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Silva GPSA, Oliveira RC, de Souza JSM, Giovanetti M, Guimarães ML, Brites C, Monteiro-Cunha JP. Tracing the relationship among HIV-1 sub-subtype F1 strains: a phylodynamic perspective. Mem Inst Oswaldo Cruz 2023; 117:e220109. [PMID: 36700579 PMCID: PMC9870255 DOI: 10.1590/0074-02760220109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/17/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The human immunodeficiency virus type 1, F1 sub-subtype (HIV-1 F1) circulates in three continents: Africa, Europe, and South America. In Brazil, this sub-subtype co-circulates with subtypes B and C and several recombinant forms, mainly BF1 variants. OBJECTIVES This study aimed to reconstruct the dynamic history of HIV-1 F1 in Brazil. METHODS HIV-1 near full-length genome and pol gene nucleotide sequences available in public databases were assembled in two datasets (POL671 and NFLG53) to cover the largest number of F1 sub-subtype sequences. Phylodynamic and temporal analyses were performed. FINDINGS Two main strains of the F1 sub-subtype are circulating worldwide. The first (F1.I) was found among Brazilian samples (75%) and the second (F1.II) among Romanian (62%) and other European and African isolates. The F1 subtype epidemic in Brazil originated from a single entry into the country around 1970. This ancestral sample is related to samples isolated in European countries (France, Finland, and Belgium), which are possibly of African origin. Moreover, further migration (1998 CI: 1994-2003) of strains from Brazil to Europe (Spain and the UK) was observed. Interestingly, all different recombinant BF patterns found, even those from outside Brazil, present the same F1 lineage (F1.I) as an ancestor, which could be related to the acquisition of adaptive advantages for the recombinant progenies. MAIN CONCLUSIONS These findings are important for the understanding of the origin and dynamics of the F1 sub-subtype and a consequent better and greater understanding of the HIV-1 F1 and BF epidemic that still spreads from Brazil to other countries.
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Affiliation(s)
| | - Rodrigo Cunha Oliveira
- Universidade Federal da Bahia, Departamento de Bioquímica e Biofísica, Salvador, BA, Brasil
| | | | - Marta Giovanetti
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Laboratório de Genética Celular e Molecular, Belo Horizonte, MG, Brasil
| | - Monick Lindenmeyer Guimarães
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS e Imunologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Carlos Brites
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, BA, Brasil
| | - Joana Paixão Monteiro-Cunha
- Universidade Federal da Bahia, Departamento de Bioquímica e Biofísica, Salvador, BA, Brasil,+ Corresponding author:
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Gil H, Delgado E, Benito S, Georgalis L, Montero V, Sánchez M, Cañada-García JE, García-Bodas E, Díaz A, Thomson MM. Transmission Clusters, Predominantly Associated With Men Who Have Sex With Men, Play a Main Role in the Propagation of HIV-1 in Northern Spain (2013–2018). Front Microbiol 2022; 13:782609. [PMID: 35432279 PMCID: PMC9009226 DOI: 10.3389/fmicb.2022.782609] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses of HIV-1-infected individuals whose transmission is related group phylogenetically in transmission clusters (TCs). The study of the phylogenetic relations of these viruses and the factors associated with these individuals is essential to analyze the HIV-1 epidemic. In this study, we examine the role of TCs in the epidemiology of HIV-1 infection in Galicia and the Basque County, two regions of northern Spain. A total of 1,158 HIV-1-infected patients from both regions with new diagnoses (NDs) in 2013–2018 were included in the study. Partial HIV-1 pol sequences were analyzed phylogenetically by approximately maximum-likelihood with FastTree 2. In this analysis, 10,687 additional sequences from samples from HIV-1-infected individuals collected in Spain in 1999–2019 were also included to assign TC membership and to determine TCs’ sizes. TCs were defined as those which included viruses from ≥4 individuals, at least 50% of them Spaniards, and with ≥0.95 Shimodaira-Hasegawa-like node support in the phylogenetic tree. Factors associated to TCs were evaluated using odds ratios (OR) and their 95% CI. Fifty-one percent of NDs grouped in 162 TCs. Male patients (OR: 2.6; 95% CI: 1.5–4.7) and men having sex with men (MSM; OR: 2.1; 95% CI: 1.4–3.2) had higher odds of belonging to a TC compared to female and heterosexual patients, respectively. Individuals from Latin America (OR: 0.3; 95% CI: 0.2–0.4), North Africa (OR: 0.4; 95% CI: 0.2–1.0), and especially Sub-Saharan Africa (OR: 0.02; 95% CI: 0.003–0.2) were inversely associated to belonging to TCs compared to native Spaniards. Our results show that TCs are important components of the HIV-1 epidemics in the two Spanish regions studied, where transmission between MSM is predominant. The majority of migrants were infected with viruses not belonging to TCs that expand in Spain. Molecular epidemiology is essential to identify local peculiarities of HIV-1 propagation. The early detection of TCs and prevention of their expansion, implementing effective control measures, could reduce HIV-1 infections.
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Affiliation(s)
- Horacio Gil
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Michael M. Thomson, ; Horacio Gil,
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sonia Benito
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Leonidas Georgalis
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Vanessa Montero
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Mónica Sánchez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Javier E. Cañada-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Elena García-Bodas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Asunción Díaz
- HIV Surveillance and Behavioral Monitoring Unit, Centro Nacional de Epidemiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Michael M. Thomson, ; Horacio Gil,
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3
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Ekpenyong ME, Adegoke AA, Edoho ME, Inyang UG, Udo IJ, Ekaidem IS, Osang F, Uto NP, Geoffery JI. Collaborative Mining of Whole Genome Sequences for Intelligent HIV-1 Sub-Strain(s) Discovery. Curr HIV Res 2022; 20:163-183. [PMID: 35142269 DOI: 10.2174/1570162x20666220210142209] [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: 08/24/2021] [Revised: 11/30/2021] [Accepted: 12/20/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Effective global antiretroviral vaccines and therapeutic strategies depend on the diversity, evolution, and epidemiology of their various strains as well as their transmission and pathogenesis. Most viral disease-causing particles are clustered into a taxonomy of subtypes to suggest pointers toward nucleotide-specific vaccines or therapeutic applications of clinical significance sufficient for sequence-specific diagnosis and homologous viral studies. These are very useful to formulate predictors to induce cross-resistance to some retroviral control drugs being used across study areas. OBJECTIVE This research proposed a collaborative framework of hybridized (Machine Learning and Natural Language Processing) techniques to discover hidden genome patterns and feature predictors, for HIV-1 genome sequences mining. METHOD 630 human HIV-1 genome sequences above 8500 bps were excavated from the National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov) for 21 countries across different continents, Antarctica exempt. These sequences were transformed and learned using a self-organizing map (SOM). To discriminate emerging/new sub-strain(s), the HIV-1 reference genome was included as part of the input isolates/samples during the training. After training the SOM, component planes defining pattern clusters of the input datasets were generated, for cognitive knowledge mining and subsequent labelling of the datasets. Additional genome features including dinucleotide transmission recurrences, codon recurrences, and mutation recurrences, were finally extracted from the raw genomes to construct output classification targets for supervised learning. RESULTS SOM training explains the inherent pattern diversity of HIV-1 genomes as well as inter- and intra-country transmissions in which mobility might play an active role, as corroborated by literature. Nine sub-strains were discovered after disassembling the SOM correlation hunting matrix space attributed to disparate clusters. Cognitive knowledge mining separated similar pattern clusters bounded by a certain degree of correlation range, discovered by the SOM. A Kruskal-Wallis rank-sum test and Wilcoxon rank-sum test showed statistically significant variations in dinucleotide, codon, and mutation patterns. CONCLUSION Results of the discovered sub-strains and response clusters visualizations corroborate existing literature, with significant haplotype variations. The proposed framework would assist in the development of decision support systems for easy contact tracing, infectious disease surveillance, and studying the progressive evolution of the reference HIV-1 genome.
