present, was not reactivated despite temporary withdrawal of ART. INTERPRETATION These findings suggest that loss of HIV suppression due to donor-derived HIV superinfection might not be a significant clinical concern in carefully monitored ART suppressed HIV-positive organ recipients. FUNDING US National Institute of Allergy and Infectious Diseases and National Cancer Institute.
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Affiliation(s)
- Tania S Bonny
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Charles Kirby
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Craig Martens
- Genomic Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Rebecca Rose
- Bioinfoexperts, Shreveport, Los Angeles, CA, USA
| | - Niraj Desai
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Seisa
- Laboratory Corporation of America (LabCorp), South San Francisco, CA, USA
| | | | - Sander Florman
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Diane Brown
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dorry L Segev
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | - Andrew D Redd
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; International HIV Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA.
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Abstract
OBJECTIVE To identify correlates of incident HIV infection in rapidly growing HIV molecular clusters. DESIGN Phylogenetic analysis of HIV public health surveillance data. METHODS High-priority HIV genetic transmission clusters with evidence of rapid growth in 2012 (i.e. clusters with a pairwise genetic distance ≤0.005 substitutions/site and at least three cases diagnosed in 2012) were identified using HIV-TRACE. Then, we investigated cluster growth, defined as HIV cases diagnosed in the following 5 years that were genetically linked to these clusters. For clusters that grew during the follow-up period, Bayesian molecular clock phylogenetic inference was performed to identify clusters with evidence of incident HIV infection (as opposed to diagnosis of previously infected cases) during this follow-up period. RESULTS Of the 116 rapidly growing clusters identified, 73 (63%) had phylogenetic evidence for an incident HIV case during the 5-year follow-up period. Correlates of an incident HIV case arising in clusters included a greater number of diagnosed but virally unsuppressed cases in 2012, a greater number of inferred undiagnosed cases in the cluster in 2012, and a younger time of most recent common ancestor for the cluster. CONCLUSION These findings suggest that incident infections in rapidly growing clusters originate equally from diagnosed but unsuppressed cases and undiagnosed infections. These results highlight the importance of promoting retention in care and viral suppression as well as partner notification and other case-finding activities when investigating and intervening on high-priority molecular transmission clusters.
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Affiliation(s)
- Joel O. Wertheim
- Department of Medicine, University of California, San Diego, CA, USA
| | - Nivedha Panneer
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anne Marie France
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Alexandra M. Oster
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Patil A, Elwitigala JP, Rajapaksa L, Gangakhedkar R, Chaturbhuj D, Pendse R, Rajapaksha DI, Rewari BB, Malliawadu N, Jayamanna K, Dombawela D, Kurle S. HIV-1 pol gene diversity and molecular dating of subtype C from Sri Lanka. PLoS One 2020; 15:e0234133. [PMID: 32525892 PMCID: PMC7289380 DOI: 10.1371/journal.pone.0234133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/19/2020] [Indexed: 11/19/2022] Open
Abstract
Background The first case of HIV infection in Sri Lanka was reported in 1987 and at the end of 2018 there were 3500 people living with HIV. There have been commendable efforts made towards the detection, treatment, and prevention of HIV in the country. Even though the genetic diversity of HIV has been shown to affect the parameters ranging from detection to vaccine development, there is no data available with respect to the molecular epidemiology of HIV-1 in Sri Lanka. Methods In this report we have performed the ancillary analysis of pol gene region sequences (n = 85) obtained primarily for the purpose of HIV-1 drug resistance genotyping. Briefly, dried blood spot specimens (DBS) collected from HIV-1 infected individuals between December 2015 and August 2018 were subjected to pol gene amplification and sequencing. These pol gene sequences were used to interpret the drug resistance mutation profiles. Further, sequences were subjected to HIV-1 subtyping using REGA 3.0, COMET, jPHMM and, RIP online subtyping tools. Moreover, Bayesian phylogenetic analysis was employed to estimate the evolutionary history of HIV-1 subtype C in Sri Lanka. Results Our analysis revealed that the majority (51.8%) of pol gene sequences were subtype C. Other than subtype C, there were sequences categorized as subtypes A1, B, D and G. In addition to pure subtypes there were sequences which were observed to be circulating recombinant forms (CRFs) and a few of the recombinants were identified as potential unique recombinants (URFs). We also observed the presence of drug resistance mutations in 56 (65.9%) out of 85 sequences. Estimates of the Bayesian evolutionary analysis suggested that the HIV-1 subtype C was introduced to Sri Lanka during the early 1970s (1972.8). Conclusion The findings presented here indicate the presence of multiple HIV-1 subtypes and the prevalence of drug resistance mutations in Sri Lanka. The majority of the sequences were subtype C, having their most recent common ancestor traced back to the early 1970s. Continuous molecular surveillance of HIV-1 molecular epidemiology will be crucial to keep track of drug resistance, genetic diversity, and evolutionary history of HIV-1 in Sri Lanka.
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Affiliation(s)
- Ajit Patil
- HIV Drug Resistance Laboratory, National AIDS Research Institute, Pune, India
| | | | | | | | - Devidas Chaturbhuj
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | | | | | - B. B. Rewari
- World Health Organization South-East Asia Region, New Delhi, India
| | | | | | | | - Swarali Kurle
- HIV Drug Resistance Laboratory, National AIDS Research Institute, Pune, India
- * E-mail:
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13
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Nazziwa J, Faria NR, Chaplin B, Rawizza H, Kanki P, Dakum P, Abimiku A, Charurat M, Ndembi N, Esbjörnsson J. Characterisation of HIV-1 Molecular Epidemiology in Nigeria: Origin, Diversity, Demography and Geographic Spread. Sci Rep 2020; 10:3468. [PMID: 32103028 PMCID: PMC7044301 DOI: 10.1038/s41598-020-59944-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 02/05/2020] [Indexed: 11/23/2022] Open
Abstract
Nigeria has the highest number of AIDS-related deaths in the world. In this study, we characterised the HIV-1 molecular epidemiology by analysing 1442 HIV-1 pol sequences collected 1999-2014 from four geopolitical zones in Nigeria using state-of-the-art maximum-likelihood and Bayesian phylogenetic analyses. The main circulating forms were the circulating recombinant form (CRF) 02_AG (44% of the analysed sequences), CRF43_02G (16%), and subtype G (8%). Twenty-three percent of the sequences represented unique recombinant forms (URFs), whereof 37 (11%) could be grouped into seven potentially novel CRFs. Bayesian phylodynamic analysis suggested that five major Nigerian HIV-1 sub-epidemics were introduced in the 1960s and 1970s, close to the Nigerian Civil War. The analysis also indicated that the number of effective infections decreased in Nigeria after the introduction of free antiretroviral treatment in 2006. Finally, Bayesian phylogeographic analysis suggested gravity-like dynamics in which virus lineages first emerge and expand within large urban centers such as Abuja and Lagos, before migrating towards smaller rural areas. This study provides novel insight into the Nigerian HIV-1 epidemic and may have implications for future HIV-1 prevention strategies in Nigeria and other severely affected countries.
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Affiliation(s)
- Jamirah Nazziwa
- Department of Translational Medicine, Lund University, Lund, Sweden
| | | | - Beth Chaplin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Holly Rawizza
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Phyllis Kanki
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Patrick Dakum
- Institute of Human Virology Nigeria, Abuja, Nigeria
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Alash'le Abimiku
- Institute of Human Virology Nigeria, Abuja, Nigeria
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Man Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Nicaise Ndembi
- Institute of Human Virology Nigeria, Abuja, Nigeria
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Lund, Sweden.
- Nuffield Department Medicine, University of Oxford, Oxford, United Kingdom.
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Gibson KM, Jair K, Castel AD, Bendall ML, Wilbourn B, Jordan JA, Crandall KA, Pérez-Losada M. A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing. Sci Rep 2020; 10:1989. [PMID: 32029767 PMCID: PMC7004982 DOI: 10.1038/s41598-020-58410-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/31/2019] [Indexed: 11/08/2022] Open
Abstract
Washington, DC continues to experience a generalized HIV-1 epidemic. We characterized the local phylodynamics of HIV-1 in DC using next-generation sequencing (NGS) data. Viral samples from 68 participants from 2016 through 2017 were sequenced and paired with epidemiological data. Phylogenetic and network inferences, drug resistant mutations (DRMs), subtypes and HIV-1 diversity estimations were completed. Haplotypes were reconstructed to infer transmission clusters. Phylodynamic inferences based on the HIV-1 polymerase (pol) and envelope genes (env) were compared. Higher HIV-1 diversity (n.s.) was seen in men who have sex with men, heterosexual, and male participants in DC. 54.0% of the participants contained at least one DRM. The 40-49 year-olds showed the highest prevalence of DRMs (22.9%). Phylogenetic analysis of pol and env sequences grouped 31.9-33.8% of the participants into clusters. HIV-TRACE grouped 2.9-12.8% of participants when using consensus sequences and 9.0-64.2% when using haplotypes. NGS allowed us to characterize the local phylodynamics of HIV-1 in DC more broadly and accurately, given a better representation of its diversity and dynamics. Reconstructed haplotypes provided novel and deeper phylodynamic insights, which led to networks linking a higher number of participants. Our understanding of the HIV-1 epidemic was expanded with the powerful coupling of HIV-1 NGS data with epidemiological data.
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Grants
- P30 AI117970 NIAID NIH HHS
- U01 AI069503 NIAID NIH HHS
- UM1 AI069503 NIAID NIH HHS
- This study was supported by the DC Cohort Study (U01 AI69503-03S2), a supplement from the Women’s Interagency Study for HIV-1 (410722_GR410708), a DC D-CFAR pilot award, and a 2015 HIV-1 Phylodynamics Supplement award from the District of Columbia for AIDS Research, an NIH funded program (AI117970), which is supported by the following NIH Co-Funding and Participating Institutes and Centers: NIAID, NCI, NICHD, NHLBI, NIDA, NIMH, NIA, FIC, NIGMS, NIDDK and OAR. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
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Affiliation(s)
- Keylie M Gibson
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA.
| | - Kamwing Jair
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Amanda D Castel
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Matthew L Bendall
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Brittany Wilbourn
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Jeanne A Jordan
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Keith A Crandall
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- Department of Biostatistics and Bioinformatics, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- Department of Biostatistics and Bioinformatics, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
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Lunar MM, Mlakar J, Zorec TM, Poljak M. HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing. Viruses 2020; 12:v12010063. [PMID: 31947872 PMCID: PMC7019782 DOI: 10.3390/v12010063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/28/2019] [Accepted: 12/31/2019] [Indexed: 11/30/2022] Open
Abstract
Surveillance of HIV circulating recombinant forms (CRFs) is important because HIV diversity can affect various aspects of HIV infection from prevention to diagnosis and patient management. A comprehensive collection of pol sequences obtained from individuals diagnosed with HIV-1 from 2000 to 2016 in Slovenia was subtyped to identify possible unique recombinant forms (URFs). Selected samples were subjected to near full-length genome (NFLG) sequencing and detailed recombination analyses. Discordant subtyping results were observed for 68/387 (17.6%) sequences and 20 sequences were identified as the most probable URFs and selected for NFLG characterization. Further, 11 NFLGs and two sequences of >7000 base pairs were obtained. Seven sequences were identified as “pure” subtypes or already characterized CRFs: subtype B (n = 5), sub-subtype A6 (n = 1), and CRF01_AE (n = 1). The remaining six sequences were determined to be URFs; four displayed a single recombination event and two exhibited a complex recombination pattern involving several subtypes or CRFs. Finally, three HIV strains were recognized as having epidemic potential and could be further characterized as new CRFs. Our study shows that the identification of new CRFs is possible, even in countries where HIV diversity is considered limited, emphasizing the importance of the surveillance of HIV recombinant forms.
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Verhofstede C, Mortier V, Dauwe K, Callens S, Deblonde J, Dessilly G, Delforge ML, Fransen K, Sasse A, Stoffels K, Van Beckhoven D, Vanroye F, Vaira D, Vancutsem E, Van Laethem K. Exploring HIV-1 Transmission Dynamics by Combining Phylogenetic Analysis and Infection Timing. Viruses 2019; 11:v11121096. [PMID: 31779195 PMCID: PMC6950120 DOI: 10.3390/v11121096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/12/2022] Open
Abstract
HIV-1 pol sequences obtained through baseline drug resistance testing of patients newly diagnosed between 2013 and 2017 were analyzed for genetic similarity. For 927 patients the information on genetic similarity was combined with demographic data and with information on the recency of infection. Overall, 48.3% of the patients were genetically linked with 11.4% belonging to a pair and 36.9% involved in a cluster of ≥3 members. The percentage of early diagnosed (≤4 months after infection) was 28.6%. Patients of Belgian origin were more frequently involved in transmission clusters (49.7% compared to 15.3%) and diagnosed earlier (37.4% compared to 12.2%) than patients of Sub-Saharan African origin. Of the infections reported to be locally acquired, 69.5% were linked (14.1% paired and 55.4% in a cluster). Equal parts of early and late diagnosed individuals (59.9% and 52.4%, respectively) were involved in clusters. The identification of a genetically linked individual for the majority of locally infected patients suggests a high rate of diagnosis in this population. Diagnosis however is often delayed for >4 months after infection increasing the opportunities for onward transmission. Prevention of local infection should focus on earlier diagnosis and protection of the still uninfected members of sexual networks with human immunodeficiency virus (HIV)-infected members.
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Affiliation(s)
- Chris Verhofstede
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium; (V.M.); (K.D.)
