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Switzer WM, Shankar A, Jia H, Knyazev S, Ambrosio F, Kelly R, Zheng H, Campbell EM, Cintron R, Pan Y, Saduvala N, Panneer N, Richman R, Singh MB, Thoroughman DA, Blau EF, Khalil GM, Lyss S, Heneine W. High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA. Virus Evol 2024; 10:veae015. [PMID: 38510920 PMCID: PMC10953796 DOI: 10.1093/ve/veae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 03/22/2024] Open
Abstract
We investigated transmission dynamics of a large human immunodeficiency virus (HIV) outbreak among persons who inject drugs (PWID) in KY and OH during 2017-20 by using detailed phylogenetic, network, recombination, and cluster dating analyses. Using polymerase (pol) sequences from 193 people associated with the investigation, we document high HIV-1 diversity, including Subtype B (44.6 per cent); numerous circulating recombinant forms (CRFs) including CRF02_AG (2.5 per cent) and CRF02_AG-like (21.8 per cent); and many unique recombinant forms composed of CRFs with major subtypes and sub-subtypes [CRF02_AG/B (24.3 per cent), B/CRF02_AG/B (0.5 per cent), and A6/D/B (6.4 per cent)]. Cluster analysis of sequences using a 1.5 per cent genetic distance identified thirteen clusters, including a seventy-five-member cluster composed of CRF02_AG-like and CRF02_AG/B, an eighteen-member CRF02_AG/B cluster, Subtype B clusters of sizes ranging from two to twenty-three, and a nine-member A6/D and A6/D/B cluster. Recombination and phylogenetic analyses identified CRF02_AG/B variants with ten unique breakpoints likely originating from Subtype B and CRF02_AG-like viruses in the largest clusters. The addition of contact tracing results from OH to the genetic networks identified linkage between persons with Subtype B, CRF02_AG, and CRF02_AG/B sequences in the clusters supporting de novo recombinant generation. Superinfection prevalence was 13.3 per cent (8/60) in persons with multiple specimens and included infection with B and CRF02_AG; B and CRF02_AG/B; or B and A6/D/B. In addition to the presence of multiple, distinct molecular clusters associated with this outbreak, cluster dating inferred transmission associated with the largest molecular cluster occurred as early as 2006, with high transmission rates during 2017-8 in certain other molecular clusters. This outbreak among PWID in KY and OH was likely driven by rapid transmission of multiple HIV-1 variants including de novo viral recombinants from circulating viruses within the community. Our findings documenting the high HIV-1 transmission rate and clustering through partner services and molecular clusters emphasize the importance of leveraging multiple different data sources and analyses, including those from disease intervention specialist investigations, to better understand outbreak dynamics and interrupt HIV spread.
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Affiliation(s)
- William M Switzer
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Anupama Shankar
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Hongwei Jia
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Sergey Knyazev
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
- Oak Ridge Institute for Science and Education, 1299 Bethel Valley Rd, Oak Ridge, TN 37830, USA
| | - Frank Ambrosio
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Reagan Kelly
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
- General Dynamics Information Technology, 3150 Fairview Park Dr, Falls Church, VA 22042, USA
| | - HaoQiang Zheng
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | | | - Roxana Cintron
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Yi Pan
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | | | - Nivedha Panneer
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Rhiannon Richman
- HIV Surveillance Program, Bureau of HIV/STI/Viral Hepatitis, Ohio Department of Health, 246 North High Street, Colombus, OH 43215, USA
| | - Manny B Singh
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
| | - Douglas A Thoroughman
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
- ORR/Division of State and Local Readiness/Field Services Branch/CEFO Program, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Erin F Blau
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
- Epidemic Intelligence Service, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - George M Khalil
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Sheryl Lyss
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
- HIV Surveillance Program, Bureau of HIV/STI/Viral Hepatitis, Ohio Department of Health, 246 North High Street, Colombus, OH 43215, USA
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
- Hamilton County Public Health, 250 William Howard Taft Rd, Cincinnati, OH 45219, USA
- Northern Kentucky Health Department, 8001 Veterans Memorial Drive, Florence, KY 41042, USA
| | - Walid Heneine
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
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Genetic characteristics of HIV-1 CRF06_cpx and CRF56_cpx strains isolated in Guangzhou, China. Arch Virol 2021; 166:2853-2857. [PMID: 34373969 DOI: 10.1007/s00705-021-05198-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/14/2021] [Indexed: 10/20/2022]
Abstract
Strains of the HIV-1 circulating recombinant forms (CRFs) 06_cpx and 56_cpx were identified for the first time in Guangzhou, China. The nearly full-length genome (NFLG) sequence was amplified, and the PCR products were sequenced by the Sanger method. The CRF06_cpx and CRF56_cpx strains were identified using the Basic Local Alignment Search Tool (BLAST) and confirmed by neighbour-joining (NJ) phylogenetic analysis. Additionally, these strains were found to contain transmitted drug resistance mutations that have little effect on first-line efavirenz (EFV)-based treatment. Genetic analysis of the detailed sequence data will provide more information on the HIV-1 epidemic in China.
