1
|
Fabeni L, Armenia D, Abbate I, Gagliardini R, Mazzotta V, Bertoli A, Gennari W, Forbici F, Berno G, Piermatteo L, Borghi V, Pinnetti C, Vergori A, Mondi A, Parruti G, Di Sora F, Iannetta M, Lichtner M, Latini A, Mussini C, Sarmati L, Perno CF, Girardi E, Antinori A, Ceccherini-Silberstein F, Maggi F, Santoro MM. HIV-1 transmitted drug resistance in newly diagnosed individuals in Italy over the period 2015-21. J Antimicrob Chemother 2024:dkae189. [PMID: 39028674 DOI: 10.1093/jac/dkae189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/22/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Transmitted drug resistance (TDR) is still a critical aspect for the management of individuals living with HIV-1. Thus, its evaluation is crucial to optimize HIV care. METHODS Overall, 2386 HIV-1 protease/reverse transcriptase and 1831 integrase sequences from drug-naïve individuals diagnosed in north and central Italy between 2015 and 2021 were analysed. TDR was evaluated over time. Phylogeny was generated by maximum likelihood. Factors associated with TDR were evaluated by logistic regression. RESULTS Individuals were mainly male (79.1%) and Italian (56.2%), with a median (IQR) age of 38 (30-48). Non-B infected individuals accounted for 44.6% (N = 1065) of the overall population and increased over time (2015-2021, from 42.1% to 51.0%, P = 0.002). TDR prevalence to any class was 8.0% (B subtype 9.5% versus non-B subtypes 6.1%, P = 0.002) and remained almost constant over time. Overall, 300 transmission clusters (TCs) involving 1155 (48.4%) individuals were identified, with a similar proportion in B and non-infected individuals (49.7% versus 46.8%, P = 0.148). A similar prevalence of TDR among individuals in TCs and those out of TCs was found (8.2% versus 7.8%, P = 0.707).By multivariable analysis, subtypes A, F, and CFR02_AG were negatively associated with TDR. No other factors, including being part of TCs, were significantly associated with TDR. CONCLUSIONS Between 2015 and 2021, TDR prevalence in Italy was 8% and remained almost stable over time. Resistant strains were found circulating regardless of being in TCs, but less likely in non-B subtypes. These results highlight the importance of a continuous surveillance of newly diagnosed individuals for evidence of TDR to inform clinical practice.
Collapse
Affiliation(s)
- Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Daniele Armenia
- Departmental Faculty, UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | - Isabella Abbate
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Roberta Gagliardini
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Valentina Mazzotta
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Ada Bertoli
- Laboratory of Virology, Department of Laboratory Medicine, University Hospital Tor Vergata, Rome, Italy
| | - William Gennari
- Molecular Microbiology and Virology Unit, Department of Laboratory Medicine and Pathological Anatomy, Policlinic of Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Federica Forbici
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Giulia Berno
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | | | - Vanni Borghi
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, Policlinico of Modena, Modena, Italy
| | - Carmela Pinnetti
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Alessandra Vergori
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Annalisa Mondi
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Giustino Parruti
- Infectious Diseases Unit, Pescara General Hospital, Pescara, Italy
| | - Fiorella Di Sora
- Unit of Clinical Immunology, San Giovanni Addolorata Hospital, Rome, Italy
| | - Marco Iannetta
- Department of Infectious Diseases, University Hospital Tor Vergata, Rome, Italy
| | - Miriam Lichtner
- Infectious Diseases Unit, Santa Maria Goretti Hospital, Sapienza University of Rome, Polo Pontino, Latina, Italy
- Sant'Andrea Hospital, Clinical Infectious Diseases, Rome, Italy
| | - Alessandra Latini
- Sexually Transmitted Infection/Human Immunodeficiency Virus Unit, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Cristina Mussini
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, Policlinico of Modena, Modena, Italy
| | - Loredana Sarmati
- Department of Infectious Diseases, University Hospital Tor Vergata, Rome, Italy
| | - Carlo Federico Perno
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesú Children's Hospital, IRCCS, Rome, Italy
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Andrea Antinori
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | | | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | | |
Collapse
|
2
|
Grant HE, Roy S, Williams R, Tutill H, Ferns B, Cane PA, Carswell JW, Ssemwanga D, Kaleebu P, Breuer J, Leigh Brown AJ. A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism. Retrovirology 2022; 19:28. [PMID: 36514107 PMCID: PMC9746199 DOI: 10.1186/s12977-022-00612-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/12/2022] [Indexed: 12/15/2022] Open
Abstract
We present 109 near full-length HIV genomes amplified from blood serum samples obtained during early 1986 from across Uganda, which to our knowledge is the earliest and largest population sample from the initial phase of the HIV epidemic in Africa. Consensus sequences were made from paired-end Illumina reads with a target-capture approach to amplify HIV material following poor success with standard approaches. In comparisons with a smaller 'intermediate' genome dataset from 1998 to 1999 and a 'modern' genome dataset from 2007 to 2016, the proportion of subtype D was significantly higher initially, dropping from 67% (73/109), to 57% (26/46) to 17% (82/465) respectively (p < 0.0001). Subtype D has previously been shown to have a faster rate of disease progression than other subtypes in East African population studies, and to have a higher propensity to use the CXCR4 co-receptor ("X4 tropism"); associated with a decrease in time to AIDS. Here we find significant differences in predicted tropism between A1 and D subtypes in all three sample periods considered, which is particularly striking the 1986 sample: 66% (53/80) of subtype D env sequences were predicted to be X4 tropic compared with none of the 24 subtype A1. We also analysed the frequency of subtype in the envelope region of inter-subtype recombinants, and found that subtype A1 is over-represented in env, suggesting recombination and selection have acted to remove subtype D env from circulation. The reduction of subtype D frequency over three decades therefore appears to be a result of selective pressure against X4 tropism and its higher virulence. Lastly, we find a subtype D specific codon deletion at position 24 of the V3 loop, which may explain the higher propensity for subtype D to utilise X4 tropism.
Collapse
Affiliation(s)
- Heather E Grant
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
| | - Sunando Roy
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Williams
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Helena Tutill
- Division of Infection and Immunity, University College London, London, UK
| | - Bridget Ferns
- Department of Virology, University College London Hospitals NHS Foundation Trust, London, UK
| | | | | | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | | |
Collapse
|
3
|
Wilbourn B, Saafir-Callaway B, Jair K, Wertheim JO, Laeyendeker O, Jordan JA, Kharfen M, Castel A. Characterization of HIV Risk Behaviors and Clusters Using HIV-Transmission Cluster Engine Among a Cohort of Persons Living with HIV in Washington, DC. AIDS Res Hum Retroviruses 2021; 37:706-715. [PMID: 34157853 PMCID: PMC8501467 DOI: 10.1089/aid.2021.0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Molecular epidemiology (ME) is one tool used to end the HIV epidemic in the United States. We combined clinical and behavioral data with HIV sequence data to identify any overlap in clusters generated from different sequence datasets; to characterize HIV transmission clusters; and to identify correlates of clustering among people living with HIV (PLWH) in Washington, District of Columbia (DC). First, Sanger sequences from DC Cohort participants, a longitudinal HIV study, were combined with next-generation sequences (NGS) from participants in a ME substudy to identify clusters. Next, demographic and self-reported behavioral data from ME substudy participants were used to identify risks of secondary transmission. Finally, we combined NGS from ME substudy participants with Sanger sequences in the DC Molecular HIV Surveillance database to identify clusters. Cluster analyses used HIV-Transmission Cluster Engine to identify linked pairs of sequences (defined as distance ≤1.5%). Twenty-eight clusters of ≥3 sequences (size range: 3-12) representing 108 (3%) participants were identified. None of the five largest clusters (size range: 5-12) included newly diagnosed PLWH. Thirty-four percent of ME substudy participants (n = 213) reported condomless sex during their last sexual encounter and 14% reported a Syphilis diagnosis in the past year. Seven transmission clusters (size range: 2-19) were identified in the final analysis, each containing at least one ME substudy participant. Substudy participants in clusters from the third analysis were present in clusters from the first analysis. Combining HIV sequence, clinical and behavioral data provided insights into HIV transmission that may not be identified using traditional epidemiological methods alone. Specifically, the sexual risk behaviors and STI diagnoses reported in the substudy survey may not have been disclosed during Partner Services activities and the survey data complemented clinical data to fully characterize transmission clusters. These findings can be used to enhance local efforts to interrupt transmission and avert new infections.
Collapse
Affiliation(s)
- Brittany Wilbourn
- Department of Epidemiology, Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, USA
| | - Brittani Saafir-Callaway
- HIV/AIDS, Hepatitis, STD and TB Administration, DC Health, Washington, District of Columbia, USA
| | - Kamwing Jair
- Department of Epidemiology, Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, USA
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, LA Jolla, California, USA
| | - Oliver Laeyendeker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, USA
| | - Jeanne A. Jordan
- Department of Epidemiology, Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, USA
| | - Michael Kharfen
- HIV/AIDS, Hepatitis, STD and TB Administration, DC Health, Washington, District of Columbia, USA
| | - Amanda Castel
- Department of Epidemiology, Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, USA
| |
Collapse
|
4
|
Bousali M, Dimadi A, Kostaki EG, Tsiodras S, Nikolopoulos GK, Sgouras DN, Magiorkinis G, Papatheodoridis G, Pogka V, Lourida G, Argyraki A, Angelakis E, Sourvinos G, Beloukas A, Paraskevis D, Karamitros T. SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic Wave. Life (Basel) 2021; 11:life11030219. [PMID: 33803490 PMCID: PMC8001481 DOI: 10.3390/life11030219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/12/2021] [Accepted: 03/03/2021] [Indexed: 12/23/2022] Open
Abstract
Background: The spatiotemporal profiling of molecular transmission clusters (MTCs) using viral genomic data can effectively identify transmission networks in order to inform public health actions targeting SARS-CoV-2 spread. Methods: We used whole genome SARS-CoV-2 sequences derived from ten European regions belonging to eight countries to perform phylogenetic and phylodynamic analysis. We developed dedicated bioinformatics pipelines to identify regional MTCs and to assess demographic factors potentially associated with their formation. Results: The total number and the scale of MTCs varied from small household clusters identified in all regions, to a super-spreading event found in Uusimaa-FI. Specific age groups were more likely to belong to MTCs in different regions. The clustered sequences referring to the age groups 50–100 years old (y.o.) were increased in all regions two weeks after the establishment of the lockdown, while those referring to the age group 0–19 y.o. decreased only in those regions where schools’ closure was combined with a lockdown. Conclusions: The spatiotemporal profiling of the SARS-CoV-2 MTCs can be a useful tool to monitor the effectiveness of the interventions and to reveal cryptic transmissions that have not been identified through contact tracing.
Collapse
Affiliation(s)
- Maria Bousali
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (M.B.); (A.D.); (V.P.)
| | - Aristea Dimadi
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (M.B.); (A.D.); (V.P.)
| | - Evangelia-Georgia Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece; (E.-G.K.); (G.M.)
| | - Sotirios Tsiodras
- 4th Department of Internal Medicine & Infectious Diseases, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece;
| | | | - Dionyssios N. Sgouras
- Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (D.N.S.); (E.A.)
| | - Gkikas Magiorkinis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece; (E.-G.K.); (G.M.)
| | - George Papatheodoridis
- Department of Gastroenterology, Medical School of National and Kapodistrian University of Athens, “Laiko” General Hospital of Athens, 11527 Athens, Greece;
| | - Vasiliki Pogka
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (M.B.); (A.D.); (V.P.)
- Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (D.N.S.); (E.A.)
| | - Giota Lourida
- Infectious Diseases Clinic A, Sotiria Chest Diseases Hospital, 11527 Athens, Greece; (G.L.); (A.A.)
| | - Aikaterini Argyraki
- Infectious Diseases Clinic A, Sotiria Chest Diseases Hospital, 11527 Athens, Greece; (G.L.); (A.A.)
| | - Emmanouil Angelakis
- Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (D.N.S.); (E.A.)
- IRD, APHM, VITROME, IHU-Mediterranean Infections, Aix Marseille University, 13005 Marseille, France
| | - George Sourvinos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71500 Heraklion, Greece;
| | - Apostolos Beloukas
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
- Correspondence: (A.B.); (D.P.); (T.K.); Tel.: +30-210-5385697 (A.B.); +30-210-7462114 (D.P.); +30-210-6478871 (T.K.)
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece; (E.-G.K.); (G.M.)
- Correspondence: (A.B.); (D.P.); (T.K.); Tel.: +30-210-5385697 (A.B.); +30-210-7462114 (D.P.); +30-210-6478871 (T.K.)
| | - Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (M.B.); (A.D.); (V.P.)
- Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (D.N.S.); (E.A.)
- Correspondence: (A.B.); (D.P.); (T.K.); Tel.: +30-210-5385697 (A.B.); +30-210-7462114 (D.P.); +30-210-6478871 (T.K.)
| |
Collapse
|
5
|
Vasylyeva TI, Zarebski A, Smyrnov P, Williams LD, Korobchuk A, Liulchuk M, Zadorozhna V, Nikolopoulos G, Paraskevis D, Schneider J, Skaathun B, Hatzakis A, Pybus OG, Friedman SR. Phylodynamics Helps to Evaluate the Impact of an HIV Prevention Intervention. Viruses 2020; 12:E469. [PMID: 32326127 PMCID: PMC7232463 DOI: 10.3390/v12040469] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/02/2020] [Accepted: 04/15/2020] [Indexed: 01/01/2023] Open
Abstract
Assessment of the long-term population-level effects of HIV interventions is an ongoing public health challenge. Following the implementation of a Transmission Reduction Intervention Project (TRIP) in Odessa, Ukraine, in 2013-2016, we obtained HIV pol gene sequences and used phylogenetics to identify HIV transmission clusters. We further applied the birth-death skyline model to the sequences from Odessa (n = 275) and Kyiv (n = 92) in order to estimate changes in the epidemic's effective reproductive number (Re) and rate of becoming uninfectious (δ). We identified 12 transmission clusters in Odessa; phylogenetic clustering was correlated with younger age and higher average viral load at the time of sampling. Estimated Re were similar in Odessa and Kyiv before the initiation of TRIP; Re started to decline in 2013 and is now below Re = 1 in Odessa (Re = 0.4, 95%HPD 0.06-0.75), but not in Kyiv (Re = 2.3, 95%HPD 0.2-5.4). Similarly, estimates of δ increased in Odessa after the initiation of TRIP. Given that both cities shared the same HIV prevention programs in 2013-2019, apart from TRIP, the observed changes in transmission parameters are likely attributable to the TRIP intervention. We propose that molecular epidemiology analysis can be used as a post-intervention effectiveness assessment tool.
Collapse
Affiliation(s)
- Tetyana I. Vasylyeva
- Department of Zoology, University of Oxford, OX1 3SY Oxford, UK
- New College, University of Oxford, OX1 3BN Oxford, UK
| | | | | | - Leslie D. Williams
- Division of Community Health Sciences, University of Illinois at Chicago School of Public Health, Chicago, IL 60612, USA
| | | | - Mariia Liulchuk
- State Institution “The L.V. Gromashevsky Institute of Epidemiology and Infectious Diseases of NAMS of Ukraine”, Kyiv 03038, Ukraine
| | - Viktoriia Zadorozhna
- State Institution “The L.V. Gromashevsky Institute of Epidemiology and Infectious Diseases of NAMS of Ukraine”, Kyiv 03038, Ukraine
| | | | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 157 72 Athens, Greece
| | - John Schneider
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Britt Skaathun
- Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 157 72 Athens, Greece
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, OX1 3SY Oxford, UK
| | - Samuel R. Friedman
- Department of Population Health, New York University, New York, NY 10003, USA
| |
Collapse
|
6
|
Abstract
PURPOSE OF REVIEW A major goal of public health in relation to HIV/AIDS is to prevent new transmissions in communities. Phylogenetic techniques have improved our understanding of the structure and dynamics of HIV transmissions. However, there is still no consensus about phylogenetic methodology, sampling coverage, gene target and/or minimum fragment size. RECENT FINDINGS Several studies use a combined methodology, which includes both a genetic or patristic distance cut-off and a branching support threshold to identify phylogenetic clusters. However, the choice about these thresholds remains an inherently subjective process, which affects the results of these studies. There is still a lack of consensus about the genomic region and the size of fragments that should be used, although there seems to be emerging a consensus that using longer segments, allied with the use of a realistic model of evolution and a codon alignment, increases the likelihood of inferring true transmission clusters. The pol gene is still the most used genomic region, but recent studies have suggested that whole genomes and/or sequences from nef and gp41 are also good targets for cluster reconstruction. SUMMARY The development and application of standard methodologies for phylogenetic clustering analysis will advance our understanding of factors associated with HIV transmission. This will lead to the design of more precise public health interventions.
Collapse
|
7
|
Vasylyeva TI, du Plessis L, Pineda-Peña AC, Kühnert D, Lemey P, Vandamme AM, Gomes P, Camacho RJ, Pybus OG, Abecasis AB, Faria NR. Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology. J Infect Dis 2020; 220:233-243. [PMID: 30805610 PMCID: PMC6581889 DOI: 10.1093/infdis/jiz085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/21/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Estimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies. METHODS Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific effective reproductive numbers (Re). Discrete trait analysis (DTA) was used to quantify mixing among transmission groups. RESULTS We identified 5 subtype B Portuguese clades (26-79 sequences) and a large monophyletic subtype G Portuguese clade (236 sequences). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval [BCI], 1998-2000) and 2000 (95% BCI, 1998-2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (95% BCI, 1.73-2.09) to 0.62 (95% BCI,.52-.72). For subtype G, Re decreased from 1.49 (95% BCI, 1.39-1.59) to 0.72 (95% BCI, .63-.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were the source of most (>80%) virus lineage transitions for subtypes G and B, respectively. CONCLUSIONS The estimated declines in Re coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for PWID. Inferred transmission events across transmission groups emphasize the importance of prevention efforts for bridging populations.
Collapse
Affiliation(s)
- Tetyana I Vasylyeva
- Department of Zoology, University of Oxford, United Kingdom.,New College, University of Oxford, United Kingdom
| | | | - Andrea C Pineda-Peña
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa.,Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia.,Basic Sciences Department, Universidad del Rosario, Bogotá, Colombia
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Anne-Mieke Vandamme
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa.,Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Perpétua Gomes
- Laboratory of Molecular Biology, LMCBM, SPC, Hospital de Egas Moniz-Centro Hospitalar de Lisboa Ocidental, Lisbon.,Center for Interdisciplinary Research Egas Moniz, CiiEM, Almada, Portugal
| | - Ricardo J Camacho
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, United Kingdom
| | - Ana B Abecasis
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa
| | - Nuno R Faria
- Department of Zoology, University of Oxford, United Kingdom
| |
Collapse
|
8
|
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] [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.
Collapse
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.
Collapse
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
| |
Collapse
|
9
|
Deletsu SD, Maina EK, Quaye O, Ampofo WK, Awandare GA, Bonney EY. High resistance to reverse transcriptase inhibitors among persons infected with human immunodeficiency virus type 1 subtype circulating recombinant form 02_AG in Ghana and on antiretroviral therapy. Medicine (Baltimore) 2020; 99:e18777. [PMID: 32049783 PMCID: PMC7035011 DOI: 10.1097/md.0000000000018777] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/30/2019] [Accepted: 12/16/2019] [Indexed: 11/26/2022] Open
Abstract
This study sought to determine the dominant circulating human immunodeficiency virus type 1 (HIV-1) subtype and associated drug resistance mutations in Ghana.This cross-sectional study was conducted with archived samples collected from patients who received care at 2 hospitals in Ghana from 2014 to 2016. Blood samples were earlier processed into plasma and peripheral blood mononuclear cells and stored at -80 °C. Ribonucleic acid (RNA) was extracted from the archived plasma. Two HIV-1 genes; protease and reverse transcriptase, were amplified, sequenced using gene-specific primers and analyzed for subtype and drug resistance mutations using the Stanford HIV Database.Of 16 patient samples successfully sequenced, we identified the predominance of HIV-1 subtype CRF02_AG (11/16, 68%). Subtypes G (2/16, 13%), dual CRF02_AG/G (2/16, 13%), and CRF01_AE (1/16, 6%) were also observed. Major nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations, M184I/V, D67N, T215F, and K70R/E were found. Non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations, K103N, Y181C, V90I, F227L, and V106A were also prevalent. Additionally, and at a lower level, protease inhibitor (PI)-resistance mutations, M46I, I54 V, V82A, L90 M, and I471 V, were also present in the sequences from antiretroviral therapy (ART)-experienced individuals. Two NRTI-associated drug resistance mutations (DRMs) (D67N and T69N) were present in sequences from 1 ART-naive individual.HIV-1 subtype CRF02_AG was most frequently detected in this study thus confirming earlier reports of dominance of this subtype in the West-African sub-region and Ghana in particular. The detection of these drug resistance mutations in individuals on first-line regimen composed of NRTI and NNRTI is an indication of prolonged drug exposure without viral load monitoring. Routine viral load monitoring is necessary for early detection of virologic failure and drug resistance testing will inform appropriate choice of regimens for such patients.
Collapse
Affiliation(s)
- Selase D. Deletsu
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology
| | - Edward K. Maina
- Department of Virology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon-Accra, Ghana
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology
| | - William K. Ampofo
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology
- Department of Virology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon-Accra, Ghana
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology
| | - Evelyn Y. Bonney
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology
- Department of Virology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon-Accra, Ghana
| |
Collapse
|
10
|
Genetic clustering analysis for HIV infection among MSM in Nigeria: implications for intervention. AIDS 2020; 34:227-236. [PMID: 31634185 DOI: 10.1097/qad.0000000000002409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The HIV epidemic continues to grow among MSM in countries across sub-Saharan Africa including Nigeria. To inform prevention efforts, we used a phylogenetic cluster method to characterize HIV genetic clusters and factors associated with cluster formation among MSM living with HIV in Nigeria. METHODS We analyzed HIV-1 pol sequences from 417 MSM living with HIV enrolled in the TRUST/RV368 cohort between 2013 and 2017 in Abuja and Lagos, Nigeria. A genetically linked cluster was defined among participants whose sequences had pairwise genetic distance of 1.5% or less. Binary and multinomial logistic regressions were used to estimate adjusted odds ratios (AORs) and 95% confidence intervals (CIs) for factors associated with HIV genetic cluster membership and size. RESULTS Among 417 MSM living with HIV, 153 (36.7%) were genetically linked. Participants with higher viral load (AOR = 1.72 95% CI: 1.04-2.86), no female partners (AOR = 3.66; 95% CI: 1.97-6.08), and self-identified as male sex (compared with self-identified as bigender) (AOR = 3.42; 95% CI: 1.08-10.78) had higher odds of being in a genetic cluster. Compared with unlinked participants, MSM who had high school education (AOR = 23.84; 95% CI: 2.66-213.49), were employed (AOR = 3.41; 95% CI: 1.89-10.70), had bacterial sexually transmitted infections (AOR = 3.98; 95% CI: 0.89-17.22) and were not taking antiretroviral therapy (AOR = 6.61; 95% CI: 2.25-19.37) had higher odds of being in a large cluster (size > 4). CONCLUSION Comprehensive HIV prevention packages should include behavioral and biological components, including early diagnosis and treatment of both HIV and bacterial sexually transmitted infections to optimally reduce the risk of HIV transmission and acquisition.
Collapse
|
11
|
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] [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.
Collapse
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
| |
Collapse
|
12
|
How are transgender women acquiring HIV? Insights from phylogenetic transmission clusters in San Francisco. AIDS 2019; 33:2073-2079. [PMID: 31335804 DOI: 10.1097/qad.0000000000002318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE We explored potential HIV transmission typologies that involve transgender women to obtain insights on sexual and needle-sharing networks as sources of HIV infection. DESIGN San Francisco residents diagnosed with HIV in care at public facilities who had available viral pol sequences from June 2001 to January 2016 were included in the analysis. METHODS Viral sequence data were matched to the San Francisco HIV/AIDS Case Registry to obtain demographic and risk classification information. Transmission clusters with at least two cases were identified by bootstrap values at least 90% and mean pairwise genetic distances 0.025 or less substitutions per site. RESULTS Transgender women represented 275 of 5200 patients; 86 were present in 70 clusters. Four typologies were hypothesized: first, transgender women in clusters with MSM; second, transgender women who inject drugs in clusters with cisgender women and men who inject drugs; third, multiple transgender women in clusters with one man; and fourth, multiple transgender women who do not inject drugs in clusters with men and cisgender women who inject drugs. CONCLUSION Transmission patterns of transgender women may stand apart from MSM epidemics. Transgender women clustered with people who inject drugs, and with men who have sex with transgender women and cisgender women. Aggregation of transgender women into the category of MSM may obscure understanding of how they acquire HIV and to whom they may transmit infection. Phylogenetic insights strengthen the case that HIV prevention programs for MSM may not be applicable to transgender women or their partners.