- Correspondence:
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium; (V.M.); (K.D.)
| | - Kenny Dauwe
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium; (V.M.); (K.D.)
| | - Steven Callens
- Aids Reference Center, Department of Internal Medicine, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Jessika Deblonde
- Epidemiology of Infectious Diseases Unit, Scientific Institute of Public Health Sciensano, 1050 Brussels, Belgium; (J.D.); (A.S.); (D.V.B.)
| | - Géraldine Dessilly
- Aids Reference Laboratory, Medical Microbiology Unit, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Marie-Luce Delforge
- Aids Reference Laboratory, Université Libre de Bruxelles, 1050 Brussels, Belgium;
| | - Katrien Fransen
- HIV/STD Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (K.F.); (F.V.)
| | - André Sasse
- Epidemiology of Infectious Diseases Unit, Scientific Institute of Public Health Sciensano, 1050 Brussels, Belgium; (J.D.); (A.S.); (D.V.B.)
| | - Karolien Stoffels
- Aids Reference Laboratory, Centre Hospitalier Universitaire St. Pierre, 1000 Brussels, Belgium;
| | - Dominique Van Beckhoven
- Epidemiology of Infectious Diseases Unit, Scientific Institute of Public Health Sciensano, 1050 Brussels, Belgium; (J.D.); (A.S.); (D.V.B.)
| | - Fien Vanroye
- HIV/STD Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (K.F.); (F.V.)
| | - Dolores Vaira
- Aids Reference Laboratory, Centre Hospitalier Universitaire de Liège, 4000 Liège, Belgium;
| | - Ellen Vancutsem
- Aids Reference Laboratory, Vrije Universiteit Brussel VUB, 1090 Brussels, Belgium;
| | - Kristel Van Laethem
- Aids Reference Laboratory, University Hospital Leuven, 3000 Leuven, Belgium;
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
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Sebastião CS, Neto Z, de Jesus CS, Mirandela M, Jandondo D, Couto-Fernandez JC, Tanuri A, Morais J, Brito M. Genetic diversity and drug resistance of HIV-1 among infected pregnant women newly diagnosed in Luanda, Angola. PLoS One 2019; 14:e0225251. [PMID: 31770425 PMCID: PMC6879122 DOI: 10.1371/journal.pone.0225251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022] Open
Abstract
Monitoring genetic diversity and drug resistance mutations (DRMs) is critical for understanding HIV epidemiology. Here, we report HIV-1 genetic diversity and DRMs in blood samples from 42 HIV-positive pregnant women naive to antiretroviral therapy (ART), in Luanda. The samples were subjected to nested-PCR, followed by sequencing of HIV-1 pol gene, targeting the protease and reverse transcriptase fragments. HIV-1 diversity was analyzed using the REGA HIV-1 subtyping tool and DRMs were identified using the Calibrated Population Resistance tool. A total of 34 sequences were obtained. The data revealed wide HIV-1 subtypes heterogeneity, with subtype C (38%, 13/34) the most frequent, followed by the subtypes F1 (18%, 6/34), A1 (9%, 3/34), G (9%, 3/34), D (6%, 2/34) and H (3%, 1/34). In addition, recombinants strains were detected, with CRF02_AG (6%, 2/34) the most frequent, followed by CRF37_cpx, F1/C, A1/G and H/G, all with 3% (1/34). A total of 6/34 (18%) of the sequences presented DRMs. The non-nucleoside reverse transcriptase inhibitors presented 15% (5/34) of resistance. Moreover, 1/34 (3%) sequence presented resistance against both non-nucleoside reverse transcriptase inhibitors and nucleoside reverse transcriptase inhibitors, simultaneously. Despite the small sample size, our results suggest the need to update currently used ART regimens. Surveillance of HIV-1 subtypes and DRMs are necessary to understand HIV epidemiology and to guide modification of ART guidelines in Angola.
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Affiliation(s)
- Cruz S. Sebastião
- NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
- Laboratório de Biologia Molecular, Instituto Nacional de Investigação em Saúde, Luanda, Angola
- Instituto Superior de Ciências da Saúde, Universidade Agostinho Neto, Luanda, Angola
- Centro de Investigação em Saúde de Angola, Luanda, Angola
| | - Zoraima Neto
- Laboratório de Biologia Molecular, Instituto Nacional de Investigação em Saúde, Luanda, Angola
| | - Carlos S. de Jesus
- Laboratorio de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marinela Mirandela
- Laboratório de Biologia Molecular, Instituto Nacional de Investigação em Saúde, Luanda, Angola
| | - Domingos Jandondo
- Laboratório de Biologia Molecular, Instituto Nacional de Investigação em Saúde, Luanda, Angola
| | | | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Joana Morais
- Laboratório de Biologia Molecular, Instituto Nacional de Investigação em Saúde, Luanda, Angola
- Centro de Investigação em Saúde de Angola, Luanda, Angola
- Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
| | - Miguel Brito
- Centro de Investigação em Saúde de Angola, Luanda, Angola
- Health and Technology Research Center, Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
- * E-mail:
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Derache A, Iwuji CC, Baisley K, Danaviah S, Marcelin AG, Calvez V, de Oliveira T, Dabis F, Porter K, Pillay D. Impact of Next-generation Sequencing Defined Human Immunodeficiency Virus Pretreatment Drug Resistance on Virological Outcomes in the ANRS 12249 Treatment-as-Prevention Trial. Clin Infect Dis 2019; 69:207-214. [PMID: 30321314 PMCID: PMC6603266 DOI: 10.1093/cid/ciy881] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 10/09/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Previous studies in human immunodeficiency virus (HIV)-positive individuals on thymidine analogue backbone antiretroviral therapy (ART) with either nevirapine or efavirenz have suggested poorer virological outcomes in the presence of pretreatment drug resistance (PDR). We assessed the impact of PDR on virological suppression (VS; <50 copies/mL) in individuals prescribed primarily tenofovir/emtricitabine/efavirenz in rural KwaZulu-Natal within a treatment-as-prevention trial. METHODS Among 1557 HIV-positive individuals who reported no prior ART at study entry and provided plasma samples, 1328 individuals with entry viral load (VL) >1000 copies/mL had next-generation sequencing (NGS) of the HIV pol gene with MiSeq technology. Results were obtained for 1148 individuals, and the presence of PDR was assessed at 5% and 20% detection thresholds. Virological outcome was assessed using Cox regression in 837 of 920 ART initiators with at least 1 follow-up VL after ART initiation. RESULTS PDR prevalence was 9.5% (109/1148) and 12.8% (147/1148) at 20% and 5% thresholds, respectively. After a median of 1.36 years (interquartile range, 0.91-2.13), mostly on fixed-dose combination tenofovir/emtricitabine/efavirenz, presence of both nonnucleoside reverse transcriptase inhibitor (NNRTI)/nucleoside reverse transcriptase inhibitor PDR vs no PDR was associated with longer time to VS (adjusted hazard ratio [aHR], 0.32; 95% confidence interval [CI], 0.12-0.86), while there was no difference between those with only NNRTI PDR vs no PDR (aHR, 1.05; 95% CI, 0.82-1.34) at the 5% threshold. Similar differences were observed for mutations detected at the 20% threshold, although without statistical significance. CONCLUSIONS NGS uncovered a high prevalence of PDR among participants enrolled in trial clinics in rural KwaZulu-Natal. Dual-class PDR to a mainly tenofovir/emtricitabine/efavirenz regimen was associated with poorer VS. However, there was no impact of NNRTI PDR alone. CLINICAL TRIALS TEGISTRATION NCT01509508; South African National Clinical Trials Register: DOH-27-0512-3974.
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Affiliation(s)
- Anne Derache
- Africa Health Research Institute, Mtubatuba, South Africa
- Sorbonne University, l’université Pierre et Marie Curie, Institut national de la santé et de la recherche médicale, Institut Pierre Louis d’Epidémiologie et de Santé Publique Unité Mixte de Recherche en Santé (IPLESP UMRS 1136), Paris, France
| | - Collins C Iwuji
- Africa Health Research Institute, Mtubatuba, South Africa
- Department of Global Health and Infection, Brighton and Sussex Medical School
- Institute for Global Health, University College London, United Kingdom
| | - Kathy Baisley
- Sorbonne University, l’université Pierre et Marie Curie, Institut national de la santé et de la recherche médicale, Institut Pierre Louis d’Epidémiologie et de Santé Publique Unité Mixte de Recherche en Santé (IPLESP UMRS 1136), Paris, France
| | - Siva Danaviah
- Africa Health Research Institute, Mtubatuba, South Africa
| | - Anne-Geneviève Marcelin
- Sorbonne University, l’université Pierre et Marie Curie, Institut national de la santé et de la recherche médicale, Institut Pierre Louis d’Epidémiologie et de Santé Publique Unité Mixte de Recherche en Santé (IPLESP UMRS 1136), Paris, France
| | - Vincent Calvez
- Sorbonne University, l’université Pierre et Marie Curie, Institut national de la santé et de la recherche médicale, Institut Pierre Louis d’Epidémiologie et de Santé Publique Unité Mixte de Recherche en Santé (IPLESP UMRS 1136), Paris, France
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - François Dabis
- Université de Bordeaux, Institut de Santé Publique d’Epidémiologie et de Développement, Centre Institut national de la santé et de la recherche médicale 1219, France
| | - Kholoud Porter
- Institute for Global Health, University College London, United Kingdom
| | - Deenan Pillay
- Africa Health Research Institute, Mtubatuba, South Africa
- Division of Infection and Immunity, University College London, United Kingdom
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Adeniyi OV, Obi CL, Goon DT, Iweriebor B, Ajayi AI, Lambert J, Okoh A. HIV-1 drug resistance surveillance among parturient women on anti-retroviral therapy in the Eastern Cape, South Africa: Implications for elimination of mother-to-child transmission. J Clin Virol 2019; 117:89-95. [PMID: 31255794 DOI: 10.1016/j.jcv.2019.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 05/20/2019] [Accepted: 06/13/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND The emergence of HIV drug resistance poses a significant threat to achieving the goal of elimination of mother-to-child transmission. OBJECTIVES We assessed the extent and patterns of HIV-1 drug resistance mutations (DRMs) within the context of the public sector prevention of mother-to-child transmission (PMTCT) programme in the Eastern Cape, South Africa. STUDY DESIGN We conducted analysis of the Pol sub-genomic sequence of RNA extracted from plasma samples of women with probable virological failure at delivery between January and May 2018 from two large maternity centres in the Eastern Cape using standard protocols. Partial pol gene covering 1030bp were amplified and sequenced according to previously reported protocol. DRMs were determined by submitting the generated partial pol sequences to the Stanford drug resistance database for query on mutations associated with drug resistance in HIV viruses. We examined the correlates of DRMs using bivariate analysis. RESULTS The age of parturient women ranged from 16 to 43 years. The majority of the parturient women were currently on Efavirenz-based regimen (first line ART) (82.5%) and had been on ART for more than 12 months (65.0%). The prevalence of DRMs was 72.5% (n = 58). The CD4 count demonstrated a negative linear association with the DRMs (p = 0.002). The predominant DRMs were K103 N (n = 43; 74.1%), M184 V (n = 28; 48.3%) and K65R (n = 11; 19%). Among the parturient women on EFV-based regimen treatment; 79.1% already had K103 N while nine patients on protease inhibitor-based regimen still harboured K103 N. The majority of the M184 V mutations were observed in parturient women on first line regimen (n = 23; 82.1%). CONCLUSIONS We found a high prevalence of DRMs in women delivering their index babies at high viral loads in the study settings. Drug resistance surveillance using point-of-care reverse transcriptase-PCR strategies for the screening of pregnant women on ART could be a game-changer in the resource-constrained settings.
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Affiliation(s)
- Oladele Vincent Adeniyi
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Fort Hare, Alice, South Africa; SAMRC Microbial Water Quality Monitoring Centre, Faculty of Science and Agriculture, University of Fort Hare, Alice, South Africa.
| | - Chikwelu Larry Obi
- School of Science and Technology, Sefako Makgatho Health Sciences University, Ga-Rankuwa, Pretoria, South Africa.
| | - Daniel Ter Goon
- Department of Public Health, Faculty of Health Sciences, University of Fort Hare, East London, South Africa.
| | - Benson Iweriebor
- School of Science and Technology, Sefako Makgatho Health Sciences University, Ga-Rankuwa, Pretoria, South Africa.
| | - Anthony Idowu Ajayi
- Population Dynamics and Sexual and Reproductive Health, African Population and Health Research Center, Nairobi, Kenya.
| | - John Lambert
- University College Dublin/Mater Misericordiae University Hospital, Catherine McAuley Education & Research Centre, Dublin, Ireland.
| | - Anthony Okoh
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Fort Hare, Alice, South Africa; SAMRC Microbial Water Quality Monitoring Centre, Faculty of Science and Agriculture, University of Fort Hare, Alice, South Africa.
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Villandré L, Labbe A, Brenner B, Ibanescu RI, Roger M, Stephens DA. Assessing the role of transmission chains in the spread of HIV-1 among men who have sex with men in Quebec, Canada. PLoS One 2019; 14:e0213366. [PMID: 30840706 PMCID: PMC6402664 DOI: 10.1371/journal.pone.0213366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 02/19/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Phylogenetics has been used to investigate HIV transmission among men who have sex with men. This study compares several methodologies to elucidate the role of transmission chains in the dynamics of HIV spread in Quebec, Canada. METHODS The Quebec Human Immunodeficiency Virus (HIV) genotyping program database now includes viral sequences from close to 4,000 HIV-positive individuals classified as Men who have Sex with Men (MSMs), collected between 1996 and early 2016. Assessment of chain expansion may depend on the partitioning scheme used, and so, we produce estimates from several methods: the conventional Bayesian and maximum likelihood-bootstrap methods, in combination with a variety of schemes for applying a maximum distance criterion, and two other algorithms, DM-PhyClus, a Bayesian algorithm that produces a measure of uncertainty for proposed partitions, and the Gap Procedure, a fast non-phylogenetic approach. Sequences obtained from individuals in the Primary HIV Infection (PHI) stage serve to identify incident cases. We focus on the period ranging from January 1st 2012 to February 1st 2016. RESULTS AND CONCLUSION The analyses reveal considerable overlap between chain estimates obtained from conventional methods, thus leading to similar estimates of recent temporal expansion. The Gap Procedure and DM-PhyClus suggest however moderately different chains. Nevertheless, all estimates stress that longer older chains are responsible for a sizeable proportion of the sampled incident cases among MSMs. Curbing the HIV epidemic will require strategies aimed specifically at preventing such growth.