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Lee JE, Lee SO, Lee S, Park S, Kim HH, Shin KH, Kang JS, Lee SH. Epidemiological and phylogenetic analysis for non-B subtypes of human immunodeficiency virus type 1 in Busan, Korea. Sci Rep 2021; 11:16000. [PMID: 34362954 PMCID: PMC8346492 DOI: 10.1038/s41598-021-94794-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 07/18/2021] [Indexed: 11/29/2022] Open
Abstract
Recent data on non-B subtypes’ epidemiology among patients infected with human immunodeficiency virus-1 (HIV-1) in Korea are lacking. We aimed to assess the changing trends in the epidemiology of non-B subtypes of HIV-1 in Korea using phyloepidemiological analyses. We analyzed the demographic records and sequencing data obtained from genotypic drug resistance tests between 2005 and 2019 from 517 patients infected with HIV attending a tertiary care hospital in Busan, Korea. Subtyping and phylogenetic analyses with reference sequences were performed. Additionally, transmission clusters were identified via maximum-likelihood trees. Non-B subtypes accounted for 21.3% of the 517 sequences. CRF01_AE (52.7%) was the most common non-B subtype, followed by CRF02_AG (16.4%), A1 (11.8%), and C (5.5%). The prevalence of non-B subtypes decreased from 36.4 to 13.4% by 2009, while it increased to 27.4% between 2015 and 2019. Among patients with non-B subtypes, the proportion of overseas sailors decreased from 66.7 to 7.5%; contrarily, the proportion of men-who-have-sex-with-men (MSM) increased from 0 to 46.9% over the study period. We identified 8 transmission clusters involving non-B subtypes, with sizes ranging from 2 to 4 patients, including 3 clusters containing MSM. Our results highlight the changes in the epidemiological trends of non-B subtypes of HIV-1 in Korea.
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Affiliation(s)
- Jeong Eun Lee
- Division of Infectious Disease, Department of Internal Medicine, Pusan National University School of Medicine and Medical Research Institute, Pusan National University Hospital, 179 Gudeok-ro, Seo-gu, Busan, 49241, Republic of Korea
| | - Soon Ok Lee
- Division of Infectious Disease, Department of Internal Medicine, Pusan National University School of Medicine and Medical Research Institute, Pusan National University Hospital, 179 Gudeok-ro, Seo-gu, Busan, 49241, Republic of Korea
| | - Shinwon Lee
- Division of Infectious Disease, Department of Internal Medicine, Pusan National University School of Medicine and Medical Research Institute, Pusan National University Hospital, 179 Gudeok-ro, Seo-gu, Busan, 49241, Republic of Korea
| | - Sohee Park
- Division of Infectious Disease, Department of Internal Medicine, Pusan National University School of Medicine and Medical Research Institute, Pusan National University Hospital, 179 Gudeok-ro, Seo-gu, Busan, 49241, Republic of Korea
| | - Hyung-Hoi Kim
- Deparment of Laboratory Medicine, Pusan National University School of Medicine, Busan, Republic of Korea.,Biomedical Informatics Unit, Pusan National University School of Medicine, Busan, Republic of Korea
| | - Kyung-Hwa Shin
- Deparment of Laboratory Medicine, Pusan National University School of Medicine, Busan, Republic of Korea
| | - Jin Suk Kang
- Division of Infectious Disease, Department of Internal Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Sun Hee Lee
- Division of Infectious Disease, Department of Internal Medicine, Pusan National University School of Medicine and Medical Research Institute, Pusan National University Hospital, 179 Gudeok-ro, Seo-gu, Busan, 49241, Republic of Korea.
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4
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Identification of a New HIV-1 BC Intersubtype Circulating Recombinant Form (CRF108_BC) in Spain. Viruses 2021; 13:v13010093. [PMID: 33445523 PMCID: PMC7826730 DOI: 10.3390/v13010093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
The extraordinary genetic variability of human immunodeficiency virus type 1 (HIV-1) group M has led to the identification of 10 subtypes, 102 circulating recombinant forms (CRFs) and numerous unique recombinant forms. Among CRFs, 11 derived from subtypes B and C have been identified in China, Brazil, and Italy. Here we identify a new HIV-1 CRF_BC in Northern Spain. Originally, a phylogenetic cluster of 15 viruses of subtype C in protease-reverse transcriptase was identified in an HIV-1 molecular surveillance study in Spain, most of them from individuals from the Basque Country and heterosexually transmitted. Analyses of near full-length genome sequences from six viruses from three cities revealed that they were BC recombinant with coincident mosaic structures different from known CRFs. This allowed the definition of a new HIV-1 CRF designated CRF108_BC, whose genome is predominantly of subtype C, with four short subtype B fragments. Phylogenetic analyses with database sequences supported a Brazilian ancestry of the parental subtype C strain. Coalescent Bayesian analyses estimated the most recent common ancestor of CRF108_BC in the city of Vitoria, Basque Country, around 2000. CRF108_BC is the first CRF_BC identified in Spain and the second in Europe, after CRF60_BC, both phylogenetically related to Brazilian subtype C strains.