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Affiliation(s)
- Moses E Ekpenyong
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
- Centre for Research and Development, University of Uyo, Uyo, Nigeria
| | - Anthony A Adegoke
- Department of Microbiology, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Mercy E Edoho
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Udoinyang G Inyang
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Ifiok J Udo
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Itemobong S Ekaidem
- Department of Chemical Pathology, College of Health Sciences, University of Uyo, Uyo, Nigeria
| | - Francis Osang
- Department of Computer Science, Faculty of Science, National Open University, Abuja, Nigeria
| | - Nseobong P Uto
- School of Mathematics and Statistics, University of St Andrews, Scotland, United Kingdom
| | - Joseph I Geoffery
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
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4
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O'Keefe KJ, Pipkin S, Fatch R, Scheer S, Liegler T, McFarland W, Grant RM, Truong HHM. Non-B variants of HIV-1 in San Francisco, California. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 90:104677. [PMID: 33321227 PMCID: PMC10686190 DOI: 10.1016/j.meegid.2020.104677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 11/26/2022]
Abstract
The HIV-1 epidemic in the US has historically been dominated by subtype B. HIV subtype diversity has not been extensively examined in most US cities to determine whether non-B variants have become established, as has been observed in many other global regions. We describe the diversity of non-B variants and present evidence of local transmission of non-B HIV in San Francisco. Viral sequences collected from patients between 2000 and 2016 were matched to the San Francisco HIV/AIDS case registry. HIV subtype was determined using COMET. Phylogenies were reconstructed using the pol region of subtypes A, C, D, G, CRF01_AE, CRF02_AG, and CRF07_BC, with reference sequences from the LANL HIV database. Associations of non-B subtypes and circulating recombinant forms (CRFs) with patient characteristics were assessed using multivariable logistic regression. Out of 11,381 sequences, 10,669 were from 7235 registry cases, of which 141 (2%) had non-B subtypes and CRFs and 72 (1%) had unique recombinant forms. CRF01_AE (0.8%) and subtype C (0.5%) were the most prevalent non-B forms. The frequency of non-B subtypes and CRFs increased in San Francisco during years 2000-2016. Out of 146 transmission events involving non-B study sequences, 18% indicated local transmission within the study population and 74% appeared to be inward migration of the virus. Compared to 7016 cases with only subtype B, 141 cases with non-B sequences were more likely to be of non-US country of birth (aOR = 11.02; p < 0.001), of Asian/Pacific-Islander race/ethnicity (aOR = 3.17; p < 0.001), and diagnosed after 2009 (aOR = 4.81; p < 0.001). Results suggest that most non-B infections were likely acquired outside the US and that local transmission of non-B forms has occurred but so far has not produced extensive transmission networks. Thus, non-B variants were not widely established in San Francisco, an observation that differs from cities worldwide with more diverse epidemics.
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Affiliation(s)
- Kara J O'Keefe
- Department of Medicine, University of California, San Francisco, CA 94158, USA.
| | - Sharon Pipkin
- Department of Public Health, San Francisco, CA 94102, USA.
| | - Robin Fatch
- Department of Epidemiology and Biostatistics, University of California, San Francisco 94158, USA.
| | - Susan Scheer
- Department of Public Health, San Francisco, CA 94102, USA.
| | - Teri Liegler
- Department of Medicine, University of California, San Francisco, CA 94158, USA
| | - Willi McFarland
- Department of Public Health, San Francisco, CA 94102, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco 94158, USA.
| | - Robert M Grant
- Department of Medicine, University of California, San Francisco, CA 94158, USA.
| | - Hong-Ha M Truong
- Department of Medicine, University of California, San Francisco, CA 94158, USA.
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Mutenherwa F, Wassenaar D, de Oliveira T. Adding a Voice to the Unique Ethical Considerations in Molecular HIV Surveillance. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2020; 20:34-36. [PMID: 33016832 DOI: 10.1080/15265161.2020.1806399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Farirai Mutenherwa
- University of KwaZulu-Natal
- KwaZulu-Natal Research Innovation and Sequencing Platform
| | - Douglas Wassenaar
- University of KwaZulu-Natal
- South African Research Ethics Training Initiative, University of KwaZulu-Natal
| | - Tulio de Oliveira
- University of KwaZulu-Natal
- KwaZulu-Natal Research Innovation and Sequencing Platform
- University of Washington
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Schlösser M, Kartashev VV, Mikkola VH, Shemshura A, Saukhat S, Kolpakov D, Suladze A, Tverdokhlebova T, Hutt K, Heger E, Knops E, Böhm M, Di Cristanziano V, Kaiser R, Sönnerborg A, Zazzi M, Bobkova M, Sierra S. HIV-1 Sub-Subtype A6: Settings for Normalised Identification and Molecular Epidemiology in the Southern Federal District, Russia. Viruses 2020; 12:v12040475. [PMID: 32331438 PMCID: PMC7232409 DOI: 10.3390/v12040475] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 01/08/2023] Open
Abstract
Russia has one of the largest and fastest growing HIV epidemics. However, epidemiological data are scarce. Sub-subtype A6 is most prevalent in Russia but its identification is challenging. We analysed protease/reverse transcriptase-, integrase-sequences, and epidemiological data from 303 patients to develop a methodology for the systematisation of A6 identification and to describe the HIV epidemiology in the Russian Southern Federal District. Drug consumption (32.0%) and heterosexual contact (27.1%) were the major reported transmission risks. This study successfully established the settings for systematic identification of A6 samples. Low frequency of subtype B (3.3%) and large prevalence of sub-subtype A6 (69.6%) and subtype G (23.4%) were detected. Transmitted PI- (8.8%) and NRTI-resistance (6.4%) were detected in therapy-naive patients. In therapy-experienced patients, 17.3% of the isolates showed resistance to PIs, 50.0% to NRTI, 39.2% to NNRTIs, and 9.5% to INSTIs. Multiresistance was identified in 52 isolates, 40 corresponding to two-class resistance and seven to three-class resistance. Two resistance-associated-mutations significantly associated to sub-subtype A6 samples: A62VRT and G190SRT. This study establishes the conditions for a systematic annotation of sub-subtype A6 to normalise epidemiological studies. Accurate knowledge on South Russian epidemiology will allow for the development of efficient regional frameworks for HIV-1 infection management.
