1
|
Zhou Z, Zhang X, Wang M, Jiang F, Tong J, Nie J, Zhao C, Zheng H, Zhang Z, Shi P, Fan W, Wang Y, Huang W. HIV-1 env gene mutations outside the targeting probe affects IPDA efficiency. iScience 2024; 27:109941. [PMID: 38812543 PMCID: PMC11133923 DOI: 10.1016/j.isci.2024.109941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/29/2024] [Accepted: 05/06/2024] [Indexed: 05/31/2024] Open
Abstract
The intact proviral DNA assay (IPDA) based on droplet digital PCR was developed to identify intact proviral DNA and quantify HIV-1 latency reservoirs in patients infected with HIV-1. However, the genetic characteristics of different HIV-1 subtypes are non-consistent due to their high mutation and recombination rates. Here, we identified that the IPDA based on the sequences features of an HIV-1 subtype could not effectively detect different HIV-1 subtypes due to the high diversity of HIV-1. Furthermore, we demonstrated that mutations in env gene outside the probe binding site affect the detection efficiency of IPDA. Since mutations in env gene outside the probe binding site may also lead to the formation of stop codons, thereby preventing the formation of viruses and ultimately overestimating the number of HIV-1 latency reservoirs, it is important to address the effect of mutations on the IPDA.
Collapse
Affiliation(s)
- Zehua Zhou
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan, China
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
- Beijing Minhai Biotechnology Co., Ltd., Beijing, China
| | - Xinyu Zhang
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
- College of Life Science, Jilin University, Changchun 130012, China
| | - Meiyu Wang
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Fei Jiang
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Jincheng Tong
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Jianhui Nie
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Chenyan Zhao
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Haifa Zheng
- Beijing Minhai Biotechnology Co., Ltd., Beijing, China
| | - Zhen Zhang
- Infection Division, the People’s Hospital of Baoding, 608 Dongfeng East Road, Lianchi District, Baoding, Hebei 071000, China
| | - Penghui Shi
- Department of Clinical Laboratory Medicine, the People’s Hospital of Baoding, 608 Dongfeng East Road, Lianchi District, Baoding, Hebei 071000, China
| | - Weiguang Fan
- Department of Clinical Laboratory Medicine, the People’s Hospital of Baoding, 608 Dongfeng East Road, Lianchi District, Baoding, Hebei 071000, China
| | - Youchun Wang
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Weijin Huang
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| |
Collapse
|
2
|
Fili M, Hu G, Han C, Kort A, Trettin J, Haim H. A classification algorithm based on dynamic ensemble selection to predict mutational patterns of the envelope protein in HIV-infected patients. Algorithms Mol Biol 2023; 18:4. [PMID: 37337202 DOI: 10.1186/s13015-023-00228-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/04/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Therapeutics against the envelope (Env) proteins of human immunodeficiency virus type 1 (HIV-1) effectively reduce viral loads in patients. However, due to mutations, new therapy-resistant Env variants frequently emerge. The sites of mutations on Env that appear in each patient are considered random and unpredictable. Here we developed an algorithm to estimate for each patient the mutational state of each position based on the mutational state of adjacent positions on the three-dimensional structure of the protein. METHODS We developed a dynamic ensemble selection algorithm designated k-best classifiers. It identifies the best classifiers within the neighborhood of a new observation and applies them to predict the variability state of each observation. To evaluate the algorithm, we applied amino acid sequences of Envs from 300 HIV-1-infected individuals (at least six sequences per patient). For each patient, amino acid variability values at all Env positions were mapped onto the three-dimensional structure of the protein. Then, the variability state of each position was estimated by the variability at adjacent positions of the protein. RESULTS The proposed algorithm showed higher performance than the base learner and a panel of classification algorithms. The mutational state of positions in the high-mannose patch and CD4-binding site of Env, which are targeted by multiple therapeutics, was predicted well. Importantly, the algorithm outperformed other classification techniques for predicting the variability state at multi-position footprints of therapeutics on Env. CONCLUSIONS The proposed algorithm applies a dynamic classifier-scoring approach that increases its performance relative to other classification methods. Better understanding of the spatiotemporal patterns of variability across Env may lead to new treatment strategies that are tailored to the unique mutational patterns of each patient. More generally, we propose the algorithm as a new high-performance dynamic ensemble selection technique.
Collapse
Affiliation(s)
- Mohammad Fili
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, 3014 Black Engineering, 2529 Union Drive, Ames, IA, 50011, USA
| | - Guiping Hu
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, 3014 Black Engineering, 2529 Union Drive, Ames, IA, 50011, USA.
| | - Changze Han
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 51 Newton Rd, 3-770 BSB, Iowa City, IA, 52242, USA
| | - Alexa Kort
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 51 Newton Rd, 3-770 BSB, Iowa City, IA, 52242, USA
| | - John Trettin
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, 3014 Black Engineering, 2529 Union Drive, Ames, IA, 50011, USA
| | - Hillel Haim
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 51 Newton Rd, 3-770 BSB, Iowa City, IA, 52242, USA.
