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Topcu C, Georgiou V, Rodosthenous JH, Siakallis G, Gavala EK, Dimitriou CR, Zeniou E, Foley BT, Kostrikis LG. Comprehensive Genetic Characterization of Four Novel HIV-1 Circulating Recombinant Forms (CRF129_56G, CRF130_A1B, CRF131_A1B, and CRF138_cpx): Insights from Molecular Epidemiology in Cyprus. Viruses 2023; 16:19. [PMID: 38275954 PMCID: PMC10819958 DOI: 10.3390/v16010019] [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] [Received: 11/14/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Molecular investigations of the HIV-1 pol region (2253-5250 in the HXB2 genome) were conducted on sequences obtained from 331 individuals infected with HIV-1 in Cyprus between 2017 and 2021. This study unveiled four distinct HIV-1 putative transmission clusters, encompassing 19 previously unidentified HIV-1 recombinants. These recombinants, each comprising eight, three, four, and four sequences, respectively, did not align with previously established Circulating Recombinant Forms (CRFs). To characterize these novel HIV-1 recombinants, near-full-length genome sequences were successfully obtained for 16 of the 19 recombinants (790-8795 in the HXB2 genome) using an in-house-developed RT-PCR assay. Phylogenetic analyses, employing MEGAX and Cluster-Picker, along with confirmatory neighbor-joining tree analyses of subregions, were conducted to identify distinct clusters and determine subtypes. The uniqueness of the HIV-1 recombinants was evident in their exclusive clustering within generated maximum likelihood trees. Recombination analyses highlighted the distinct chimeric nature of these recombinants, with consistent mosaic patterns observed across all sequences within each of the four putative transmission clusters. Conclusive genetic characterization identified four novel HIV-1 CRFs: CRF129_56G, CRF130_A1B, CRF131_A1B, and CRF138_cpx. CRF129_56G exhibited two recombination breakpoints and three fragments of subtypes CRF56_cpx and G. Both CRF130_A1B and CRF131_A1B featured seven recombination breakpoints and eight fragments of subtypes A1 and B. CRF138_cpx displayed five recombination breakpoints and six fragments of subtypes CRF22_01A1 and F2, along with an unclassified fragment. Additional BLAST analyses identified a Unique Recombinant Form (URF) of CRF138_cpx with three additional recombination sites, involving subtype F2, a fragment of unknown subtype origin, and CRF138_cpx. Post-identification, all putative transmission clusters remained active, with CRF130_A1B, CRF131_A1B, and CRF138_cpx clusters exhibiting further growth. Furthermore, international connections were identified through BLAST analyses, linking one sequence from the USA to the CRF130_A1B strain, and three sequences from Belgium and Cameroon to the CRF138_cpx strain. This study contributes valuable insights into the dynamic landscape of HIV-1 diversity and transmission patterns, emphasizing the need for ongoing molecular surveillance and global collaboration in tracking emerging viral variants.
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Affiliation(s)
- Cicek Topcu
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus
| | - Vasilis Georgiou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus
| | - Johana Hezka Rodosthenous
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus
| | | | - Elena Katerina Gavala
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus
| | - Christiana Reveka Dimitriou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus
| | - Evgenia Zeniou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus
| | - Brian Thomas Foley
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60–68 Phaneromenis Street, 1011 Nicosia, Cyprus
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2
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Topcu C, Georgiou V, Rodosthenous JH, Demetriades I, Foley BT, G Kostrikis L. Characterization of a novel HIV-1 circulating recombinant form, CRF91_cpx, comprising CRF02_AG, G, J, and U, mostly among men who have sex with men. Virulence 2022; 13:1331-1348. [PMID: 35979885 PMCID: PMC9397478 DOI: 10.1080/21505594.2022.2106021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Prospective molecular studies of HIV-1 pol region (2253-5250 in HXB2 genome) sequences from sequenced samples of 269 HIV-1-infected patients in Cyprus (2017-2021) revealed a transmission cluster of 14 unknown HIV-1 recombinants that were not classified as previously established CRFs. The earliest recombinant was collected in September 2017, and the transmission cluster continued to grow until November 2020. Near full-length HIV-1 genome sequences of the 11 of the 14 