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Affiliation(s)
- Madita Schlösser
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Vladimir V. Kartashev
- Russian Southern Federal Center for HIV Control, 344000 Rostov-na-Donu, Russia; (V.V.K.); (D.K.); (A.S.); (T.T.)
- Department of Infectious Diseases, Rostov State Medical University, 344022 Rostov-na-Donu, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Visa H. Mikkola
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Andrey Shemshura
- Clinical Center of HIV/AIDS of the Ministry of Health of Krasnodar Region, 350015 Krasnodar, Russia;
| | - Sergey Saukhat
- Department of Infectious Diseases, Rostov State Medical University, 344022 Rostov-na-Donu, Russia;
| | - Dmitriy Kolpakov
- Russian Southern Federal Center for HIV Control, 344000 Rostov-na-Donu, Russia; (V.V.K.); (D.K.); (A.S.); (T.T.)
| | - Alexandr Suladze
- Russian Southern Federal Center for HIV Control, 344000 Rostov-na-Donu, Russia; (V.V.K.); (D.K.); (A.S.); (T.T.)
| | - Tatiana Tverdokhlebova
- Russian Southern Federal Center for HIV Control, 344000 Rostov-na-Donu, Russia; (V.V.K.); (D.K.); (A.S.); (T.T.)
| | - Katharina Hutt
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Eva Heger
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Elena Knops
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Michael Böhm
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Veronica Di Cristanziano
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Rolf Kaiser
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, 17177 Stockholm, Sweden;
| | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy;
| | - Marina Bobkova
- Department of General Virology, Gamaleya Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia;
| | - Saleta Sierra
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50935 Cologne, Germany; (M.S.); (V.H.M.); (K.H.); (E.H.); (E.K.); (M.B.); (V.D.C.); (R.K.)
- Correspondence: ; Tel.: +49-221-4788-5807
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Analysis of HIV-1 diversity, primary drug resistance and transmission networks in Croatia. Sci Rep 2019; 9:17307. [PMID: 31754119 PMCID: PMC6872562 DOI: 10.1038/s41598-019-53520-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/31/2019] [Indexed: 01/23/2023] Open
Abstract
Molecular epidemiology of HIV-1 infection in treatment-naive HIV-1 infected persons from Croatia was investigated. We included 403 persons, representing 92.4% of all HIV-positive individuals entering clinical care in Croatia in 2014–2017. Overall prevalence of transmitted drug resistance (TDR) was estimated at 16.4%. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside RTI (NNRTIs) and protease inhibitors (PIs) was found in 11.4%, 6.7% and 2.5% of persons, respectively. Triple-class resistance was determined in 2.2% of individuals. In addition, a single case (1.0%) of resistance to integrase strand-transfer inhibitors (InSTIs) was found. Deep sequencing was performed on 48 randomly selected samples and detected additional TDR mutations in 6 cases. Phylogenetic inference showed that 347/403 sequences (86.1%) were part of transmission clusters and identified forward transmission of resistance in Croatia, even that of triple-class resistance. The largest TDR cluster of 53 persons with T215S was estimated to originate in the year 1992. Our data show a continuing need for pre-treatment HIV resistance testing in Croatia. Even though a low prevalence of resistance to InSTI was observed, surveillance of TDR to InSTI should be continued.
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Beamud B, Bracho MA, González-Candelas F. Characterization of New Recombinant Forms of HIV-1 From the Comunitat Valenciana (Spain) by Phylogenetic Incongruence. Front Microbiol 2019; 10:1006. [PMID: 31191463 PMCID: PMC6540936 DOI: 10.3389/fmicb.2019.01006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 04/18/2019] [Indexed: 11/13/2022] Open
Abstract
Recombination is one of the main processes shaping the evolution of HIV-1, with relevant consequences for its epidemiology. In fact, Circulating and Unique Recombinant Forms (CRFs and URFs) cause 23% of current infections. The routine analyses of antiretroviral resistance yield partial pol gene sequences that can be exploited for molecular epidemiology surveillance but also to study viral diversity and to detect potential recombinant samples. Among the pol sequences derived from a large sample dataset from the Comunitat Valenciana (Spain), we identified nine putative recombinant samples. We aimed at fully characterizing these samples and performing a detailed analysis of the corresponding recombination events. We obtained nearly full-genome sequences and used jpHMM and RDP4 to detect and characterize recombinant fragments. We assessed the confidence of these inferences by likelihood mapping and phylogenetic placement with topology congruence tests. Next, we performed a phylogenetic analysis of each putative recombinant fragment to determine its relationships to previously described recombinant forms. We found that two samples related to CRF44_BF whereas the rest corresponded to new URFs (two URF_AD, one URF_BG that can constitute a new CRF resulting from subtype B and CRF24_BG, and two URF_cpx composed of A, G, K, H, and J subtypes). These URFs have a complex recombination pattern that cannot be determined accurately. They seem to have arisen by successive recombination events among lineages, including other CRFs. Our results highlight the usefulness of routine surveillance analysis for the detection of new HIV-1 recombination forms and, at the same time, the need for full-genome sequencing and recombination detection guidelines to properly characterize this complex process.