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Affiliation(s)
- Luc Villandré
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, Québec, Canada
- Department of Decision Sciences, HEC Montréal, Montreal, Québec, Canada
| | - Aurélie Labbe
- Department of Decision Sciences, HEC Montréal, Montreal, Québec, Canada
| | - Bluma Brenner
- McGill AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Québec, Canada
| | | | - Michel Roger
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, Québec, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montreal, Québec, Canada
| | - David A. Stephens
- Department of Mathematics and Statistics, McGill University, Montréal, Québec, Canada
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Ragonnet-Cronin M, Hu YW, Morris SR, Sheng Z, Poortinga K, Wertheim JO. HIV transmission networks among transgender women in Los Angeles County, CA, USA: a phylogenetic analysis of surveillance data. Lancet HIV 2019; 6:e164-e172. [PMID: 30765313 PMCID: PMC6887514 DOI: 10.1016/s2352-3018(18)30359-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND Transgender women are among the groups at highest risk for HIV infection, with a prevalence of 27·7% in the USA; and despite this known high risk, undiagnosed infection is common in this population. We set out to identify transgender women and their partners in a molecular transmission network to prioritise public health activities. METHODS Since 2006, HIV protease and reverse transcriptase gene (pol) sequences from drug resistance testing have been reported to the Los Angeles County Department of Public Health and linked to demographic data, gender, and HIV transmission risk factor data for each case in the enhanced HIV/AIDS Reporting System. We reconstructed a molecular transmission network by use of HIV-TRAnsmission Cluster Engine (with a pairwise genetic distance threshold of 0·015 substitutions per site) from the earliest pol sequences from 22 398 unique individuals, including 412 (2%) self-identified transgender women. We examined the possible predictors of clustering with multivariate logistic regression. We characterised the genetically linked partners of transgender women and calculated assortativity (the tendency for people to link to other people with the same attributes) for each transmission risk group. FINDINGS 8133 (36·3%) of 22 398 individuals clustered in the network across 1722 molecular transmission clusters. Transgender women who indicated a sexual risk factor clustered at the highest frequency in the network, with 147 (43%) of 345 being linked to at least one other person (adjusted odds ratio [aOR] 2·0, p=0·0002). Transgender women were assortative in the network (assortativity 0·06, p<0·001), indicating that they tended to link to other transgender women. Transgender women were more likely than expected to link to other transgender women (OR 4·65, p<0·001) and cisgender men who did not identify as men who have sex with men (MSM; OR 1·53, p<0·001). Transgender women were less likely than expected to link to MSM (OR 0·75, p<0·001), despite the high prevalence of HIV among MSM. Transgender women were distributed across 126 clusters, and cisgender individuals linked to one transgender woman were 9·2 times more likely to link to a second transgender woman than other individuals in the surveillance database. Reconstruction of the transmission network is limited by sample availability, but sequences were available for more than 40% of diagnoses. INTERPRETATION Clustering of transgender women and the observed tendency for linkage with cisgender men who did not identify as MSM, shows the potential to use molecular epidemiology both to identify clusters that are likely to include undiagnosed transgender women with HIV and to improve the targeting of public health prevention and treatment services to transgender women. FUNDING California HIV and AIDS Research Program and National Institutes of Health-National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- Manon Ragonnet-Cronin
- Department of Medicine, University of California, San Diego, CA, USA; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Yunyin W Hu
- Division of HIV and STD Programs, Department of Public Health, Los Angeles, CA, USA
| | - Sheldon R Morris
- Department of Medicine, University of California, San Diego, CA, USA
| | - Zhijuan Sheng
- Division of HIV and STD Programs, Department of Public Health, Los Angeles, CA, USA
| | - Kathleen Poortinga
- Division of HIV and STD Programs, Department of Public Health, Los Angeles, CA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, CA, USA
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22
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BRUMME ZL, SUDDERUDDIN H, ZIEMNIAK C, LUZURIAGA K, JONES BR, JOY JB, CUNNINGHAM CK, GREENOUGH T, PERSAUD D. Genetic complexity in the replication-competent latent HIV reservoir increases with untreated infection duration in infected youth. AIDS 2019; 33:211-218. [PMID: 30325763 PMCID: PMC6298800 DOI: 10.1097/qad.0000000000002045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Timely initiation of combination antiretroviral therapy (ART) limits latent HIV reservoir size and should also limit reservoir genetic complexity. However, the relationship between these two factors remains unclear, particularly among HIV-infected youth. DESIGN Retrospective analysis of replication-competent latent HIV clones serially isolated by limiting-dilution culture from resting CD4 T-cell reservoirs from ART-suppressed, young adult participants of a historic phase I therapeutic vaccine trial (PACTG/IMPAACT-P1059). METHODS Replication-competent latent HIV clones isolated from resting CD4 T cells of four perinatally and 10 nonperinatally infected young adults (average 22 versus 6 years uncontrolled infection, respectively) were sequenced in Pol and Nef. Within-host HIV sequence datasets were characterized with respect to their genetic diversity and inferred immune escape mutation burden. RESULTS Although participants were comparable in terms of sociodemographic and HIV sampling characteristics (e.g. on average, a mean 17 Pol sequences were recovered at five timepoints over up to 70 weeks) and the length of ART suppression at study entry (average 3 years), replication-competent HIV reservoir size, genetic diversity, immune escape mutation burden and variant complexity were significantly higher among the perinatally infected participants who experienced longer durations of uncontrolled viremia. Nevertheless, viral sequences inferred to retain susceptibility to host cellular immune responses were detected in all participants, irrespective of uncontrolled viremia duration. CONCLUSION HIV elimination in late-suppressed youth may be doubly challenged by larger and more genetically complex reservoirs. Strategies that integrate host and viral genetic complexity to achieve HIV remission or cure may merit consideration in such cases.
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Affiliation(s)
- Zabrina L. BRUMME
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC Canada
- BC Centre for Excellence in HIV/AIDS, Vancouver BC, Canada
| | | | | | | | - Bradley R. JONES
- BC Centre for Excellence in HIV/AIDS, Vancouver BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC Canada
| | - Jeffrey B. JOY
- BC Centre for Excellence in HIV/AIDS, Vancouver BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC Canada
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Rawson JMO, Nikolaitchik OA, Keele BF, Pathak VK, Hu WS. Recombination is required for efficient HIV-1 replication and the maintenance of viral genome integrity. Nucleic Acids Res 2018; 46:10535-10545. [PMID: 30307534 PMCID: PMC6237782 DOI: 10.1093/nar/gky910] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 09/20/2018] [Accepted: 10/08/2018] [Indexed: 01/24/2023] Open
Abstract
Retroviruses package two complete RNA genomes into a viral particle but generate only one provirus after each infection. This pseudodiploid replication strategy facilitates frequent recombination, which occurs during DNA synthesis when reverse transcriptase switches templates between two copackaged RNA genomes, generating chimeric DNA. Recombination has played an important role in shaping the current HIV-1 pandemic; however, whether recombination is required for HIV-1 replication is currently unknown. In this report, we examined viral replication when recombination was blocked in defined regions of the HIV-1 genome. We found that blocking recombination reduced viral titers. Furthermore, a significant proportion of the resulting proviruses contained large deletions. Analyses of the deletion junctions indicated that these deletions were the direct consequence of blocking recombination. Thus, our findings illustrate that recombination is a major mechanism to maintain HIV-1 genome integrity. Our study also shows that both obligatory and nonobligatory crossovers occur during reverse transcription, thereby supporting both the forced and dynamic copy-choice models of retroviral recombination. Taken together, our results demonstrate that, in most viruses, both packaged RNA genomes contribute to the genetic information in the DNA form. Furthermore, recombination allows generation of the intact HIV-1 DNA genome and is required for efficient viral replication.
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Affiliation(s)
- Jonathan M O Rawson
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Olga A Nikolaitchik
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, U.S.A
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, U.S.A
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Peng BJ, Carlson JM, Liu MKP, Gao F, Goonetilleke N, McMichael AJ, Borrow P, Gilmour J, Heath SL, Hunter E, Bansal A, Goepfert PA. Antisense-Derived HIV-1 Cryptic Epitopes Are Not Major Drivers of Viral Evolution during the Acute Phase of Infection. J Virol 2018; 92:e00711-18. [PMID: 30021907 PMCID: PMC6146806 DOI: 10.1128/jvi.00711-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/07/2018] [Indexed: 01/31/2023] Open
Abstract
While prior studies have demonstrated that CD8 T cell responses to cryptic epitopes (CE) are readily detectable during HIV-1 infection, their ability to drive escape mutations following acute infection is unknown. We predicted 66 CE in a Zambian acute infection cohort based on escape mutations occurring within or near the putatively predicted HLA-I-restricted epitopes. The CE were evaluated for CD8 T cell responses for patients with chronic and acute HIV infections. Of the 66 predicted CE, 10 were recognized in 8/32 and 4/11 patients with chronic and acute infections, respectively. The immunogenic CE were all derived from a single antisense reading frame within pol However, when these CE were tested using longitudinal study samples, CE-specific T cell responses were detected but did not consistently select for viral escape mutations. Thus, while we demonstrated that CE are immunogenic in acute infection, the immune responses to CE are not major drivers of viral escape in the initial stages of HIV infection. The latter finding may be due to either the subdominant nature of CE-specific responses, the low antigen sensitivity, or the magnitude of CE responses during acute infections.IMPORTANCE Although prior studies demonstrated that cryptic epitopes of HIV-1 induce CD8 T cell responses, evidence that targeting these epitopes drives HIV escape mutations has been substantially limited, and no studies have addressed this question following acute infection. In this comprehensive study, we utilized longitudinal viral sequencing data obtained from three separate acute infection cohorts to predict potential cryptic epitopes based on HLA-I-associated viral escape. Our data show that cryptic epitopes are immunogenic during acute infection and that many of the responses they elicit are toward translation products of HIV-1 antisense reading frames. However, despite cryptic epitope targeting, our study did not find any evidence of early CD8-mediated immune escape. Nevertheless, improving cryptic epitope-specific CD8 T cell responses may still be beneficial in both preventative and therapeutic HIV-1 vaccines.
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Affiliation(s)
- Binghao J Peng
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Michael K P Liu
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Feng Gao
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Nilu Goonetilleke
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew J McMichael
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Sonya L Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Anju Bansal
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Paul A Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Mendoza Y, García-Morales C, Bello G, Garrido-Rodríguez D, Tapia-Trejo D, Pascale JM, Girón-Callejas AC, Mendizábal-Burastero R, Escobar-Urias IY, García-González BL, Navas-Castillo JS, Quintana-Galindo MC, Pinzón-Meza R, Mejía-Villatoro CR, Avila-Ríos S, Reyes-Terán G. Evolutionary history and spatiotemporal dynamics of the HIV-1 subtype B epidemic in Guatemala. PLoS One 2018; 13:e0203916. [PMID: 30212548 PMCID: PMC6136800 DOI: 10.1371/journal.pone.0203916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/30/2018] [Indexed: 11/22/2022] Open
Abstract
Different explanations exist on how HIV-1 subtype B spread in Central America, but the role of Guatemala, the Central American country with the highest number of people living with the virus, in this scenario is unknown. We investigated the evolutionary history and spatiotemporal dynamics of HIV-1 subtype B in Guatemala. A total of 1,047 HIV-1 subtype B pol sequences, from newly diagnosed ART-naïve, HIV-infected Guatemalan subjects enrolled between 2011 and 2013 were combined with published subtype B sequences from other Central American countries (n = 2,101) and with reference sequences representative of the BPANDEMIC and BCAR lineages from the United States (n = 465), France (n = 344) and the Caribbean (n = 238). Estimates of evolutionary, demographic, and phylogeographic parameters were obtained from sequence data using maximum likelihood and Bayesian coalescent-based methods. The majority of Guatemalan sequences (98.9%) belonged to the BPANDEMIC clade, and 75.2% of these sequences branched within 10 monophyletic clades: four also included sequences from other Central American countries (BCAM-I to BCAM-IV) and six were mostly (>99%) composed by Guatemalan sequences (BGU clades). Most clades mainly comprised sequences from heterosexual individuals. Bayesian coalescent-based analyses suggested that BGU clades originated during the 1990s and 2000s, whereas BCAM clades originated between the late 1970s and mid 1980s. The major hub of dissemination of all BGU, and of BCAM-II, and BCAM-IV clades was traced to the Department of Guatemala, while the root location of BCAM-I and BCAM-III was traced to Honduras. Most Guatemalan clades experienced initial phases of exponential growth (0.23 and 3.6 year-1), followed by recent growth declines. Our observations suggest that the Guatemalan HIV-1 subtype B epidemic is driven by dissemination of multiple BPANDEMIC founder viral strains, some restricted to Guatemala and others widely disseminated in the Central American region, with Guatemala City identified as a major hub of viral dissemination. Our results also suggest the existence of different sub-epidemics within Guatemala for which different targeted prevention efforts might be needed.
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Affiliation(s)
- Yaxelis Mendoza
- Gorgas Memorial Institute for Health Studies, Panama City, Panama
- Department of Genetics and Molecular Biology, University of Panama, Panama City, Panama
| | - Claudia García-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Daniela Garrido-Rodríguez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Daniela Tapia-Trejo
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | | | | | | | | | | | | | | | | | | | - Santiago Avila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
- * E-mail: (GRT); (SAR)
| | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
- * E-mail: (GRT); (SAR)
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Diphoko T, Gaseitsiwe S, Kasvosve I, Moyo S, Okatch H, Musonda R, Wainberg M, Makhema J, Marlink R, Novitsky V, Essex M. Prevalence of Rilpivirine and Etravirine Resistance Mutations in HIV-1 Subtype C-Infected Patients Failing Nevirapine or Efavirenz-Based Combination Antiretroviral Therapy in Botswana. AIDS Res Hum Retroviruses 2018; 34:667-671. [PMID: 29732907 PMCID: PMC6079649 DOI: 10.1089/aid.2017.0135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Rilpivirine (RPV) and Etravirine (ETR) are approved second-generation non-nucleoside reverse transcriptase inhibitors (NNRTIs) for HIV treatment. There is a cross-resistance HIV mutation profile between first- and second-generation NNRTI drugs. We determined the prevalence of HIV-1 drug resistance mutations (DRMs) to RPV and ETR in Botswana. A total of 168 HIV-1 polymerase gene sequences from participants failing nevirapine (NVP)- or efavirenz (EFV)-containing regimens were analyzed for DRMs using the Stanford University HIV drug resistance database. Forty-one sequences were from an adult antiretroviral therapy (ART) study, the Tshepo study, and 127 from a prevention of mother-to-child transmission (PMTCT) study, the Mashi study, all conducted in Botswana. Prevalence of RPV and ETR highest DRM in the adult ART study (n = 41) were K101E (26.2%), E138A (23.8%), and Y181C (26.2%). The PMTCT cohort's (n = 127) high prevalence mutations were Y181C (15.7%), E138A (15%), and K101E (11%). A total of 42.9% and 3.2% of patients in the adult ART study and PMTCT study, respectively, had three or more NNRTI mutations at virologic failure. We identified HIV-1 mutations conferring resistance to RPV and ETR even though they have not been used in Botswana. Of concern was the high proportion of sequences from the adult ART study that displayed multiple DRMs; as the number of NNRTI mutations increases, the level of cross-resistance increases. It is plausible that patients displaying such profiles maybe at increased risk of failing second-generation NNRTI drugs, hence, calls for genotyping in patients with prior NVP or efavirenz exposure before prescription of RPV- or ETR-containing cART.