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New Subtype B Containing HIV-1 Circulating Recombinant of sub-Saharan Africa Origin in Nigerian Men Who Have Sex With Men. J Acquir Immune Defic Syndr 2020; 81:578-584. [PMID: 31107298 DOI: 10.1097/qai.0000000000002076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND HIV-1 circulating recombinant forms (CRF) containing subtype B are uncommon in sub-Saharan Africa. Prevalent infections observed during enrollment of a prospective study of men who have sex with men (MSM) from Lagos, Nigeria, revealed the presence of a family of subtype B and CRF02_AG recombinants. This report describes the HIV-1 genetic diversity within a high-risk, high-prevalence, and previously undersampled cohort of Nigerian MSM. METHODS Between 2013 and 2016, 672 MSM were enrolled at the Lagos site of the TRUST/RV368 study. Prevalent HIV-1 infections were initially characterized by pol sequencing and phylogenetic subtyping analysis. Samples demonstrating the presence of subtype B were further characterized by near full-length sequencing, phylogenetic, and Bayesian analyses. RESULTS Within this cohort, HIV-1 prevalence was 59%. The major subtype was CRF02_AG (57%), followed by CRF02/B recombinants (15%), subtype G (13%), and smaller amounts of A1, B, and other recombinants. Nine clusters of closely related pol sequences indicate ongoing transmission events within this cohort. Among the CRF02_AG/B, a new CRF was identified and termed CRF95_02B. Shared risk factors and Bayesian phylogenetic inference of the new CRF95_02B and the similarly structured CRF56_cpx indicate a Nigerian or West African origin of CRF56_cpx before its observation in France. CONCLUSION With high HIV-1 prevalence, new strains, and multiple transmission networks, this cohort of Nigerian MSM represents a previously hidden reservoir of HIV-1 strains, including the newly identified CRF95_02B and closely related CRF56_cpx. These strains will need to be considered during vaccine selection and development to optimize the design of a globally effective HIV-1 vaccine.
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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] [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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7
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Wirden M, De Oliveira F, Bouvier-Alias M, Lambert-Niclot S, Chaix ML, Raymond S, Si-Mohammed A, Alloui C, André-Garnier E, Bellecave P, Malve B, Mirand A, Pallier C, Poveda JD, Rabenja T, Schneider V, Signori-Schmuck A, Stefic K, Calvez V, Descamps D, Plantier JC, Marcelin AG, Visseaux B. New HIV-1 circulating recombinant form 94: from phylogenetic detection of a large transmission cluster to prevention in the age of geosocial-networking apps in France, 2013 to 2017. Euro Surveill 2019; 24:1800658. [PMID: 31576801 PMCID: PMC6774227 DOI: 10.2807/1560-7917.es.2019.24.39.1800658] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BackgroundEnding the HIV pandemic must involve new tools to rapidly identify and control local outbreaks and prevent the emergence of recombinant strains with epidemiological advantages.AimThis observational study aimed to investigate in France a cluster of HIV-1 cases related to a new circulating recombinant form (CRF). The confirmation this CRF's novelty as well as measures to control its spread are presented.MethodsPhylogenetic analyses of HIV sequences routinely generated for drug resistance genotyping before 2018 in French laboratories were employed to detect the transmission chain. The CRF involved was characterised by almost full-length viral sequencing for six cases. Cases' clinical data were reviewed. Where possible, epidemiological information was collected with a questionnaire.ResultsThe transmission cluster comprised 49 cases, mostly diagnosed in 2016-2017 (n = 37). All were infected with a new CRF, CRF94_cpx. The molecular proximity of this CRF to X4 strains and the high median viraemia, exceeding 5.0 log10 copies/mL, at diagnosis, even in chronic infection, raise concerns of enhanced virulence. Overall, 41 cases were diagnosed in the Ile-de-France region and 45 were men who have sex with men. Among 24 cases with available information, 20 reported finding partners through a geosocial networking app. Prevention activities in the area and population affected were undertaken.ConclusionWe advocate the systematic use of routinely generated HIV molecular data by a dedicated reactive network, to improve and accelerate targeted prevention interventions. Geosocial networking apps can play a role in the spread of outbreaks, but could also deliver local targeted preventive alerts.
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Affiliation(s)
- Marc Wirden
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, AP-HP, Hôpital Pitié Salpêtrière, Laboratoire de virologie, Paris, France
| | - Fabienne De Oliveira
- Normandie Université, UNIROUEN, EA2656 GRAM, CHU de Rouen, Laboratoire de virologie associé au CNR VIH, Rouen, France
| | | | | | - Marie-Laure Chaix
- AP-HP, Hôpital Saint-Louis, Laboratoire de virologie, INSERM U944, Paris, France
| | | | | | - Chakib Alloui
- Laboratoire de virologie, Hôpital Avicenne, Bobigny, France
| | | | | | - Brice Malve
- Laboratoire de virologie CHU de Nancy, Nancy, France
| | - Audrey Mirand
- Laboratoire de virologie CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - Coralie Pallier
- Laboratoire de virologie, Hôpital P. Brousse, Villejuif, France
| | | | - Theresa Rabenja
- Laboratoire du Grand Hôpital de l’Est Francilien, Jossigny, France
| | | | | | - Karl Stefic
- Laboratoire de virologie CHU de Tours, Tours, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, AP-HP, Hôpital Pitié Salpêtrière, Laboratoire de virologie, Paris, France
| | - Diane Descamps
- Laboratoire de virologie, AP-HP, Hopital Bichat Claude Bernard, Univ Paris-Diderot, INSERM, IAME, CNR VIH, Paris, France
| | - Jean-Christophe Plantier
- Normandie Université, UNIROUEN, EA2656 GRAM, CHU de Rouen, Laboratoire de virologie associé au CNR VIH, Rouen, France
| | - Anne-Genevieve Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, AP-HP, Hôpital Pitié Salpêtrière, Laboratoire de virologie, Paris, France