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Affiliation(s)
- Beatriz Beamud
- Instituto de Biología Integrativa de Sistemas, Consejo Superior de Investigaciones Científicas, Universitat de València, Valencia, Spain.,Unidad Mixta de Investigación Infección y Salud Pública, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Universitat de València, Valencia, Spain
| | - María Alma Bracho
- Unidad Mixta de Investigación Infección y Salud Pública, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Universitat de València, Valencia, Spain.,Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Valencia, Spain
| | - Fernando González-Candelas
- Instituto de Biología Integrativa de Sistemas, Consejo Superior de Investigaciones Científicas, Universitat de València, Valencia, Spain.,Unidad Mixta de Investigación Infección y Salud Pública, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Universitat de València, Valencia, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Valencia, Spain
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9
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Pérez-Parra S, Álvarez M, Fernandez-Caballero JA, Pérez AB, Santos J, Bisbal O, Aguilera A, Rivero M, García-Fraile L, García F. Continued propagation of the CRF19_cpx variant among HIV-positive MSM patients in Spain. J Antimicrob Chemother 2019; 73:1031-1038. [PMID: 29325134 DOI: 10.1093/jac/dkx474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/15/2017] [Indexed: 01/15/2023] Open
Abstract
Objectives The HIV-1 CRF19_cpx genetic form has been recently associated with greater pathogenicity. We used CoRIS, a national cohort of 31 reference hospitals in Spain, to investigate the current epidemiological situation of this variant in Spain. Patients and methods We analysed 4734 naive HIV-1-positive patients diagnosed during the 2007-15 period with an available pol gene sequence in the CoRIS resistance database. HIV-1 CRF19_cpx was ascribed through REGA3.0 and confirmed by a phylogenetic analysis. We analysed the presence of the transmission clusters of HIV-1 CRF19_cpx by maximum likelihood [with the randomized accelerated maximum likelihood (RAxML) program] and the time to the most recent common ancestor using Bayesian inference (BEAST, v. 1.7.5). Results Nineteen patients were infected with CRF19_cpx: all were male, they had a mean age of 42.9 years (95% CI: 36.4-52.5 years), the majority were MSM [n = 18 (95%)] and of Spanish nationality [n = 16 (84.2%)] and they had high CD4+ T cell counts (∼415 cells/mm3). Fifteen patients were grouped into four different transmission clusters: two clusters (two patients each) grouped the patients from Valencia and another cluster grouped one patient from Madrid and another from Seville. We found a larger cluster that grouped nine patients from southern Spain (Malaga and Seville), of which six presented mutation G190A. We estimated the origin of all the transmission clusters to take place between 2009 and 2010. Conclusions We demonstrate that this variant has spread in Spain in recent years among young HIV-positive MSM and we note a recent expansion in southern Spain in patients who carry mutation G190A. We alert healthcare managers to enhance preventive measures to prevent the continuous spread of HIV-1 CRF19_cpx.
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Affiliation(s)
- S Pérez-Parra
- Clinical Microbiology & Infectious Disease Unit, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs, Granada, Spain
| | - M Álvarez
- Clinical Microbiology & Infectious Disease Unit, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs, Granada, Spain
| | - J A Fernandez-Caballero
- Clinical Microbiology & Infectious Disease Unit, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs, Granada, Spain
| | - A B Pérez
- Clinical Microbiology & Infectious Disease Unit, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs, Granada, Spain
| | - J Santos
- Infectious Diseases Unit, Hospital Universitario Virgen de la Victoria, Malaga, Spain
| | - O Bisbal
- Infectious Diseases Unit, Hospital 12 de Octubre, Madrid, Spain
| | - A Aguilera
- Clinical Microbiology Dept, Complexo Hospitalario Santiago de Compostela, Spain
| | - M Rivero
- Infectious Diseases Unit, Hospital de Navarra, Pamplona, Spain
| | - L García-Fraile
- Infectious Diseases Unit, Hospital de la Princesa, Madrid, Spain
| | - F García
- Clinical Microbiology & Infectious Disease Unit, Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs, Granada, Spain
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10
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Murzakova A, Kireev D, Baryshev P, Lopatukhin A, Serova E, Shemshura A, Saukhat S, Kolpakov D, Matuzkova A, Suladze A, Nosik M, Eremin V, Shipulin G, Pokrovsky V. Molecular Epidemiology of HIV-1 Subtype G in the Russian Federation. Viruses 2019; 11:E348. [PMID: 30995717 PMCID: PMC6521041 DOI: 10.3390/v11040348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 01/02/2023] Open
Abstract
Although HIV-1 subtype A has predominated in Russia since the end of the 20th century, other viral variants also circulate in this country. The dramatic outbreak of HIV-1 subtype G in 1988-1990 represents the origin of this variant spreading in Russia. However, full genome sequencing of the nosocomial viral variant and an analysis of the current circulating variants have not been conducted. We performed near full-length genome sequencing and phylogenetic and recombination analyses of 11 samples; the samples were determined to be subtype G based on an analysis of the pol region. Three samples were reliably obtained from patients infected during the nosocomial outbreak. The other 8 samples were obtained from patients who were diagnosed in 2010-2015. Phylogenetic analysis confirmed that a man from the Democratic Republic of the Congo was the origin of the outbreak. We also found that currently circulating viral variants that were genotyped as subtype G according to their pol region are in fact unique recombinant forms. These recombinant forms are similar to the BG-recombinants from Western Europe, particularly Spain and Portugal. The limitations of subtyping based on the pol region suggest that these viral variants are more widespread in Europe than is currently supposed.
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Affiliation(s)
| | - Dmitry Kireev
- Central Research Institute of Epidemiology, 111123 Moscow, Russia.
| | - Pavel Baryshev
- Central Research Institute of Epidemiology, 111123 Moscow, Russia.
| | | | - Ekaterina Serova
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia.
| | - Andrey Shemshura
- Clinical Center of HIV/AIDS of the Ministry of Health of Krasnodar Region, 350015 Krasnodar, Russia.
| | - Sergey Saukhat
- Department of Epidemiology, Rostov State Medical University, 344022 Rostov-on-Don, Russia.
| | - Dmitry Kolpakov
- Rostov Research Institute of Microbiology and Parasitology, 344000 Rostov-on-Don, Russia.
| | - Anna Matuzkova
- Rostov Research Institute of Microbiology and Parasitology, 344000 Rostov-on-Don, Russia.
| | - Alexander Suladze
- Rostov Research Institute of Microbiology and Parasitology, 344000 Rostov-on-Don, Russia.
| | - Marina Nosik
- Ilya Ilyich Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia.
| | - Vladimir Eremin
- Republican Research and Practical Center for Epidemiology and Microbiology, 220114 Minsk, Belarus.
| | - German Shipulin
- Center of Strategical Planning and Management of Biomedical Health Risks of the Ministry of Health, 119121 Moscow, Russia.
| | - Vadim Pokrovsky
- Central Research Institute of Epidemiology, 111123 Moscow, Russia.
- Department of infectious diseases with courses of epidemiology and phthisiology, RUDN University, 117198 Moscow, Russia.