recombinants were successfully obtained (790-8795 in HXB2 genome) and aligned against a reference dataset of HIV-1 subtypes and CRFs. We employed MEGAX for maximum-likelihood tree construction (GTR model, 1000 bootstrap replicates), Cluster-Picker for phylogenetic clustering analysis (genetic distance ≤0.045, bootstrap support value ≥70%), and REGA-3.0 for subtype determination. Bootscan and similarity plot analyses (sliding window of 400 nucleotides overlapped by 40 nucleotides) were conducted using SimPlot-v3.5.1, and subregion confirmatory neighbour-joining tree analyses were conducted using MEGAX (Kimura two-parameter model, 1000 bootstrap replicates, ≥70% bootstrap-support value). Exclusive clustering of the HIV-1 recombinants revealed their uniqueness. The recombination analyses illustrated the same unique mosaic pattern with six putative intersubtype recombination breakpoints, seven fragments of subtypes CRF02_AG, G, J and an unclassified fragment. We conclusively characterized the mosaic structure of the novel HIV-1 CRF, named CRF91_cpx, by the Los Alamos HIV Sequence Database. Additionally, we identified a URF of CRF91_cpx with two additional recombination sites, generated by a recombination event between subtype B and CRF91_cpx. Since the identification of CRF91_cpx, two additional patient samples have been entered into the CRF91_cpx transmission cluster, demonstrating active growth.
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Affiliation(s)
- Cicek Topcu
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, Nicosia, Cyprus
| | - Vasilis Georgiou
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, Nicosia, Cyprus
| | - Johana Hezka Rodosthenous
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, Nicosia, Cyprus
| | | | - Brian Thomas Foley
- Los Alamos National Laboratory, T-6 Theoretical Biology and Biophysics, Los Alamos, NM, USA
| | - Leondios G Kostrikis
- Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, Nicosia, Cyprus.,Cyprus Academy of Sciences, Letters, and Arts, Nicosia, Cyprus
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3
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Jia M, Shaw T, Zhang X, Liu D, Shen Y, Ezeamama AE, Yang C, Zhang M. Decoding noises in HIV computational genotyping. Virology 2017; 511:249-255. [PMID: 28918303 DOI: 10.1016/j.virol.2017.08.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 08/22/2017] [Accepted: 08/23/2017] [Indexed: 10/18/2022]
Abstract
Lack of a consistent and reliable genotyping system can critically impede HIV genomic research on pathogenesis, fitness, virulence, drug resistance, and genomic-based healthcare and treatment. At present, mis-genotyping, i.e., background noises in molecular genotyping, and its impact on epidemic surveillance is unknown. For the first time, we present a comprehensive assessment of HIV genotyping quality. HIV sequence data were retrieved from worldwide published records, and subjected to a systematic genotyping assessment pipeline. Results showed that mis-genotyped cases occurred at 4.6% globally, with some regional and high-risk population heterogeneities. Results also revealed a consistent mis-genotyping pattern in gp120 in all studied populations except the group of men who have sex with men. Our study also suggests novel virus diversities in the mis-genotyped cases. Finally, this study reemphasizes the importance of implementing a standardized genotyping pipeline to avoid genotyping disparity and to advance our understanding of virus evolution in various epidemiological settings.
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Affiliation(s)
- MingRui Jia
- Department of Pain Management, Shandong Provincial Hospital Affiliated to Shandong University, 324 Jingwu Road, Jinan, Shandong Province 250021, China; Department of Epidemiology and Biostatistics, University of Georgia, GA 30602, USA
| | - Timothy Shaw
- Department of Epidemiology and Biostatistics, University of Georgia, GA 30602, USA
| | - Xing Zhang
- Diagnostic Imaging center, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dong Liu
- Department of Epidemiology and Biostatistics, University of Georgia, GA 30602, USA; Laboratory of Ichthyology, Shanghai Ocean University, Shanghai 201306, China
| | - Ye Shen
- Department of Epidemiology and Biostatistics, University of Georgia, GA 30602, USA
| | - Amara E Ezeamama
- Department of Psychiatry, Michigan State University, MI 48824, USA
| | - Chunfu Yang
- International Laboratory Branch, Division of Global HIV/TB, Center for Global Health, Centers for Diseases Control and Prevention, GA 30333, USA
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, University of Georgia, GA 30602, USA.