| |
Collapse
|
3
|
Baxter J, Langhorne S, Shi T, Tully DC, Villabona-Arenas CJ, Hué S, Albert J, Leigh Brown A, Atkins KE. Inferring the multiplicity of founder variants initiating HIV-1 infection: a systematic review and individual patient data meta-analysis. THE LANCET. MICROBE 2023; 4:e102-e112. [PMID: 36642083 DOI: 10.1016/s2666-5247(22)00327-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 01/15/2023]
Abstract
BACKGROUND HIV-1 infections initiated by multiple founder variants are characterised by a higher viral load and a worse clinical prognosis than those initiated with single founder variants, yet little is known about the routes of exposure through which transmission of multiple founder variants is most probable. Here we used individual patient data to calculate the probability of multiple founders stratified by route of HIV exposure and study methodology. METHODS We conducted a systematic review and meta-analysis of studies that estimated founder variant multiplicity in HIV-1 infection, searching MEDLINE, Embase, and Global Health databases for papers published between Jan 1, 1990, and Sept 14, 2020. Eligible studies must have reported original estimates of founder variant multiplicity in people with acute or early HIV-1 infections, have clearly detailed the methods used, and reported the route of exposure. Studies were excluded if they reported data concerning people living with HIV-1 who had known or suspected superinfection, who were documented as having received pre-exposure prophylaxis, or if the transmitting partner was known to be receiving antiretroviral treatment. Individual patient data were collated from all studies, with authors contacted if these data were not publicly available. We applied logistic meta-regression to these data to estimate the probability that an HIV infection is initiated by multiple founder variants. We calculated a pooled estimate using a random effects model, subsequently stratifying this estimate across exposure routes in a univariable analysis. We then extended our model to adjust for different study methods in a multivariable analysis, recalculating estimates across the exposure routes. This study is registered with PROSPERO, CRD42020202672. FINDINGS We included 70 publications in our analysis, comprising 1657 individual patients. Our pooled estimate of the probability that an infection is initiated by multiple founder variants was 0·25 (95% CI 0·21-0·29), with moderate heterogeneity (Q=132·3, p<0·0001, I2=64·2%). Our multivariable analysis uncovered differences in the probability of multiple variant infection by exposure route. Relative to a baseline of male-to-female transmission, the predicted probability for female-to-male multiple variant transmission was significantly lower at 0·13 (95% CI 0·08-0·20), and the probabilities were significantly higher for transmissions in people who inject drugs (0·37 [0·24-0·53]) and men who have sex with men (0·30 [0·33-0·40]). There was no significant difference in the probability of multiple variant transmission between male-to-female transmission (0·21 [0·14-0·31]), post-partum transmission (0·18 [0·03-0·57]), pre-partum transmission (0·17 [0·08-0·33]), and intra-partum transmission (0·27 [0·14-0·45]). INTERPRETATION We identified that transmissions in people who inject drugs and men who have sex with men are significantly more likely to result in an infection initiated by multiple founder variants, and female-to-male infections are significantly less probable. Quantifying how the routes of HIV infection affect the transmission of multiple variants allows us to better understand how the evolution and epidemiology of HIV-1 determine clinical outcomes. FUNDING Medical Research Council Precision Medicine Doctoral Training Programme and a European Research Council Starting Grant.
Collapse
Affiliation(s)
- James Baxter
- Usher Institute, The University of Edinburgh, Edinburgh, UK.
| | - Sarah Langhorne
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Ting Shi
- Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Damien C Tully
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Ch Julián Villabona-Arenas
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Stéphane Hué
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Andrew Leigh Brown
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
| | - Katherine E Atkins
- Usher Institute, The University of Edinburgh, Edinburgh, UK; Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| |
Collapse
|
4
|
Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa JM, Yebra G, Esquivel Gomez LR, Frampton D, Gall A, Kellam P, de Oliveira T, Bbosa N, Nsubuga RN, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh Brown AJ. Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evol 2020; 6:veaa004. [PMID: 32395255 PMCID: PMC7204518 DOI: 10.1093/ve/veaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recombination is an important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes). The Ugandan epidemic is primarily composed of two subtypes, A1 and D, that have been co-circulating for 50 years, frequently recombining in dually infected patients. Here, we investigate the frequency of recombinants in this population and the location of breakpoints along the genome. As part of the PANGEA-HIV consortium, 1,472 consensus genome sequences over 5 kb have been obtained from 1,857 samples collected by the MRC/UVRI & LSHTM Research unit in Uganda, 465 (31.6 per cent) of which were near full-length sequences (>8 kb). Using the subtyping tool SCUEAL, we find that of the near full-length dataset, 233 (50.1 per cent) genomes contained only one subtype, 30.8 per cent A1 (n = 143), 17.6 per cent D (n = 82), and 1.7 per cent C (n = 8), while 49.9 per cent (n = 232) contained more than one subtype (including A1/D (n = 164), A1/C (n = 13), C/D (n = 9); A1/C/D (n = 13), and 33 complex types). K-means clustering of the recombinant A1/D genomes revealed a section of envelope (C2gp120-TMgp41) is often inherited intact, whilst a generalized linear model was used to demonstrate significantly fewer breakpoints in the gag-pol and envelope C2-TM regions compared with accessory gene regions. Despite similar recombination patterns in many recombinants, no clearly supported circulating recombinant form (CRF) was found, there was limited evidence of the transmission of breakpoints, and the vast majority (153/164; 93 per cent) of the A1/D recombinants appear to be unique recombinant forms. Thus, recombination is pervasive with clear biases in breakpoint location, but CRFs are not a significant feature, characteristic of a complex, and diverse epidemic.