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11
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Mbondji-wonje C, Dong M, Wang X, Zhao J, Ragupathy V, Sanchez AM, Denny TN, Hewlett I. Distinctive variation in the U3R region of the 5' Long Terminal Repeat from diverse HIV-1 strains. PLoS One 2018; 13:e0195661. [PMID: 29664930 PMCID: PMC5903597 DOI: 10.1371/journal.pone.0195661] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/27/2018] [Indexed: 12/14/2022] Open
Abstract
Functional mapping of the 5’LTR has shown that the U3 and the R regions (U3R) contain a cluster of regulatory elements involved in the control of HIV-1 transcription and expression. As the HIV-1 genome is characterized by extensive variability, here we aimed to describe mutations in the U3R from various HIV-1 clades and CRFs in order to highlight strain specific differences that may impact the biological properties of diverse HIV-1 strains. To achieve our purpose, the U3R sequence of plasma derived virus belonging to different clades (A1, B, C, D, F2) and recombinants (CRF02_AG, CRF01_AE and CRF22_01A1) was obtained using Illumina technology. Overall, the R region was very well conserved among and across different strains, while in the U3 region the average inter-strains nucleotide dissimilarity was up to 25%. The TAR hairpin displayed a strain-distinctive cluster of mutations affecting the bulge and the loop, but mostly the stem. Like in previous studies we found a TATAA motif in U3 promoter region from the majority of HIV-1 strains and a TAAAA motif in CRF01_AE; but also in LTRs from CRF22_01A1 isolates. Although LTRs from CRF22_01A1 specimens were assigned CRF01_AE, they contained two NF-kB sites instead of the single TFBS described in CRF01_AE. Also, as previously describe in clade C isolates, we found no C/EBP binding site directly upstream of the enhancer region in CRF22_01A1 specimens. In our study, one-third of CRF02_AG LTRs displayed three NF-kB sites which have been mainly described in clade C isolates. Overall, the number, location and binding patterns of potential regulatory elements found along the U3R might be specific to some HIV-1 strains such as clade F2, CRF02_AG, CRF01_AE and CRF22_01A1. These features may be worth consideration as they may be involved in distinctive regulation of HIV-1 transcription and replication by different and diverse infecting strains.
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Affiliation(s)
- Christelle Mbondji-wonje
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- Department of Molecular Biology, Faculty of Medicine, Pharmacy and Biomedical sciences, University of Douala, Douala, Cameroon
- * E-mail: (CM); (IH)
| | - Ming Dong
- U.S. Military HIV Research Program, Silver Spring, Maryland United States of America
| | - Xue Wang
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Jiangqin Zhao
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Viswanath Ragupathy
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Ana M. Sanchez
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States
| | - Thomas N. Denny
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States
| | - Indira Hewlett
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail: (CM); (IH)
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12
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Trends in Drug Resistance Prevalence, HIV-1 Variants and Clinical Status in HIV-1-infected Pediatric Population in Madrid: 1993 to 2015 Analysis. Pediatr Infect Dis J 2018; 37:e48-e57. [PMID: 28991889 DOI: 10.1097/inf.0000000000001760] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND The expanded use of long-term antiretroviral treatments in infected children may exacerbate the problem of drug resistance mutations selection, which can compromise treatment efficiency. OBJECTIVE We describe the temporal trends of HIV drug resistance mutations and the HIV-1 variants during 23 years (1993 to March 2016) in the Madrid cohort of HIV-infected children and adolescents. METHODS We selected patients with at least one available HIV-1 pol sequence/genotypic resistance profile, establishing different groups according to the sampling year of first resistance data. We determined the prevalence of transmitted drug resistance mutations or acquired drug resistance mutations (DRM), the drug susceptibility among resistant viruses and HIV-1 variants characterized by phylogeny across time. RESULTS A total of 245 pediatric patients were selected, being mainly female, Spanish native, perinatally infected and carrying HIV-1 subtype B. At first sampling, most pediatric patients were on antiretroviral therapy and heavily pretreated. During 1993 to 2016, transmitted drug resistance mutations was found in 13 (26%) of 50 naive children [non-nucleoside reverse transcriptase inhibitors (NNRTI), 14.6%; nucleoside reverse transcriptase inhibitors (NRTI), 10.4%; protease inhibitors, 8.7%]. DRM appeared in 139 (73.2%) of 190 pretreated patients (NRTI, 64.5%; NNRTI, 36%; protease inhibitors, 35.1%). DRM to NNRTI was higher in last 5 years. Non-B variants infected 14.5% of children and adolescents of the Madrid Cohort, being mainly intersubtype recombinants (76.5%), including complex unique recombinant strains. They caused 3.4% infections before 2000, rising to 85.7% during 2011 to 2016. CONCLUSIONS Periodic surveillance resistance and molecular epidemiology studies in long-term pretreated HIV-infected pediatric populations are required to optimize treatment regimens. Results will permit a better understanding of long-time dynamics of viral resistance and HIV-1 variants in Spain.
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13
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Pérez-Parra S, Chueca N, Álvarez M, Pasquau J, Omar M, Collado A, Vinuesa D, Lozano AB, Yebra G, García F. High prevalence and diversity of HIV-1 non-B genetic forms due to immigration in southern Spain: A phylogeographic approach. PLoS One 2017; 12:e0186928. [PMID: 29084239 PMCID: PMC5662216 DOI: 10.1371/journal.pone.0186928] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 10/10/2017] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic studies are a valuable tool to understand viral transmission patterns and the role of immigration in HIV-1 spread. We analyzed the spatio-temporal relationship of different HIV-1 non-B subtype variants over time using phylogenetic analysis techniques. We collected 693 pol (PR+RT) sequences that were sampled from 2005 to 2012 from naïve patients in different hospitals in southern Spain. We used REGA v3.0 to classify them into subtypes and recombinant forms, which were confirmed by phylogenetic analysis through maximum likelihood (ML) using RAxML. For the main HIV-1 non-B variants, publicly available, genetically similar sequences were sought using HIV-BLAST. The presence of HIV-1 lineages circulating in our study population was established using ML and Bayesian inference (BEAST v1.7.5) and transmission networks were identified. We detected 165 (23.4%) patients infected with HIV-1 non-B variants: 104 (63%) with recombinant viruses in pol: CRF02_AG (71, 43%), CRF14_BG (8, 4.8%), CRF06_cpx (5, 3%) and nine other recombinant forms (11, 6.7%) and unique recombinants (9, 5.5%). The rest (61, 37%) were infected with non-recombinant subtypes: A1 (30, 18.2%), C (7, [4.2%]), D (3, [1.8%]), F1 (9, 5.5%) and G (12, 7.3%). Most patients infected with HIV-1 non-B variants were men (63%, p < 0.001) aged over 35 (73.5%, p < 0.001), heterosexuals (92.2%, p < 0.001), from Africa (59.5%, p < 0.001) and living in the El Ejido area (62.4%, p<0.001). We found lineages of epidemiological relevance (mainly within Subtype A1), imported primarily through female sex workers from East Europe. We detected 11 transmission clusters of HIV-1 non-B Subtypes, which included patients born in Spain in half of them. We present the phylogenetic profiles of the HIV-1 non-B variants detected in southern Spain, and explore their putative geographical origins. Our data reveals a high HIV-1 genetic diversity likely due to the import of viral lineages that circulate in other countries. The highly immigrated El Ejido area acts as a gateway through which different subtypes are introduced into other regions, hence the importance of setting up epidemiological control measures to prevent future outbreaks.