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Affiliation(s)
- Thabo Diphoko
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts
| | - Harriet Okatch
- Centre for Public Health Initiatives, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rosemary Musonda
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts
| | - Mark Wainberg
- Lady Davis Institute for Medical Research, McGill University, Montreal, Canada
| | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts
| | - Richard Marlink
- Rutgers Global Health Institute, Rutgers Biomedical and Health Sciences, Rutgers University, New Brunswick, New Jersey
| | - Vladimir Novitsky
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts
| | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts
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27
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Chen M, Ma Y, Chen H, Dai J, Dong L, Yang C, Li Y, Luo H, Zhang R, Jin X, Yang L, Cheung AKL, Jia M, Song Z. HIV-1 genetic transmission networks among men who have sex with men in Kunming, China. PLoS One 2018; 13:e0196548. [PMID: 29698467 PMCID: PMC5919538 DOI: 10.1371/journal.pone.0196548] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 04/15/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Yunnan has the greatest share of reported human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) cases in China. In recent years, HIV prevalence and incidence remained stubbornly high in men who have sex with men (MSM). To follow the dynamics of the HIV-1 epidemic among MSM, HIV-1 genetic characteristics and genetic transmission networks were investigated. METHODS Blood samples from 190 newly diagnosed HIV-1 cases among MSM were continuously collected at fixed sites from January 2013 to December 2015 in Kunming City, Yunnan Province. Partial gag, pol and env genes were sequenced and used for phylogenetic and genotypic drug resistance analyses. The genetic characteristics of the predominant HIV-1 strains were analyzed by the Bayesian Markov Chain Monte Carlo (MCMC) method. The genetic transmission networks were identified with a genetic distance of 0.03 substitutions/site and 90% bootstrap support. RESULTS Among the 190 HIV-1 positive MSM reported during 2013-2105, various genotypes were identified, including CRF01_AE (45.3%), CRF07_BC (35.8%), unique recombinant forms (URFs) (11.6%), CRF08_BC (3.2%), CRF55_01B (2.1%), subtype B (1.6%) and CRF59_01B (0.5%). The effective population sizes (EPS) for CRF01_AE and CRF07_BC increased exponentially from approximately 2001-2010 and 2005-2009, respectively. Genetic transmission networks were constructed with 308 pol sequences from MSM diagnosed during 2010-2015. Of the 308 MSM, 109 (35.4%) were identified in 38 distinct clusters. Having multiple male partners was associated with a high probability of identification in the genetic transmission networks. Of the 38 clusters, 27 (71.1%) contained individuals diagnosed in different years. Of the 109 individuals in the networks, 26 (23.9%) had ≥2 potential transmission partners (≥2 links). The proportion of MSM with ≥2 links was higher among those diagnosed from 2010-2012. The constituent ratios of their potential transmission partners by areas showed no significant difference among MSM from Kunming, other cities in Yunnan and other provinces. Additionally, surveillance drug resistance mutations (SDRMs) were identified in 5% of individuals. CONCLUSION This study revealed the various HIV-a genotypes circulating among MSM in Kunming. MSM with more partners were more easily detected in transmission networks, and early-diagnosed MSM remained active in transmission networks. These findings suggested that the routine interventions should be combined with HIV testing and linkage to care and early antiretroviral therapy among HIV-positive MSM.
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MESH Headings
- Adolescent
- Adult
- Aged
- China
- Drug Resistance, Viral/genetics
- Genotype
- HIV Infections/diagnosis
- HIV Infections/transmission
- HIV Infections/virology
- HIV-1/genetics
- HIV-1/isolation & purification
- Homosexuality, Male
- Humans
- Male
- Middle Aged
- Monte Carlo Method
- Probability
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- Sequence Analysis, DNA
- Young Adult
- env Gene Products, Human Immunodeficiency Virus/classification
- env Gene Products, Human Immunodeficiency Virus/genetics
- gag Gene Products, Human Immunodeficiency Virus/classification
- gag Gene Products, Human Immunodeficiency Virus/genetics
- pol Gene Products, Human Immunodeficiency Virus/classification
- pol Gene Products, Human Immunodeficiency Virus/genetics
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Affiliation(s)
- Min Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yanling Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Huichao Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Jie Dai
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Lijuan Dong
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Chaojun Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Youfang Li
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Hongbing Luo
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Renzhong Zhang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Xiaomei Jin
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Li Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Allen Ka Loon Cheung
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Manhong Jia
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- * E-mail: (ZS); (MJ)
| | - Zhizhong Song
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- * E-mail: (ZS); (MJ)
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28
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Aggeli D, Karas VO, Sinnott-Armstrong NA, Varghese V, Shafer RW, Greenleaf WJ, Sherlock G. Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery. Nucleic Acids Res 2018; 46:e42. [PMID: 29361139 PMCID: PMC5909455 DOI: 10.1093/nar/gky022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/15/2017] [Accepted: 01/16/2018] [Indexed: 01/15/2023] Open
Abstract
Much of the within species genetic variation is in the form of single nucleotide polymorphisms (SNPs), typically detected by whole genome sequencing (WGS) or microarray-based technologies. However, WGS produces mostly uninformative reads that perfectly match the reference, while microarrays require genome-specific reagents. We have developed Diff-seq, a sequencing-based mismatch detection assay for SNP discovery without the requirement for specialized nucleic-acid reagents. Diff-seq leverages the Surveyor endonuclease to cleave mismatched DNA molecules that are generated after cross-annealing of a complex pool of DNA fragments. Sequencing libraries enriched for Surveyor-cleaved molecules result in increased coverage at the variant sites. Diff-seq detected all mismatches present in an initial test substrate, with specific enrichment dependent on the identity and context of the variation. Application to viral sequences resulted in increased observation of variant alleles in a biologically relevant context. Diff-Seq has the potential to increase the sensitivity and efficiency of high-throughput sequencing in the detection of variation.
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Affiliation(s)
- Dimitra Aggeli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Vlad O Karas
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Vici Varghese
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert W Shafer
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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29
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Lemoine F, Domelevo Entfellner JB, Wilkinson E, Correia D, Dávila Felipe M, De Oliveira T, Gascuel O. Renewing Felsenstein's phylogenetic bootstrap in the era of big data. Nature 2018; 556:452-456. [PMID: 29670290 PMCID: PMC6030568 DOI: 10.1038/s41586-018-0043-0] [Citation(s) in RCA: 321] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 03/01/2018] [Indexed: 12/29/2022]
Abstract
Felsenstein's application of the bootstrap method to evolutionary trees is one of the most cited scientific papers of all time. The bootstrap method, which is based on resampling and replications, is used extensively to assess the robustness of phylogenetic inferences. However, increasing numbers of sequences are now available for a wide variety of species, and phylogenies based on hundreds or thousands of taxa are becoming routine. With phylogenies of this size Felsenstein's bootstrap tends to yield very low supports, especially on deep branches. Here we propose a new version of the phylogenetic bootstrap in which the presence of inferred branches in replications is measured using a gradual 'transfer' distance rather than the binary presence or absence index used in Felsenstein's original version. The resulting supports are higher and do not induce falsely supported branches. The application of our method to large mammal, HIV and simulated datasets reveals their phylogenetic signals, whereas Felsenstein's bootstrap fails to do so.
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Affiliation(s)
- F Lemoine
- Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France
- Hub Bioinformatique et Biostatistique, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France
| | - J-B Domelevo Entfellner
- Department of Computer Science, University of the Western Cape, Cape Town, South Africa
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - E Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - D Correia
- Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France
| | - M Dávila Felipe
- Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France
| | - T De Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - O Gascuel
- Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France.
- Méthodes et Algorithmes pour la Bioinformatique, LIRMM UMR 5506, Université de Montpellier & CNRS, Montpellier, France.
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30
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Mehta SR, Chaillon A, Gaines TL, Gonzalez-Zuniga PE, Stockman JK, Almanza-Reyes H, Chavez JR, Vera A, Wagner KD, Patterson TL, Scott B, Smith DM, Strathdee SA. Impact of Public Safety Policies on Human Immunodeficiency Virus Transmission Dynamics in Tijuana, Mexico. Clin Infect Dis 2018; 66:758-764. [PMID: 29045592 PMCID: PMC5848227 DOI: 10.1093/cid/cix884] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/09/2017] [Indexed: 11/15/2022] Open
Abstract
Background North Tijuana, Mexico is home to many individuals at high risk for transmitting and acquiring human immunodeficiency virus (HIV). Recently, policy shifts by local government impacted how these individuals were handled by authorities. Here we examined how this affected regional HIV transmission dynamics. Methods HIV pol sequences and associated demographic information were collected from 8 research studies enrolling persons in Tijuana and were used to infer viral transmission patterns. To evaluate the impact of recent policy changes on HIV transmission dynamics, qualitative interviews were performed on a subset of recently infected individuals. Results Between 2004 and 2016, 288 unique HIV pol sequences were obtained from individuals in Tijuana, including 46.4% from men who have sex with men, 42.1% from individuals reporting transactional sex, and 27.8% from persons who inject drugs (some individuals had >1 risk factor). Forty-two percent of sequences linked to at least 1 other sequence, forming 37 transmission clusters. Thirty-two individuals seroconverted during the observation period, including 8 between April and July 2016. Three of these individuals were putatively linked together. Qualitative interviews suggested changes in policing led individuals to shift locations of residence and injection drug use, leading to increased risk taking (eg, sharing needles). Conclusions Near real-time molecular epidemiologic analyses identified a cluster of linked transmissions temporally associated with policy shifts. Interviews suggested these shifts may have led to increased risk taking among individuals at high risk for HIV acquisition. With all public policy shifts, downstream impacts need to be carefully considered, as even well-intentioned policies can have major public health consequences.
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Affiliation(s)
- Sanjay R Mehta
- Departments of Medicine University of California, La Jolla
- Departments of Pathology, University of California, La Jolla
- San Diego Veterans Affairs Medical Center, California
| | | | - Tommi L Gaines
- Departments of Medicine University of California, La Jolla
| | | | | | - Horatio Almanza-Reyes
- Escuela de Ciencias de la Salud Valle de Las Palmas, Universidad Autónoma de Baja California, Tijuana, Baja California, México
| | - Jose Roman Chavez
- Escuela de Ciencias de la Salud Valle de Las Palmas, Universidad Autónoma de Baja California, Tijuana, Baja California, México
| | - Alicia Vera
- Departments of Medicine University of California, La Jolla
| | - Karla D Wagner
- School of Community Health Sciences, University of Nevada, Reno
| | | | - Brianna Scott
- Departments of Medicine University of California, La Jolla
| | - Davey M Smith
- Departments of Medicine University of California, La Jolla
- San Diego Veterans Affairs Medical Center, California
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Abstract
The Brazilian AIDS epidemic has been characterized by an increasing rate of BF1 recombinants and so far eight circulating recombinant forms/CRFs_BF1 have been described countrywide. In this study, pol sequences (protease/PR, reverse transcriptase/RT) of 87 BF1 mosaic isolates identified among 828 patients living in six Brazilian States from three geographic regions (Central West, North, Northeast) were analyzed. Phylogenetic and bootscan analyses were performed to investigate the evolutionary relationship and mosaic structure of BF1 isolates. Those analyses showed that 20.7% of mosaics (18 out of 87) were CRFs-like isolates, mostly represented by CRF28/CRF29_BF-like viruses (14 out of 18). We also identified five highly supported clusters that together comprise 42 out of 87 (48.3%) BF1 sequences, each cluster containing at least five sequences sharing a similar mosaic structure, suggesting possible new unidentified CRFs_BF1. The divergence time of these five potential new CRFs_BF1 clusters was estimated using a Bayesian approach and indicate that they probably originated between the middle 1980s and the middle 1990s. DNA was extracted from whole blood and four overlapping fragments were amplified by PCR providing full/near full length genomes (FLG/NFLG) and partial genomes. Eleven HIV-1 isolates from Cluster # 5 identified in epidemiologically unlinked individuals living in Central West and North regions provided FLG/NFLG/partial genome sequences with identical mosaic structure. These viruses differ from any known CRF_BF1 reported to date and were named CRF90_BF1 by the Los Alamos National Laboratory. This is the 9th CRF_BF1 described in Brazil and the first one identified in Central West and North regions. Our results highlight the importance of continued molecular screening and surveillance studies, especially of full genome sequences to understand the evolutionary dynamics of the HIV-1 epidemic in a country of continental dimensions as Brazil.