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4
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Foley BT, Leitner T, Paraskevis D, Peeters M. Primate immunodeficiency virus classification and nomenclature: Review. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 46:150-158. [PMID: 27789390 PMCID: PMC5136504 DOI: 10.1016/j.meegid.2016.10.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 12/25/2022]
Abstract
The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature system, while at the same time it presents challenges such that many of the rules need to be flexibly applied or modified over time. This review outlines the nomenclature system for primate lentiviruses and provides an update on new findings since the last review was written in 2000.
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Affiliation(s)
- Brian T Foley
- Theoretical Biology and Biophysics Group, T-6 Mail Stop K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, T-6 Mail Stop K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Dimitrios Paraskevis
- National and Kapodistrian University of Athens, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, Athens, Greece
| | - Martine Peeters
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France; IBC, Computational Biology Institute, 34095 Montpellier, France
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5
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Delatorre E, de Azevedo SSD, Rodrigues-Pedro A, Velasco-de-Castro CA, Couto-Fernandez JC, Pilotto JH, Morgado MG. Tracing the origin of a singular HIV-1 CRF45_cpx clade identified in Brazil. INFECTION GENETICS AND EVOLUTION 2016; 46:223-232. [PMID: 27259365 DOI: 10.1016/j.meegid.2016.05.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 05/26/2016] [Accepted: 05/30/2016] [Indexed: 01/10/2023]
Abstract
The HIV-1 epidemiology has changed over the past decade toward a marked increase in the circulation of strains previously restricted to local epidemics. Recent molecular epidemiological surveys identified some HIV-1 strains of probable African origin circulating in Brazil, including the Circulating Recombinant Form (CRF) 45_cpx, a complex A1/K/U recombinant that circulates in Central Africa. Here, we characterize partial genomic sequences and reconstruct the evolutionary history of HIV-1 CRF45_cpx-related recombinant samples identified in independent studies carried out with HIV+ individuals in Brazil. The sequences were obtained by overlapping PCR amplifications followed by direct sequencing. Recombination profiles were determined by phylogenetic and bootscaning analyses. The evolutionary history was estimated by a Bayesian coalescent-based method using datasets representing the gag, pol and env gene fragments. Six of the 10 samples isolated in Rio de Janeiro showed a CRF45_cpx-like pattern throughout the sequenced genome. The remaining were classified as second-generation recombinants, showing the mosaic patterns: CRF45_cpx/B/D/F1/U, CRF45_cpx/B/F1/U, CRF45_cpx/B/U and CRF45_cpx/F1. All Brazilian CRF45_cpx sequences, except one, formed a monophyletic clade (CRF45-BR), which seems to be the result of a single introduction event that has spread to the Rio de Janeiro, São Paulo and Minas Gerais states and is related to sequences from Argentina, Italy and Belgium. The Bayesian analyses pointed out quite consistent onset dates for CRF45-BR clade (~1984: 1976-1996) in the three gene datasets. These results indicate that the CRF45-BR clade has been circulating in the Southeastern Brazilian region for about 30years, although its presence was not detected until recently due to its very low prevalence. This reinforces the relevance of large-scale molecular surveillance data to identify the emergence of new HIV variants and their impact on local epidemics.