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Affiliation(s)
- Santiago Pérez-Parra
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Campus de la Salud e Instituto de Investigación IBS, Granada, Spain
| | - Natalia Chueca
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Campus de la Salud e Instituto de Investigación IBS, Granada, Spain
| | - Marta Álvarez
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Campus de la Salud e Instituto de Investigación IBS, Granada, Spain
| | - Juan Pasquau
- Servicio de Infecciosas, Hospital Virgen de las Nieves, Granada, Spain
| | - Mohamed Omar
- Servicio de Infecciosas, Hospital Ciudad de Jaén, Jaén, Spain
| | - Antonio Collado
- Servicio de Medicina Interna, Hospital de Torrecárdenas, Almería, Spain
| | - David Vinuesa
- Servicio de Infecciosas, Hospital Universitario San Cecilio, Granada, Spain
| | | | - Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Edinburgh, the United Kingdom
| | - Federico García
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Campus de la Salud e Instituto de Investigación IBS, Granada, Spain
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14
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Patiño-Galindo JÁ, Torres-Puente M, Bracho MA, Alastrué I, Juan A, Navarro D, Galindo MJ, Ocete D, Ortega E, Gimeno C, Belda J, Domínguez V, Moreno R, González-Candelas F. The molecular epidemiology of HIV-1 in the Comunidad Valenciana (Spain): analysis of transmission clusters. Sci Rep 2017; 7:11584. [PMID: 28912478 PMCID: PMC5599654 DOI: 10.1038/s41598-017-10286-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/07/2017] [Indexed: 11/09/2022] Open
Abstract
HIV infections are still a very serious concern for public heath worldwide. We have applied molecular evolution methods to study the HIV-1 epidemics in the Comunidad Valenciana (CV, Spain) from a public health surveillance perspective. For this, we analysed 1804 HIV-1 sequences comprising protease and reverse transcriptase (PR/RT) coding regions, sampled between 2004 and 2014. These sequences were subtyped and subjected to phylogenetic analyses in order to detect transmission clusters. In addition, univariate and multinomial comparisons were performed to detect epidemiological differences between HIV-1 subtypes, and risk groups. The HIV epidemic in the CV is dominated by subtype B infections among local men who have sex with men (MSM). 270 transmission clusters were identified (>57% of the dataset), 12 of which included ≥10 patients; 11 of subtype B (9 affecting MSMs) and one (n = 21) of CRF14, affecting predominately intravenous drug users (IDUs). Dated phylogenies revealed these large clusters to have originated from the mid-80s to the early 00 s. Subtype B is more likely to form transmission clusters than non-B variants and MSMs to cluster than other risk groups. Multinomial analyses revealed an association between non-B variants, which are not established in the local population yet, and different foreign groups.
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Affiliation(s)
- Juan Ángel Patiño-Galindo
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP/Universidad de Valencia-I2SysBio, Valencia, 46180, Spain.,CIBER of Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Manoli Torres-Puente
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP/Universidad de Valencia-I2SysBio, Valencia, 46180, Spain
| | - María Alma Bracho
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP/Universidad de Valencia-I2SysBio, Valencia, 46180, Spain.,CIBER of Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | | | - Amparo Juan
- Unidad Prevención del SIDA y otras ITS, Valencia, 46017, Spain
| | - David Navarro
- Hospital Clínico Universitario, Valencia, 46010, Spain.,Dpto. Microbiología, Universidad de Valencia, 46080, Valencia, Spain
| | | | - Dolores Ocete
- Consorcio Hospital General Universitario, Valencia, 46014, Spain
| | - Enrique Ortega
- Consorcio Hospital General Universitario, Valencia, 46014, Spain
| | - Concepción Gimeno
- Dpto. Microbiología, Universidad de Valencia, 46080, Valencia, Spain.,Consorcio Hospital General Universitario, Valencia, 46014, Spain
| | - Josefina Belda
- Unidad Prevención del SIDA y otras ITS, Alicante, 03010, Spain
| | | | | | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP/Universidad de Valencia-I2SysBio, Valencia, 46180, Spain. .,CIBER of Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, 28029, Spain.
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15
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HIV surveillance combining an assay for identification of very recent infection and phylogenetic analyses on dried spots. AIDS 2017; 31:407-416. [PMID: 27831948 DOI: 10.1097/qad.0000000000001325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Transmitted/founder viruses isolated at the early stage of infection are indicators of the variants that are spreading within a population. The French reporting system for new HIV diagnoses is linked to a virological surveillance using dried serum spots. METHODS We combined an immunoassay for very recent infection (less than 31 days) to a phylogenetic analysis of transmitted/founder viruses and sociodemographic information to analyze the dynamics of the HIV-1 epidemic during a 3-year period. Bayesian coalescent-based methods were used to explore the temporal and spatial dynamics of the identified clusters. RESULTS Of 17 010 dried serum spots collected, 549 very recent infections were identified for which both env sequences and sociodemographic data were available. Non-B transmitted/founder viruses were found in 196 cases (35.7%), belonging to six subtypes and seven circulating recombinant forms. Forty-three dyads/clusters were identified (range 2-11 cases), including 107 individuals (19.5%), mainly MSM. The largest cluster involved MSM infected by a CRF02_AG variant. Reconstruction of viral migrations across time suggests that Paris was the major hub of dissemination. CONCLUSION The study shows the feasibility of the surveillance of the HIV epidemic using this methodology. The observation of actively growing spatiotemporal clusters allows identification of specific networks that may be targets for intervention.
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16
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Beloukas A, Psarris A, Giannelou P, Kostaki E, Hatzakis A, Paraskevis D. Molecular epidemiology of HIV-1 infection in Europe: An overview. INFECTION GENETICS AND EVOLUTION 2016; 46:180-189. [PMID: 27321440 DOI: 10.1016/j.meegid.2016.06.033] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Abstract
Human Immunodeficiency Virus type 1 (HIV-1) is characterised by vast genetic diversity. Globally circulating HIV-1 viruses are classified into distinct phylogenetic strains (subtypes, sub-subtypes) and several recombinant forms. Here we describe the characteristics and evolution of European HIV-1 epidemic over time through a review of published literature and updated queries of existing HIV-1 sequence databases. HIV-1 in Western and Central Europe was introduced in the early-1980s in the form of subtype B, which is still the predominant clade. However, in Eastern Europe (Former Soviet Union (FSU) countries and Russia) the predominant strain, introduced into Ukraine in the mid-1990s, is subtype A (AFSU) with transmission mostly occurring in People Who Inject Drugs (PWID). In recent years, the epidemic is evolving towards a complex tapestry with an increase in the prevalence of non-B subtypes and recombinants in Western and Central Europe. Non-B epidemics are mainly associated with immigrants, heterosexuals and females but more recently, non-B clades have also spread amongst groups where non-B strains were previously absent - non-immigrant European populations and amongst men having sex with men (MSM). In some countries, non-B clades have spread amongst the native population, for example subtype G in Portugal and subtype A in Greece, Albania and Cyprus. Romania provides a unique case where sub-subtype F1 has predominated throughout the epidemic. In contrast, HIV-1 epidemic in FSU countries remains more homogeneous with AFSU clade predominating in all countries. The differences between the evolution of the Western epidemic and the Eastern epidemic may be attributable to differences in transmission risk behaviours, lifestyle and the patterns of human mobility. The study of HIV-1 epidemic diversity provides a useful tool by which we can understand the history of the pandemic in addition to allowing us to monitor the spread and growth of the epidemic over time.