Collapse
Affiliation(s)
- Heather E Grant
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - 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
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Dan Frampton
- Division of Infection and Immunity, University College London, London, UK
| | - Astrid Gall
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Paul Kellam
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Tulio de Oliveira
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Rebecca N Nsubuga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Freddie Kibengo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Tsz Ho Kwan
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rowland Kao
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Deenan Pillay
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - 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
- Uganda Virus Research Institute, Entebbe, Uganda
| | | |
Collapse
|
5
|
Leoz M, Feyertag F, Kfutwah A, Mauclère P, Lachenal G, Damond F, De Oliveira F, Lemée V, Simon F, Robertson DL, Plantier JC. The Two-Phase Emergence of Non Pandemic HIV-1 Group O in Cameroon. PLoS Pathog 2015; 11:e1005029. [PMID: 26241860 PMCID: PMC4524642 DOI: 10.1371/journal.ppat.1005029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 06/17/2015] [Indexed: 01/17/2023] Open
Abstract
Unlike the pandemic form of HIV-1 (group M), group O viruses are endemic in west central Africa, especially in Cameroon. However, little is known about group O's genetic evolution, and why this highly divergent lineage has not become pandemic. Using a unique and large set of group O sequences from samples collected from 1987 to 2012, we find that this lineage has evolved in successive slow and fast phases of diversification, with a most recent common ancestor estimated to have existed around 1930 (1914-1944). The most rapid periods of diversification occurred in the 1950s and in the 1980s, and could be linked to favourable epidemiological contexts in Cameroon. Group O genetic diversity reflects this two-phase evolution, with two distinct populations potentially having different viral properties. The currently predominant viral population emerged in the 1980s, from an ancient population which had first developed in the 1950s, and is characterized by higher growth and evolutionary rates, and the natural presence of the Y181C resistance mutation, thought to confer a phenotypic advantage. Our findings show that although this evolutionary pattern is specific to HIV-1 group O, it paralleled the early spread of HIV-1 group M in the Democratic Republic of Congo. Both viral lineages are likely to have benefited from similar epidemiological contexts. The relative role of virological and social factors in the distinct epidemic histories of HIV-1 group O and M needs to be reassessed.
Collapse
Affiliation(s)
- Marie Leoz
- Laboratoire de Virologie, CHU Charles Nicolle, Rouen, France
- EA 2656 GRAM, Université de Rouen, Rouen, France
| | - Felix Feyertag
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Anfumbom Kfutwah
- Service de Virologie, Centre Pasteur du Cameroun, Yaoundé, Cameroun
| | - Philippe Mauclère
- Service de Virologie, Centre Pasteur du Cameroun, Yaoundé, Cameroun
- Direction Interarmées du Service de Santé, Nouméa, Nouvelle Calédonie
| | - Guillaume Lachenal
- Laboratoire SPHERE, UMR 7219, Université Paris Diderot & Institut Universitaire de France, Paris, France
| | - Florence Damond
- Service de Virologie, APHP CHU Bichat Claude Bernard, Faculté de Médecine Paris Diderot, Paris, France
| | | | - Véronique Lemée
- EA 2656 GRAM, Université de Rouen, Rouen, France
- Laboratoire associé au Centre National de Référence du VIH, CHU Charles Nicolle, Rouen, France
| | - François Simon
- Service de Microbiologie, APHP CHU Saint Louis, Faculté de Médecine Paris Diderot, Paris, France
| | - David L Robertson
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Jean-Christophe Plantier
- Laboratoire de Virologie, CHU Charles Nicolle, Rouen, France
- EA 2656 GRAM, Université de Rouen, Rouen, France
- Laboratoire associé au Centre National de Référence du VIH, CHU Charles Nicolle, Rouen, France
- * E-mail:
| |
Collapse
|
6
|
de Pina-Araujo IIM, Delatorre E, Guimarães ML, Morgado MG, Bello G. Origin and Population Dynamics of a Novel HIV-1 Subtype G Clade Circulating in Cape Verde and Portugal. PLoS One 2015; 10:e0127384. [PMID: 25993094 PMCID: PMC4439163 DOI: 10.1371/journal.pone.0127384] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/15/2015] [Indexed: 01/04/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) subtype G is the most prevalent and second most prevalent HIV-1 clade in Cape Verde and Portugal, respectively; but there is no information about the origin and spatiotemporal dispersal pattern of this HIV-1 clade circulating in those countries. To this end, we used Maximum Likelihood and Bayesian coalescent-based methods to analyze a collection of 578 HIV-1 subtype G pol sequences sampled throughout Portugal, Cape Verde and 11 other countries from West and Central Africa over a period of 22 years (1992 to 2013). Our analyses indicate that most subtype G sequences from Cape Verde (80%) and Portugal (95%) branched together in a distinct monophyletic cluster (here called GCV-PT). The GCV-PT clade probably emerged after a single migration of the virus out of Central Africa into Cape Verde between the late 1970s and the middle 1980s, followed by a rapid dissemination to Portugal a couple of years later. Reconstruction of the demographic history of the GCV-PT clade circulating in Cape Verde and Portugal indicates that this viral clade displayed an initial phase of exponential growth during the 1980s and 1990s, followed by a decline in growth rate since the early 2000s. Our data also indicate that during the exponential growth phase the GCV-PT clade recombined with a preexisting subtype B viral strain circulating in Portugal, originating the CRF14_BG clade that was later disseminated to Spain and Cape Verde. Historical and recent human population movements between Angola, Cape Verde and Portugal probably played a key role in the origin and dispersal of the GCV-PT and CRF14_BG clades.