Collapse
|
13
|
Wu J, Zhang Y, Shen Y, Wang X, Xing H, Yang X, Ding X, Hu B, Li H, Han J, Li J, Su B, Liu Y, Li L. Phylogenetic analysis highlights the role of older people in the transmission of HIV-1 in Fuyang, Anhui Province, China. BMC Infect Dis 2019; 19:562. [PMID: 31248372 PMCID: PMC6598234 DOI: 10.1186/s12879-019-4187-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/12/2019] [Indexed: 01/16/2023] Open
Abstract
Background The proportion of older HIV-1 infected people in China has increased rapidly in recent years. Elucidation of the transmission characteristics of this high-risk population subgroup is helpful for the development of tailored interventions. Methods A phylogenetic analysis was performed that uses available HIV-1 pol sequences amplified with nested RT-PCR from plasma samples of all newly diagnosed participants spanning from October 2017 to September 2018 in Fuyang, Anhui Province. Transmission clusters were identified as two or more sequences that shared a corresponding node with an aLRT-SH value ≥90 in the maximum-likelihood phylogenetic tree and had an overall mean genetic distance of ≤1.5%. A local transmission cluster was defined as a cluster that had more than 80% of its sequences from Fuyang. The role of older people in local HIV-1 transmission was determined using an integration of molecular and demographic data. Results Of 362 available sequences, 14 subtypes, and 28 local transmission clusters were identified. It was found that the proportion of older people in the local transmission cluster (69/77, 89.61%) was much higher than that of younger people (46/114, 40.35%) (χ2 test, P < 0.001). In the pretreatment drug resistance analysis, the proportion of sequences with PDRMs in the local transmission cluster was not significantly different between the older people group (57.14%, 4/7) and non-old-aged group (11.11%, 1/9) (Fisher’s exact test, P > 0.05). Conclusion By combining phylogenetic analyses with demographic data, more detailed information was provided about the local transmission structure in Fuyang. These findings suggested that older people play an important role in local transmission, and more tailored interventions for this population subgroup are urgently needed.
Collapse
Affiliation(s)
- Jianjun Wu
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Yu Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yuelan Shen
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xiaohui Yang
- Fuyang Center for Disease Control and Prevention, Fuyang, 236069, China
| | - Xinping Ding
- Fuyang Center for Disease Control and Prevention, Fuyang, 236069, China
| | - Bing Hu
- Fuyang Center for Disease Control and Prevention, Fuyang, 236069, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Bin Su
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China.
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| |
Collapse
|
14
|
Abstract
PURPOSE OF REVIEW This review summarizes the use of genetic similarity clusters to understand HIV transmission and inform prevention efforts. RECENT FINDINGS Recent emphases include the development of real-time cluster identification in order to interrupt transmission chains, the use of clusters to estimate rates of transmission along the HIV care cascade, and the extension of cluster analyses to understand transmission in the generalized epidemics of sub-Saharan Africa. Importantly, this recent empirical work has been accompanied by theoretical work that elucidates the processes that underlie HIV genetic similarity clusters; multiple studies suggest that clusters are not necessarily enriched with individuals with high transmission rates, but rather can reflect variation in sampling times within a population, with individuals sampled early in infection more likely to cluster. Analyses of genetic similarity clusters have great promise to inform HIV epidemiology and prevention. Future emphases should include the collection of additional sequence data from underrepresented populations, such as those in sub-Saharan Africa, and further development and evaluation of clustering methods.
Collapse
Affiliation(s)
- Mary Kate Grabowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Rakai Health Sciences Program, Baltimore, MD, USA
| | - Joshua T Herbeck
- International Clinical Research Center, Department of Global Health, University of Washington, Seattle, WA, USA.
| | - Art F Y Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| |
Collapse
|
15
|
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.
Collapse
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
| | | |
Collapse
|
16
|
Vinken L, Fransen K, Cuypers L, Alexiev I, Balotta C, Debaisieux L, Seguin-Devaux C, García Ribas S, Gomes P, Incardona F, Kaiser R, Ruelle J, Sayan M, Paraschiv S, Paredes R, Peeters M, Sönnerborg A, Vancutsem E, Vandamme AM, Van den Wijngaert S, Van Ranst M, Verhofstede C, Stadler T, Lemey P, Van Laethem K. Earlier Initiation of Antiretroviral Treatment Coincides With an Initial Control of the HIV-1 Sub-Subtype F1 Outbreak Among Men-Having-Sex-With-Men in Flanders, Belgium. Front Microbiol 2019; 10:613. [PMID: 30972053 PMCID: PMC6443750 DOI: 10.3389/fmicb.2019.00613] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 03/11/2019] [Indexed: 11/17/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) non-B subtype infections occurred in Belgium since the 1980s, mainly amongst migrants and heterosexuals, whereas subtype B predominated in men-having-sex-with-men (MSM). In the last decade, the diagnosis of F1 sub-subtype in particular has increased substantially, which prompted us to perform a detailed reconstruction of its epidemiological history. To this purpose, the Belgian AIDS Reference Laboratories collected HIV-1 pol sequences from all sub-subtype F1-infected patients for whom genotypic drug resistance testing was requested as part of routine clinical follow-up. This data was complemented with HIV-1 pol sequences from countries with a high burden of F1 infections or a potential role in the global origin of sub-subtype F1. The molecular epidemiology of the Belgian subtype F1 epidemic was investigated using Bayesian phylogenetic inference and transmission dynamics were characterized based on birth-death models. F1 sequences were retained from 297 patients diagnosed and linked to care in Belgium between 1988 and 2015. Phylogenetic inference indicated that among the 297 Belgian F1 sequences, 191 belonged to a monophyletic group that mainly contained sequences from people likely infected in Belgium (OR 26.67, 95% CI 9.59–74.15), diagnosed in Flanders (OR 7.28, 95% CI 4.23–12.53), diagnosed at a recent stage of infection (OR 7.19, 95% CI 2.88-17.95) or declared to be MSM (OR 34.8, 95% CI 16.0–75.6). Together with a Spanish clade, this Belgian clade was embedded in the genetic diversity of Brazilian subtype F1 strains and most probably emerged after one or only a few migration events from Brazil to the European continent before 2002. The origin of the Belgian outbreak was dated back to 2002 (95% higher posterior density 2000–2004) and birth-death models suggested that its extensive growth had been controlled (Re < 1) by 2012, coinciding with a time period where delay in antiretroviral treatment initiation substantially declined. In conclusion, phylogenetic reconstruction of the Belgian HIV-1 sub-subtype F1 epidemic illustrates the introduction and substantial dissemination of viral strains in a geographically restricted risk group that was most likely controlled by effective treatment as prevention.
Collapse
Affiliation(s)
- Lore Vinken
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Katrien Fransen
- AIDS Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Lize Cuypers
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Ivailo Alexiev
- National Reference Confirmatory Laboratory of HIV, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Claudia Balotta
- Infectious Diseases and Immunopathology Section, 'L. Sacco' Department of Biomedical and Clinical Sciences, 'L. Sacco' Hospital, University of Milan, Milan, Italy
| | - Laurent Debaisieux
- AIDS Reference Laboratory, CUB-Hopital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Carole Seguin-Devaux
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Sergio García Ribas
- AIDS Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Perpétua Gomes
- Serviço de Patologia Clínica, Laboratorio de Biologia Molecular, LMCBM, Centro Hospitalar Lisboa Ocidental, Hospital Egas Moniz, Lisbon, Portugal.,Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Almada, Portugal
| | | | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Jean Ruelle
- Unit of Medical Microbiology, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Murat Sayan
- PCR Unit, Clinical Laboratory, Kocaeli University, İzmit, Turkey.,Research Center of Experimental Health Sciences, Near East University, Nicosia, Cyprus
| | - Simona Paraschiv
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases 'Matei Bals', Bucharest, Romania
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Martine Peeters
- UMI 233 TransVIHMI/INSERM1175, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ellen Vancutsem
- AIDS Reference Laboratory, Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Anne-Mieke Vandamme
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,Unidade de Microbiologia, Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Sigi Van den Wijngaert
- AIDS Reference Laboratory, Department of Microbiology, Saint-Pierre University Hospital, Brussels, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,AIDS Reference Laboratory, University Hospitals Leuven, Leuven, Belgium
| | - Chris Verhofstede
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Philippe Lemey
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Kristel Van Laethem
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,AIDS Reference Laboratory, University Hospitals Leuven, Leuven, Belgium
| |
Collapse
|
17
|
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] [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.
Collapse
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
| |
Collapse
|
18
|
Osbak KK, Meehan CJ, G Ribas S, Heyndrickx L, Ariën KK, Tsoumanis A, Florence E, Esbroeck MV, Fransen K, Kenyon CR. Superimposing incident sexually transmitted infections on HIV phylogram to investigate possible misclassification of men who have sex with men as heterosexuals in a cohort in Antwerp, Belgium. Int J STD AIDS 2019; 30:486-495. [PMID: 30999835 DOI: 10.1177/0956462418821752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In this study, we assessed if the superimposition of incident sexually transmitted infections (STIs) on HIV phylogenetic analyses could reveal possible sexual behaviour misclassifications in our HIV-infected population. HIV-1 sequences collected between 1997 and 2014 from 1169 individuals attending a HIV clinic in Antwerp, Belgium were analysed to infer a partial HIV transmission network. Individual demographic, clinical and laboratory data collected during routine HIV follow-up were used to compare clustered and non-clustered individuals using logistic regression analyses. In total, 438 (37.5%) individuals were identified in 136 clusters, including 76 transmission pairs and 60 clusters consisting of three or more individuals. Individuals in a cluster were more likely to have a history of syphilis, Chlamydia and/or gonorrhoea (P < 0.05); however, when analyses were stratified by HIV transmission risk groups (heterosexual and men who have sex with men [MSM]), this association only remained significant for heterosexuals with syphilis (P = 0.001). Under closer scrutiny, this association was driven by six heterosexual men who were located in six almost exclusively MSM clusters. A parsimonious conclusion is that these six individuals were potentially misclassified as heterosexual. Improving the accuracy of sexual behaviour reporting could improve care.
Collapse
Affiliation(s)
- Kara K Osbak
- 1 Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J Meehan
- 2 Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sergio G Ribas
- 1 Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leo Heyndrickx
- 1 Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,2 Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Kevin K Ariën
- 2 Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Achilleas Tsoumanis
- 1 Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Eric Florence
- 1 Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Marjan Van Esbroeck
- 1 Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Katrien Fransen
- 1 Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Chris R Kenyon
- 1 Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,3 Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
19
|
Transmission dynamics among participants initiating antiretroviral therapy upon diagnosis of early acute HIV-1 infection in Thailand. AIDS 2018; 32:2373-2381. [PMID: 30096068 DOI: 10.1097/qad.0000000000001956] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To assess transmission characteristics in a predominantly MSM cohort initiating antiretroviral therapy (ART) immediately following diagnosis of acute HIV-1infection (AHI). METHODS A longitudinal study (2009-2017) was performed in participants with AHI (n = 439) attending a single clinic in Bangkok. Plasma samples obtained prior to ART were used to obtain HIV-1 pol sequences and combined with clinical and epidemiologic data to assess transmission dynamics (cluster formation and size) using phylogenetic analysis. Clusters were estimated using maximum likelihood, genetic distance of 1.5% and visual inspection. The potential transmitter(s) in a cluster was determined using time to viral suppression and interview data. RESULTS The cohort was predominantly MSM (93%) and infected with HIV-1 CRF01_AE (87%). Medians (ranges) for age and viral load prior to ART were 26 (18-70) years and 5.9 (2.5-8.2) log10 HIV-1 RNA copies/ml. Median time from history of HIV-1 exposure to diagnosis was 19 (3-61) days. Viral suppression was observed in 388 of 412 (94%) participants at a median time of 12 weeks following ART. Twenty-six clusters with median cluster size of 2 (2-5) representing 62 of 439 (14%) participants were observed. Younger age was associated with cluster formation: median 28 versus 30 years for unique infections (P = 0.01). A potential transmitter was identified in 11 of 26 (42%) clusters. CONCLUSION Despite high rates of viral suppression following diagnosis and treatment of AHI within a cohort of young Thai MSM, HIV-1 transmission continued, reflecting the need to expand awareness and treatment access to the entire MSM population.