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Affiliation(s)
- Mônica Nogueira da Guarda Reis
- Laboratório de Imunologia da AIDS e da Hanseníase, Instituto de Patologia Tropical e Saúde Pública, UFG, Goiânia, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Mariane Martins Araújo Stefani
- Laboratório de Imunologia da AIDS e da Hanseníase, Instituto de Patologia Tropical e Saúde Pública, UFG, Goiânia, Brazil
- * E-mail:
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32
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Yin C, Zhang T, Qu X, Zhang Y, Putatunda R, Xiao X, Li F, Xiao W, Zhao H, Dai S, Qin X, Mo X, Young WB, Khalili K, Hu W. In Vivo Excision of HIV-1 Provirus by saCas9 and Multiplex Single-Guide RNAs in Animal Models. Mol Ther 2017; 25:1168-1186. [PMID: 28366764 PMCID: PMC5417847 DOI: 10.1016/j.ymthe.2017.03.012] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 02/05/2023] Open
Abstract
CRISPR-associated protein 9 (Cas9)-mediated genome editing provides a promising cure for HIV-1/AIDS; however, gene delivery efficiency in vivo remains an obstacle to overcome. Here, we demonstrate the feasibility and efficiency of excising the HIV-1 provirus in three different animal models using an all-in-one adeno-associated virus (AAV) vector to deliver multiplex single-guide RNAs (sgRNAs) plus Staphylococcus aureus Cas9 (saCas9). The quadruplex sgRNAs/saCas9 vector outperformed the duplex vector in excising the integrated HIV-1 genome in cultured neural stem/progenitor cells from HIV-1 Tg26 transgenic mice. Intravenously injected quadruplex sgRNAs/saCas9 AAV-DJ/8 excised HIV-1 proviral DNA and significantly reduced viral RNA expression in several organs/tissues of Tg26 mice. In EcoHIV acutely infected mice, intravenously injected quadruplex sgRNAs/saCas9 AAV-DJ/8 reduced systemic EcoHIV infection, as determined by live bioluminescence imaging. Additionally, this quadruplex vector induced efficient proviral excision, as determined by PCR genotyping in the liver, lungs, brain, and spleen. Finally, in humanized bone marrow/liver/thymus (BLT) mice with chronic HIV-1 infection, successful proviral excision was detected by PCR genotyping in the spleen, lungs, heart, colon, and brain after a single intravenous injection of quadruplex sgRNAs/saCas9 AAV-DJ/8. In conclusion, in vivo excision of HIV-1 proviral DNA by sgRNAs/saCas9 in solid tissues/organs can be achieved via AAV delivery, a significant step toward human clinical trials.
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MESH Headings
- Animals
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- Dependovirus/genetics
- Dependovirus/metabolism
- Disease Models, Animal
- Endonucleases/genetics
- Endonucleases/metabolism
- Gene Editing/methods
- Genetic Therapy/methods
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Genome, Viral
- HIV Infections/pathology
- HIV Infections/therapy
- HIV Infections/virology
- HIV Long Terminal Repeat
- HIV-1/genetics
- HIV-1/metabolism
- Humans
- Mice
- Mice, Transgenic
- Oligonucleotides/genetics
- Oligonucleotides/metabolism
- Proviruses/genetics
- Proviruses/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Staphylococcus aureus/chemistry
- Staphylococcus aureus/enzymology
- gag Gene Products, Human Immunodeficiency Virus/genetics
- gag Gene Products, Human Immunodeficiency Virus/metabolism
- pol Gene Products, Human Immunodeficiency Virus/genetics
- pol Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Chaoran Yin
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Ting Zhang
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Xiying Qu
- Department of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Yonggang Zhang
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Raj Putatunda
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Xiao Xiao
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Fang Li
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Weidong Xiao
- Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Huaqing Zhao
- Department of Clinical Science, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Shen Dai
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Xuebin Qin
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Xianming Mo
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Won-Bin Young
- Department of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Kamel Khalili
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA.
| | - Wenhui Hu
- Department of Neuroscience, Center for Neurovirology and the Comprehensive NeuroAIDS Center, Temple University Lewis Katz School of Medicine, 3500 N. Broad Street, Philadelphia, PA 19140, USA.
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Onywera H, Maman D, Inzaule S, Auma E, Were K, Fredrick H, Owiti P, Opollo V, Etard JF, Mukui I, Kim AA, Zeh C. Surveillance of HIV-1 pol transmitted drug resistance in acutely and recently infected antiretroviral drug-naïve persons in rural western Kenya. PLoS One 2017; 12:e0171124. [PMID: 28178281 PMCID: PMC5298248 DOI: 10.1371/journal.pone.0171124] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/16/2017] [Indexed: 11/21/2022] Open
Abstract
HIV-1 transmitted drug resistance (TDR) is of increasing public health concern in sub-Saharan Africa with the rollout of antiretroviral (ARV) therapy. Such data are, however, limited in Kenya, where HIV-1 drug resistance testing is not routinely performed. From a population-based household survey conducted between September and November 2012 in rural western Kenya, we retrospectively assessed HIV-1 TDR baseline rates, its determinants, and genetic diversity among drug-naïve persons aged 15–59 years with acute HIV-1 infections (AHI) and recent HIV-1 infections (RHI) as determined by nucleic acid amplification test and both Limiting Antigen and BioRad avidity immunoassays, respectively. HIV-1 pol sequences were scored for drug resistance mutations using Stanford HIVdb and WHO 2009 mutation guidelines. HIV-1 subtyping was computed in MEGA6. Eighty seven (93.5%) of the eligible samples were successfully sequenced. Of these, 8 had at least one TDR mutation, resulting in a TDR prevalence of 9.2% (95% CI 4.7–17.1). No TDR was observed among persons with AHI (n = 7). TDR prevalence was 4.6% (95% CI 1.8–11.2) for nucleoside reverse transcriptase inhibitors (NRTIs), 6.9% (95% CI 3.2–14.2) for non- nucleoside reverse transcriptase inhibitors (NNRTIs), and 1.2% (95% CI 0.2–6.2) for protease inhibitors. Three (3.4% 95% CI 0.8–10.1) persons had dual-class NRTI/NNRTI resistance. Predominant TDR mutations in the reverse transcriptase included K103N/S (4.6%) and M184V (2.3%); only M46I/L (1.1%) occurred in the protease. All the eight persons were predicted to have different grades of resistance to the ARV regimens, ranging from potential low-level to high-level resistance. HIV-1 subtype distribution was heterogeneous: A (57.5%), C (6.9%), D (21.8%), G (2.3%), and circulating recombinant forms (11.5%). Only low CD4 count was associated with TDR (p = 0.0145). Our findings warrant the need for enhanced HIV-1 TDR monitoring in order to inform on population-based therapeutic guidelines and public health interventions.
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Affiliation(s)
- Harris Onywera
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
- * E-mail: (CZ); (HO)
| | - David Maman
- Epicentre, Médecins Sans Frontières (MSF), Paris, France
| | - Seth Inzaule
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Erick Auma
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Kennedy Were
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Harrison Fredrick
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Prestone Owiti
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Valarie Opollo
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Jean-François Etard
- TransVIHMI IRD UMI 233 –INSERM U 1175 –Université de Montpellier, Montpellier, France
| | - Irene Mukui
- National AIDS and STI Control Programme (NASCOP), Ministry of Health, Nairobi, Kenya
| | - Andrea A. Kim
- US Centers for Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Clement Zeh
- US Centers for Disease Control and Prevention (CDC), Kisumu, Kenya
- * E-mail: (CZ); (HO)
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Patiño-Galindo JÁ, Torres-Puente M, Bracho MA, Alastrué I, Juan A, Navarro D, Galindo MJ, Gimeno C, Ortega E, González-Candelas F. Identification of a large, fast-expanding HIV-1 subtype B transmission cluster among MSM in Valencia, Spain. PLoS One 2017; 12:e0171062. [PMID: 28152089 PMCID: PMC5289541 DOI: 10.1371/journal.pone.0171062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 01/16/2017] [Indexed: 11/19/2022] Open
Abstract
We describe and characterize an exceptionally large HIV-1 subtype B transmission cluster occurring in the Comunidad Valenciana (CV, Spain). A total of 1806 HIV-1 protease-reverse transcriptase (PR/RT) sequences from different patients were obtained in the CV between 2004 and 2014. After subtyping and generating a phylogenetic tree with additional HIV-1 subtype B sequences, a very large transmission cluster which included almost exclusively sequences from the CV was detected (n = 143 patients). This cluster was then validated and characterized with further maximum-likelihood phylogenetic analyses and Bayesian coalescent reconstructions. With these analyses, the CV cluster was delimited to 113 patients, predominately men who have sex with men (MSM). Although it was significantly located in the city of Valencia (n = 105), phylogenetic analyses suggested this cluster derives from a larger HIV lineage affecting other Spanish localities (n = 194). Coalescent analyses estimated its expansion in Valencia to have started between 1998 and 2004. From 2004 to 2009, members of this cluster represented only 1.46% of the HIV-1 subtype B samples studied in Valencia (n = 5/143), whereas from 2010 onwards its prevalence raised to 12.64% (n = 100/791). In conclusion, we have detected a very large transmission cluster in the CV where it has experienced a very fast growth in the recent years in the city of Valencia, thus contributing significantly to the HIV epidemic in this locality. Its transmission efficiency evidences shortcomings in HIV control measures in Spain and particularly in Valencia.
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Affiliation(s)
- Juan Ángel Patiño-Galindo
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP / Universidad de Valencia and CIBER Epidemiología y Salud Pública, Valencia, Spain
| | - Manoli Torres-Puente
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP / Universidad de Valencia and CIBER Epidemiología y Salud Pública, Valencia, Spain
| | - María Alma Bracho
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP / Universidad de Valencia and CIBER Epidemiología y Salud Pública, Valencia, Spain
| | | | - Amparo Juan
- Unidad Prevención del SIDA y otras ITS, Valencia, Spain
| | - David Navarro
- Hospital Clínico Universitario-Universidad de Valencia, Valencia, Spain
| | | | | | | | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP / Universidad de Valencia and CIBER Epidemiología y Salud Pública, Valencia, Spain
- * E-mail:
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Pérez-Parra S, Chueca N, Álvarez M, Pasquau J, Omar M, Collado A, Vinuesa D, Lozano AB, Yebra G, García F. Phylodynamic and Phylogeographic Profiles of Subtype B HIV-1 Epidemics in South Spain. PLoS One 2016; 11:e0168099. [PMID: 28002469 PMCID: PMC5176287 DOI: 10.1371/journal.pone.0168099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 11/23/2016] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Since 1982, HIV-1 epidemics have evolved to different scenarios in terms of transmission routes, subtype distribution and characteristics of transmission clusters. We investigated the evolutionary history of HIV-1 subtype B in south Spain. PATIENTS & METHODS We studied all newly diagnosed HIV-1 subtype B patients in East Andalusia during the 2005-2012 period. For the analysis, we used the reverse transcriptase and protease sequences from baseline resistance, and the Trugene® HIV Genotyping kit (Siemens, Barcelona, Spain). Subtyping was done with REGA v3.0. The maximum likelihood trees constructed with RAxML were used to study HIV-1 clustering. Phylogeographic and phylodynamic profiles were studied by Bayesian inference methods with BEAST v1.7.5 and SPREAD v1.0.6. RESULTS Of the 493 patients infected with HIV-1 subtype B, 234 grouped into 55 clusters, most of which were small (44 clusters ≤ 5 patients, 31 with 2 patients, 13 with 3). The rest (133/234) were grouped into 11 clusters with ≥ 5 patients, and most (82%, 109/133) were men who have sex with men (MSM) grouped into 8 clusters. The association with clusters was more frequent in Spanish (p = 0.02) men (p< 0.001), MSM (p<0.001) younger than 35 years (p = 0.001) and with a CD4+ T-cell count above 350 cells/ul (p<0.001). We estimated the date of HIV-1 subtype B regional epidemic diversification around 1970 (95% CI: 1965-1987), with an evolutionary rate of 2.4 (95%CI: 1.7-3.1) x 10-3 substitutions/site/year. Most clusters originated in the 1990s in MSMs. We observed exponential subtype B HIV-1 growth in 1980-1990 and 2005-2008. The most significant migration routes for subtype B went from inland cities to seaside locations. CONCLUSIONS We provide the first data on the phylodynamic and phylogeographic profiles of HIV-1 subtype B in south Spain. Our findings of transmission clustering among MSMs should alert healthcare managers to enhance preventive measures in this risk group in order to prevent future outbreaks.
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Affiliation(s)
- Santiago Pérez-Parra
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
| | - Natalia Chueca
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
| | - Marta Álvarez
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
| | - Juan Pasquau
- Servicio de Infecciosas, Hospital Virgen de las Nieves, Granada, Spain
| | - Mohamed Omar
- Servicio de Infecciosas, Hospital Ciudad de Jaén, Jaén, Spain
| | - Antonio Collado
- Servicio de Medicina Interna, Hospital de Torrecárdenas, Almería, Spain
| | - David Vinuesa
- Servicio de Infecciosas, Hospital Universitario San Cecilio, Granada, Spain
| | - Ana B. Lozano
- Servicio de Infecciosas, Hospital de Poniente, Almería, Spain
| | - Gonzalo Yebra
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Federico García
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain
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Dinesha TR, Gomathi S, Boobalan J, Sivamalar S, Solomon SS, Pradeep A, Poongulali S, Solomon S, Balakrishnan P, Saravanan S. Genotypic HIV-1 Drug Resistance Among Patients Failing Tenofovir-Based First-Line HAART in South India. AIDS Res Hum Retroviruses 2016; 32:1234-1236. [PMID: 27334566 DOI: 10.1089/aid.2016.0110] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
According to 2013 WHO guidelines, tenofovir (TDF) is the preferred first-line regimen for adults and adolescents. A total of 167 HIV-1-infected patients attaining immunological failure after TDF-based first-line HAART were included in this study, RT region of HIV-1 pol gene was sequenced for them, IAS-USA 2014 list and Stanford HIV drug resistance database were used for mutation interpretation. REGA V3.0 was used for HIV subtyping. The predominant NRTI and NNRTI mutations observed were M184IV (59.9%), K65R (28.1%), and thymidine analogue mutations (TAMs, 29.3%) and K103NS (54.5%), V106AM (39.5%), and Y181CIV (19.8%), respectively. Mutational association shows, K65R was negatively associated with TAMs (OR 0.31, p .008), M184V (OR 0.14, p .57), and K70E (OR 0.29, p .02). Genotypically predicted level of drug resistance based on mutation pattern shows 88% can be opted for azidothymidine (AZT) and still 65% can be opted for TDF. Considering the nature of K65R mutation in increasing susceptibility to AZT and its low prevalence, we conclude that in most patients failing TDF-based first-line therapy, AZT can be considered for second-line therapy followed by TDF itself.