Collapse
Affiliation(s)
| | - Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Monick L. Guimarães
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Mariza G. Morgado
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
| |
Collapse
|
7
|
Frangoulidis D, Walter MC, Antwerpen M, Zimmermann P, Janowetz B, Alex M, Böttcher J, Henning K, Hilbert A, Ganter M, Runge M, Münsterkötter M, Splettstoesser WD, Hanczaruk M. Molecular analysis of Coxiella burnetii in Germany reveals evolution of unique clonal clusters. Int J Med Microbiol 2014; 304:868-76. [DOI: 10.1016/j.ijmm.2014.06.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
8
|
Delatorre E, Mir D, Bello G. Spatiotemporal dynamics of the HIV-1 subtype G epidemic in West and Central Africa. PLoS One 2014; 9:e98908. [PMID: 24918930 PMCID: PMC4053352 DOI: 10.1371/journal.pone.0098908] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/03/2014] [Indexed: 01/25/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) subtype G is the second most prevalent HIV-1 clade in West Africa, accounting for nearly 30% of infections in the region. There is no information about the spatiotemporal dynamics of dissemination of this HIV-1 clade in Africa. To this end, we analyzed a total of 305 HIV-1 subtype G pol sequences isolated from 11 different countries from West and Central Africa over a period of 20 years (1992 to 2011). Evolutionary, phylogeographic and demographic parameters were jointly estimated from sequence data using a Bayesian coalescent-based method. Our analyses indicate that subtype G most probably emerged in Central Africa in 1968 (1956–1976). From Central Africa, the virus was disseminated to West and West Central Africa at multiple times from the middle 1970s onwards. Two subtype G strains probably introduced into Nigeria and Togo between the middle and the late 1970s were disseminated locally and to neighboring countries, leading to the origin of two major western African clades (GWA-I and GWA-II). Subtype G clades circulating in western and central African regions displayed an initial phase of exponential growth followed by a decline in growth rate since the early/middle 1990s; but the mean epidemic growth rate of GWA-I (0.75 year−1) and GWA-II (0.95 year−1) clades was about two times higher than that estimated for central African lineages (0.47 year−1). Notably, the overall evolutionary and demographic history of GWA-I and GWA-II clades was very similar to that estimated for the CRF06_cpx clade circulating in the same region. These results support the notion that the spatiotemporal dissemination dynamics of major HIV-1 clades circulating in western Africa have probably been shaped by the same ecological factors.
Collapse
Affiliation(s)
- Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Daiana Mir
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
| |
Collapse
|
9
|
Huang Y, Li Z, Xing H, Jiao Y, Ouyang Y, Liao L, Jiang S, Armstrong R, Shao Y, Ma L. Identification of the critical sites of NNRTI-resistance in reverse transcriptase of HIV-1 CRF_BC strains. PLoS One 2014; 9:e93804. [PMID: 24743727 PMCID: PMC3990534 DOI: 10.1371/journal.pone.0093804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 03/07/2014] [Indexed: 11/26/2022] Open
Abstract
Background The polymorphisms involved in drug resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) in HIV-1 CRF_BC, the most prevalent HIV-1 strain in China, have been poorly characterized. Results To reveal the drug resistance mutations, we compared the gene sequences of pol region of HIV-1 CRF_BC from 631 treatment-naïve and 363 treatment-experienced patients using the selection pressure-based method. We calculated an individual Ka/Ks value for each specific amino acid mutation. Result showed that eight polymorphic mutations (W88C, K101Q, I132L, R135L, T139K/R, H221Y and L228R) in RT for treatment-experienced patients were identified, while they, except for R135L, were completely absent in those from treatment-naïve patients. The I132L and T139K/R mutants exhibited high-level resistance to DLV and NVP and moderate resistance to TMC-125 and EFV, while the K101Q and H221Y mutants exhibited an increased resistance to all four NNRTIs tested. The W88C, R135L, and L228R may be RTI-induced adaptive mutations. Y181C+K101Q mutant showed a 2.5-, 4.4-, and 4.7-fold higher resistance to TMC-125, NVP and EFV, respectively, than Y181C alone mutant, while Y181C+H221Y or K103N+H221Y mutants had significantly higher resistance to all four NNRTIs than Y181C or K103N mutants. K103N+T139K and G190A+T139K mutant induce higher resistance (2.0∼14.2-fold and 1.5∼7.2-fold, respectively) to all four NNRTIs than K103N or G190A alone mutation. Conclusions I132L and T139K/R are rare but critical mutations associated with NNRTI-resistance for some NNRTIs. K101Q, H221Y and T139K can enhance K103N/Y181C/G190A-assocated NNRTI-resistance. Monitoring these mutations will provide useful information for rational design of the NNRTI-based antiretroviral regimen for HIV-1 CRF_BC-infected patients.
Collapse
Affiliation(s)
- Yang Huang
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China
| | - Zhenpeng Li
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China
| | - Hui Xing
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China
| | - Yang Jiao
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China
| | - Yabo Ouyang
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China
| | - Lingjie Liao
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai, China
| | - Rebecca Armstrong
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China
| | - Yiming Shao
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China
- * E-mail: (YS); (LM)
| | - Liying Ma
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China-CDC), Beijing, China
- * E-mail: (YS); (LM)
| |
Collapse
|
10
|
Abstract
The AIDS pandemic that started in the early 1980s is due to human immunodeficiency virus type 1 (HIV-1) group M (HIV-M), but apart from this major group, many divergent variants have been described (HIV-1 groups N, O, and P and HIV-2). The four HIV-1 groups arose from independent cross-species transmission of the simian immunodeficiency viruses (SIVs) SIVcpz, infecting chimpanzees, and SIVgor, infecting gorillas. This, together with human adaptation, accounts for their genomic, phylogenetic, and virological specificities. Nevertheless, the natural course of non-M HIV infection seems similar to that of HIV-M. The virological monitoring of infected patients is now possible with commercial kits, but their therapeutic management remains complex. All non-M variants were principally described for patients linked to Cameroon, where HIV-O accounts for 1% of all HIV infections; only 15 cases of HIV-N infection and 2 HIV-P infections have been reported. Despite improvements in our knowledge, many fascinating questions remain concerning the origin, genetic evolution, and slow spread of these variants. Other variants may already exist or may arise in the future, calling for close surveillance. This review provides a comprehensive, up-to-date summary of the current knowledge on these pathogens, including the historical background of their discovery; the latest advances in the comprehension of their origin and spread; and clinical, therapeutic, and laboratory aspects that may be useful for the management and the treatment of patients infected with these divergent viruses.