Collapse
|
20
|
Villandré L, Labbe A, Brenner B, Roger M, Stephens DA. DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference. BMC Bioinformatics 2018; 19:324. [PMID: 30217139 PMCID: PMC6137936 DOI: 10.1186/s12859-018-2347-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 08/29/2018] [Indexed: 12/24/2022] Open
Abstract
Background Conventional phylogenetic clustering approaches rely on arbitrary cutpoints applied a posteriori to phylogenetic estimates. Although in practice, Bayesian and bootstrap-based clustering tend to lead to similar estimates, they often produce conflicting measures of confidence in clusters. The current study proposes a new Bayesian phylogenetic clustering algorithm, which we refer to as DM-PhyClus (Dirichlet-Multinomial Phylogenetic Clustering), that identifies sets of sequences resulting from quick transmission chains, thus yielding easily-interpretable clusters, without using any ad hoc distance or confidence requirement. Results Simulations reveal that DM-PhyClus can outperform conventional clustering methods, as well as the Gap procedure, a pure distance-based algorithm, in terms of mean cluster recovery. We apply DM-PhyClus to a sample of real HIV-1 sequences, producing a set of clusters whose inference is in line with the conclusions of a previous thorough analysis. Conclusions DM-PhyClus, by eliminating the need for cutpoints and producing sensible inference for cluster configurations, can facilitate transmission cluster detection. Future efforts to reduce incidence of infectious diseases, like HIV-1, will need reliable estimates of transmission clusters. It follows that algorithms like DM-PhyClus could serve to better inform public health strategies. Electronic supplementary material The online version of this article (10.1186/s12859-018-2347-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Luc Villandré
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, 1020 avenue des Pins Ouest, Montreal, H3A 1A2, QC, Canada.
| | - Aurélie Labbe
- Department of Decision Science, HEC Montréal, 3000, chemin de la Côte-Sainte-Catherine, Montreal, H3T 2A7, QC, Canada
| | - Bluma Brenner
- McGill AIDS Centre, Lady Davis Institute, Jewish General Hospital, 3755 chemin de la Côte-Sainte-Catherine, Montreal, H3T 1E2, QC, Canada
| | - Michel Roger
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue Saint-Denis, Pavillon R, Montreal, H2X 0A9, QC, Canada.,Département de microbiologie, infectiologie et immunologie, Université de Montréal, 2900 boul. Edouard-Montpetit, Montreal, H3T 1J4, QC, Canada
| | - David A Stephens
- Department of Mathematics and Statistics, McGill University, 805 rue Sherbrooke Ouest, Montreal, H3A 0B9, QC, Canada
| |
Collapse
|
21
|
Fabeni L, Alteri C, Di Carlo D, Orchi N, Carioti L, Bertoli A, Gori C, Forbici F, Continenza F, Maffongelli G, Pinnetti C, Vergori A, Mondi A, Ammassari A, Borghi V, Giuliani M, De Carli G, Pittalis S, Grisetti S, Pennica A, Mastroianni CM, Montella F, Cristaudo A, Mussini C, Girardi E, Andreoni M, Antinori A, Ceccherini-Silberstein F, Perno CF, Santoro MM. Dynamics and phylogenetic relationships of HIV-1 transmitted drug resistance according to subtype in Italy over the years 2000-14. J Antimicrob Chemother 2018; 72:2837-2845. [PMID: 29091206 DOI: 10.1093/jac/dkx231] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/09/2017] [Indexed: 11/14/2022] Open
Abstract
Background Transmitted drug-resistance (TDR) remains a critical aspect for the management of HIV-1-infected individuals. Thus, studying the dynamics of TDR is crucial to optimize HIV care. Methods In total, 4323 HIV-1 protease/reverse-transcriptase sequences from drug-naive individuals diagnosed in north and central Italy between 2000 and 2014 were analysed. TDR was evaluated over time. Maximum-likelihood and Bayesian phylogenetic trees with bootstrap and Bayesian-probability supports defined transmission clusters. Results Most individuals were males (80.2%) and Italian (72.1%), with a median (IQR) age of 37 (30-45) years. MSM accounted for 42.2% of cases, followed by heterosexuals (36.4%). Non-B subtype infections accounted for 30.8% of the overall population and increased over time (<2005-14: 19.5%-38.5%, P < 0.0001), particularly among Italians (<2005-14: 6.5%-28.8%, P < 0.0001). TDR prevalence was 8.8% and increased over time in non-B subtypes (<2005-14: 2%-7.1%, P = 0.018). Overall, 467 transmission clusters (involving 1207 individuals; 27.9%) were identified. The prevalence of individuals grouping in transmission clusters increased over time in both B (<2005-14: 12.9%-33.5%, P = 0.001) and non-B subtypes (<2005-14: 18.4%-41.9%, P = 0.006). TDR transmission clusters were 13.3% within the overall cluster observed and dramatically increased in recent years (<2005-14: 14.3%-35.5%, P = 0.005). This recent increase was mainly due to non-B subtype-infected individuals, who were also more frequently involved in large transmission clusters than those infected with a B subtype [median number of individuals in transmission clusters: 7 (IQR 6-19) versus 4 (3-4), P = 0.047]. Conclusions The epidemiology of HIV transmission changed greatly over time; the increasing number of transmission clusters (sometimes with drug resistance) shows that detection and proper treatment of the multi-transmitters is a major target for controlling HIV spread.
Collapse
Affiliation(s)
- L Fabeni
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - C Alteri
- University of Rome Tor Vergata, Rome, Italy
| | - D Di Carlo
- University of Rome Tor Vergata, Rome, Italy
| | - N Orchi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - L Carioti
- University of Rome Tor Vergata, Rome, Italy
| | - A Bertoli
- University of Rome Tor Vergata, Rome, Italy
| | - C Gori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - F Forbici
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - F Continenza
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | - C Pinnetti
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Vergori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Mondi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Ammassari
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - V Borghi
- Modena University Hospital, Modena, Italy
| | - M Giuliani
- San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - G De Carli
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - S Pittalis
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - S Grisetti
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | | | - F Montella
- S. Giovanni Addolorata Hospital, Rome, Italy
| | - A Cristaudo
- San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - C Mussini
- Modena University Hospital, Modena, Italy
| | - E Girardi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - M Andreoni
- University Hospital Tor Vergata, Rome, Italy
| | - A Antinori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | - C F Perno
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | | | | |
Collapse
|
22
|
Hebberecht L, Vancoillie L, Schauvliege M, Staelens D, Dauwe K, Mortier V, Verhofstede C. Frequency of occurrence of HIV-1 dual infection in a Belgian MSM population. PLoS One 2018; 13:e0195679. [PMID: 29624605 PMCID: PMC5889168 DOI: 10.1371/journal.pone.0195679] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/27/2018] [Indexed: 12/20/2022] Open
Abstract
Introduction HIV-1 dual infection is a condition that results from infection with at least two HIV-1 variants from different sources. The scarceness of information on this condition is partly due to the fact that its detection is technically challenging. Using next-generation sequencing we defined the extent of HIV-1 dual infection in a cohort of men who have sex with men (MSM). Material & methods Eighty-six MSM, diagnosed with HIV-1 subtype B infection between 2008 and 2013 were selected for next-generation sequencing of the HIV-1 envelope V3. Sequencing was performed on 2 plasma samples collected with an interval of > 6 months before the initiation of antiretroviral therapy. Maximum likelihood phylogenetic trees were inspected for dual infection, defined as the presence of two or more monophyletic clusters with ≥ 90% bootstrap support and a mean between-cluster genetic distance of ≥ 10%. To confirm dual infection, deep V3 sequencing of intermediate samples was performed as well as clonal sequencing of the HIV-1 protease-reverse transcriptase gene. Results Five of the 74 patients (6.8%) for whom deep sequencing was successful, showed clear evidence of dual infection. In 4 of them, the second strain was absent in the first sample but occurred in subsequent samples. This was highly suggestive for superinfection. In 3 patients both virus variants were of subtype B, in 2 patients at least one of the variants was a subtype B/non-B recombinant virus. Conclusions Dual infection was confirmed in 6.8% of MSM diagnosed with HIV-1 in Belgium. This prevalence is probably an underestimation, because stringent criteria were used to classify viral variants as originating from a new infection event.
Collapse
Affiliation(s)
- Laura Hebberecht
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Leen Vancoillie
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Delfien Staelens
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Kenny Dauwe
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
- * E-mail:
| |
Collapse
|
23
|
Phylogenetic analysis of the Belgian HIV-1 epidemic reveals that local transmission is almost exclusively driven by men having sex with men despite presence of large African migrant communities. INFECTION GENETICS AND EVOLUTION 2018. [PMID: 29522828 DOI: 10.1016/j.meegid.2018.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To improve insight in the drivers of local HIV-1 transmission in Belgium, phylogenetic, demographic, epidemiological and laboratory data from patients newly diagnosed between 2013 and 2015 were combined and analyzed. Characteristics of clustered patients, paired patients and patients on isolated branches in the phylogenetic tree were compared. The results revealed an overall high level of clustering despite the short time frame of sampling, with 47.6% of all patients having at least one close genetic counterpart and 36.6% belonging to a cluster of 3 or more individuals. Compared to patients on isolated branches, patients in clusters more frequently reported being infected in Belgium (95.1% vs. 47.6%; p < 0.001), were more frequently men having sex with men (MSM) (77.9% vs. 42.8%; p < 0.001), of Belgian origin (68.2% vs. 32.9%; p < 0.001), male gender (92.6% vs. 65.8%; p < 0.001), infected with subtype B or F (87.8% vs. 43.4%; p < 0.001) and diagnosed early after infection (55.4% vs. 29.0%; p < 0.001). Strikingly, Sub-Saharan Africans (SSA), overall representing 27.1% of the population were significantly less frequently found in clusters than on individual branches (6.0% vs. 41.8%; p < 0.001). Of the SSA that participated in clustered transmission, 66.7% were MSM and this contrasts sharply with the overall 12.0% of SSA reporting MSM. Transmission clusters with SSA were more frequently non-B clusters than transmission clusters without SSA (44.4% versus 18.2%). MSM-driven clusters with patients of mixed origin may account, at least in part, for the increasing spread of non-B subtypes to the native MSM population, a cross-over that has been particularly successful for subtype F and CRF02_AG. The main conclusions from this study are that clustered transmission in Belgium remains almost exclusively MSM-driven with very limited contribution of SSA. There were no indications for local ongoing clustered transmission of HIV-1 among SSA.
Collapse
|
24
|
Pérez-Losada M, Castel AD, Lewis B, Kharfen M, Cartwright CP, Huang B, Maxwell T, Greenberg AE, Crandall KA. Characterization of HIV diversity, phylodynamics and drug resistance in Washington, DC. PLoS One 2017; 12:e0185644. [PMID: 28961263 PMCID: PMC5621693 DOI: 10.1371/journal.pone.0185644] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 09/16/2017] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Washington DC has a high burden of HIV with a 2.0% HIV prevalence. The city is a national and international hub potentially containing a broad diversity of HIV variants; yet few sequences from DC are available on GenBank to assess the evolutionary history of HIV in the US capital. Towards this general goal, here we analyze extensive sequence data and investigate HIV diversity, phylodynamics, and drug resistant mutations (DRM) in DC. METHODS Molecular HIV-1 sequences were collected from participants infected through 2015 as part of the DC Cohort, a longitudinal observational study of HIV+ patients receiving care at 13 DC clinics. Sequences were paired with Cohort demographic, risk, and clinical data and analyzed using maximum likelihood, Bayesian and coalescent approaches of phylogenetic, network and population genetic inference. We analyzed 601 sequences from 223 participants for int (~864 bp) and 2,810 sequences from 1,659 participants for PR/RT (~1497 bp). RESULTS Ninety-nine and 94% of the int and PR/RT sequences, respectively, were identified as subtype B, with 14 non-B subtypes also detected. Phylodynamic analyses of US born infected individuals showed that HIV population size varied little over time with no significant decline in diversity. Phylogenetic analyses grouped 13.5% of the int sequences into 14 clusters of 2 or 3 sequences, and 39.0% of the PR/RT sequences into 203 clusters of 2-32 sequences. Network analyses grouped 3.6% of the int sequences into 4 clusters of 2 sequences, and 10.6% of the PR/RT sequences into 76 clusters of 2-7 sequences. All network clusters were detected in our phylogenetic analyses. Higher proportions of clustered sequences were found in zip codes where HIV prevalence is highest (r = 0.607; P<0.00001). We detected a high prevalence of DRM for both int (17.1%) and PR/RT (39.1%), but only 8 int and 12 PR/RT amino acids were identified as under adaptive selection. We observed a significant (P<0.0001) association between main risk factors (men who have sex with men and heterosexuals) and genotypes in the five well-supported clusters with sufficient sample size for testing. DISCUSSION Pairing molecular data with clinical and demographic data provided novel insights into HIV population dynamics in Washington, DC. Identification of populations and geographic locations where clustering occurs can inform and complement active surveillance efforts to interrupt HIV transmission.