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Affiliation(s)
- Thongadi Ramesh Dinesha
- 1 Y.R. Gaitonde Centre for AIDS Research and Education, Voluntary Health Services , Taramani, Chennai, India
| | - Selvamurthi Gomathi
- 1 Y.R. Gaitonde Centre for AIDS Research and Education, Voluntary Health Services , Taramani, Chennai, India
| | - Jayaseelan Boobalan
- 1 Y.R. Gaitonde Centre for AIDS Research and Education, Voluntary Health Services , Taramani, Chennai, India
| | - Sathasivam Sivamalar
- 1 Y.R. Gaitonde Centre for AIDS Research and Education, Voluntary Health Services , Taramani, Chennai, India
| | - Sunil S Solomon
- 1 Y.R. Gaitonde Centre for AIDS Research and Education, Voluntary Health Services , Taramani, Chennai, India
- 2 Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Ambrose Pradeep
- 1 Y.R. Gaitonde Centre for AIDS Research and Education, Voluntary Health Services , Taramani, Chennai, India
| | - Selvamuthu Poongulali
- 1 Y.R. Gaitonde Centre for AIDS Research and Education, Voluntary Health Services , Taramani, Chennai, India
| | - Suniti Solomon
- 1 Y.R. Gaitonde Centre for AIDS Research and Education, Voluntary Health Services , Taramani, Chennai, India
| | - Pachamuthu Balakrishnan
- 1 Y.R. Gaitonde Centre for AIDS Research and Education, Voluntary Health Services , Taramani, Chennai, India
| | - Shanmugam Saravanan
- 1 Y.R. Gaitonde Centre for AIDS Research and Education, Voluntary Health Services , Taramani, Chennai, India
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Musumeci G, Magnani G, Bon I, Longo S, Bertoldi A, Degli Antoni AM, Rossi MR, Ruggeri A, Sambri V, Semprini S, Sighinolfi L, Ursitti MA, Zerbini A, Colangeli V, Calza L, Finarelli AC, Massimiliani E, Re MC. HIV-1 early and late diagnosis in the Emilia Romagna Region (Italy): a three year study. New Microbiol 2016; 39:241-246. [PMID: 27727402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/19/2016] [Indexed: 06/06/2023]
Abstract
It is crucial to establish the timing of infection and distinguish between early and long-lasting HIV-1 infections not only for partner notification and epidemiological surveillance, but also to offer early drug treatment and contain the spread of infection. This study analyzed serum and/or plasma samples with a first positive HIV antibody/antigen result coming from different Medical Centers in the Emilia Romagna Region, North East Italy, using the avidity assay, Western Blotting, RNA viral load, CD4 cell counts and genotyping assay. From May 2013 to May 2016, we certified 845 new HIV-1 infections, 18.7% of which were classified on the basis of avidity index as recent infections and 81.3% as long-lasting infections, with an estimated conversion time exceeding six months at the time of study. Western Blotting showed reactivity to only one or two HIV-1 proteins in recently infected patients (RIPs), while a complete pattern to gag, env and pol proteins was observed in most long-lasting infected patients (LLIPs). The median age, gender, nationality and risk transmission factors were comparable in RIPs and LLIPs. Phylogenetic analysis performed in available plasma disclosed B strains, non-B subtypes and circulating recombinant forms (CRFs) in both groups of patients, with a major presence of CRFs in non-Italian HIV subjects. The large number of patients unaware of their HIV status makes it crucial to discover hidden epidemics and implement appropriate targeted public health interventions.
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Affiliation(s)
- Giuseppina Musumeci
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Microbiology Section, University of Bologna, Bologna, Italy
| | - Giacomo Magnani
- Department of Infectious Diseases, S. Maria Nuova IRCCS Hospital, Reggio Emilia, Italy
| | - Isabella Bon
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Microbiology Section, University of Bologna, Bologna, Italy
| | - Serena Longo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Microbiology Section, University of Bologna, Bologna, Italy
| | - Alessia Bertoldi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Microbiology Section, University of Bologna, Bologna, Italy
| | | | - Maria Rita Rossi
- Department of Infectious Diseases and Microbiology, Arcispedale S. Anna, Ferrara, Italy
| | | | - Vittorio Sambri
- The Greater Romagna Hub Laboratory, Unit of Microbiology, Pievesestina, Cesena and Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Microbiology Section, University of Bologna
| | - Simona Semprini
- The Greater Romagna Hub Laboratory, Unit of Microbiology, Pievesestina, Cesena and Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Microbiology Section, University of Bologna
| | - Laura Sighinolfi
- Department of Infectious Diseases, S. Anna Hospital, Ferrara, Italy
| | | | - Alessandro Zerbini
- Clinical Immunology, Allergy, and Advanced Biotechnologies Unit, Diagnostic Imaging and Laboratory Medicine Department, IRCCS-Arcispedale Santa Maria Nuova, Reggio Emilia, Italy
| | - Vincenzo Colangeli
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, S. Orsola-Malpighi Hospital, University of Bologna
| | - Leonardo Calza
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, S. Orsola-Malpighi Hospital, University of Bologna
| | - Alba Carola Finarelli
- Public Health Service - Directorate General for Health and Social Policy - Emilia-Romagna Region, Italy
| | - Erika Massimiliani
- Public Health Service - Directorate General for Health and Social Policy - Emilia-Romagna Region, Italy
| | - Maria Carla Re
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Microbiology Section, University of Bologna, Bologna, Italy
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Chow WZ, Bon AH, Keating S, Anderios F, Halim HA, Takebe Y, Kamarulzaman A, Busch MP, Tee KK. Extensive Genetic Diversity of HIV-1 in Incident and Prevalent Infections among Malaysian Blood Donors: Multiple Introductions of HIV-1 Genotypes from Highly Prevalent Countries. PLoS One 2016; 11:e0161853. [PMID: 27575746 PMCID: PMC5004849 DOI: 10.1371/journal.pone.0161853] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/14/2016] [Indexed: 11/21/2022] Open
Abstract
Transfusion-transmissible infections including HIV-1 continue to pose major risks for unsafe blood transfusions due to both window phase infections and divergent viruses that may not be detected by donor screening assays. Given the recent emergence of several HIV-1 circulating recombinant forms (CRFs) in high-risk populations in the Southeast Asia region, we investigated the genetic diversity of HIV-1 among the blood donors in Kuala Lumpur, Malaysia. A total of 211 HIV-positive plasma samples detected among 730,188 donations to the National Blood Centre between 2013 and 2014 were provided (90.5% male, median age: 27.0 years old). Recent or long-term infection status at the time of donation was determined using a limiting antigen avidity enzyme immunoassay (LAg-Avidity EIA). HIV-1 gag-pol genes were amplified and sequenced from residual plasma for 149 cases followed by genotype determination using phylogenetic and recombination analyses. Transmitted antiretroviral resistance mutations were not observed among the blood donors, among which 22.7% were classified as recent or incident infections. Major circulating HIV-1 genotypes determined by neighbour-joining phylogenetic inference included CRF01_AE at 40.9% (61/149), CRF33_01B at 21.5% (32/149), and subtype B at 10.1% (15/149). Newly-described CRFs including CRF54_01B circulated at 4.0%, CRF74_01B at 2.0%, and CRF53_01B and CRF48_01B at 0.7% each. Interestingly, unique HIV-1 genotypes including African subtype G (8.7%), CRF45_cpx (1.3%), CRF02_AG (0.7%) and CRF07_BC (0.7%) from China were detected for the first time in the country. A cluster of subtype G sequences formed a distinct founder sub-lineage within the African strains. In addition, 8.7% (13/149) of HIV-infected donors had unique recombinant forms (URFs) including CRF01_AE/B' (4.7%), B'/C (2.7%) and B'/G (1.3%) recombinants. Detailed analysis identified similar recombinant structures with shared parental strains among the B'/C and B'/G URFs, some of which were sequenced from recently infected individuals, indicating the possible emergence and on-going spread of foreign clades of CRF candidates among the local population. The findings demonstrate extensive molecular complexity of HIV-1 among the infected blood donors in Malaysia, driven in part by the increased spread of recently described CRFs and multiple introductions of previously unreported genotypes from highly prevalent countries.
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Affiliation(s)
- Wei Zhen Chow
- Centre of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Abdul Hamid Bon
- National Blood Centre of Kuala Lumpur (NBCKL), Kuala Lumpur, Malaysia
| | - Sheila Keating
- Blood Systems Research Institute (BSRI), San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco (UCSF), California, United States of America
| | - Fread Anderios
- National Blood Centre of Kuala Lumpur (NBCKL), Kuala Lumpur, Malaysia
| | | | - Yutaka Takebe
- Centre of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- AIDS Research Center, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, Japan
| | - Adeeba Kamarulzaman
- Centre of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Michael P. Busch
- Blood Systems Research Institute (BSRI), San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco (UCSF), California, United States of America
| | - Kok Keng Tee
- Centre of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hoenigl M, Chaillon A, Kessler HH, Haas B, Stelzl E, Weninger K, Little SJ, Mehta SR. Characterization of HIV Transmission in South-East Austria. PLoS One 2016; 11:e0151478. [PMID: 26967154 PMCID: PMC4788428 DOI: 10.1371/journal.pone.0151478] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/29/2016] [Indexed: 11/18/2022] Open
Abstract
To gain deeper insight into the epidemiology of HIV-1 transmission in South-East Austria we performed a retrospective analysis of 259 HIV-1 partial pol sequences obtained from unique individuals newly diagnosed with HIV infection in South-East Austria from 2008 through 2014. After quality filtering, putative transmission linkages were inferred when two sequences were ≤1.5% genetically different. Multiple linkages were resolved into putative transmission clusters. Further phylogenetic analyses were performed using BEAST v1.8.1. Finally, we investigated putative links between the 259 sequences from South-East Austria and all publicly available HIV polymerase sequences in the Los Alamos National Laboratory HIV sequence database. We found that 45.6% (118/259) of the sampled sequences were genetically linked with at least one other sequence from South-East Austria forming putative transmission clusters. Clustering individuals were more likely to be men who have sex with men (MSM; p<0.001), infected with subtype B (p<0.001) or subtype F (p = 0.02). Among clustered males who reported only heterosexual (HSX) sex as an HIV risk, 47% clustered closely with MSM (either as pairs or within larger MSM clusters). One hundred and seven of the 259 sequences (41.3%) from South-East Austria had at least one putative inferred linkage with sequences from a total of 69 other countries. In conclusion, analysis of HIV-1 sequences from newly diagnosed individuals residing in South-East Austria revealed a high degree of national and international clustering mainly within MSM. Interestingly, we found that a high number of heterosexual males clustered within MSM networks, suggesting either linkage between risk groups or misrepresentation of sexual risk behaviors by subjects.