Collapse
|
11
|
Mouinga-Ondémé A, Mabika-Mabika A, Alalade P, Mongo AD, Sica J, Liégeois F, Rouet F. Significant impact of non-B HIV-1 variants genetic diversity in Gabon on plasma HIV-1 RNA quantitation. J Med Virol 2013; 86:52-7. [PMID: 24127290 DOI: 10.1002/jmv.23770] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2013] [Indexed: 11/06/2022]
Abstract
Evaluations of HIV-1 RNA viral load assays are lacking in Central Africa. The main objective of our study was to assess the reliability of HIV-1 RNA results obtained with three different assays for samples collected in Gabon. A total of 137 plasma specimens were assessed for HIV-1 RNA using the Abbott RealTime HIV-1® and Nuclisens HIV-1 EasyQ® version 2.0 assays. It included HIV-1 non-B samples (n = 113) representing six subtypes, 10 CRFs and 18 URFs from patients infected with HIV-1 and treated with antiretrovirals that were found HIV-1 RNA positive (≥300 copies/ml) with the Generic HIV viral load® assay; and samples (n = 24) from untreated individuals infected with HIV-1 but showing undetectable (<300 copies/ml) results with the Biocentric kit. For samples found positive with the Generic HIV viral load® test, correlation coefficients obtained between the three techniques were relatively low (R = 0.65 between Generic HIV viral load® and Abbott RealTime HIV-1®, 0.50 between Generic HIV viral load® and Nuclisens HIV-1 EasyQ®, and 0.66 between Abbott RealTime HIV-1® and Nuclisens HIV-1 EasyQ®). Discrepancies by at least one log10 were obtained for 19.6%, 33.7%, and 20% of samples, respectively, irrespective of genotype. Most of samples (22/24) from untreated study patients, found negative with the Biocentric kit, were also found negative with the two other techniques. In Central Africa, HIV-1 genetic diversity remains challenging for viral load testing. Further studies are required in the same area to confirm the presence of HIV-1 strains that are not amplified with at least two different viral load assays.
Collapse
|
12
|
Tracing the origin and northward dissemination dynamics of HIV-1 subtype C in Brazil. PLoS One 2013; 8:e74072. [PMID: 24069269 PMCID: PMC3771961 DOI: 10.1371/journal.pone.0074072] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/26/2013] [Indexed: 11/19/2022] Open
Abstract
Previous studies indicate that the HIV-1 subtype C epidemic in southern Brazil was initiated by the introduction of a single founder strain probably originating from east Africa. However, the exact country of origin of such a founder strain as well as the origin of the subtype C viruses detected outside the Brazilian southern region remains unknown. HIV-1 subtype C pol sequences isolated in the southern, southeastern and central-western Brazilian regions (n = 209) were compared with a large number (n ~ 2,000) of subtype C pol sequences of African origin. Maximum-likelihood analyses revealed that most HIV-1 subtype C Brazilian sequences branched in a single monophyletic clade (CBR-I), nested within a larger monophyletic lineage characteristic of east Africa. Bayesian analyses indicate that the CBR-I clade most probably originated in Burundi and was introduced into the Paraná state (southern region) around the middle 1970s, after which it rapidly disseminated to neighboring regions. The states of Paraná and Santa Catarina have been the most important hubs of subtype C dissemination, and routine travel and spatial accessibility seems to have been the major driving forces of this process. Five additional introductions of HIV-1 subtype C strains probably originated in eastern (n = 2), southern (n = 2) and central (n = 1) African countries were detected in the Rio de Janeiro state (southeastern region). These results indicate a continuous influx of HIV-1 subtype C strains of African origin into Brazil and also unveil the existence of unrecognized transmission networks linking this country to east Africa.
Collapse
|
13
|
Thomson MM, Fernández-García A. Phylogenetic structure in African HIV-1 subtype C revealed by selective sequential pruning. Virology 2011; 415:30-8. [PMID: 21507449 DOI: 10.1016/j.virol.2011.03.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 03/11/2011] [Accepted: 03/17/2011] [Indexed: 10/18/2022]
Abstract
Subtype C is the most prevalent clade in the HIV-1 pandemic. Previous studies suggested that African HIV-1 subtype C lacks a well-defined phylogenetic structure. Here we show that, by sequential pruning of ambiguously positioned taxa, a well-defined intrasubtype C phylogenetic structure becomes apparent, with 52% African HIV-1 subtype C isolates analyzed in envelope sequences branching within 11 clusters, also supported in a tree of full-length genomes, and all with geographical associations. Among 46 viruses recently transmitted in South Africa, 70% branched within 7 clusters (41% in the largest one) and 15% additional isolates were intercluster recombinants. Choice of the outgroup sequence and inclusion of intrasubtype recombinant viruses in the analyses could greatly affect support of clusters. The identification of clusters comprising a large proportion of African HIV-1 subtype C viruses may have implications for the design of vaccines intended for use in areas where subtype C is prevalent.