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Affiliation(s)
- Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Suwellen S D de Azevedo
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Adriana Rodrigues-Pedro
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Carlos Augusto Velasco-de-Castro
- Laboratório de Virologia, Departamento de Patologia Clínica, Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Jose H Pilotto
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil; Hospital Geral de Nova Iguaçu, Rio de Janeiro, Brazil
| | - Mariza G Morgado
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
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Jia L, Li L, Li H, Liu S, Wang X, Bao Z, Li T, Zhuang D, Liu Y, Li J. Recombination pattern reanalysis of some HIV-1 circulating recombination forms suggest the necessity and difficulty of revision. PLoS One 2014; 9:e107349. [PMID: 25203725 PMCID: PMC4159329 DOI: 10.1371/journal.pone.0107349] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 08/09/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Recombination is one of the major mechanisms underlying the generation of HIV-1 variability. Currently 61 circulating recombinant forms of HIV-1 have been identified. With the development of recombination detection techniques and accumulation of HIV-1 reference stains, more accurate mosaic structures of circulating recombinant forms (CRFs), like CRF04 and CRF06, have undergone repeated analysis and upgrades. Such revisions may also be necessary for other CRFs. Unlike previous studies, whose results are based primarily on a single recombination detection program, the current study was based on multiple recombination analysis, which may have produced more impartial results. METHODS Representative references of 3 categories of intersubtype recombinants were selected, including BC recombinants (CRF07 and CRF08), BG recombinants (CRF23 and CRF24), and BF recombinants (CRF38 and CRF44). They were reanalyzed in detail using both the jumping profile hidden Markov model and RDP3. RESULTS The results indicate that revisions and upgrades are very necessary and the entire re-analysis suggested 2 types of revision: (i) length of inserted fragments; and (ii) number of inserted fragments. The reanalysis also indicated that determination of small regions of about 200 bases or fewer should be performed with more caution. CONCLUSION Results indicated that the involvement of multiple recombination detection programs is very necessary. Additionally, results suggested two major challenges, one involving the difficulty of accurately determining the locations of breakpoints and the second involving identification of small regions of about 200 bases or fewer with greater caution. Both indicate the complexity of HIV-1 recombination. The resolution would depend critically on development of a recombination analysis algorithm, accumulation of HIV-1 stains, and a higher sequencing quality. With the changes in recombination pattern, phylogenetic relationships of some CRFs may also change. All these results may be critical to understand the role of recombination in a complex and dynamic HIV evolution.
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Affiliation(s)
- Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, China
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Bulla I, Schultz AK, Chesneau C, Mark T, Serea F. A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection. BMC Bioinformatics 2014; 15:205. [PMID: 24946781 PMCID: PMC4230192 DOI: 10.1186/1471-2105-15-205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 06/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In many applications, a family of nucleotide or protein sequences classified into several subfamilies has to be modeled. Profile Hidden Markov Models (pHMMs) are widely used for this task, modeling each subfamily separately by one pHMM. However, a major drawback of this approach is the difficulty of dealing with subfamilies composed of very few sequences. One of the most crucial bioinformatical tasks affected by the problem of small-size subfamilies is the subtyping of human immunodeficiency virus type 1 (HIV-1) sequences, i.e., HIV-1 subtypes for which only a small number of sequences is known. RESULTS To deal with small samples for particular subfamilies of HIV-1, we introduce a novel model-based information sharing protocol. It estimates the emission probabilities of the pHMM modeling a particular subfamily not only based on the nucleotide frequencies of the respective subfamily but also incorporating the nucleotide frequencies of all available subfamilies. To this end, the underlying probabilistic model mimics the pattern of commonality and variation between the subtypes with regards to the biological characteristics of HI viruses. In order to implement the proposed protocol, we make use of an existing HMM architecture and its associated inference engine. CONCLUSIONS We apply the modified algorithm to classify HIV-1 sequence data in the form of partial HIV-1 sequences and semi-artificial recombinants. Thereby, we demonstrate that the performance of pHMMs can be significantly improved by the proposed technique. Moreover, we show that our algorithm performs significantly better than Simplot and Bootscanning.
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Affiliation(s)
- Ingo Bulla
- Institut für Mathematik und Informatik, Universität Greifswald, Walther-Rathenau-Straße 47, 17487 Greifswald, Germany.