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Affiliation(s)
- Martin Hoenigl
- Division of Infectious Diseases, University of California San Diego, San Diego, California, United States of America
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Antoine Chaillon
- Division of Infectious Diseases, University of California San Diego, San Diego, California, United States of America
| | - Harald H. Kessler
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- * E-mail:
| | - Bernhard Haas
- Department of Infectious Diseases, Landeskrankenhaus Graz West, Graz, Austria
| | - Evelyn Stelzl
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Karin Weninger
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Susan J. Little
- Division of Infectious Diseases, University of California San Diego, San Diego, California, United States of America
| | - Sanjay R. Mehta
- Division of Infectious Diseases, University of California San Diego, San Diego, California, United States of America
- Veterans Affairs Healthcare System, San Diego, California, United States of America
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Panpradist N, Beck IA, Chung MH, Kiarie JN, Frenkel LM, Lutz BR. Simplified Paper Format for Detecting HIV Drug Resistance in Clinical Specimens by Oligonucleotide Ligation. PLoS One 2016; 11:e0145962. [PMID: 26751207 PMCID: PMC4713472 DOI: 10.1371/journal.pone.0145962] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 12/10/2015] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus (HIV) is a chronic infection that can be managed by antiretroviral treatment (ART). However, periods of suboptimal viral suppression during lifelong ART can select for HIV drug resistant (DR) variants. Transmission of drug resistant virus can lessen or abrogate ART efficacy. Therefore, testing of individuals for drug resistance prior to initiation of treatment is recommended to ensure effective ART. Sensitive and inexpensive HIV genotyping methods are needed in low-resource settings where most HIV infections occur. The oligonucleotide ligation assay (OLA) is a sensitive point mutation assay for detection of drug resistance mutations in HIV pol. The current OLA involves four main steps from sample to analysis: (1) lysis and/or nucleic acid extraction, (2) amplification of HIV RNA or DNA, (3) ligation of oligonucleotide probes designed to detect single nucleotide mutations that confer HIV drug resistance, and (4) analysis via oligonucleotide surface capture, denaturation, and detection (CDD). The relative complexity of these steps has limited its adoption in resource-limited laboratories. Here we describe a simplification of the 2.5-hour plate-format CDD to a 45-minute paper-format CDD that eliminates the need for a plate reader. Analysis of mutations at four HIV-1 DR codons (K103N, Y181C, M184V, and G190A) in 26 blood specimens showed a strong correlation of the ratios of mutant signal to total signal between the paper CDD and the plate CDD. The assay described makes the OLA easier to perform in low resource laboratories.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Ingrid A. Beck
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Michael H. Chung
- Department of Internal Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - James N. Kiarie
- Departments of Obstetrics and Gynecology, University of Nairobi, Nairobi, Kenya
| | - Lisa M. Frenkel
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Departments of Pediatrics and Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Huang Y, Follmann D, Nason M, Zhang L, Huang Y, Mehrotra DV, Moodie Z, Metch B, Janes H, Keefer MC, Churchyard G, Robb ML, Fast PE, Duerr A, McElrath MJ, Corey L, Mascola JR, Graham BS, Sobieszczyk ME, Kublin JG, Robertson M, Hammer SM, Gray GE, Buchbinder SP, Gilbert PB. Effect of rAd5-Vector HIV-1 Preventive Vaccines on HIV-1 Acquisition: A Participant-Level Meta-Analysis of Randomized Trials. PLoS One 2015; 10:e0136626. [PMID: 26332672 PMCID: PMC4558095 DOI: 10.1371/journal.pone.0136626] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/05/2015] [Indexed: 11/28/2022] Open
Abstract
Background Three phase 2b, double-blind, placebo-controlled, randomized efficacy trials have tested recombinant Adenovirus serotype-5 (rAd5)-vector preventive HIV-1 vaccines: MRKAd5 HIV-1 gag/pol/nef in Step and Phambili, and DNA/rAd5 HIV-1 env/gag/pol in HVTN505. Due to efficacy futility observed at the first interim analysis in Step and HVTN505, participants of all three studies were unblinded to their vaccination assignments during the study but continued follow–up. Rigorous meta-analysis can provide crucial information to advise the future utility of rAd5-vector vaccines. Methods We included participant-level data from all three efficacy trials, and three Phase 1–2 trials evaluating the HVTN505 vaccine regimen. We predefined two co-primary analysis cohorts for assessing the vaccine effect on HIV-1 acquisition. The modified-intention-to-treat (MITT) cohort included all randomly assigned participants HIV-1 uninfected at study entry, who received at least the first vaccine/placebo, and the Ad5 cohort included MITT participants who received at least one dose of rAd5-HIV vaccine or rAd5-placebo. Multivariable Cox regression models were used to estimate hazard ratios (HRs) of HIV-1 infection (vaccine vs. placebo) and evaluate HR variation across vaccine regimens, time since vaccination, and subgroups using interaction tests. Findings Results are similar for the MITT and Ad5 cohorts; we summarize MITT cohort results. Pooled across the efficacy trials, over all follow-up time 403 (n = 224 vaccine; n = 179 placebo) of 6266 MITT participants acquired HIV-1, with a non-significantly higher incidence in vaccine recipients (HR 1.21, 95% CI 0.99–1.48, P = 0.06). The HRs significantly differed by vaccine regimen (interaction P = 0.03; MRKAd5 HR 1.41, 95% CI 1.11–1.78, P = 0.005 vs. DNA/rAd5 HR 0.88, 95% CI 0.61–1.26, P = 0.48). Results were similar when including the Phase 1–2 trials. Exploratory analyses based on the efficacy trials supported that the MRKAd5 vaccine-increased risk was concentrated in Ad5-positive or uncircumcised men early in follow-up, and in Ad5-negative or circumcised men later. Overall, MRKAd5 vaccine-increased risk was evident across subgroups except in circumcised Ad5-negative men (HR 0.97, 95% CI 0.58−1.63, P = 0.91); there was little evidence that the DNA/rAd5 vaccine, that was tested in this subgroup, increased risk (HR 0.88, 95% CI 0.61–1.26, P = 0.48). When restricting the analysis of Step and Phambili to follow-up time before unblinding, 114 (n = 65 vaccine; n = 49 placebo) of 3770 MITT participants acquired HIV-1, with a non-significantly higher incidence in MRKAd5 vaccine recipients (HR 1.30, 95% CI 0.89–1.14, P = 0.18). Interpretation and Significance The data support increased risk of HIV-1 infection by MRKAd5 over all follow-up time, but do not support increased risk of HIV-1 infection by DNA/rAd5. This study provides a rationale for including monitoring plans enabling detection of increased susceptibility to infection in HIV-1 at-risk populations.
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Affiliation(s)
- Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Dean Follmann
- National Institute of Allergy and Infectious Diseases and Biostatistics Research Branch, National Institutes of Health, Bethesda, MD, United States of America
| | - Martha Nason
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Lily Zhang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ying Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Devan V. Mehrotra
- Merck Research Laboratories, North Wales, PA, United States of America
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Barbara Metch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael C. Keefer
- Infectious Disease Division, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America
| | | | - Merlin L. Robb
- HJF HIV Program, US Military HIV Research Program, Bethesda, MD, United States of America
| | - Patricia E. Fast
- Research and Development, International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Ann Duerr
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States of America
| | - Barney S. Graham
- Viral Pathogenesis Laboratory, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States of America
| | - Magdalena E. Sobieszczyk
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, New York, United States of America
| | - James G. Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael Robertson
- Infectious Disease Clinical Research, Merck, Philadelphia, Pennsylvania, United States of America
| | - Scott M. Hammer
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, New York, United States of America
| | - Glenda E. Gray
- University of the Witwatersrand, Johannesburg, South Africa
| | - Susan P. Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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Dvali N, Chkhartishvili N, Sharvadze L, Karchava M, Tsertsvadze T. MOLECULAR TRACING OF HETEROSEXUAL HIV-1 TRANSMISSION IN GEORGIA. Georgian Med News 2015:54-59. [PMID: 26355316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
HIV epidemic in Georgia has entered a new phase with number of heterosexually acquired infections rising each year. Epidemiological data indicates that this switch in epidemic trends is largely due to HIV positive male IDUs transmitting the virus to their female sexual partners. However, no genetic studies confirming linkage between IDUs and their sex partners were done in Georgia before. The objective of our study was to investigate molecular epidemiology of HIV-1 transmission events between heterosexual couples. Viral genotypes were obtained from plasma specimens of 36 heterosexual HIV-1 positive antiretroviral treatment (ART) naive persons representing 18 epidemiologically linked transmission events were genotyped and phylogenetic analyses were done on HIV pol sequences. HIV infection among all women was attributed to heterosexual transmission from their partners. None of 18 women had history of IDU. Fourteen pairs had subtype A virus, three - subtype B and one - subtype G viruses. Phylogenetic analysis confirmed the existing epidemiological link in 16 pairs with bootstrap values ranging from 88% to 100%. Of these 16 events, viruses from 14 pairs had genetic distance less than 0.015.Mutation A62V was seen in samples from 5 pairs, of them samples from 4 pairs additionally had V77I mutation. All 5 pairs were infected with the subtype Avirus. Women, who are sexual partners of IDUs or other men with high risk heterosexual behaviors, are at increased risk of HIV acquisition. HIV epidemic in Georgia has not spread to general population and remains concentrated around key populations at risk. Our work confirms that female sexual partners can serve as a bridge between key affected populations and general community, such as heterosexually active adults. Therefore, prevention efforts targeting key populations at risk and their sexual partners need to be expanded to avoid the spread of the infection within specific communities and beyond.
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Affiliation(s)
- N Dvali
- Infectious Diseases, AIDS and Clinical Immunology Research Center; I. Javakhishvili Tbilisi State University, Georgia
| | - N Chkhartishvili
- Infectious Diseases, AIDS and Clinical Immunology Research Center; I. Javakhishvili Tbilisi State University, Georgia
| | - L Sharvadze
- Infectious Diseases, AIDS and Clinical Immunology Research Center; I. Javakhishvili Tbilisi State University, Georgia
| | - M Karchava
- Infectious Diseases, AIDS and Clinical Immunology Research Center; I. Javakhishvili Tbilisi State University, Georgia
| | - T Tsertsvadze
- Infectious Diseases, AIDS and Clinical Immunology Research Center; I. Javakhishvili Tbilisi State University, Georgia
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Dvali N, Chkhartishvili N, Karchava M, Sharvadze L, Tsertsvadze T. Distinct drug resistance profile of HIV-1 subtype A strain circulating in Georgia. Georgian Med News 2015:19-24. [PMID: 25879553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Emergence of HIV-1 drug resistance limits effectiveness of antiretroviral therapy (ART). Since 2004 Georgia provides free ART to all patients in need. We aimed to evaluate drug resistance patterns of Georgian HIV-1 variants among patients with virologic failure. Study included adult HIV-1 patients, who experienced virologic failure and were found to carry drug resistant strains based on genotypic resistance testing in 2005-2013. HIV-1 pol gene sequences were examined for the presence of resistance-associated mutations. Stanford HIV Sequence Database was used for interpretation of resistance data. A total 193 patients were included in the study. Among them majority (86.5%) carried subtype A virus and nearly 80% were on Efavirenz-based regimen. The most common nucleoside reverse transcriptase inhibitor (NRTI) mutation was M184V - 86.0% (n=166). The most frequent non-nucleoside reverse transcriptase inhibitor (NNRTI) mutation was G190S, found in 105 (54.4%) of samples. Other significant NNRTI mutations included K101E (31.6%, n=61), K103N (30.1%, n=58) and Y181CI (26.9%, n=52). The prevalence of G190S was 62.3% in subtype A viruses compared to 3.8% in non-A variants (p<0.0001). Frequency of K101E was also significantly higher in subtype A (36.5% vs. 0%, p<0.0001). ). In 69 samples G190S co-occurred with either K101E or Y181C or with both: 39 genotypes G190S/K101E; 10 genotypes G190S/Y181CI and 20 genotypes G190S/K101E/Y181CI. High prevalence of G190S and K101 mutations suggests subtype A specific response to currently approved first-line NNRTIs. Frequent co-occurrence of G190S with Y181C and K101E may limit the use of novel generation NNRTIs in subtype A infected patients with previous exposure to this drug class.
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Affiliation(s)
- N Dvali
- 1Infectious Diseases, AIDS and Clinical Immunology Research Center; 2Ivane Javakhishvili Tbilisi State University, Georgia
| | - N Chkhartishvili
- 1Infectious Diseases, AIDS and Clinical Immunology Research Center; 2Ivane Javakhishvili Tbilisi State University, Georgia
| | - M Karchava
- 1Infectious Diseases, AIDS and Clinical Immunology Research Center; 2Ivane Javakhishvili Tbilisi State University, Georgia
| | - L Sharvadze
- 1Infectious Diseases, AIDS and Clinical Immunology Research Center; 2Ivane Javakhishvili Tbilisi State University, Georgia
| | - T Tsertsvadze
- 1Infectious Diseases, AIDS and Clinical Immunology Research Center; 2Ivane Javakhishvili Tbilisi State University, Georgia
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Roberts HE, Hurst J, Robinson N, Brown H, Flanagan P, Vass L, Fidler S, Weber J, Babiker A, Phillips RE, McLean AR, Frater J. Structured observations reveal slow HIV-1 CTL escape. PLoS Genet 2015; 11:e1004914. [PMID: 25642847 PMCID: PMC4333731 DOI: 10.1371/journal.pgen.1004914] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/23/2014] [Indexed: 01/11/2023] Open
Abstract
The existence of viral variants that escape from the selection pressures imposed by cytotoxic T-lymphocytes (CTLs) in HIV-1 infection is well documented, but it is unclear when they arise, with reported measures of the time to escape in individuals ranging from days to years. A study of participants enrolled in the SPARTAC (Short Pulse Anti-Retroviral Therapy at HIV Seroconversion) clinical trial allowed direct observation of the evolution of CTL escape variants in 125 adults with primary HIV-1 infection observed for up to three years. Patient HLA-type, longitudinal CD8+ T-cell responses measured by IFN-γ ELISpot and longitudinal HIV-1 gag, pol, and nef sequence data were used to study the timing and prevalence of CTL escape in the participants whilst untreated. Results showed that sequence variation within CTL epitopes at the first time point (within six months of the estimated date of seroconversion) was consistent with most mutations being transmitted in the infecting viral strain rather than with escape arising within the first few weeks of infection. Escape arose throughout the first three years of infection, but slowly and steadily. Approximately one third of patients did not drive any new escape in an HLA-restricted epitope in just under two years. Patients driving several escape mutations during these two years were rare and the median and modal numbers of new escape events in each patient were one and zero respectively. Survival analysis of time to escape found that possession of a protective HLA type significantly reduced time to first escape in a patient (p = 0.01), and epitopes escaped faster in the face of a measurable CD8+ ELISpot response (p = 0.001). However, even in an HLA matched host who mounted a measurable, specific, CD8+ response the average time before the targeted epitope evolved an escape mutation was longer than two years.
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Affiliation(s)
- Hannah E. Roberts
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Jacob Hurst
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- The Institute for Emerging Infections, The Oxford Martin School, Oxford, Oxford United Kingdom
| | - Nicola Robinson
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford, United Kingdom
| | - Helen Brown
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford, United Kingdom
| | - Peter Flanagan
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Laura Vass
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Sarah Fidler
- Division of Medicine, Wright Fleming Institute, Imperial College, London, United Kingdom
| | - Jonathan Weber
- Division of Medicine, Wright Fleming Institute, Imperial College, London, United Kingdom
| | - Abdel Babiker
- Medical Research Council Clinical Trials Unit, London, United Kingdom
| | - Rodney E. Phillips
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- The Institute for Emerging Infections, The Oxford Martin School, Oxford, Oxford United Kingdom
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford, United Kingdom
- * E-mail:
| | - Angela R. McLean
- The Institute for Emerging Infections, The Oxford Martin School, Oxford, Oxford United Kingdom
- Department of Zoology, Oxford University, Oxford, United Kingdom
| | - John Frater
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- The Institute for Emerging Infections, The Oxford Martin School, Oxford, Oxford United Kingdom
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford, United Kingdom
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Huang Y, Duerr A, Frahm N, Zhang L, Moodie Z, De Rosa S, McElrath MJ, Gilbert PB. Immune-correlates analysis of an HIV-1 vaccine efficacy trial reveals an association of nonspecific interferon-γ secretion with increased HIV-1 infection risk: a cohort-based modeling study. PLoS One 2014; 9:e108631. [PMID: 25369172 PMCID: PMC4219669 DOI: 10.1371/journal.pone.0108631] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 08/19/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Elevated risk of HIV-1 infection among recipients of an adenovirus serotype 5 (Ad5)-vectored HIV-1 vaccine was previously reported in the Step HIV-1 vaccine efficacy trial. We assessed pre-infection cellular immune responses measured at 4 weeks after the second vaccination to determine their roles in HIV-1 infection susceptibility among Step study male participants. METHODS We examined ex vivo interferon-γ (IFN-γ) secretion from peripheral blood mononuclear cells (PBMC) using an ELISpot assay in 112 HIV-infected and 962 uninfected participants. In addition, we performed flow cytometric assays to examine T-cell activation, and ex vivo IFN-γ and interleukin-2 secretion from CD4(+) and CD8(+) T cells. We accounted for the sub-sampling design in Cox proportional hazards models to estimate hazard ratios (HRs) of HIV-1 infection per 1-log(e) increase of the immune responses. FINDINGS We found that HIV-specific immune responses were not associated with risk of HIV-1 infection. However, each 1-log(e) increase of mock responses measured by the ELISpot assay (i.e., IFN-γ secretion in the absence of antigen-specific stimulation) was associated with a 62% increase of HIV-1 infection risk among vaccine recipients (HR = 1.62, 95% CI: (1.28, 2.04), p<0.001). This association remains after accounting for CD4(+) or CD8(+) T-cell activation. We observed a moderate correlation between ELISpot mock responses and CD4(+) T-cells secreting IFN-γ (ρ = 0.33, p = 0.007). In addition, the effect of the Step vaccine on infection risk appeared to vary with ELISpot mock response levels, especially among participants who had pre-existing anti-Ad5 antibodies (interaction p = 0.04). CONCLUSIONS The proportion of cells, likely CD4(+) T-cells, producing IFN-γ without stimulation by exogenous antigen appears to carry information beyond T-cell activation and baseline characteristics that predict risk of HIV-1 infection. These results motivate additional investigation to understand the potential link between IFN-γ secretion and underlying causes of elevated HIV-1 infection risk among vaccine recipients in the Step study.