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Affiliation(s)
- Apostolos Beloukas
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Alexandros Psarris
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Polina Giannelou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
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17
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Dauwe K, Mortier V, Schauvliege M, Van Den Heuvel A, Fransen K, Servais JY, Bercoff DP, Seguin-Devaux C, Verhofstede C. Characteristics and spread to the native population of HIV-1 non-B subtypes in two European countries with high migration rate. BMC Infect Dis 2015; 15:524. [PMID: 26572861 PMCID: PMC4647655 DOI: 10.1186/s12879-015-1217-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/14/2015] [Indexed: 12/13/2022] Open
Abstract
Background Non-B subtypes account for at least 50 % of HIV-1 infections diagnosed in Belgium and Luxembourg. They are considered to be acquired through heterosexual contacts and infect primarily individuals of foreign origin. Information on the extent to which non-B subtypes spread to the local population is incomplete. Methods Pol and env gene sequences were collected from 410 non-subtype B infections. Profound subtyping was performed using 5 subtyping tools and sequences of both pol and env. Demographic information, disease markers (viral load, CD4 count) and viral characteristics (co-receptor tropism) were compared between subtypes. Maximum likelihood phylogenetic trees were constructed and examined for clustering. Results The majority of non-B infections were diagnosed in patients originating from Africa (55.8 %), individuals born in Western Europe represented 30.5 %. Heterosexual transmission was the most frequently reported transmission route (79.9 %), MSM transmission accounted for 12.2 % and was significantly more frequently reported for Western Europeans (25.7 % versus 4.3 % for individuals originating from other regions; p < 0.001). Subtypes A and C and the circulating recombinant forms CRF01_AE and CRF02_AG were the most represented and were included in the comparative analysis. Native Western Europeans were underrepresented for subtype A (14.5 %) and overrepresented for CRF01_AE (38.6 %). The frequency of MSM transmission was the highest for CRF01_AE (18.2 %) and the lowest for subtype A (0 %). No differences in age, gender, viral load or CD4 count were observed. Prevalence of CXCR4-use differed between subtypes but largely depended on the tropism prediction algorithm applied. Indications for novel intersubtype recombinants were found in 20 patients (6.3 %). Phylogenetic analysis revealed only few and small clusters of local transmission but could document one cluster of CRF02_AG transmission among Belgian MSM. Conclusions The extent to which non-B subtypes spread in the native Belgian-Luxembourg population is higher than expected, with 30.5 % of the non-B infections diagnosed in native Western Europeans. These infections resulted from hetero- as well as homosexual transmission. Introduction of non-B variants in the local high at risk population of MSM may lead to new sub-epidemics and/or increased genetic variability and is an evolution that needs to be closely monitored.
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Affiliation(s)
- Kenny Dauwe
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
| | - Annelies Van Den Heuvel
- Aids Reference laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Nationalestraat 155, B-2000, Antwerp, Belgium.
| | - Katrien Fransen
- Aids Reference laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Nationalestraat 155, B-2000, Antwerp, Belgium.
| | - Jean-Yves Servais
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Danielle Perez Bercoff
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Carole Seguin-Devaux
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Val Fleuri 84, L-1526, Luxembourg, Luxembourg.
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000, Ghent, Belgium.
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18
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Dennis AM, Hué S, Pasquale D, Napravnik S, Sebastian J, Miller WC, Eron JJ. HIV Transmission Patterns Among Immigrant Latinos Illuminated by the Integration of Phylogenetic and Migration Data. AIDS Res Hum Retroviruses 2015. [PMID: 26214548 DOI: 10.1089/aid.2015.0089] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Latinos represent a growing proportion of HIV cases in North Carolina (NC). Understanding how immigrants are involved in local HIV transmission is important to guide interventions. We used phylogenetics to characterize Latino involvement in local HIV transmission chains. Transmission clusters were identified from maximum-likelihood phylogenies constructed with HIV pol sequences from 177 Latinos and 1,496 non-Latinos receiving care in NC. Highly supported clusters involving one or more Latinos were characterized. Migration data were obtained from interviews and chart review. Factors associated with cluster membership were identified using log-binomial regression. Most Latinos were male (76%), immigrants (83%), and had HIV-1B (99%). Immigrants were more likely to report heterosexual risk (67% vs. 23%) than U.S.-born Latinos (p < 0.01). We identified 32 clusters that included one or more Latinos; these involved 53 Latinos (30%) and 41 non-Latinos. Immigrant and U.S.-born Latinos were equally likely to be in clusters, but immigrants were more likely to be in clusters with another Latino (78% vs. 29%; p = 0.02). Cluster composition by ethnicity and risk behavior varied by cluster size; larger clusters contained fewer immigrants and more men who have sex with men (MSM). Factors associated with immigrant membership in local transmission clusters included age <30 years [RR 2.34 (95% CI 1.47-3.73)], Mexican origin [RR 2.55 (95% CI 1.29-6.88)], and residing in the United States longer before diagnosis [RR 1.53 (95% CI 1.09-2.15), per 10 years]. While some Latinos immigrate with HIV infection, many immigrants are involved in transmission networks after arrival, particularly MSM. HIV testing and prevention interventions must consider this heterogeneity and may be better targeted by integrating phylogenetic analyses.
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Affiliation(s)
- Ann M. Dennis
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Stéphane Hué
- Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dana Pasquale
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Sonia Napravnik
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Joseph Sebastian
- Laboratory Corporation of America, Research Triangle Park, North Carolina
| | - William C. Miller
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Joseph J. Eron
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
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Dennis AM, Herbeck JT, Brown AL, Kellam P, de Oliveira T, Pillay D, Fraser C, Cohen MS. Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest? J Acquir Immune Defic Syndr 2014; 67:181-95. [PMID: 24977473 PMCID: PMC4304655 DOI: 10.1097/qai.0000000000000271] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Efficient and effective HIV prevention measures for generalized epidemics in sub-Saharan Africa have not yet been validated at the population level. Design and impact evaluation of such measures requires fine-scale understanding of local HIV transmission dynamics. The novel tools of HIV phylogenetics and molecular epidemiology may elucidate these transmission dynamics. Such methods have been incorporated into studies of concentrated HIV epidemics to identify proximate and determinant traits associated with ongoing transmission. However, applying similar phylogenetic analyses to generalized epidemics, including the design and evaluation of prevention trials, presents additional challenges. Here we review the scope of these methods and present examples of their use in concentrated epidemics in the context of prevention. Next, we describe the current uses for phylogenetics in generalized epidemics and discuss their promise for elucidating transmission patterns and informing prevention trials. Finally, we review logistic and technical challenges inherent to large-scale molecular epidemiological studies of generalized epidemics and suggest potential solutions.