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An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol 2009; 5:e1000581. [PMID: 19956739 PMCID: PMC2776870 DOI: 10.1371/journal.pcbi.1000581] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 10/28/2009] [Indexed: 11/19/2022] Open
Abstract
Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1) are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes. Computational identification of such subtypes is helpful in surveillance, epidemiological analysis and detection of novel variants, e.g., circulating recombinant forms in HIV-1. A number of conceptually and technically different techniques have been proposed for determining the subtype of a query sequence, but there is not a universally optimal approach. We present a model-based phylogenetic method for automatically subtyping an HIV-1 (or other viral or bacterial) sequence, mapping the location of breakpoints and assigning parental sequences in recombinant strains as well as computing confidence levels for the inferred quantities. Our Subtype Classification Using Evolutionary ALgorithms (SCUEAL) procedure is shown to perform very well in a variety of simulation scenarios, runs in parallel when multiple sequences are being screened, and matches or exceeds the performance of existing approaches on typical empirical cases. We applied SCUEAL to all available polymerase (pol) sequences from two large databases, the Stanford Drug Resistance database and the UK HIV Drug Resistance Database. Comparing with subtypes which had previously been assigned revealed that a minor but substantial (≈5%) fraction of pure subtype sequences may in fact be within- or inter-subtype recombinants. A free implementation of SCUEAL is provided as a module for the HyPhy package and the Datamonkey web server. Our method is especially useful when an accurate automatic classification of an unknown strain is desired, and is positioned to complement and extend faster but less accurate methods. Given the increasingly frequent use of HIV subtype information in studies focusing on the effect of subtype on treatment, clinical outcome, pathogenicity and vaccine design, the importance of accurate, robust and extensible subtyping procedures is clear. There are nine different subtypes of the main group of HIV-1, each originating as a distinct subepidemic of HIV-1. The distribution of subtypes is often unique to a given geographic region of the world and constitutes a useful epidemiological and surveillance resource. The effects of viral subtype on disease progression, treatment outcome and vaccine design are being actively researched, and the importance of accurate subtyping procedures is clear. In HIV-1, subtype assignment is complicated by frequent recombination among co-circulating strains, creating new genetic mosaics or recombinant forms: 43 have been characterized to date, and many more likely exist. We present an automated phylogenetic method (SCUEAL) to accurately characterize both simple and complex HIV-1 mosaics. Using computer simulations and biological data we demonstrate that SCUEAL performs very well under various conditions, especially when some of the existing classification procedures fail. Furthermore, we show that a small, but noticeable proportion of subtype characterization stored in public databases may be incomplete or incorrect. The computational technique introduced here should provide a much more accurate characterization of HIV-1 strains, especially novel recombinants, and lead to new insights into molecular history, epidemiology and geographical distribution of the virus.
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van der Hoek L, Pollakis G, Lukashov VV, Jebbink MF, Jeeninga RE, Bakker M, Dukers N, Jurriaans S, Paxton WA, Back NKT, Berkhout B. Characterization of an HIV-1 group M variant that is distinct from the known subtypes. AIDS Res Hum Retroviruses 2007; 23:466-70. [PMID: 17411380 DOI: 10.1089/aid.2006.0184] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We identified an HIV-1 variant that belongs to the M group, with limited similarity of short genetic regions (100-200 nt) to subtype K, but the remainder of the genome is unrelated to any established HIV-1 subtype. The isolate was obtained from an HIV-1-positive male, living in the Netherlands, who encountered the virus before 1989, most probably via heterosexual contact in Africa. We describe the full-length genome sequence of four biological clones that were obtained from two samples collected 5 years apart. At both time points all open reading frames were intact. Within the 5-year interval, the person received antiretroviral therapy with zalcitabine and zidovudine for almost 4 years. Evolution of drug-resistant variants is likely given the increase in viral RNA load to +/-10,000 copies/ml during the last year of treatment. Surprisingly, the only regular RT mutation acquired during this period was K70R, which suggests that the genetic background of this variant is perhaps not suitable for the generation of the standard 41L, 67N, and 215Y/F mutations that typically arise during prolonged, nonsuccessful, zidovudine treatment. Awaiting the discovery of at least two additional, epidemiologically unrelated patients with a phylogenetically related HIV-1 variant, we can designate this variant a new HIV-1 subtype, or a distinct branch of subtype K.
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Affiliation(s)
- Lia van der Hoek
- Laboratory of Experimental Virology, and Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands.