Collapse
Affiliation(s)
- Michael M Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo Km. 2, Majadahonda, Madrid, Spain.
| | | |
Collapse
|
14
|
Rouet F, Liégeois F, Mouinga-Ondémé A, Kania D, Viljoen J, Wambua S, Ngo-Giang-Huong N, Ménan H, Peeters M, Nerrienet E. Current challenges to viral load testing in the context of emerging genetic diversity of HIV-1. ACTA ACUST UNITED AC 2011; 5:183-202. [PMID: 23484497 DOI: 10.1517/17530059.2011.566860] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION One of the major characteristics of HIV-1 is its extreme genetic diversity. A key factor in assessing the sensitivity of a molecular-based assay measuring HIV-1 RNA viral load (VL) in plasma is its ability to detect/quantify all (or most of) relevant HIV-1 genetic subtype/recombinant forms accurately. AREAS COVERED This review provides an overview of the current commercially available quantitative real-time assays (the Abbott RealTime HIV-1, Roche TaqMan HIV-1 versions 1.0 and 2.0, BioMérieux Nuclisens EasyQ HIV-1, Siemens VERSANT HIV-1 RNA 1.0 kinetic PCR, and Biocentric Generic HIV Viral Load assays). For each assay, studies from 2005 to 2010 assessing the impact of HIV-1 genetic diversity on the reliability of HIV-1 RNA quantification are described. EXPERT OPINION In light of HIV-1 genetic diversity, a general recommendation to favor one test over the other cannot categorically be made. Larger field evaluations of HIV-1 RNA assays should be conducted in areas where HIV-1 genetic diversity is the highest. The large-scale implementation of HIV-1 VL testing is urgently required in the developing world to change HIV infection from a likely death sentence into a manageable chronic infection, as done in Northern countries.
Collapse
Affiliation(s)
- François Rouet
- Laboratoire de Rétrovirologie, Centre International de Recherches Médicales de Franceville (CIRMF) , BP 769, Franceville, Gabon , France +241 677 092/096 ; +241 677 295 ;
| | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Impact of HIV-1 group O genetic diversity on genotypic resistance interpretation by algorithms designed for HIV-1 group M. J Acquir Immune Defic Syndr 2011; 56:139-45. [PMID: 21233638 DOI: 10.1097/qai.0b013e318201a904] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND HIV-1 group O (HIV-O) is characterized by a high genetic divergence from HIV-1 group M viruses. Little is known about the therapeutic impact of this diversity. The aim of this study was to assess in a large series of samples (1) the genotypic impact of natural polymorphism of the HIV-O reverse transcriptase and protease genes; and (2) the predictive value of resistance interpretation algorithms developed for HIV-1 group M when used for highly mutated HIV-O viruses. METHODS Sixty-eight antiretroviral-naive and 9 highly antiretroviral-experienced HIV-O-infected patients were included. The viruses were sequenced and resistance-associated mutations were identified using 3 different algorithms (Agence Nationale de Recherches sur le SIDA et les hépatites virales, Rega, Stanford). RESULTS All HIV-O samples naturally exhibited the A98G and V179E resistance mutations in the reverse transcriptase region; 54% of samples presented the Y181C mutation, conferring resistance to nonnucleoside reverse transcriptase inhibitors. Twelve minor resistance mutations, present in more than 75% of the protease sequences, led to the different algorithms giving discrepant results for nelfinavir and saquinavir susceptibility. A marked virological response was observed in 8 of the 9 antiretroviral-experienced patients, despite the prediction of limited activity of the combination for 5 to 8 patients according to the algorithm used. CONCLUSIONS The high level of natural polymorphism in HIV-O genes, and the important discrepancies between genotypic resistance interpretation and the virological response, emphasize the need for resistance algorithm rules better adapted to HIV-O.
Collapse
|
16
|
Archer J, Rambaut A, Taillon BE, Harrigan PR, Lewis M, Robertson DL. The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time--an ultra-deep approach. PLoS Comput Biol 2010; 6:e1001022. [PMID: 21187908 PMCID: PMC3002995 DOI: 10.1371/journal.pcbi.1001022] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 11/01/2010] [Indexed: 01/09/2023] Open
Abstract
Large-scale parallel pyrosequencing produces unprecedented quantities of sequence data. However, when generated from viral populations current mapping software is inadequate for dealing with the high levels of variation present, resulting in the potential for biased data loss. In order to apply the 454 Life Sciences' pyrosequencing system to the study of viral populations, we have developed software for the processing of highly variable sequence data. Here we demonstrate our software by analyzing two temporally sampled HIV-1 intra-patient datasets from a clinical study of maraviroc. This drug binds the CCR5 coreceptor, thus preventing HIV-1 infection of the cell. The objective is to determine viral tropism (CCR5 versus CXCR4 usage) and track the evolution of minority CXCR4-using variants that may limit the response to a maraviroc-containing treatment regimen. Five time points (two prior to treatment) were available from each patient. We first quantify the effects of divergence on initial read k-mer mapping and demonstrate the importance of utilizing population-specific template sequences in relation to the analysis of next-generation sequence data. Then, in conjunction with coreceptor prediction algorithms that infer HIV tropism, our software was used to quantify the viral population structure pre- and post-treatment. In both cases, low frequency CXCR4-using variants (2.5-15%) were detected prior to treatment. Following phylogenetic inference, these variants were observed to exist as distinct lineages that were maintained through time. Our analysis, thus confirms the role of pre-existing CXCR4-using virus in the emergence of maraviroc-insensitive HIV. The software will have utility for the study of intra-host viral diversity and evolution of other fast evolving viruses, and is available from http://www.bioinf.manchester.ac.uk/segminator/.
Collapse
Affiliation(s)
- John Archer
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Bruce E. Taillon
- 454 Life Sciences, Branford, Connecticut, United States of America
| | - P. Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marilyn Lewis
- Pfizer Global Research and Development, Sandwich, United Kingdom
| | - David L. Robertson
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
| |
Collapse
|
17
|
Abstract
The high rate of HIV-1 evolution contributes to immune escape, enables the virus to escape drug therapy, and may underlie the difficulty of producing an effective vaccine. Identifying constraints on HIV evolution is therefore of prime importance. To investigate this problem, we examined the relationships between sequence diversity, selection, and protein structure. We found that while there was an increase in sequence diversity over time, this variation had a tendency to be limited to specific structural regions. When individual sites were analyzed, there was, in contrast, substantial and widespread evolutionary constraint over gag and env. This constraint was present even in the highly variable envelope proteins. The evolutionary significance of an individual site is indicated by the change in selection pressure along the time course: increasing entropy indicates that the site is evolving predominantly in a more "clock"-like manner, low entropy values with no increase indicate a high degree of constraint, and high entropy values indicate a lack of constraint. Few sites display high degrees of turnover. Mapping these sites onto the three-dimensional protein structure, we found a significant difference between evolutionary rates for regions buried in the core of the protein and those on the surface. This constraint did not change over the time period analyzed and was not subtype dependent, as similar results were found for subtypes B and C. This link between sequence and structure not only demonstrates the limits of recent HIV-1 evolution but also highlights the origins of evolutionary constraint on viral change.