| | - Benoit Visseaux
- Laboratoire de virologie, AP-HP, Hopital Bichat Claude Bernard, Univ Paris-Diderot, INSERM, IAME, CNR VIH, Paris, France
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8
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Lai A, Simonetti FR, Brindicci G, Bergna A, Di Giambenedetto S, Sterrantino G, Mussini C, Menzo S, Bagnarelli P, Zazzi M, Angarano G, Galli M, Monno L, Balotta C. Local Epidemics Gone Viral: Evolution and Diffusion of the Italian HIV-1 Recombinant Form CRF60_BC. Front Microbiol 2019; 10:769. [PMID: 31031735 PMCID: PMC6474184 DOI: 10.3389/fmicb.2019.00769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/26/2019] [Indexed: 12/15/2022] Open
Abstract
The molecular epidemiology of HIV-1 in Italy is becoming increasingly complex, mainly due to the spread of non-B subtypes and the emergence of new recombinant forms. We previously characterized the outbreak of the first Italian circulating recombinant form (CRF60_BC), occurring among young MSM living in Apulia between the years 2009 and 2011. Here we show a 5-year follow-up surveillance to trace the evolution of CRF60_BC and to investigate its further spread in Italy. We collected additional sequences and clinical data from patients harboring CRF60_BC, enrolled at the Infectious Diseases Clinic of the University of Bari. In addition to the 24 previously identified sequences, we retrieved 27 CRF60_BC sequences from patients residing in Apulia, whose epidemiological and clinical features did not differ from those of the initial outbreak, i.e., the Italian origin, young age at HIV diagnosis (median: 24 years; range: 18–37), MSM risk factor (23/25, 92%) and recent infection (from 2008 to 2017). Sequence analysis revealed a growing overall nucleotide diversity, with few nucleotide changes that were fixed over time. Twenty-seven additional sequences were detected across Italy, spanning multiple distant regions. Using a BLAST search, we also identified a CRF60_BC sequence isolated in United Kingdom in 2013. Three patients harbored a unique second generation recombinant form in which CRF60_BC was one of the parental strains. Our data show that CRF60_BC gained epidemic importance, spreading among young MSM in multiple Italian regions and increasing its population size in few years, as the number of sequences identified so far has triplicated since our first report. The observed further divergence of CRF60_BC is likely due to evolutionary bottlenecks and host adaptation during transmission chains. Of note, we detected three second-generation recombinants, further supporting a widespread circulation of CRF60_BC and the increasing complexity of the HIV-1 epidemic in Italy.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetano Brindicci
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetana Sterrantino
- Division of Tropical and Infectious Diseases, Careggi Hospital, Florence, Italy
| | - Cristina Mussini
- Clinic of Infectious Diseases, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Menzo
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Patrizia Bagnarelli
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Massimo Galli
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Laura Monno
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Claudia Balotta
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
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Delgado E, Benito S, Montero V, Cuevas MT, Fernández-García A, Sánchez-Martínez M, García-Bodas E, Díez-Fuertes F, Gil H, Cañada J, Carrera C, Martínez-López J, Sintes M, Pérez-Álvarez L, Thomson MM. Diverse Large HIV-1 Non-subtype B Clusters Are Spreading Among Men Who Have Sex With Men in Spain. Front Microbiol 2019; 10:655. [PMID: 31001231 PMCID: PMC6457325 DOI: 10.3389/fmicb.2019.00655] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/15/2019] [Indexed: 11/23/2022] Open
Abstract
In Western Europe, the HIV-1 epidemic among men who have sex with men (MSM) is dominated by subtype B. However, recently, other genetic forms have been reported to circulate in this population, as evidenced by their grouping in clusters predominantly comprising European individuals. Here we describe four large HIV-1 non-subtype B clusters spreading among MSM in Spain. Samples were collected in 9 regions. A pol fragment was amplified from plasma RNA or blood-extracted DNA. Phylogenetic analyses were performed via maximum likelihood, including database sequences of the same genetic forms as the identified clusters. Times and locations of the most recent common ancestors (MRCA) of clusters were estimated with a Bayesian method. Five large non-subtype B clusters associated with MSM were identified. The largest one, of F1 subtype, was reported previously. The other four were of CRF02_AG (CRF02_1; n = 115) and subtypes A1 (A1_1; n = 66), F1 (F1_3; n = 36), and C (C_7; n = 17). Most individuals belonging to them had been diagnosed of HIV-1 infection in the last 10 years. Each cluster comprised viruses from 3 to 8 Spanish regions and also comprised or was related to viruses from other countries: CRF02_1 comprised a Japanese subcluster and viruses from 8 other countries from Western Europe, Asia, and South America; A1_1 comprised viruses from Portugal, United Kingom, and United States, and was related to the A1 strain circulating in Greece, Albania and Cyprus; F1_3 was related to viruses from Romania; and C_7 comprised viruses from Portugal and was related to a virus from Mozambique. A subcluster within CRF02_1 was associated with heterosexual transmission. Near full-length genomes of each cluster were of uniform genetic form. Times of MRCAs of CRF02_1, A1_1, F1_3, and C_7 were estimated around 1986, 1989, 2013, and 1983, respectively. MRCA locations for CRF02_1 and A1_1 were uncertain (however initial expansions in Spain in Madrid and Vigo, respectively, were estimated) and were most probable in Bilbao, Spain, for F1_3 and Portugal for C_7. These results show that the HIV-1 epidemic among MSM in Spain is becoming increasingly diverse through the expansion of diverse non-subtype B clusters, comprising or related to viruses circulating in other countries.