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10
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Yilmaz G, Midilli K, Türkoğlu S, Bayraktaroğlu Z, Kuşkucu AM, Ozkan E, Atasever L, Calangu S, Altaş K. Genetic subtypes of human immunodeficiency virus type 1 (HIV-1) in Istanbul, Turkey. Int J Infect Dis 2006; 10:286-90. [PMID: 16516519 DOI: 10.1016/j.ijid.2005.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Revised: 06/03/2005] [Accepted: 06/14/2005] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Epidemiological surveillance of HIV-1 subtypes is an important and ongoing element of preparation for global antiviral interventions. OBJECTIVE To assess the molecular epidemiology of HIV-1 in Istanbul, Turkey. STUDY DESIGN 27 HIV/AIDS patients were investigated. Data on age, sex, country of birth, and HIV acquisition route were collected. Following amplification with PCR the sequences of the gp41 region of the env gene were determined using a 310 DNA sequencer (ABI prism, Foster City, USA) and phylogenetically analyzed. RESULTS Among the 27 patients (26 adults and 1 infant), 22 were male, born in Turkey, and 20 infected through heterosexual contact. Two patients acquired the virus through blood and/or blood transfusion and one infant by vertical transmission. The distribution of the subtypes was as follows: four were subtype A, 19 subtype B, one subtype C, one subtype D, and two subtype F1. According to our results, although the B subtype is still predominant, non-B subtypes are also present, even though the number of registered HIV/AIDS patients is low. CONCLUSION These are the first subtyped HIV-1 strains in Turkey where a low level of HIV prevalence has been observed since the first reported case in 1985. These findings and Turkey's specific geographic localization indicate the need for a nationwide surveillance to detect all subtypes including the new recombinant ones.
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Affiliation(s)
- Gülden Yilmaz
- Department of Microbiology and Clinical Microbiology, Cerrahpasa Faculty of Medicine, Istanbul University, Istanbul 34303, Turkey.
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11
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Paraskevis D, Magiorkinis E, Magiorkinis G, Kiosses VG, Lemey P, Vandamme AM, Rambaut A, Hatzakis A. Phylogenetic reconstruction of a known HIV-1 CRF04_cpx transmission network using maximum likelihood and Bayesian methods. J Mol Evol 2005; 59:709-17. [PMID: 15693627 DOI: 10.1007/s00239-004-2651-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The CRF04_cpx strains of HIV-1 accounts for approximately 2-10% of the infected population in Greece, across different transmission risk groups. CRF04_cpx was the lineage documented in an HIV-1 transmission network in Thessalonica, northern Greece. Most of the transmissions occurred through unprotected heterosexual contacts between 1989 and 1993. Blood samples were available for six patients, obtained 6-10 years later, except for one patient sampled in 1991. Our objective was to examine whether the transmission history is compatible with the evolutionary tree of the virus, in partial gag, partial env, and partial gag+env. The inferred phylogenetic tree obtained using maximum likelihood and Bayesian methods in partial gag+env was much closer to the transmission tree than that using either env or gag separately. Our findings suggest that the epidemiological relationships among patients who have been infected by a common source correspond almost exactly to the evolutionary trees of the virus, given that enough phylogenetic signal is present in the alignment. Moreover, we found evidence that recombination is not the most parsimonious explanation for the phylogenetic incongruence between gag and env. For patients with known infection dates, the estimated dates of the coalescent events obtained using molecular clock calculations based on a newly developed Bayesian method in gag + env were in agreement with the actual infection dates.
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Affiliation(s)
- Dimitrios Paraskevis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece.
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Papa A, Papadimitriou E, Papoutsi A, Malissiovas N, Kiosses VG, Antoniadis A. Genetic variation of the protease and reverse transcriptase genes in HIV-1 CRF04_cpx strains. AIDS Res Hum Retroviruses 2002; 18:677-80. [PMID: 12079565 DOI: 10.1089/088922202760019392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To gain information about the genetic variation of the protease and reverse transcriptase gene-coding regions in HIV-1 strains belonging to CRF04_cpx, genotyping and drug susceptibility testing were performed on serum samples derived from seven patients carrying sequences belonging to this circulating recombinant form. Substitutions classically associated with resistance to antiretroviral drugs were observed in six of seven samples, including G48V, V82A, L90M, M46I in the protease protein, and K70R, D69D/N, M184V, T215F, K103N in the reverse transcriptase protein. Genotypic resistance patterns of CRF04_cpx samples were found to be similar to those identified in subtype B viruses, suggesting that the drug-selective pressure has similar effects on both subtype B and CRF04_cpx.
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Affiliation(s)
- Anna Papa
- National AIDS Reference Laboratory of Northern Greece, A Department of Microbiology, School of Medicine, Aristotelian University of Thessaloniki, Thessaloniki 54006, Greece.