Collapse
|
18
|
Distinct mutation pathways of non-subtype B HIV-1 during in vitro resistance selection with nonnucleoside reverse transcriptase inhibitors. Antimicrob Agents Chemother 2010; 54:4812-24. [PMID: 20805392 DOI: 10.1128/aac.00829-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Studies were conducted to investigate mutation pathways among subtypes A, B, and C of human immunodeficiency virus type 1 (HIV-1) during resistance selection with nonnucleoside reverse transcriptase inhibitors (NNRTIs) in cell culture under low-multiplicity of infection (MOI) conditions. The results showed that distinct pathways were selected by different virus subtypes under increasing selective pressure of NNRTIs. F227C and Y181C were the major mutations selected by MK-4965 in subtype A and C viruses during resistance selection. With efavirenz (EFV), F227C and V106M were the major mutations responsible for viral breakthrough in subtype A viruses, whereas a single pathway (G190A/V106M) accounted for mutation development in subtype C viruses. Y181C was the dominant mutation in the resistance selection with etravirine (ETV) in subtype A, and E138K/H221Y were the mutations detected in the breakthrough viruses from subtype C viruses with ETV. In subtype B viruses, on the other hand, known NNRTI-associated mutations (e.g., Y181C, P236L, L100I, V179D, and K103N) were selected by the NNRTIs. The susceptibility of the subtype A and B mutant viruses to NNRTIs was determined in order to gain insight into the potential mechanisms of mutation development. Collectively, these results suggest that minor differences may exist in conformation of the residues within the NNRTI binding pocket (NNRTIBP) of reverse transcriptase (RT) among the three subtypes of viruses. Thus, the interactions between NNRTIs and the residues in the NNRTIBPs of different subtypes may not be identical, leading to distinct mutation pathways during resistance selection in cell culture.
Collapse
|
19
|
Depatureaux A, Leoz M, De Oliveira F, Gueudin M, Damond F, Descamps D, Brun-Vézinet F, Lemée V, Simon F, Barin F, Plantier JC. [Specific diagnosis and follow-up of HIV-1 group O infection: RES-O data]. Med Mal Infect 2010; 40:669-76. [PMID: 20646884 DOI: 10.1016/j.medmal.2010.04.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2009] [Revised: 01/04/2010] [Accepted: 04/21/2010] [Indexed: 10/19/2022]
Abstract
INTRODUCTION HIV-1 group O (HIV-O), mainly found in Cameroon, has a very high genetic diversity with consequences on the diagnosis and treatment of patients, requiring the development of specific tools. OBJECTIVE We present the currently available tools for the specific detection of HIV-O and its therapeutic monitoring, and the first RES-O data, a French network for the identification and monitoring of patients infected by HIV-O. METHOD The diagnosis of infection was confirmed by group-specific envelope serotyping. The viral load was assessed by a specific technique, LTR-O, developed in the laboratory and compared to the nonspecific kit RealTime HIV-1 (Abbott). The sequencing of antiretroviral target regions (Protease, Reverse Transcriptase (RT), Integrase and Gp41), was performed by specific primers. The analysis of resistance mutations was performed with the ANRS algorithm used for HIV-M. RESULTS HIV-O infection was confirmed for 117 patients. Measuring viral load showed the two techniques were equivalent, but with a tendency to under-quantification for the Abbott technique greater than 1 log for 5% of samples. 70 to 100% of the studied strains had at least 10 mutations in the Protease, four 4 in the RT, and one in Gp41, resulting in a natural genotypic resistance to some anti-retroviral molecules. DISCUSSION The diagnosis and monitoring of HIV-O infection is now possible. However, the impact of this variant's natural polymorphism on response to treatment remains undocumented.