Collapse
Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
- CIBIO-InBIO, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Amanda D. Castel
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Brittany Lewis
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Michael Kharfen
- District of Columbia Department of Health, Washington, DC, United States of America
| | | | - Bruce Huang
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
| | - Taylor Maxwell
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
| | - Alan E. Greenberg
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Keith A. Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
| | | |
Collapse
|
25
|
Morgan E, Nyaku AN, D’Aquila RT, Schneider JA. Determinants of HIV Phylogenetic Clustering in Chicago Among Young Black Men Who Have Sex With Men From the uConnect Cohort. J Acquir Immune Defic Syndr 2017; 75:265-270. [PMID: 28328553 PMCID: PMC5472497 DOI: 10.1097/qai.0000000000001379] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTION Phylogenetic analysis determines similarities among HIV genetic sequences from persons infected with HIV, identifying clusters of transmission. We determined characteristics associated with both membership in an HIV transmission cluster and the number of clustered sequences among a cohort of young black men who have sex with men (YBMSM) in Chicago. METHODS Pairwise genetic distances of HIV-1 pol sequences were collected during 2013-2016. Potential transmission ties were identified among HIV-infected persons whose sequences were ≤1.5% genetically distant. Putative transmission pairs were defined as ≥1 tie to another sequence. We then determined demographic and risk attributes associated with both membership in an HIV transmission cluster and the number of ties to the sequences from other persons in the cluster. RESULTS Of 86 available sequences, 31 (36.0%) were tied to ≥1 other sequence. Through multivariable analyses, we determined that those who reported symptoms of depression and those who had a higher number of confidants in their network had significantly decreased odds of membership in transmission clusters. We found that those who had unstable housing and who reported heavy marijuana use had significantly more ties to other individuals within transmission clusters, whereas those identifying as bisexual, those participating in group sex, and those with higher numbers of sexual partners had significantly fewer ties. CONCLUSIONS This study demonstrates the potential for combining phylogenetic and individual and network attributes to target HIV control efforts to persons with potentially higher transmission risk, as well as suggesting some unappreciated specific predictors of transmission risk among YBMSM in Chicago for future study.
Collapse
Affiliation(s)
- Ethan Morgan
- Department of Public Health Sciences, University of Chicago, Chicago, USA
| | - Amesika N Nyaku
- Department of Medicine, Northwestern University, Chicago, USA
| | | | - John A Schneider
- Department of Public Health Sciences, University of Chicago, Chicago, USA
- Department of Medicine, University of Chicago, Chicago, USA
| |
Collapse
|
26
|
Abstract
Understanding HIV-1 transmission dynamics is relevant to both screening and intervention strategies of HIV-1 infection. Commonly, HIV-1 transmission chains are determined based on sequence similarity assessed either directly from a sequence alignment or by inferring a phylogenetic tree. This review is aimed at both nonexperts interested in understanding and interpreting studies of HIV-1 transmission, and experts interested in finding the most appropriate cluster definition for a specific dataset and research question. We start by introducing the concepts and methodologies of how HIV-1 transmission clusters usually have been defined. We then present the results of a systematic review of 105 HIV-1 molecular epidemiology studies summarizing the most common methods and definitions in the literature. Finally, we offer our perspectives on how HIV-1 transmission clusters can be defined and provide some guidance based on examples from real life datasets.
Collapse
|
27
|
A national study of the molecular epidemiology of HIV-1 in Australia 2005-2012. PLoS One 2017; 12:e0170601. [PMID: 28489920 PMCID: PMC5425008 DOI: 10.1371/journal.pone.0170601] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/06/2017] [Indexed: 12/12/2022] Open
Abstract
Introduction Rates of new HIV-1 diagnoses are increasing in Australia, with evidence of an increasing proportion of non-B HIV-1 subtypes reflecting a growing impact of migration and travel. The present study aims to define HIV-1 subtype diversity patterns and investigate possible HIV-1 transmission networks within Australia. Methods The Australian Molecular Epidemiology Network (AMEN) HIV collaborating sites in Western Australia, South Australia, Victoria, Queensland and western Sydney (New South Wales), provided baseline HIV-1 partial pol sequence, age and gender information for 4,873 patients who had genotypes performed during 2005–2012. HIV-1 phylogenetic analyses utilised MEGA V6, with a stringent classification of transmission pairs or clusters (bootstrap ≥98%, genetic distance ≤1.5% from at least one other sequence in the cluster). Results HIV-1 subtype B represented 74.5% of the 4,873 sequences (WA 59%, SA 68.4%, w-Syd 73.8%, Vic 75.6%, Qld 82.1%), with similar proportion of transmission pairs and clusters found in the B and non-B cohorts (23% vs 24.5% of sequences, p = 0.3). Significantly more subtype B clusters were comprised of ≥3 sequences compared with non-B clusters (45.0% vs 24.0%, p = 0.021) and significantly more subtype B pairs and clusters were male-only (88% compared to 53% CRF01_AE and 17% subtype C clusters). Factors associated with being in a cluster of any size included; being sequenced in a more recent time period (p<0.001), being younger (p<0.001), being male (p = 0.023) and having a B subtype (p = 0.02). Being in a larger cluster (>3) was associated with being sequenced in a more recent time period (p = 0.05) and being male (p = 0.008). Conclusion This nationwide HIV-1 study of 4,873 patient sequences highlights the increased diversity of HIV-1 subtypes within the Australian epidemic, as well as differences in transmission networks associated with these HIV-1 subtypes. These findings provide epidemiological insights not readily available using standard surveillance methods and can inform the development of effective public health strategies in the current paradigm of HIV prevention in Australia.
Collapse
|
28
|
van de Laar TJ, Bezemer D, van Laethem K, Vandewalle G, de Smet A, van Wijngaerden E, Claas EC, van Sighem AI, Vandamme AM, Compernolle V, Zaaijer HL. Phylogenetic evidence for underreporting of male-to-male sex among human immunodeficiency virus-infected donors in the Netherlands and Flanders. Transfusion 2017; 57:1235-1247. [PMID: 28375576 DOI: 10.1111/trf.14097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/14/2016] [Accepted: 01/08/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND Separate transmission networks for human immunodeficiency virus (HIV) coexist. Molecular typing of viral genomes can provide insight in HIV transmission routes in donors for whom risk behavior-based donor selection failed. STUDY DESIGN AND METHODS This study includes all HIV-infected Dutch and Flemish donors in the period 2005 to 2014 (n = 55). Part of the HIV polymerase (pol) gene was amplified, sequenced, and compared with more than 10,000 HIV strains obtained from HIV-infected Dutch and Flemish patients. The most likely transmission route was determined based on HIV phylogeny and the donor's self-reported risk behavior during the exit interview. RESULTS HIV-infected donors were predominantly male (69%), were repeat donors (73%), were born in the Netherlands or Belgium (95%), and harbored HIV Subtype B (68%). Seventy-five percent of HIV-infected male donors were part of robust phylogenetic clusters linked to male-to-male sex, while only 24% of HIV-infected male donors reported male-to-male sex during posttest counseling. Sex between men and women accounted for 13% of HIV infections in male donors and 93% of HIV infections in female donors based on phylogenetic analysis. Only 40% of HIV-infected female donors had HIV Subtype B; 65% of female donors reported a foreign partner and indeed HIV sequences interspersed with sequences from HIV-endemic areas abroad, in particular sub-Saharan Africa. CONCLUSION HIV typing helps to understand HIV transmission routes in donor populations. We found substantial underreporting of male-to-male sex among HIV-infected male donors. Donor education on HIV risk factors and the danger of window-period donations and a donor environment that encourages frank disclosure of sexual behavior will contribute to a decrease of HIV-infected donors.
Collapse
Affiliation(s)
- Thijs J van de Laar
- Department of Blood-borne Infections, Sanquin Research, Amsterdam, the Netherlands
| | | | - Kristel van Laethem
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven-Leuven University, Leuven, Belgium.,AIDS Reference Laboratory, University Hospitals Leuven, Leuven, Belgium
| | | | - Annie de Smet
- Blood Service, Belgian Red Cross-Flanders, Mechelen, Belgium
| | - Eric van Wijngaerden
- AIDS Reference Center, University Hospitals Leuven, Leuven, Belgium.,Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology and Immunology, KU Leuven-Leuven University, Leuven, Belgium
| | - Eric C Claas
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands.,Department of Molecular Biology, MC Slotervaart, Amsterdam, the Netherlands
| | | | - Anne-Mieke Vandamme
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven-Leuven University, Leuven, Belgium.,Center for Global Health and Tropical Medicine, Microbiology Unit, Institute for Hygiene and Tropical Medicine, University Nova de Lisboa, Lisbon, Portugal
| | - Veerle Compernolle
- Blood Service, Belgian Red Cross-Flanders, Mechelen, Belgium.,Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Hans L Zaaijer
- Department of Blood-borne Infections, Sanquin Research, Amsterdam, the Netherlands.,Department of Medical Microbiology (CINIMA), Academic Medical Center/University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
29
|
Rose R, Lamers SL, Dollar JJ, Grabowski MK, Hodcroft EB, Ragonnet-Cronin M, Wertheim JO, Redd AD, German D, Laeyendecker O. Identifying Transmission Clusters with Cluster Picker and HIV-TRACE. AIDS Res Hum Retroviruses 2017; 33:211-218. [PMID: 27824249 DOI: 10.1089/aid.2016.0205] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We compared the behavior of two approaches (Cluster Picker and HIV-TRACE) at varying genetic distances to identify transmission clusters. We used three HIV gp41 sequence datasets originating from the Rakai Community Cohort Study: (1) next-generation sequence (NGS) data from nine linked couples; (2) NGS data from longitudinal sampling of 14 individuals; and (3) Sanger consensus sequences from a cross-sectional dataset (n = 1,022) containing 91 epidemiologically linked heterosexual couples. We calculated the optimal genetic distance threshold to separate linked versus unlinked NGS datasets using a receiver operating curve analysis. We evaluated the number, size, and composition of clusters detected by Cluster Picker and HIV-TRACE at six genetic distance thresholds (1%-5.3%) on all three datasets. We further tested the effect of using all NGS, versus only a single variant for each patient/time point, for datasets (1) and (2). The optimal gp41 genetic distance threshold to distinguish linked and unlinked couples and individuals was 5.3% and 4%, respectively. HIV-TRACE tended to detect larger and fewer clusters, whereas Cluster Picker detected more clusters containing only two sequences. For NGS datasets (1) and (2), HIV-TRACE and Cluster Picker detected all linked pairs at 3% and 4% genetic distances, respectively. However, at 5.3% genetic distance, 20% of couples in dataset (3) did not cluster using either program, and for >1/3 of couples cluster assignment were discordant. We suggest caution in choosing thresholds for clustering analyses in a generalized epidemic.
Collapse
Affiliation(s)
| | | | | | - Mary K. Grabowski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Emma B. Hodcroft
- Institute for Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Manon Ragonnet-Cronin
- Institute for Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Joel O. Wertheim
- Department of Medicine, University of California, San Diego, California
| | - Andrew D. Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
- School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Danielle German
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Oliver Laeyendecker
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
- School of Medicine, Johns Hopkins University, Baltimore, Maryland
| |
Collapse
|
30
|
Parczewski M, Leszczyszyn-Pynka M, Witak-Jędra M, Szetela B, Gąsiorowski J, Knysz B, Bociąga-Jasik M, Skwara P, Grzeszczuk A, Jankowska M, Barałkiewicz G, Mozer-Lisewska I, Łojewski W, Kozieł K, Grąbczewska E, Jabłonowska E, Urbańska A. Expanding HIV-1 subtype B transmission networks among men who have sex with men in Poland. PLoS One 2017; 12:e0172473. [PMID: 28234955 PMCID: PMC5325290 DOI: 10.1371/journal.pone.0172473] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/05/2017] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Reconstruction of HIV transmission links allows to trace the spread and dynamics of infection and guide epidemiological interventions. The aim of this study was to characterize transmission networks among subtype B infected patients from Poland. MATERIAL AND METHODS Maximum likelihood phylogenenetic trees were inferred from 966 HIV-1 subtype B protease/reverse transcriptase sequences from patients followed up in nine Polish HIV centers. Monophyletic clusters were identified using 3% within-cluster distance and 0.9 bootstrap values. Interregional links for the clusters were investigated and time from infection to onward transmission estimated using Bayesian dated MCMC phylogeny. RESULTS Three hundred twenty one (33.2%) sequences formed 109 clusters, including ten clusters of ≥5 sequences (n = 81, 8.4%). Transmission networks were more common among MSM (234 sequences, 68.6%) compared to other infection routes (injection drug use: 28 (8.2%) and heterosexual transmissions: 59 (17.3%) cases, respectively [OR:3.5 (95%CI:2.6-4.6),p<0.001]. Frequency of clustering increased from 26.92% in 2009 to 50.6% in 2014 [OR:1.18 (95%CI:1.06-1.31),p = 0.0026; slope +2.8%/year] with median time to onward transmission within clusters of 1.38 (IQR:0.59-2.52) years. In multivariate models clustering was associated with both MSM transmission route [OR:2.24 (95%CI:1.38-3.65),p<0.001] and asymptomatic stage of HIV infection [OR:1.93 (95%CI:1.4-2.64),p<0.0001]. Additionally, interregional networks were linked to MSM transmissions [OR:4.7 (95%CI:2.55-8.96),p<0.001]. CONCLUSIONS Reconstruction of the HIV-1 subtype B transmission patterns reveals increasing degree of clustering and existence of interregional networks among Polish MSM. Dated phylogeny confirms the association between onward transmission and recent infections. High transmission dynamics among Polish MSM emphasizes the necessity for active testing and early treatment in this group.