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Affiliation(s)
- Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sonia Benito
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Vanessa Montero
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María Teresa Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Aurora Fernández-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Mónica Sánchez-Martínez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Elena García-Bodas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco Díez-Fuertes
- AIDS Immunopathogenesis Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Horacio Gil
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,European Program for Public Health Microbiology Training, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Javier Cañada
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Carrera
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Martínez-López
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Marcos Sintes
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Michael M Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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Recordon-Pinson P, Alves BM, Tumiotto C, Bellecave P, Bonnet F, Neau D, Soares EA, Soares MA, Fleury H. A New HIV-1 Circulating Recombinant Form (CRF98_cpx) Between CRF06_cpx and Subtype B Identified in Southwestern France. AIDS Res Hum Retroviruses 2018; 34:1005-1009. [PMID: 29947242 DOI: 10.1089/aid.2018.0122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
During a recent study on the sequencing data of our database between 2012 and 2016 in Southwestern France, we observed that eight patients harbored what seemed to be the same virus. Indeed, routine genotyping at the time of HIV diagnosis showed that protease and reverse transcriptase were related to CRF06_cpx and subtype B, respectively. The integrase sequences (available for three patients) were clustering with CRF06_cpx and envelope (Env) gp120 sequences (available for two patients) with subtype B. Since such a recombinant has not been recorded in the Los Alamos database, we decided to characterize the full-length genome of this virus. The data suggest the identification of a new circulating recombinant form (CRF) between CRF06_cpx and subtype B, the structure of which is very complex with multiple breakpoints. We will refer this CRF as CRF98_cpx.
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Affiliation(s)
| | | | - Camille Tumiotto
- CNRS MFP-UMR 5234, Bordeaux, France
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
| | - Pantxika Bellecave
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
| | - Fabrice Bonnet
- Department of Internal Medicine, University Hospital of Bordeaux, Bordeaux, France
| | - Didier Neau
- Department of Infectious and Tropical Diseases, University Hospital of Bordeaux, Bordeaux, France
| | | | | | - Hervé Fleury
- CNRS MFP-UMR 5234, Bordeaux, France
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
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Tariq U, Parveen A, Akhtar F, Mahmood F, Ali S, Abidi SH. Emergence of Circulating Recombinant Form 56_cpx in Pakistan. AIDS Res Hum Retroviruses 2018; 34:1002-1004. [PMID: 29947245 DOI: 10.1089/aid.2018.0128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In Pakistan, HIV has converted from outbreak to concentrated epidemic and has also bridged into the low-risk population. The HIV epidemic in Pakistan mainly comprises subtype A. Here, we present the first case and genetic analysis of a circulating recombinant form 56_cpx in a Pakistani HIV-infected patient. Genetic analysis of the sequence indicated that Pakistani 56_cpx sequence had more drug resistance mutation than the other 56_cpx sequences available in the database.
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Affiliation(s)
- Uroosa Tariq
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Azra Parveen
- Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Furqana Akhtar
- Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Faisal Mahmood
- Department of Medicine, Aga Khan University, Karachi, Pakistan
| | - Syed Ali
- Department of Biomedical Sciences, Nazarbayev School of Medicine Nazarbayev University, Astana, Kazakhstan
| | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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12
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Trends in Drug Resistance Prevalence, HIV-1 Variants and Clinical Status in HIV-1-infected Pediatric Population in Madrid: 1993 to 2015 Analysis. Pediatr Infect Dis J 2018; 37:e48-e57. [PMID: 28991889 DOI: 10.1097/inf.0000000000001760] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND The expanded use of long-term antiretroviral treatments in infected children may exacerbate the problem of drug resistance mutations selection, which can compromise treatment efficiency. OBJECTIVE We describe the temporal trends of HIV drug resistance mutations and the HIV-1 variants during 23 years (1993 to March 2016) in the Madrid cohort of HIV-infected children and adolescents. METHODS We selected patients with at least one available HIV-1 pol sequence/genotypic resistance profile, establishing different groups according to the sampling year of first resistance data. We determined the prevalence of transmitted drug resistance mutations or acquired drug resistance mutations (DRM), the drug susceptibility among resistant viruses and HIV-1 variants characterized by phylogeny across time. RESULTS A total of 245 pediatric patients were selected, being mainly female, Spanish native, perinatally infected and carrying HIV-1 subtype B. At first sampling, most pediatric patients were on antiretroviral therapy and heavily pretreated. During 1993 to 2016, transmitted drug resistance mutations was found in 13 (26%) of 50 naive children [non-nucleoside reverse transcriptase inhibitors (NNRTI), 14.6%; nucleoside reverse transcriptase inhibitors (NRTI), 10.4%; protease inhibitors, 8.7%]. DRM appeared in 139 (73.2%) of 190 pretreated patients (NRTI, 64.5%; NNRTI, 36%; protease inhibitors, 35.1%). DRM to NNRTI was higher in last 5 years. Non-B variants infected 14.5% of children and adolescents of the Madrid Cohort, being mainly intersubtype recombinants (76.5%), including complex unique recombinant strains. They caused 3.4% infections before 2000, rising to 85.7% during 2011 to 2016. CONCLUSIONS Periodic surveillance resistance and molecular epidemiology studies in long-term pretreated HIV-infected pediatric populations are required to optimize treatment regimens. Results will permit a better understanding of long-time dynamics of viral resistance and HIV-1 variants in Spain.