Collapse
Affiliation(s)
- A Depatureaux
- Laboratoire associé au CNR du VIH, EA 2656, CHU Charles-Nicolle, 76031 Rouen, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Increased Thermostability and Fidelity of DNA Synthesis of Wild-Type and Mutant HIV-1 Group O Reverse Transcriptases. J Mol Biol 2009; 392:872-84. [DOI: 10.1016/j.jmb.2009.07.081] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 07/24/2009] [Accepted: 07/28/2009] [Indexed: 11/18/2022]
|
21
|
Archer J, Pinney JW, Fan J, Simon-Loriere E, Arts EJ, Negroni M, Robertson DL. Identifying the important HIV-1 recombination breakpoints. PLoS Comput Biol 2008; 4:e1000178. [PMID: 18787691 PMCID: PMC2522274 DOI: 10.1371/journal.pcbi.1000178] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Accepted: 08/04/2008] [Indexed: 11/19/2022] Open
Abstract
Recombinant HIV-1 genomes contribute significantly to the diversity of variants within the HIV/AIDS pandemic. It is assumed that some of these mosaic genomes may have novel properties that have led to their prevalence, particularly in the case of the circulating recombinant forms (CRFs). In regions of the HIV-1 genome where recombination has a tendency to convey a selective advantage to the virus, we predict that the distribution of breakpoints—the identifiable boundaries that delimit the mosaic structure—will deviate from the underlying null distribution. To test this hypothesis, we generate a probabilistic model of HIV-1 copy-choice recombination and compare the predicted breakpoint distribution to the distribution from the HIV/AIDS pandemic. Across much of the HIV-1 genome, we find that the observed frequencies of inter-subtype recombination are predicted accurately by our model. This observation strongly indicates that in these regions a probabilistic model, dependent on local sequence identity, is sufficient to explain breakpoint locations. In regions where there is a significant over- (either side of the env gene) or under- (short regions within gag, pol, and most of env) representation of breakpoints, we infer natural selection to be influencing the recombination pattern. The paucity of recombination breakpoints within most of the envelope gene indicates that recombinants generated in this region are less likely to be successful. The breakpoints at a higher frequency than predicted by our model are approximately at either side of env, indicating increased selection for these recombinants as a consequence of this region, or at least part of it, having a tendency to be recombined as an entire unit. Our findings thus provide the first clear indication of the existence of a specific portion of the genome that deviates from a probabilistic null model for recombination. This suggests that, despite the wide diversity of recombinant forms seen in the viral population, only a minority of recombination events appear to be of significance to the evolution of HIV-1. Multiple variants of HIV can infect the same cell, and because each viral particle contains two copies of the viral genomic RNA, RNAs from different viruses can occasionally be incorporated together within a viral particle. When this virus subsequently infects another cell, genetic exchange (recombination) may occur between these two divergent copies of genomic RNA as a result of a switch between the RNA molecules while they are copied into DNA. This process is very important to understand as it contributes to the generation of new HIV variants. In this study, we have analysed a set of recombinant HIV genomes generated in the laboratory to construct a probabilistic model of the propensity for the switch to take place in specific regions of the genome, dependent on the local similarity of the parental viral sequences. This model allows us to predict the locations where recombination should occur more frequently. By comparing these predictions to the patterns of recombination observed in the HIV-1 pandemic, we identify the genomic regions in which recombination has been more important, in that it has provided an evolutionary advantage to the virus.
Collapse
Affiliation(s)
- John Archer
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - John W. Pinney
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Jun Fan
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Etienne Simon-Loriere
- Architecture et Réactivité des ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Eric J. Arts
- Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Matteo Negroni
- Architecture et Réactivité des ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, Strasbourg, France
- Institut Pasteur, Paris, France
| | - David L. Robertson
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
| |
Collapse
|
22
|
|
23
|
Vidal N, Frange P, Chaix ML, Mulanga C, Lepira F, Bazepeo SE, Goujard C, Meyer L, Rouzioux C, Delaporte E, Peeters M. Characterization of an old complex circulating recombinant form, CRF27_cpx, originating from the Democratic Republic of Congo (DRC) and circulating in France. AIDS Res Hum Retroviruses 2008; 24:315-21. [PMID: 18257687 DOI: 10.1089/aid.2007.0241] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Full-length genomes were characterized for two samples, 02CD-LBR024 from the Democratic Republic of Congo (DRC) and 04FR-CD-KZS from France, that formed a separate subcluster with a previously characterized env subtype E isolate from DRC with a recombinant structure different from CRF01-AE. Since the three viruses are clearly epidemiologically unlinked and share the same complex recombinant structure, they represent a circulating recombinant form, designated as CRF27-cpx. The recombination pattern involves six different HIV-1 subtypes (A, E, G, H, J, and K) and a small unclassified fragment. The genetic distances are relatively high, indicating that CRF27-cpx evolved over a long time. Their prevalence is low (0.75%) and remained stable over time in the DRC. The existence of the 04FR.CD.KZS virus, in a patient who recently seroconverted in France, confirmed that these strains now circulate outside the DRC. Continuous monitoring of HIV-1 strains thus remains important to allow early identification of the introduction of new variants.
Collapse
Affiliation(s)
- Nicole Vidal
- UMR145, Institut de Recherches pour le Développement (IRD) and University of Montpellier 1, Montpellier, France
| | - Pierre Frange
- EA 3620, Université Paris Descartes, Service de Virologie, CHU Necker-Enfants Malades, Paris, France
| | - Marie-Laure Chaix
- EA 3620, Université Paris Descartes, Service de Virologie, CHU Necker-Enfants Malades, Paris, France
| | - Claire Mulanga
- UMR145, Institut de Recherches pour le Développement (IRD) and University of Montpellier 1, Montpellier, France
| | - François Lepira
- PNLS, Ministère de la Santé, Kinshasa, Democratic Republic of Congo
| | | | | | | | - Christine Rouzioux
- EA 3620, Université Paris Descartes, Service de Virologie, CHU Necker-Enfants Malades, Paris, France
| | - Eric Delaporte
- UMR145, Institut de Recherches pour le Développement (IRD) and University of Montpellier 1, Montpellier, France
| | - Martine Peeters
- UMR145, Institut de Recherches pour le Développement (IRD) and University of Montpellier 1, Montpellier, France
| |
Collapse
|
24
|
Abstract
SUMMARY CTree has been designed for the quantification of clusters within viral phylogenetic tree topologies. Clusters are stored as individual data structures from which statistical data, such as the Subtype Diversity Ratio (SDR), Subtype Diversity Variance (SDV) and pairwise distances can be extracted. This simplifies the quantification of tree topologies in relation to inter- and intra-cluster diversity. Here the novel features incorporated within CTree, including the implementation of a heuristic algorithm for identifying clusters, are outlined along with the more usual features found within general tree viewing software. AVAILABILITY CTree is available as an executable jar file from: http://www.manchester.ac.uk/bioinformatics/ctree
Collapse
Affiliation(s)
- John Archer
- Faculty of Life Science, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
| | | |
Collapse
|