Collapse
Affiliation(s)
- Miłosz Parczewski
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Magdalena Leszczyszyn-Pynka
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Magdalena Witak-Jędra
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Bartosz Szetela
- Department of Infectious Diseases, Hepatology and Acquired Immune Deficiencies, Wrocław Medical University, Wrocław, Poland
| | - Jacek Gąsiorowski
- Department of Infectious Diseases, Hepatology and Acquired Immune Deficiencies, Wrocław Medical University, Wrocław, Poland
| | - Brygida Knysz
- Department of Infectious Diseases, Hepatology and Acquired Immune Deficiencies, Wrocław Medical University, Wrocław, Poland
| | - Monika Bociąga-Jasik
- Department of Infectious Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - Paweł Skwara
- Department of Infectious Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - Anna Grzeszczuk
- Department of Infectious Diseases and Hepatology, Medical University of Bialystok, Białystok, Poland
| | - Maria Jankowska
- Department of Infectious Diseases, Medical University in Gdańsk, Gdańsk, Poland
| | | | - Iwona Mozer-Lisewska
- Department of Infectious Diseases, Poznań University of Medical Sciences, Poznań, Poland
| | - Władysław Łojewski
- Department of Infectious Diseases, Regional Hospital in Zielona Gora, Zielona Góra, Poland
| | - Katarzyna Kozieł
- Department of Infectious Diseases, Regional Hospital in Zielona Gora, Zielona Góra, Poland
| | - Edyta Grąbczewska
- Department of Infectious Diseases and Hepatology Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - Elżbieta Jabłonowska
- Department of Infectious Diseases and Hepatology, Medical University of Łódź, Łódź, Poland
| | - Anna Urbańska
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| |
Collapse
|
31
|
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.
Collapse
|
32
|
Morgan E, Oster AM, Townsell S, Peace D, Benbow N, Schneider JA. HIV-1 Infection and Transmission Networks of Younger People in Chicago, Illinois, 2005-2011. Public Health Rep 2017; 132:48-55. [PMID: 28005480 PMCID: PMC5298503 DOI: 10.1177/0033354916679988] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE Analysis of HIV nucleotide sequences can be used to identify people with highly similar HIV strains and understand transmission patterns. The objective of this study was to identify groups of people highly connected by HIV transmission and the extent to which transmission occurred within and between geographic areas in Chicago, Illinois. METHODS We analyzed genetic sequences in the HIV-1 pol region in samples collected from people participating in the VARHS program in Chicago during 2005-2011. We determined pairwise genetic distance, inferred potential transmission events between HIV-infected people whose sequences were ≤1.5% genetically distant, and identified clusters of connected people. We used multivariable analysis to determine demographic characteristics and risk attributes associated with degree of connectivity. RESULTS Of 1154 sequences, 177 (15.3%) were tied to at least 1 other sequence. We determined that younger people, men, non-Hispanic black people, and men who have sex with men were more highly connected than other HIV-infected people. We also identified a high degree of geographic heterogeneity-48 of 67 clusters (71.6%) contained people from >1 Chicago region (north, south, or west sides). CONCLUSION Our results indicate a need to address HIV transmission through the networks of younger non-Hispanic black men who have sex with men. The high level of geographic heterogeneity observed suggests that HIV prevention programs should be targeted toward networks of younger people rather than geographic areas of high incidence. This study could also guide prevention efforts in other diverse metropolitan regions with characteristics similar to those of Chicago.
Collapse
Affiliation(s)
- Ethan Morgan
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
- Chicago Center for HIV Elimination, University of Chicago, Chicago, IL, USA
| | - Alexandra M. Oster
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Donna Peace
- Chicago Department of Public Health, Chicago, IL, USA
| | | | - John A. Schneider
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
- Chicago Center for HIV Elimination, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| |
Collapse
|
33
|
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] [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.
Collapse
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
| |
Collapse
|
34
|
Steegen K, Carmona S, Bronze M, Papathanasopoulos MA, van Zyl G, Goedhals D, MacLeod W, Sanne I, Stevens WS. Moderate Levels of Pre-Treatment HIV-1 Antiretroviral Drug Resistance Detected in the First South African National Survey. PLoS One 2016; 11:e0166305. [PMID: 27907009 PMCID: PMC5132262 DOI: 10.1371/journal.pone.0166305] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 10/26/2016] [Indexed: 11/29/2022] Open
Abstract
Background In order to assess the level of transmitted and/or pre-treatment antiretroviral drug resistance to HIV-1, the World Health Organization (WHO) recommends that regular surveys are conducted. This study’s objective was to assess the frequency of HIV-1 antiretroviral drug resistance in patients initiating antiretroviral treatment (ART) in the public sector throughout South Africa. Methods A prospective cross-sectional survey was conducted using probability proportional to size sampling. This method ensured that samples from each province were proportionally collected, based on the number of patients receiving ART in each region. Samples were collected between March 2013 and October 2014. Pol sequences were obtained using RT-PCR and Sanger sequencing and submitted to the Stanford Calibrated Population Resistance tool v6.0. Results A total of 277 sequences were available for analysis. Most participants were female (58.8%) and the median age was 34 years (IQR: 29–42). The median baseline CD4-count was 149 cells/mm3 (IQR: 62–249) and, based on self-reporting, participants had been diagnosed as HIV-positive approximately 44 days prior to sample collection (IQR: 23–179). Subtyping revealed that 98.2% were infected with HIV-1 subtype C. Overall, 25 out of 277 patients presented with ≥1 surveillance drug resistance mutation (SDRM, 9.0%, 95% CI: 6.1–13.0%). Non-nucleoside reverse transcriptase inhibitor (NNRTI) mutations were the most numerous mutations detected (n = 23). Only two patients presented with a protease inhibitor (PI) mutation. In four patients ≥4 SDRMs were detected, which might indicate that these patients were not truly ART-naïve or were infected with a multi-resistant virus. Conclusions These results show that the level of antiretroviral drug resistance in ART-naïve South Africans has reached moderate levels, as per the WHO classification. Therefore, regular surveys of pre-treatment drug resistance levels in all regions of South Africa is highly recommended to monitor the changing levels of pre-treatment antiretroviral drug resistance.
Collapse
Affiliation(s)
- Kim Steegen
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Sergio Carmona
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - Michelle Bronze
- National Health Laboratory Services, Johannesburg, South Africa
| | - Maria A. Papathanasopoulos
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Gert van Zyl
- National Health Laboratory Services, Johannesburg, South Africa
- Division of Medical Virology, Stellenbosch University, Stellenbosch, South Africa
| | - Dominique Goedhals
- National Health Laboratory Services, Johannesburg, South Africa
- Department of Medical Microbiology and Virology, University of the Free State, Bloemfontein, South Africa
| | - William MacLeod
- Center for Global Health and Development, Boston University School of Public Health, Boston, Massachusetts, United States of America
- Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ian Sanne
- Right to Care, Johannesburg, South Africa
| | - Wendy S. Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| |
Collapse
|
35
|
Junqueira DM, de Medeiros RM, Gräf T, Almeida SEDM. Short-Term Dynamic and Local Epidemiological Trends in the South American HIV-1B Epidemic. PLoS One 2016; 11:e0156712. [PMID: 27258369 PMCID: PMC4892525 DOI: 10.1371/journal.pone.0156712] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/18/2016] [Indexed: 01/07/2023] Open
Abstract
The human displacement and sexual behavior are the main factors driving the HIV-1 pandemic to the current profile. The intrinsic structure of the HIV transmission among different individuals has valuable importance for the understanding of the epidemic and for the public health response. The aim of this study was to characterize the HIV-1 subtype B (HIV-1B) epidemic in South America through the identification of transmission links and infer trends about geographical patterns and median time of transmission between individuals. Sequences of the protease and reverse transcriptase coding regions from 4,810 individuals were selected from GenBank. Maximum likelihood phylogenies were inferred and submitted to ClusterPicker to identify transmission links. Bayesian analyses were applied only for clusters including ≥5 dated samples in order to estimate the median maximum inter-transmission interval. This study analyzed sequences sampled from 12 South American countries, from individuals of different exposure categories, under different antiretroviral profiles, and from a wide period of time (1989–2013). Continentally, Brazil, Argentina and Venezuela were revealed important sites for the spread of HIV-1B among countries inside South America. Of note, from all the clusters identified about 70% of the HIV-1B infections are primarily occurring among individuals living in the same geographic region. In addition, these transmissions seem to occur early after the infection of an individual, taking in average 2.39 years (95% CI 1.48–3.30) to succeed. Homosexual/Bisexual individuals transmit the virus as quickly as almost half time of that estimated for the general population sampled here. Public health services can be broadly benefitted from this kind of information whether to focus on specific programs of response to the epidemic whether as guiding of prevention campaigns to specific risk groups.
Collapse
Affiliation(s)
- Dennis Maletich Junqueira
- Centro Universitário Ritter dos Reis—Uniritter, Departamento de Ciências da Saúde, Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Porto Alegre, RS, Brazil
- * E-mail: ;
| | - Rubia Marília de Medeiros
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Porto Alegre, RS, Brazil
| | - Tiago Gräf
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Porto Alegre, RS, Brazil
- Programa de Pós-graduação em Biotecnologia e Biociências, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Sabrina Esteves de Matos Almeida
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Porto Alegre, RS, Brazil
- Instituto de Ciências da Saúde, Universidade FEEVALE, Novo Hamburgo, RS, Brazil
| |
Collapse
|
36
|
Lima K, de Souza Leal É, Cavalcanti AMS, Salustiano DM, de Medeiros LB, da Silva SP, Lacerda HR. Epidemiological, Clinical and Antiretroviral Susceptibility Characterization of Human Immunodeficiency Virus Subtypes B and Non-B in Pernambuco, Northeast Brazil. PLoS One 2016; 11:e0155854. [PMID: 27218259 PMCID: PMC4878750 DOI: 10.1371/journal.pone.0155854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/05/2016] [Indexed: 01/15/2023] Open
Abstract
Background HIV-1 diversity causes important differences in the virus’ biological properties and their interactions with hosts, such as cell tropism, responses to antiretroviral therapy, drug-resistance, and disease progression. Objectives We evaluated the interrelationship of phylogenetic inference with epidemiological and laboratory data for HIV-1 isolates circulating in Pernambuco, Northeast Region—Brazil. Study design A total of 168 HIV-1 pol sequences were analysed, 64 were obtained from 2002–2003, and 104, from 2007–2009. Socio-demographic, clinical, and behavioural data were obtained from medical records. Laboratory testing enabled the determination of recent HIV-1 infections and co-infections with HBV, HCV, HTLV, or syphilis. Surveillance drug-resistance mutation analysis and antiretroviral susceptibility profiling were performed using HIV Drug-Resistance Database. Results HIV-1 non-B was associated with female, lower education, lower viral loads, and higher T cell counts mean. Frequencies of co-infection HIV-HBV, HIV-HCV, and HIV-syphilis were 27.8% (95% CI: 19.8–37.7), 1.04% (95% CI: 0.05–5.00) and 14.7% (95% CI: 8.6–23.0), respectively. Drug-resistant mutations rate was 2.98% (95% CI: 1.10–6.47). HIV-HBV subtype B co-infection was associated with men who have sex with men (MSM), higher education, higher viral loads and males. HIV-syphilis subtype non-B co-infection was associated with MSM status, lower T cell counts and males. Conclusions Data showed the importance of molecular characterisations of the HIV-1 epidemic and its relation with epidemiological and clinical characteristics of the population, as well as its association with other infectious diseases, so they can effort to improve preventive measures for health services and more information about the progress and effects of the epidemic in Northeastern–Brazil.