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Yebra G, Frampton D, Gallo Cassarino T, Raffle J, Hubb J, Ferns RB, Waters L, Tong CYW, Kozlakidis Z, Hayward A, Kellam P, Pillay D, Clark D, Nastouli E, Leigh Brown AJ. A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project. PLoS One 2018; 13:e0192081. [PMID: 29389981 PMCID: PMC5794160 DOI: 10.1371/journal.pone.0192081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/28/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND & METHODS The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospitals NHS Trust and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker. RESULTS The pipeline generated sequences of at least 1Kb of length (median = 7.46Kb, IQR = 4.01Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n = 149, 40.8%) and C (n = 77, 21.1%) and the circulating recombinant form CRF02_AG (n = 32, 8.8%). We found 14 different CRFs (n = 66, 18.1%) and multiple URFs (n = 32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RT pol region, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similar pol sequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset. CONCLUSIONS The initial analysis of genome sequences detected substantial hidden variability in the London HIV epidemic. Analysing full genome sequences, as opposed to only PR+RT, identified previously undetected recombinants. It provided a more reliable description of CRFs (that would be otherwise misclassified) and transmission clusters.
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Affiliation(s)
- Gonzalo Yebra
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Dan Frampton
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
| | | | - Jade Raffle
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
- Department of Clinical Virology, UCL Hospital NHS Foundation Trust, London, United Kingdom
| | - Jonathan Hubb
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
| | - R. Bridget Ferns
- Department of Clinical Virology, UCL Hospital NHS Foundation Trust, London, United Kingdom
- NIHR UCLH/UCL Biomedical Research Centre, London, United Kingdom
| | - Laura Waters
- Department of HIV Medicine, Mortimer Market Centre, Central & North West London NHS Trust, London, United Kingdom
| | - C. Y. William Tong
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
- Queen Mary University, London, United Kingdom
| | - Zisis Kozlakidis
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
- UCL Institute of Disease Informatics, Farr Institute of Health Informatics Research, London, United Kingdom
| | - Andrew Hayward
- UCL Institute of Epidemiology and Health Care, London, United Kingdom
| | - Paul Kellam
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
| | - Deenan Pillay
- UCL Division of Infection and Immunity, Faculty of Medical Sciences, London, United Kingdom
| | - Duncan Clark
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
- School of Life Sciences, University of Glasgow. Glasgow, United Kingdom
| | - Eleni Nastouli
- Department of Clinical Virology, UCL Hospital NHS Foundation Trust, London, United Kingdom
- Department of Population, Policy and Practice, UCL GOS Institute of Child Health, London, United Kingdom
| | - Andrew J. Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
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14
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HIV surveillance combining an assay for identification of very recent infection and phylogenetic analyses on dried spots. AIDS 2017; 31:407-416. [PMID: 27831948 DOI: 10.1097/qad.0000000000001325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Transmitted/founder viruses isolated at the early stage of infection are indicators of the variants that are spreading within a population. The French reporting system for new HIV diagnoses is linked to a virological surveillance using dried serum spots. METHODS We combined an immunoassay for very recent infection (less than 31 days) to a phylogenetic analysis of transmitted/founder viruses and sociodemographic information to analyze the dynamics of the HIV-1 epidemic during a 3-year period. Bayesian coalescent-based methods were used to explore the temporal and spatial dynamics of the identified clusters. RESULTS Of 17 010 dried serum spots collected, 549 very recent infections were identified for which both env sequences and sociodemographic data were available. Non-B transmitted/founder viruses were found in 196 cases (35.7%), belonging to six subtypes and seven circulating recombinant forms. Forty-three dyads/clusters were identified (range 2-11 cases), including 107 individuals (19.5%), mainly MSM. The largest cluster involved MSM infected by a CRF02_AG variant. Reconstruction of viral migrations across time suggests that Paris was the major hub of dissemination. CONCLUSION The study shows the feasibility of the surveillance of the HIV epidemic using this methodology. The observation of actively growing spatiotemporal clusters allows identification of specific networks that may be targets for intervention.
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De Oliveira F, Mourez T, Vessiere A, Ngoupo PA, Alessandri-Gradt E, Simon F, Rousset D, Plantier JC. Multiple HIV-1/M + HIV-1/O dual infections and new HIV-1/MO inter-group recombinant forms detected in Cameroon. Retrovirology 2017; 14:1. [PMID: 28086923 PMCID: PMC5237259 DOI: 10.1186/s12977-016-0324-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 12/15/2016] [Indexed: 11/10/2022] Open
Abstract
Background
Due to the prevalence of HIV-1 group M and the endemicity of HIV-1 group O infections in Cameroon, patients may be infected with both viruses and/or with HIV-1/MO recombinant forms. Such atypical infections may be deleterious in terms of diagnosis and therapeutic management due to the high divergence of HIV-1/O. The aim of this study was to identify prospectively such atypical infections in Cameroon. Results
Based on serological screening by env-V3 serotyping and a molecular strategy using group-specific (RT)-PCRs, we identified 10 Cameroonian patients harboring three different profiles of infection: (1) 4 HIV-1/M + O dual infections without evidence of recombinant; (2) 5 recombinants associated with one or both parental strains; and (3) 1 new recombinant form without parental strains. Conclusions This work highlights the dynamic co-evolution of these two HIV groups in Cameroon that could lead to the emergence of a circulating recombinant form MO, and the need for accurate identification of such atypical infections for precise diagnosis, virological monitoring and therapeutic management with adapted tools.