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MESH Headings
- AIDS Vaccines/immunology
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Cohort Studies
- Follow-Up Studies
- HIV Infections/pathology
- HIV Infections/prevention & control
- HIV-1/metabolism
- Humans
- Immunoassay
- Interferon-gamma/metabolism
- Interleukin-2/metabolism
- Leukocytes, Mononuclear/immunology
- Leukocytes, Mononuclear/metabolism
- Lymphocyte Activation
- Male
- Proportional Hazards Models
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Risk
- gag Gene Products, Human Immunodeficiency Virus/genetics
- gag Gene Products, Human Immunodeficiency Virus/immunology
- gag Gene Products, Human Immunodeficiency Virus/metabolism
- nef Gene Products, Human Immunodeficiency Virus/genetics
- nef Gene Products, Human Immunodeficiency Virus/immunology
- nef Gene Products, Human Immunodeficiency Virus/metabolism
- pol Gene Products, Human Immunodeficiency Virus/genetics
- pol Gene Products, Human Immunodeficiency Virus/immunology
- pol Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| | - Ann Duerr
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Lily Zhang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Steve De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
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Armitage AE, Deforche K, Welch JJ, Van Laethem K, Camacho R, Rambaut A, Iversen AKN. Possible footprints of APOBEC3F and/or other APOBEC3 deaminases, but not APOBEC3G, on HIV-1 from patients with acute/early and chronic infections. J Virol 2014; 88:12882-94. [PMID: 25165112 PMCID: PMC4248940 DOI: 10.1128/jvi.01460-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/21/2014] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED Members of the apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like-3 (APOBEC3) innate cellular cytidine deaminase family, particularly APOBEC3F and APOBEC3G, can cause extensive and lethal G-to-A mutations in HIV-1 plus-strand DNA (termed hypermutation). It is unclear if APOBEC3-induced mutations in vivo are always lethal or can occur at sublethal levels that increase HIV-1 diversification and viral adaptation to the host. The viral accessory protein Vif counteracts APOBEC3 activity by binding to APOBEC3 and promoting proteasome degradation; however, the efficiency of this interaction varies, since a range of hypermutation frequencies are observed in HIV-1 patient DNA. Therefore, we examined "footprints" of APOBEC3G and APOBEC3F activity in longitudinal HIV-1 RNA pol sequences from approximately 3,000 chronically infected patients by determining whether G-to-A mutations occurred in motifs that were favored or disfavored by these deaminases. G-to-A mutations were more frequent in APOBEC3G-disfavored than in APOBEC3G-favored contexts. In contrast, mutations in APOBEC3F-disfavored contexts were relatively rare, whereas mutations in contexts favoring APOBEC3F (and possibly other deaminases) occurred 16% more often than average G-to-A mutations. These results were supported by analyses of >500 HIV-1 env sequences from acute/early infection. IMPORTANCE Collectively, our results suggest that APOBEC3G-induced mutagenesis is lethal to HIV-1, whereas mutagenesis caused by APOBEC3F and/or other deaminases may result in sublethal mutations that might facilitate viral diversification. Therefore, Vif-specific cytotoxic T lymphocyte (CTL) responses and drugs that manipulate the interplay between Vif and APOBEC3 may have beneficial or detrimental clinical effects depending on how they affect the binding of Vif to various members of the APOBEC3 family.
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Affiliation(s)
- Andrew E Armitage
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
| | - Koen Deforche
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Kristel Van Laethem
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
| | - Ricardo Camacho
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Andrew Rambaut
- Institute of Evolutionary Biology. University of Edinburgh, Edinburgh, United Kingdom
| | - Astrid K N Iversen
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
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Chen Y, Chen S, Kang J, Fang H, Dao H, Guo W, Lai C, Lai M, Fan J, Fu L, Andrieu JM, Lu W. Evolving molecular epidemiological profile of human immunodeficiency virus 1 in the southwest border of China. PLoS One 2014; 9:e107578. [PMID: 25207977 PMCID: PMC4160289 DOI: 10.1371/journal.pone.0107578] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 08/19/2014] [Indexed: 11/23/2022] Open
Abstract
Background We have previously reported in Xishuangbanna (Banna) Dai Autonomous Prefecture, a well-developed tourist destination in the southwest border of China, that HIV-1 transmitted dominantly through heterosexual contact with less divergent genotypes and few drug resistant mutations [1]. Due to the rapid increase of newly diagnosed HIV-1 cases per year in Banna in recent years, it’s important to evaluate the evolution of HIV-1 molecular epidemiology for the better understanding of ongoing HIV-1 outbreak in this region. Methodology/Principal Findings By sequencing of HIV-1 pol genes and phylogenetic analysis, we conducted a molecular epidemiologic study in 352 HIV-1-seropositive highly active antiretroviral treatment (HAART)-naïve individuals newly diagnosed at the Banna Center for Disease Control and Prevention between 2009 and 2011. Of 283 samples (84.1% taken from heterosexually acquired adults, 10.6% from needle-sharing drug users, 2.8% from men who have sex with men, 0.4% from children born from HIV-1-infected mothers, and 2.1% remained unknown) with successful sequencing for pol gene, we identified 108 (38.2%) HIV-1 subtype CRF08_BC, 101 (35.7%) CRF01_AE, 49 (17.3%) CRF07_BC, 5 (1.8%) C/CRF57_BC, 3 (1.1%) B’, 1 (0.4%) B/CRF51_01B, and 16 (5.7%) unique recombinants forms. Among these infected individuals, 104 (36.7%) cases showed drug resistant or resistance-relevant mutations, and 4 of them conferring high-level resistance to 3TC/FTC, EFV/NVP or NFV. Phylogenetic analysis revealed 21 clusters (2–7 sequences) with only 21.2% (60/283) sequences involved. Conclusion/Significance In contrast to our previous findings, CRF08_BC, replaced CRF01_AE, became the dominant genotype of HIV-1 in Banna prefecture. The viral strains with drug resistance mutations were detected frequently in newly diagnosed HIV-1-infected individuals in this region.
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Affiliation(s)
- Yingyu Chen
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Song Chen
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
- Institut de Recherche sur les Vaccins et l’Immunologie des Cancers et du Sida, Université Paris Descartes/Institut de Recherche pour le Développement, Paris, France
| | - Jun Kang
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Hua Fang
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Hong Dao
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Weizhong Guo
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chunhui Lai
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Mingyue Lai
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Jianhua Fan
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Linchun Fu
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jean-Marie Andrieu
- Institut de Recherche sur les Vaccins et l’Immunologie des Cancers et du Sida, Université Paris Descartes/Institut de Recherche pour le Développement, Paris, France
| | - Wei Lu
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
- Institut de Recherche sur les Vaccins et l’Immunologie des Cancers et du Sida, Université Paris Descartes/Institut de Recherche pour le Développement, Paris, France
- * E-mail:
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Cabello M, Mendoza Y, Bello G. Spatiotemporal dynamics of dissemination of non-pandemic HIV-1 subtype B clades in the Caribbean region. PLoS One 2014; 9:e106045. [PMID: 25148215 PMCID: PMC4141835 DOI: 10.1371/journal.pone.0106045] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/29/2014] [Indexed: 11/18/2022] Open
Abstract
The Human immunodeficiency virus type-1 (HIV-1) epidemic in the Caribbean region is mostly driven by subtype B; but information about the pattern of viral spread in this geographic region is scarce and different studies point to quite divergent models of viral dissemination. In this study, we reconstructed the spatiotemporal and population dynamics of the HIV-1 subtype B epidemic in the Caribbean. A total of 1,806 HIV-1 subtype B pol sequences collected from 17 different Caribbean islands between 1996 and 2011 were analyzed together with sequences from the United States (n = 525) and France (n = 340) included as control. Maximum Likelihood phylogenetic analyses revealed that HIV-1 subtype B infections in the Caribbean are driven by dissemination of the pandemic clade (BPANDEMIC) responsible for most subtype B infections across the world, and older non-pandemic lineages (BCAR) characteristics of the Caribbean region. The non-pandemic BCAR strains account for >40% of HIV-1 infections in most Caribbean islands; with exception of Cuba and Puerto Rico. Bayesian phylogeographic analyses indicate that BCAR strains probably arose in the island of Hispaniola (Haiti/Dominican Republic) around the middle 1960s and were later disseminated to Trinidad and Tobago and to Jamaica between the late 1960s and the early 1970s. In the following years, the BCAR strains were also disseminated from Hispaniola and Trinidad and Tobago to other Lesser Antilles islands at multiple times. The BCAR clades circulating in Hispaniola, Jamaica and Trinidad and Tobago appear to have experienced an initial phase of exponential growth, with mean estimated growth rates of 0.35-0.45 year(-1), followed by a more recent stabilization since the middle 1990s. These results demonstrate that non-pandemic subtype B lineages have been widely disseminated through the Caribbean since the late 1960s and account for an important fraction of current HIV-1 infections in the region.
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Affiliation(s)
- Marina Cabello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Yaxelis Mendoza
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur City, Andhra Pradesh, India
- Department of Genetics and Molecular Biology, University of Panama, Panama City, Panama
- INDICASAT-AIP, City of Knowledge, Clayton, Panama City, Panama
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
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Kiwelu IE, Novitsky V, Kituma E, Margolin L, Baca J, Manongi R, Sam N, Shao J, McLane MF, Kapiga SH, Essex M. HIV-1 pol diversity among female bar and hotel workers in Northern Tanzania. PLoS One 2014; 9:e102258. [PMID: 25003939 PMCID: PMC4087014 DOI: 10.1371/journal.pone.0102258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 06/16/2014] [Indexed: 11/18/2022] Open
Abstract
A national ART program was launched in Tanzania in October 2004. Due to the existence of multiple HIV-1 subtypes and recombinant viruses co-circulating in Tanzania, it is important to monitor rates of drug resistance. The present study determined the prevalence of HIV-1 drug resistance mutations among ART-naive female bar and hotel workers, a high-risk population for HIV-1 infection in Moshi, Tanzania. A partial HIV-1 pol gene was analyzed by single-genome amplification and sequencing in 45 subjects (622 pol sequences total; median number of sequences per subject, 13; IQR 5-20) in samples collected in 2005. The prevalence of HIV-1 subtypes A1, C, and D, and inter-subtype recombinant viruses, was 36%, 29%, 9% and 27%, respectively. Thirteen different recombination patterns included D/A1/D, C/A1, A1/C/A1, A1/U/A1, C/U/A1, C/A1, U/D/U, D/A1/D, A1/C, A1/C, A2/C/A2, CRF10_CD/C/CRF10_CD and CRF35_AD/A1/CRF35_AD. CRF35_AD was identified in Tanzania for the first time. All recombinant viruses in this study were unique, suggesting ongoing recombination processes among circulating HIV-1 variants. The prevalence of multiple infections in this population was 16% (n = 7). Primary HIV-1 drug resistance mutations to RT inhibitors were identified in three (7%) subjects (K65R plus Y181C; N60D; and V106M). In some subjects, polymorphisms were observed at the RT positions 41, 69, 75, 98, 101, 179, 190, and 215. Secondary mutations associated with NNRTIs were observed at the RT positions 90 (7%) and 138 (6%). In the protease gene, three subjects (7%) had M46I/L mutations. All subjects in this study had HIV-1 subtype-specific natural polymorphisms at positions 36, 69, 89 and 93 that are associated with drug resistance in HIV-1 subtype B. These results suggested that HIV-1 drug resistance mutations and natural polymorphisms existed in this population before the initiation of the national ART program. With increasing use of ARV, these results highlight the importance of drug resistance monitoring in Tanzania.
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Affiliation(s)
- Ireen E. Kiwelu
- Kilimanjaro Christian Medical Centre and College, Tumaini University, Moshi, Tanzania
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Vladimir Novitsky
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Elimsaada Kituma
- Kilimanjaro Christian Medical Centre and College, Tumaini University, Moshi, Tanzania
- Kilimanjaro Reproductive Health Program, Moshi, Tanzania
| | - Lauren Margolin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Jeannie Baca
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Rachel Manongi
- Kilimanjaro Christian Medical Centre and College, Tumaini University, Moshi, Tanzania
- Kilimanjaro Reproductive Health Program, Moshi, Tanzania
| | - Noel Sam
- Kilimanjaro Christian Medical Centre and College, Tumaini University, Moshi, Tanzania
- Kilimanjaro Reproductive Health Program, Moshi, Tanzania
| | - John Shao
- Kilimanjaro Christian Medical Centre and College, Tumaini University, Moshi, Tanzania
| | - Mary F. McLane
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Saidi H. Kapiga
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- Kilimanjaro Reproductive Health Program, Moshi, Tanzania
| | - M. Essex
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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