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Affiliation(s)
- I D Tatt
- Sexually Transmitted and Blood Borne Virus Laboratory, Central Public Health Laboratory, Public Health Laboratory Service, London, UK
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14
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Magiorkinis G, Paraskevis D, Magiorkinis E, Vandamme AM, Hatzakis A. Reanalysis of the HIV-1 circulating recombinant form A/E (CRF01_AE): evidence of A/E/G recombination. J Acquir Immune Defic Syndr 2002; 30:124-9. [PMID: 12048373 DOI: 10.1097/00042560-200205010-00017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Circulating recombinant form (CRF) 01_AE caused an extensive HIV-1 epidemic in Thailand and Southeast Asia. Reanalysis of the recombination pattern of CRF01_AE suggested a more complicated pattern of mosaicism consisting of subtypes A, G, and E. These findings provide evidence that CRF01_AE originated from recombination between at least three different subtypes.
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Affiliation(s)
- Gkikas Magiorkinis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece
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15
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Papa A, Papadimitriou E, Papoutsi A, Kiosses V, Antoniadis A. HIV-1 subtypes and circulating recombinant forms (CRFs) in Northern Greece. Virus Res 2002; 85:85-93. [PMID: 11955641 DOI: 10.1016/s0168-1702(02)00020-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In order to understand the genetic diversity of virus isolates associated with the human immunodeficiency virus type one (HIV-1) epidemic in Northern Greece, 51 specimens from HIV-1 infected individuals were classified into subtypes by sequence-based phylogenetic analysis of the polymerase (pol) region of the viral genome. Forty two (82.3%) specimens were identified as pol subtype B, three (5.9%) as A, and one (2%) as CRF01_AE, while the remaining five (9.8%) specimens appeared to be complex recombinants, belonging to the Cypriot/Greek form CRF04_cpx. The proportion of CRF04_cpx strains is larger than previously reported, suggesting that the CRF04_cpx is significantly contributing to the Greek HIV-1 epidemic.
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Affiliation(s)
- Anna Papa
- Department of Microbiology, National AIDS Reference Laboratory of Northern Greece, School of Medicine, Aristotelian University of Thessaloniki, 54006, Greece.
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16
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Paraskevis D, Magiorkinis E, Magiorkinis G, Anastassopoulou C, Lazanas M, Chrysos G, Vandamme AM, Hatzakis A. Molecular characterization of a complex, recombinant human immunodeficiency virus type 1 (HIV-1) isolate (A/G/J/K/?): evidence to support the existence of a novel HIV-1 subtype. J Gen Virol 2001; 82:2509-2514. [PMID: 11562543 DOI: 10.1099/0022-1317-82-10-2509] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recombination is one of several factors that contribute to the great genetic diversity of human immunodeficiency virus type 1 (HIV-1). In the current study, analysis of the full-length genome of a novel complex mosaic HIV-1 isolate (99GR303) from a Greek sailor who was possibly infected in Sierra Leone, Africa is presented. The 99GR303 isolate was found to comprise genomic regions belonging to subtypes A, G, J and K as well as of regions of a subtype that remains unclassified. For a partial region of env as well as vpr, no apparent similarity to the known HIV-1 subtypes or to any of the circulating recombinant forms was found. In fact, in the partial env gene, including the C2-V3 region, the 99GR303 isolate formed a new clade, suggesting the existence of an additional HIV-1 subtype. Thus, novel recombinants embody partial genomic regions which may have originated either from subtypes that existed in the past and became extinct or from contemporary subtypes that are extremely rare.
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Affiliation(s)
- D Paraskevis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, 75 Mikras Asias Street, GR-115 27 Athens (Goudi), Greece1
| | - E Magiorkinis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, 75 Mikras Asias Street, GR-115 27 Athens (Goudi), Greece1
| | - G Magiorkinis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, 75 Mikras Asias Street, GR-115 27 Athens (Goudi), Greece1
| | - C Anastassopoulou
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, 75 Mikras Asias Street, GR-115 27 Athens (Goudi), Greece1
| | | | - G Chrysos
- Tzanio General Hospital, Piraeus, Greece3
| | - A M Vandamme
- Rega Institute for Medical Research and University Hospitals, Katholieke Universiteit Leuven, Belgium4
| | - A Hatzakis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, 75 Mikras Asias Street, GR-115 27 Athens (Goudi), Greece1
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