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Affiliation(s)
- Fabienne De Oliveira
- GRAM EA2656, Université de Rouen, Rouen, France.,Laboratoire de Virologie, Laboratoire associé au Centre National de Référence du VIH, CHU Charles Nicolle, 76031, Rouen Cedex, France
| | - Thomas Mourez
- GRAM EA2656, Université de Rouen, Rouen, France.,Laboratoire de Virologie, Laboratoire associé au Centre National de Référence du VIH, CHU Charles Nicolle, 76031, Rouen Cedex, France
| | - Aurélia Vessiere
- Centre Pasteur du Cameroun, Yaoundé, Cameroon.,Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - Elodie Alessandri-Gradt
- GRAM EA2656, Université de Rouen, Rouen, France.,Laboratoire de Virologie, Laboratoire associé au Centre National de Référence du VIH, CHU Charles Nicolle, 76031, Rouen Cedex, France
| | - François Simon
- Service de Microbiologie, APHP, CHU Saint Louis, INSERM U941, Faculté de Médecine Paris Diderot, Paris, France
| | - Dominique Rousset
- Centre Pasteur du Cameroun, Yaoundé, Cameroon.,Laboratoire de Virologie, Institut Pasteur de le Guyane, Cayenne, Guyane française, France
| | - Jean-Christophe Plantier
- GRAM EA2656, Université de Rouen, Rouen, France. .,Laboratoire de Virologie, Laboratoire associé au Centre National de Référence du VIH, CHU Charles Nicolle, 76031, Rouen Cedex, France.
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Genetic diversity and transmission networks of HIV-1 strains among men having sex with men (MSM) in Lomé, Togo. INFECTION GENETICS AND EVOLUTION 2016; 46:279-285. [PMID: 27235597 DOI: 10.1016/j.meegid.2016.05.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/19/2016] [Accepted: 05/22/2016] [Indexed: 11/24/2022]
Abstract
Understanding the HIV epidemic in key populations is important. Today only scarce information is available on HIV-1 strains that circulate in men having sex with men (MSM) in sub-Saharan Africa. Here, we studied for the first time the genetic diversity of HIV-1 strains circulating in the MSM population in Lomé, the capital city from Togo. The overall subtype/CRF distribution in pol (protease and/or partial reverse transcriptase (RT)) among the 79 HIV-1 strains from MSM was as follows: CRF02_AG (72%, n=57), subtype G (2.5%, n=2), sub-subtype A3 (1.3%, n=1), and unique recombinant forms (URF) (24%, n=19). Among the 19 URFs four different mosaic structures were observed, annotated as URF1 to URF4. Fifteen sequences (URF1) had the same mosaic structure in pol (G/CRF02_AG) and could represent a new circulating recombinant form (CRF). Phylogenetic analysis of the RT sequences showed that there were several introductions of CRF02_AG strains in the MSM population, however half of the CRF02_AG and all URF1 strains formed a separate, well-supported cluster suggesting one major introduction of CRF02_AG in the MSM population followed by efficient transmission and emergence of a possible new CRF. At least 40% of the strains fell into recent transmission chains involving two to seven MSM. Comparison with >950 HIV-1 sequences from previous studies in Togo showed intermixing of the HIV-1 epidemics between MSM and the general population. Moreover, an HIV-1 strain from a recently HIV-1 infected male patient from Germany, fell within a cluster of HIV-1 strains from MSM from Togo, illustrating recent exchange between MSM from Africa and people from other geographic regions. With growing evidence of the importance of MSM in the dynamic of the HIV epidemic in Africa there is an urgent need for appropriate interventions to limit HIV transmission in this population group.
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Tamalet C, Ravaux I, Moreau J, Brégigeon S, Tourres C, Richet H, Abat C, Colson P. Emergence of clusters of CRF02_AG and B human immunodeficiency viral strains among men having sex with men exhibiting HIV primary infection in southeastern France. J Med Virol 2015; 87:1327-33. [PMID: 25873310 DOI: 10.1002/jmv.24184] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2015] [Indexed: 11/05/2022]
Abstract
The number of new HIV diagnoses is increasing in the western world and transmission clusters have been recently identified among men having sex with men despite Highly Active Antiretroviral Therapy efficacy. The objective of this study was to assess temporal trends, epidemiological, clinical and virological characteristics of primary HIV infections. A retrospective analysis of 79 patients presenting primary HIV infections from 2005 to 2012 was performed in Marseille University Hospitals, southeastern France. Clinical, epidemiological and immunovirological data including phylogeny based on the polymerase gene were collected. 65 males and 14 females were enrolled. The main transmission route was homosexual contact (60.8%). Patients were mostly infected with subtype B (73.4%) and CRF02_AG (21.5%) HIV-1 strains. An increase in the annual number of HIV seroconversions among new HIV diagnoses from 5% in 2005 to 11.2% in 2012 (P = 0.06) and of the proportion of CRF02_AG HIV strains among primary HIV infections in 2011-2012 as compared to 2005-2010 (P = 0.055) was observed. Phylogenetic analysis revealed four transmission clusters including three transmission clusters among men having sex with men: two large clusters of nine CRF02_AG, six B HIV strains; and one small cluster of three B HIV strains. Clusters involved more frequently men (P = 0.01) belonging to caucasian ethicity (P = 0.05), with a higher HIV RNA load at inclusion (P = 0.03). These data highlight the importance of improving epidemiological surveillance and of implementing suitable prevention strategies to control the spread of HIV transmission among men having sex with men.