Collapse
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
| |
Collapse
|
37
|
Chin BS, Chaillon A, Mehta SR, Wertheim JO, Kim G, Shin HS, Smith DM. Molecular epidemiology identifies HIV transmission networks associated with younger age and heterosexual exposure among Korean individuals. J Med Virol 2016; 88:1832-5. [PMID: 26990771 DOI: 10.1002/jmv.24523] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2016] [Indexed: 11/10/2022]
Abstract
To evaluate if HIV transmission networks could be elucidated from data collected in a short time frame, 131 HIV-1 pol sequences were analyzed which were generated from treatment-naïve Korean individuals who were sequentially identified over 1 year. A transmission linkage was inferred when there was a genetic distance <1.5% and a total of 16 clusters, involving 39/131 (29.8%), were identified. Younger age and heterosexual exposure were independently related with clustering in the inferred network, which demonstrated that molecular epidemiology with currently generated data (i.e., drug resistance genotypes) can be used to identify local transmission networks, even over a short timeframe. J. Med. Virol. 88:1832-1835, 2016. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Bum Sik Chin
- Center for Infectious Diseases, National Medical Center, Seoul, Republic of Korea.,Department of Medicine, University of California San Diego, La Jolla, California
| | - Antoine Chaillon
- Department of Medicine, University of California San Diego, La Jolla, California
| | - Sanjay R Mehta
- Department of Medicine, University of California San Diego, La Jolla, California
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, California
| | - Gayeon Kim
- Center for Infectious Diseases, National Medical Center, Seoul, Republic of Korea
| | - Hyoung-Shik Shin
- Center for Infectious Diseases, National Medical Center, Seoul, Republic of Korea
| | - Davey M Smith
- Department of Medicine, University of California San Diego, La Jolla, California.,Veterans Affairs San Diego Healthcare System, San Diego, California
| |
Collapse
|
38
|
Delgado E, Cuevas MT, Domínguez F, Vega Y, Cabello M, Fernández-García A, Pérez-Losada M, Castro MÁ, Montero V, Sánchez M, Mariño A, Álvarez H, Ordóñez P, Ocampo A, Miralles C, Pérez-Castro S, López-Álvarez MJ, Rodríguez R, Trigo M, Diz-Arén J, Hinojosa C, Bachiller P, Hernáez-Crespo S, Cisterna R, Garduño E, Pérez-Álvarez L, Thomson MM. Phylogeny and Phylogeography of a Recent HIV-1 Subtype F Outbreak among Men Who Have Sex with Men in Spain Deriving from a Cluster with a Wide Geographic Circulation in Western Europe. PLoS One 2015; 10:e0143325. [PMID: 26599410 PMCID: PMC4658047 DOI: 10.1371/journal.pone.0143325] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 11/03/2015] [Indexed: 11/18/2022] Open
Abstract
We recently reported the rapid expansion of an HIV-1 subtype F cluster among men who have sex with men (MSM) in the region of Galicia, Northwest Spain. Here we update this outbreak, analyze near full-length genomes, determine phylogenetic relationships, and estimate its origin. For this study, we used sequences of HIV-1 protease-reverse transcriptase and env V3 region, and for 17 samples, near full-length genome sequences were obtained. Phylogenetic analyses were performed via maximum likelihood. Locations and times of most recent common ancestors were estimated using Bayesian inference. Among samples analyzed by us, 100 HIV-1 F1 subsubtype infections of monophyletic origin were diagnosed in Spain, including 88 in Galicia and 12 in four other regions. Most viruses (n = 90) grouped in a subcluster (Galician subcluster), while 7 from Valladolid (Central Spain) grouped in another subcluster. At least 94 individuals were sexually-infected males and at least 71 were MSM. Seventeen near full-length genomes were uniformly of F1 subsubtype. Through similarity searches and phylogenetic analyses, we identified 18 viruses from four other Western European countries [Switzerland (n = 8), Belgium (n = 5), France (n = 3), and United Kingdom (n = 2)] and one from Brazil, from samples collected in 2005–2011, which branched within the subtype F cluster, outside of both Spanish subclusters, most of them corresponding to recently infected individuals. The most probable geographic origin and age of the Galician subcluster was Ferrol, Northwest Galicia, around 2007, while the Western European cluster probably emerged in Switzerland around 2002. In conclusion, a recently expanded HIV-1 subtype F cluster, the largest non-subtype B cluster reported in Western Europe, continues to spread among MSM in Spain; this cluster is part of a larger cluster with a wide geographic circulation in diverse Western European countries.
Collapse
Affiliation(s)
- Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - María Teresa Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Francisco Domínguez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Yolanda Vega
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Marina Cabello
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Aurora Fernández-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Marcos Pérez-Losada
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Vairão, Portugal
| | - María Ángeles Castro
- Department of Internal Medicine, Complejo Hospitalario Universitario de A Coruña, A Coruña, Spain
| | - Vanessa Montero
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Mónica Sánchez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ana Mariño
- Infectious Diseases Unit, Department of Internal Medicine, Complejo Hospitalario Universitario Arquitecto Marcide, Ferrol, A Coruña, Spain
| | - Hortensia Álvarez
- Infectious Diseases Unit, Department of Internal Medicine, Complejo Hospitalario Universitario Arquitecto Marcide, Ferrol, A Coruña, Spain
| | - Patricia Ordóñez
- Department of Microbiology, Complejo Hospitalario Universitario Arquitecto Marcide, Ferrol, A Coruña, Spain
| | - Antonio Ocampo
- Department of Internal Medicine, Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain
| | - Celia Miralles
- Department of Internal Medicine, Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain
| | - Sonia Pérez-Castro
- Department of Microbiology, Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain
| | | | - Raúl Rodríguez
- Department of Internal Medicine, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | - Matilde Trigo
- Department of Microbiology, Complejo Hospitalario Provincial de Pontevedra, Pontevedra, Spain
| | - Julio Diz-Arén
- Department of Internal Medicine, Complejo Hospitalario Provincial de Pontevedra, Pontevedra, Spain
| | - Carmen Hinojosa
- Department of Internal Medicine, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Pablo Bachiller
- Department of Internal Medicine, Hospital Universitario Río Hortega, Valladolid, Spain
| | - Silvia Hernáez-Crespo
- Department of Clinical Microbiology and Infection Control, Hospital Universitario de Basurto, Bilbao, Vizcaya, Spain
| | - Ramón Cisterna
- Department of Clinical Microbiology and Infection Control, Hospital Universitario de Basurto, Bilbao, Vizcaya, Spain
| | - Eugenio Garduño
- Department of Microbiology, Hospital Infanta Cristina, Badajoz, Spain
| | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- * E-mail:
| |
Collapse
|
39
|
Transmission Networks of HIV-1 Among Men Who Have Sex With Men in East and Southeast Asia. J Acquir Immune Defic Syndr 2015; 70:e28-30. [PMID: 25835606 DOI: 10.1097/qai.0000000000000614] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
40
|
Dauwe K, Mortier V, Schauvliege M, Van Den Heuvel A, Fransen K, Servais JY, Bercoff DP, Seguin-Devaux C, Verhofstede C. Characteristics and spread to the native population of HIV-1 non-B subtypes in two European countries with high migration rate. BMC Infect Dis 2015; 15:524. [PMID: 26572861 PMCID: PMC4647655 DOI: 10.1186/s12879-015-1217-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/14/2015] [Indexed: 12/13/2022] Open
Abstract
Background Non-B subtypes account for at least 50 % of HIV-1 infections diagnosed in Belgium and Luxembourg. They are considered to be acquired through heterosexual contacts and infect primarily individuals of foreign origin. Information on the extent to which non-B subtypes spread to the local population is incomplete. Methods Pol and env gene sequences were collected from 410 non-subtype B infections. Profound subtyping was performed using 5 subtyping tools and sequences of both pol and env. Demographic information, disease markers (viral load, CD4 count) and viral characteristics (co-receptor tropism) were compared between subtypes. Maximum likelihood phylogenetic trees were constructed and examined for clustering. Results The majority of non-B infections were diagnosed in patients originating from Africa (55.8 %), individuals born in Western Europe represented 30.5 %. Heterosexual transmission was the most frequently reported transmission route (79.9 %), MSM transmission accounted for 12.2 % and was significantly more frequently reported for Western Europeans (25.7 % versus 4.3 % for individuals originating from other regions; p < 0.001). Subtypes A and C and the circulating recombinant forms CRF01_AE and CRF02_AG were the most represented and were included in the comparative analysis. Native Western Europeans were underrepresented for subtype A (14.5 %) and overrepresented for CRF01_AE (38.6 %). The frequency of MSM transmission was the highest for CRF01_AE (18.2 %) and the lowest for subtype A (0 %). No differences in age, gender, viral load or CD4 count were observed. Prevalence of CXCR4-use differed between subtypes but largely depended on the tropism prediction algorithm applied. Indications for novel intersubtype recombinants were found in 20 patients (6.3 %). Phylogenetic analysis revealed only few and small clusters of local transmission but could document one cluster of CRF02_AG transmission among Belgian MSM. Conclusions The extent to which non-B subtypes spread in the native Belgian-Luxembourg population is higher than expected, with 30.5 % of the non-B infections diagnosed in native Western Europeans. These infections resulted from hetero- as well as homosexual transmission. Introduction of non-B variants in the local high at risk population of MSM may lead to new sub-epidemics and/or increased genetic variability and is an evolution that needs to be closely monitored.
Collapse
Affiliation(s)
- Kenny Dauwe
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Annelies Van Den Heuvel
- Aids Reference laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Nationalestraat 155, B-2000, Antwerp, Belgium.
| | - Katrien Fransen
- Aids Reference laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Nationalestraat 155, B-2000, Antwerp, Belgium.
| | - Jean-Yves Servais
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Danielle Perez Bercoff
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Carole Seguin-Devaux
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| |
Collapse
|
41
|
Vrbik I, Stephens DA, Roger M, Brenner BG. The Gap Procedure: for the identification of phylogenetic clusters in HIV-1 sequence data. BMC Bioinformatics 2015; 16:355. [PMID: 26538192 PMCID: PMC4634160 DOI: 10.1186/s12859-015-0791-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 10/22/2015] [Indexed: 11/29/2022] Open
Abstract
Background In the context of infectious disease, sequence clustering can be used to provide important insights into the dynamics of transmission. Cluster analysis is usually performed using a phylogenetic approach whereby clusters are assigned on the basis of sufficiently small genetic distances and high bootstrap support (or posterior probabilities). The computational burden involved in this phylogenetic threshold approach is a major drawback, especially when a large number of sequences are being considered. In addition, this method requires a skilled user to specify the appropriate threshold values which may vary widely depending on the application. Results This paper presents the Gap Procedure, a distance-based clustering algorithm for the classification of DNA sequences sampled from individuals infected with the human immunodeficiency virus type 1 (HIV-1). Our heuristic algorithm bypasses the need for phylogenetic reconstruction, thereby supporting the quick analysis of large genetic data sets. Moreover, this fully automated procedure relies on data-driven gaps in sorted pairwise distances to infer clusters, thus no user-specified threshold values are required. The clustering results obtained by the Gap Procedure on both real and simulated data, closely agree with those found using the threshold approach, while only requiring a fraction of the time to complete the analysis. Conclusions Apart from the dramatic gains in computational time, the Gap Procedure is highly effective in finding distinct groups of genetically similar sequences and obviates the need for subjective user-specified values. The clusters of genetically similar sequences returned by this procedure can be used to detect patterns in HIV-1 transmission and thereby aid in the prevention, treatment and containment of the disease. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0791-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Irene Vrbik
- Department of Mathematics & Statistics, McGill University, 805 Sherbrooke Street West, Montreal, H3A 0B9, Canada.
| | - David A Stephens
- Department of Mathematics & Statistics, McGill University, 805 Sherbrooke Street West, Montreal, H3A 0B9, Canada.
| | - Michel Roger
- Centre de recherche du CHUM, 900 rue Saint-Denis Tour Viger, H2X 0A9, Montreal, Canada.
| | - Bluma G Brenner
- Faculty of Surgery (Medicine), McGill University, 1010 Sherbrooke Street West, Montreal, H3A 2R7, Canada. .,McGill University AIDS Centre, Jewish General Hospital, Côte-Sainte-Catherine, Montreal, H3T1E2, Canada.
| |
Collapse
|
42
|
Brief Report: Recent Infection, Sexually Transmitted Infections, and Transmission Clusters Frequently Observed Among Persons Newly Diagnosed With HIV in San Francisco. J Acquir Immune Defic Syndr 2015; 69:606-9. [PMID: 25967271 DOI: 10.1097/qai.0000000000000681] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
There were 1311 newly diagnosed HIV cases in San Francisco between 2005 and 2011 that were linked to care at publicly funded facilities and had viral sequences available for analysis. Of the 214 cases characterized as recently infected with HIV at the time of diagnosis, 25% had a recent sexually transmitted infection diagnosis (vs. 10% among longer-standing HIV infections, P < 0.001) and 57% were part of a phylogenetic transmission cluster (vs. 42% among longer-standing HIV infection, P < 0.001). The association observed between recent HIV infection and having a sexually transmitted infection diagnosis during the interval overlapping likely HIV acquisition points to potential opportunities to interrupt HIV transmission.