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Affiliation(s)
- Catherine Tamalet
- Mediterranean Institute for Infectious Diseases, Timone Hospital, Virology Department, Marseille, Cedex 05, France
| | - Isabelle Ravaux
- Mediterranean Institute for Infectious Diseases, Conception Hospital, Infectious Diseases Department, Marseille, France
| | - Jacques Moreau
- Mediterranean Institute for Infectious Diseases, Nord Hospital, Tropical and Infectious Diseases Department, Marseille, France
| | - Sylvie Brégigeon
- Immunohematology Unit, Sainte-Marguerite Hospital, INSERM U912 (SESSTIM), Marseille, France
| | - Christian Tourres
- Mediterranean Institute for Infectious Diseases, Timone Hospital, Virology Department, Marseille, Cedex 05, France
| | - Hervé Richet
- Mediterranean Institute for Infectious Diseases, Timone Hospital, Virology Department, Marseille, Cedex 05, France
| | - Cedric Abat
- Mediterranean Institute for Infectious Diseases, Timone Hospital, Virology Department, Marseille, Cedex 05, France
| | - Philippe Colson
- Mediterranean Institute for Infectious Diseases, Timone Hospital, Virology Department, Marseille, Cedex 05, France
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Colson P, Ravaux I, Tourrès C, Stein A, Tamalet C. Detection of the newly characterized HIV CRF56_cpx in Marseille, southeastern France. Int J Infect Dis 2014; 29:241-3. [PMID: 25461665 DOI: 10.1016/j.ijid.2014.10.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 09/18/2014] [Accepted: 10/04/2014] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES We aimed to seek HIV sequences highly similar to CRF56-cpx, a recently described newly circulating B/CRF02/G recombinant HIV, in our local clinical microbiology laboratory sequence database. METHODS A recently implemented tool that combines a databank of all HIV nucleotide sequences obtained at our clinical microbiology laboratory with a search tool that uses BLAST was used. A comparative and phylogenetic analysis of HIV protease and reverse transcriptase fragments was performed. RESULTS We identified two sequences that were clustered with CRF56-cpx with a bootstrap value of 99% in phylogenetic analyses; these were obtained from two patients diagnosed with HIV in 2009-2011. HIV protease-reverse transcriptase sequences obtained from these two patients shared a mean identity of 98.2±0.2% with previously described CRF56-cpx sequences. Both case patients diagnosed with HIV in our centre were highly sexually active men who have sex with men. CONCLUSIONS Our findings highlight the continuous expansion of HIV diversity in France and indicate that real-time surveillance of HIV molecular epidemiology, including the comparison of sequences from laboratory, national, and international databases, might be helpful to identify the emergence, circulation, and transmission of viral strains.
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Affiliation(s)
- Philippe Colson
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, 27 boulevard Jean Moulin, 13385, Marseille Cedex 05, France; Fondation IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique - Hôpitaux de Marseille, 264 rue Saint-Pierre, 13385, Marseille Cedex 05, France.
| | - Isabelle Ravaux
- Fondation IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Conception, Assistance Publique - Hôpitaux de Marseille, 147 boulevard Baille, 13385, Marseille Cedex 05, France
| | - Christian Tourrès
- Fondation IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique - Hôpitaux de Marseille, 264 rue Saint-Pierre, 13385, Marseille Cedex 05, France
| | - Andréas Stein
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, 27 boulevard Jean Moulin, 13385, Marseille Cedex 05, France; Fondation IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Conception, Assistance Publique - Hôpitaux de Marseille, 147 boulevard Baille, 13385, Marseille Cedex 05, France
| | - Catherine Tamalet
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, 27 boulevard Jean Moulin, 13385, Marseille Cedex 05, France; Fondation IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique - Hôpitaux de Marseille, 264 rue Saint-Pierre, 13385, Marseille Cedex 05, France
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Characteristics of patients recently infected with HIV-1 non-B subtypes in France: a nested study within the mandatory notification system for new HIV diagnoses. J Clin Microbiol 2014; 52:4010-6. [PMID: 25232163 DOI: 10.1128/jcm.01141-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The presence of HIV-1 non-B subtypes in Western Europe is commonly attributed to migration of individuals from non-European countries, but the possible role of domestic infections with non-B subtypes is not well investigated. The French mandatory anonymous reporting system for HIV is linked to a virological surveillance using assays for recent infection (<6 months) and serotyping. During the first semester of years 2007 to 2010, any sample corresponding to a non-B recent infection was analyzed by sequencing a 415-bp env region, followed by phylogenetic analysis and search for transmission clusters. Two hundred thirty-three recent HIV-1 infections with non-B variants were identified. They involved 5 subtypes and 7 circulating recombinant forms (CRFs). Ninety-two cases (39.5%) were due to heterosexual transmissions, of which 39 occurred in patients born in France. Eighty-five cases (36.5%) were identified in men having sex with men (MSM). Forty-three recent non-B infections (18.5%) segregated into 14 clusters, MSM being involved in 11 of them. Clustered transmission events included 2 to 7 cases per cluster. The largest cluster involved MSM infected by a CRF02_AG variant. In conclusion, we found that the spread of non-B subtypes in France occurs in individuals of French origin and that MSM are particularly involved in this dynamic.
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