Collapse
|
43
|
Recent Transmission Clustering of HIV-1 C and CRF17_BF Strains Characterized by NNRTI-Related Mutations among Newly Diagnosed Men in Central Italy. PLoS One 2015; 10:e0135325. [PMID: 26270824 PMCID: PMC4535860 DOI: 10.1371/journal.pone.0135325] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/21/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Increased evidence of relevant HIV-1 epidemic transmission in European countries is being reported, with an increased circulation of non-B-subtypes. Here, we present two recent HIV-1 non-B transmission clusters characterized by NNRTI-related amino-acidic mutations among newly diagnosed HIV-1 infected men, living in Rome (Central-Italy). METHODS Pol and V3 sequences were available at the time of diagnosis for all individuals. Maximum-Likelihood and Bayesian phylogenetic-trees with bootstrap and Bayesian-probability supports defined transmission-clusters. HIV-1 drug-resistance and V3-tropism were also evaluated. RESULTS Among 534 new HIV-1 non-B cases, diagnosed from 2011 to 2014, in Central-Italy, 35 carried virus gathering in two distinct clusters, including 27 HIV-1 C and 8 CRF17_BF subtypes, respectively. Both clusters were centralized in Rome, and their origin was estimated to have been after 2007. All individuals within both clusters were males and 37.1% of them had been recently-infected. While C-cluster was entirely composed by Italian men-who-have-sex-with-men, with a median-age of 34 years (IQR:30-39), individuals in CRF17_BF-cluster were older, with a median-age of 51 years (IQR:48-59) and almost all reported sexual-contacts with men and women. All carried R5-tropic viruses, with evidence of atypical or resistance amino-acidic mutations related to NNRTI-drugs (K103Q in C-cluster, and K101E+E138K in CRF17_BF-cluster). CONCLUSIONS These two epidemiological clusters provided evidence of a strong and recent circulation of C and CRF17_BF strains in central Italy, characterized by NNRTI-related mutations among men engaging in high-risk behaviours. These findings underline the role of molecular epidemiology in identifying groups at increased risk of HIV-1 transmission, and in enhancing additional prevention efforts.
Collapse
|
44
|
López P, Rivera-Amill V, Paulino-Ramirez R, Yamamura Y. Short Communication: HIV-1 Subtype B in the Dominican Republic: Evolution and Molecular Epidemiology. AIDS Res Hum Retroviruses 2015; 31:679-84. [PMID: 25941939 DOI: 10.1089/aid.2014.0304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Caribbean region has the world second highest incidence rate of acquired immunodeficiency syndrome. The island of Hispaniola is composed of two sovereign nations: the Dominican Republic and Haiti. Together, they account for more than 85% of HIV/AIDS cases in the Caribbean; and the Dominican Republic alone has approximately 46,000 (33,000-59,000) HIV-1-infected adults and children. Despite this, the magnitude of the genetic variability and evolution of the HIV-1 virus in the Dominican Republic is unclear. In the current study, we analyzed 195 reverse transcriptase (RT) sequences obtained from the Los Alamos HIV database. The data were used to assess the course of the viral epidemic over time in the Dominican Republic, using a coalescent approach. Based on the data, we estimated that the timing of the most recent common ancestor (tMRCA) of local HIV-1 subtype B emerged in 1963, approximately. In addition, the Bayesian analysis provided new information that suggests that the epidemic in the Dominican Republic experienced a significant decrease in relative genetic diversity in the past 2 decades. The results suggest that adherence to antiretroviral therapy, adequate prevention campaigns, and better access to health care may be altering the virus's evolution in the Dominican Republic.
Collapse
Affiliation(s)
- Pablo López
- Ponce Health Sciences University-School of Medicine, Ponce Research Institute, AIDS Research Program, Ponce, Puerto Rico
| | - Vanessa Rivera-Amill
- Ponce Health Sciences University-School of Medicine, Ponce Research Institute, AIDS Research Program, Ponce, Puerto Rico
| | - Robert Paulino-Ramirez
- Universidad Iberoamericana, School of Medicine, Research Department, Santo Domingo, Dominican Republic
| | - Yasuhiro Yamamura
- Ponce Health Sciences University-School of Medicine, Ponce Research Institute, AIDS Research Program, Ponce, Puerto Rico
| |
Collapse
|
45
|
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.
Collapse
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
| |
Collapse
|
46
|
Transmission clustering among newly diagnosed HIV patients in Chicago, 2008 to 2011: using phylogenetics to expand knowledge of regional HIV transmission patterns. J Acquir Immune Defic Syndr 2015; 68:46-54. [PMID: 25321182 DOI: 10.1097/qai.0000000000000404] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION HIV transmission cluster analyses can inform HIV prevention efforts. We describe the first such assessment for transmission clustering among HIV patients in Chicago. METHODS We performed transmission cluster analyses using HIV pol sequences from newly diagnosed patients presenting to Chicago's largest HIV clinic between 2008 and 2011. We compared sequences through progressive pairwise alignment, using neighbor joining to construct an unrooted phylogenetic tree. We defined clusters as >2 sequences among which each sequence had at least 1 partner within a genetic distance of ≤1.5%. We used multivariable regression to examine factors associated with clustering and used geospatial analysis to assess geographic proximity of phylogenetically clustered patients. RESULTS We compared sequences from 920 patients, median age of 35 years, 75% male, 67% black, 23% Hispanic, and 8% had a rapid plasma reagin titer ≥1:16 concurrent with their HIV diagnosis. We had HIV transmission risk data for 54%; 43% identified as men who have sex with men (MSM). Phylogenetic analysis demonstrated 123 patients (13%) grouped into 26 clusters, the largest having 20 members. In multivariable regression, age <25, black race, MSM status, male gender, higher HIV viral load, and rapid plasma reagin ≥1:16 associated with clustering. We did not observe geographic grouping of genetically clustered patients. DISCUSSION Our results demonstrate high rates of HIV transmission clustering, without local geographic foci, among young black MSM in Chicago. Applied prospectively, phylogenetic analyses could guide prevention efforts and help break the cycle of transmission.
Collapse
|
47
|
Analysis of a local HIV-1 epidemic in portugal highlights established transmission of non-B and non-G subtypes. J Clin Microbiol 2015; 53:1506-14. [PMID: 25694526 DOI: 10.1128/jcm.03611-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/10/2015] [Indexed: 12/24/2022] Open
Abstract
The existing data support Portugal as the western European country with the highest HIV-1 subtype diversity. However, detailed phylogenetic studies of Portuguese HIV-1 epidemics are still scarce. Thus, our main goal was to analyze the phylodynamics of a local HIV-1 infection in the Portuguese region of Minho. Molecular epidemiological analysis was applied to data from 289 HIV-1-infected individuals followed at the reference hospital of the province of Minho, Portugal, at which isolated viruses had been sequenced between 2000 and 2012. Viruses of the G (29.1%) and B (27.0%) subtypes were the most frequent, followed by recombinant forms (17.6%) and the C (14.5%), F1 (7.3%), and A1 (4.2%) subtypes. Multinomial logistic regression revealed that the odds of being infected with the A1 and F1 subtypes increased over the years compared with those with B, G, or C subtypes or recombinant viruses. As expected, polyphyletic patterns suggesting multiple and old introductions of the B and G subtypes were found. However, transmission clusters of non-B and non-G viruses among native individuals were also found, with the dates of the most recent common ancestor estimated to be in the early 2000s. Our study supports that the HIV-1 subtype diversity in the Portuguese region of Minho is high and has been increasing in a manner that is apparently driven by factors other than immigration and international travel. Infections with A1 and F1 viruses in the region of Minho are becoming established and are mainly found in sexually transmitted clusters, reinforcing the need for more efficacious control measures targeting this infection route.
Collapse
|
48
|
Bártolo I, Zakovic S, Martin F, Palladino C, Carvalho P, Camacho R, Thamm S, Clemente S, Taveira N. HIV-1 diversity, transmission dynamics and primary drug resistance in Angola. PLoS One 2014; 9:e113626. [PMID: 25479241 PMCID: PMC4257534 DOI: 10.1371/journal.pone.0113626] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/29/2014] [Indexed: 11/30/2022] Open
Abstract
Objectives To assess HIV-1 diversity, transmission dynamics and prevalence of transmitted drug resistance (TDR) in Angola, five years after ART scale-up. Methods Population sequencing of the pol gene was performed on 139 plasma samples collected in 2009 from drug-naive HIV-1 infected individuals living in Luanda. HIV-1 subtypes were determined using phylogenetic analysis. Drug resistance mutations were identified using the Calibrated Population Resistance Tool (CPR). Transmission networks were determined using phylogenetic analysis of all Angolan sequences present in the databases. Evolutionary trends were determined by comparison with a similar survey performed in 2001. Results 47.1% of the viruses were pure subtypes (all except B), 47.1% were recombinants and 5.8% were untypable. The prevalence of subtype A decreased significantly from 2001 to 2009 (40.0% to 10.8%, P = 0.0019) while the prevalence of unique recombinant forms (URFs) increased>2-fold (40.0% to 83.1%, P<0.0001). The most frequent URFs comprised untypable sequences with subtypes H (U/H, n = 7, 10.8%), A (U/A, n = 6, 9.2%) and G (G/U, n = 4, 6.2%). Newly identified U/H recombinants formed a highly supported monophyletic cluster suggesting a local and common origin. TDR mutation K103N was found in one (0.7%) patient (1.6% in 2001). Out of the 364 sequences sampled for transmission network analysis, 130 (35.7%) were part of a transmission network. Forty eight transmission clusters were identified; the majority (56.3%) comprised sequences sampled in 2008–2010 in Luanda which is consistent with a locally fuelled epidemic. Very low genetic distance was found in 27 transmission pairs sampled in the same year, suggesting recent transmission events. Conclusions Transmission of drug resistant strains was still negligible in Luanda in 2009, five years after the scale-up of ART. The dominance of small and recent transmission clusters and the emergence of new URFs are consistent with a rising HIV-1 epidemics mainly driven by heterosexual transmission.
Collapse
Affiliation(s)
- Inês Bártolo
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular e Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal
| | - Suzana Zakovic
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal
| | - Francisco Martin
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular e Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal
| | - Claudia Palladino
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular e Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Patrícia Carvalho
- Laboratório de Biologia Molecular, Centro Hospitalar Lisboa Ocidental, Hospital Egas Moniz, Lisboa, Portugal
| | - Ricardo Camacho
- Laboratório de Biologia Molecular, Centro Hospitalar Lisboa Ocidental, Hospital Egas Moniz, Lisboa, Portugal
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Sven Thamm
- Abbott GmbH & Co. KG, Wiesbaden, Germany
| | - Sofia Clemente
- Hospital da Divina Providência, Serviço de Doenças Infecciosas, Luanda, Angola
| | - Nuno Taveira
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular e Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal
- * E-mail:
| |
Collapse
|
49
|
Dennis AM, Herbeck JT, Brown AL, Kellam P, de Oliveira T, Pillay D, Fraser C, Cohen MS. Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest? J Acquir Immune Defic Syndr 2014; 67:181-95. [PMID: 24977473 PMCID: PMC4304655 DOI: 10.1097/qai.0000000000000271] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Efficient and effective HIV prevention measures for generalized epidemics in sub-Saharan Africa have not yet been validated at the population level. Design and impact evaluation of such measures requires fine-scale understanding of local HIV transmission dynamics. The novel tools of HIV phylogenetics and molecular epidemiology may elucidate these transmission dynamics. Such methods have been incorporated into studies of concentrated HIV epidemics to identify proximate and determinant traits associated with ongoing transmission. However, applying similar phylogenetic analyses to generalized epidemics, including the design and evaluation of prevention trials, presents additional challenges. Here we review the scope of these methods and present examples of their use in concentrated epidemics in the context of prevention. Next, we describe the current uses for phylogenetics in generalized epidemics and discuss their promise for elucidating transmission patterns and informing prevention trials. Finally, we review logistic and technical challenges inherent to large-scale molecular epidemiological studies of generalized epidemics and suggest potential solutions.
Collapse
Affiliation(s)
- Ann M. Dennis
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Andrew Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Tulio de Oliveira
- Wellcome Trust-Africa Centre for Health and Population Studies, University of Kwazula-Natal, ZA
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, UK
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Myron S. Cohen
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC
| |
Collapse
|
50
|
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.
Collapse
|