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Affiliation(s)
- Ann M. Dennis
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Andrew Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Tulio de Oliveira
- Wellcome Trust-Africa Centre for Health and Population Studies, University of Kwazula-Natal, ZA
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, UK
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Myron S. Cohen
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Characteristics of patients recently infected with HIV-1 non-B subtypes in France: a nested study within the mandatory notification system for new HIV diagnoses. J Clin Microbiol 2014; 52:4010-6. [PMID: 25232163 DOI: 10.1128/jcm.01141-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The presence of HIV-1 non-B subtypes in Western Europe is commonly attributed to migration of individuals from non-European countries, but the possible role of domestic infections with non-B subtypes is not well investigated. The French mandatory anonymous reporting system for HIV is linked to a virological surveillance using assays for recent infection (<6 months) and serotyping. During the first semester of years 2007 to 2010, any sample corresponding to a non-B recent infection was analyzed by sequencing a 415-bp env region, followed by phylogenetic analysis and search for transmission clusters. Two hundred thirty-three recent HIV-1 infections with non-B variants were identified. They involved 5 subtypes and 7 circulating recombinant forms (CRFs). Ninety-two cases (39.5%) were due to heterosexual transmissions, of which 39 occurred in patients born in France. Eighty-five cases (36.5%) were identified in men having sex with men (MSM). Forty-three recent non-B infections (18.5%) segregated into 14 clusters, MSM being involved in 11 of them. Clustered transmission events included 2 to 7 cases per cluster. The largest cluster involved MSM infected by a CRF02_AG variant. In conclusion, we found that the spread of non-B subtypes in France occurs in individuals of French origin and that MSM are particularly involved in this dynamic.
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Parczewski M, Urbanska A, Grzeszczuk A, Maciejewska K, Witak-Jedra M, Leszczyszyn-Pynka M. Phylogeographic analysis on the travel-related introduction of HIV-1 non-B subtypes to Northern Poland. INFECTION GENETICS AND EVOLUTION 2014; 27:121-30. [PMID: 25038296 DOI: 10.1016/j.meegid.2014.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/27/2014] [Accepted: 07/05/2014] [Indexed: 11/16/2022]
Abstract
Phylodynamic, sequence data based reconstructions for the surveillance of the geographic spatial spread are a powerful tool in molecular epidemiology. In this study region of origin for the set of 57 partial pol sequences derived from the patients the history of travel-related HIV transmission was analyzed using phylogeographic approach. Maximum likelihood trees based on the sets of country-annotated reference sequences were inferred for identified non-B variants. Region of sequence import was assigned using on the highest approximate likelihood ratios. Import of the A1 clades was traced to the Eastern Europe and associated with immigration from this region. Subtype C infections clustered most frequently with sequences of the South African origin while majority of subtype Ds were similar to the European clades. Subtype G sequences clustered with Portuguese lineage, CRF01_AE with Eastern or South-Eastern Asian. Eastern European, Middle African or Western African lineage was assigned for the CFR02_AG. Rare circulating recombinants originated either from Central Africa (CRF11_cpx - Democratic Republic of Congo, CRF13_cpx - Central African Republic, CRF37_cpx - Cameroon) or South America (CRF28_BF and CRF46_BF - Brazil). Import of the HIV-1 non-B variants, including recombinant forms previously rarely found in Poland and Europe is frequent among travelers. Observed founder events result in the heterosexually-driven introduction of the novel HIV-1 variants into the population.
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Affiliation(s)
- Milosz Parczewski
- Department of Infectious Diseases and Hepatology, Pomeranian Medical University, Szczecin, Poland.
| | - Anna Urbanska
- Department of Infectious Diseases and Hepatology, Pomeranian Medical University, Szczecin, Poland
| | - Anna Grzeszczuk
- Department of Infectious Diseases and Hepatology, Medical University of Bialystok, Bialystok, Poland
| | - Katarzyna Maciejewska
- Department of Infectious Diseases and Hepatology, Pomeranian Medical University, Szczecin, Poland
| | - Magdalena Witak-Jedra
- Department of Infectious Diseases and Hepatology, Pomeranian Medical University, Szczecin, Poland
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22
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Rojas Sánchez P, Holguín A. Drug resistance in the HIV-1-infected paediatric population worldwide: a systematic review. J Antimicrob Chemother 2014; 69:2032-42. [PMID: 24788658 DOI: 10.1093/jac/dku104] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Drug resistance monitoring of the paediatric HIV-1-infected population is required to optimize treatment success and preserve future treatment options. OBJECTIVES To explore the current knowledge of HIV drug resistance (HIVDR) in naive and pretreated HIV-1-infected paediatric populations across diverse settings and sampling time periods. METHODS PubMed database screened until May 2013. We selected publications including data on transmitted (TDR) and acquired drug resistance mutation (DRM) rates and/or pol sequences for HIVDR testing in paediatric patients. We recorded the children's country, age, study period, number of children with pol sequences, presence or absence of antiretroviral treatment (ART) at sampling time, viral region sequenced, HIVDR rate to the three main drug classes (single, double or triple), the considered resistance mutation list and performed assay, specimen type, HIV-1 variants and subtyping methodology when available. RESULTS Forty-one selected studies showed HIVDR data from 2538 paediatric HIV-1-infected patients (558 naive and 1980 pretreated) from 30 countries in Africa (11), Asia (6), America (10) and Europe (3). Both TDR and DRM prevalence were reported in 9 studies, only TDR in 6 and only DRM in 26. HIVDR prevalence varied across countries and periods. Most studies used in-house resistance assays using plasma or infected cells. HIV-1 non-B variants were prevalent in 18 paediatric cohorts of the 24 countries with reported subtypes. Only five countries (Uganda, Spain, the UK, Brazil and Thailand) presented resistance data in ≥200 patients. CONCLUSIONS Systematic and periodic studies among infected children are crucial to design a more suitable first- or second-line therapy.
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Affiliation(s)
- Patricia Rojas Sánchez
- HIV-1 Molecular Epidemiology Laboratory, Microbiology Department, Hospital Ramón y Cajal-IRYCIS and CIBERESP, Madrid, Spain
| | - Africa Holguín
- HIV-1 Molecular Epidemiology Laboratory, Microbiology Department, Hospital Ramón y Cajal-IRYCIS and CIBERESP, Madrid, Spain
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Emerging trends in CRF02_AG variants transmission among men who have sex with men in Spain. J Acquir Immune Defic Syndr 2014; 65:e130-3. [PMID: 24091696 DOI: 10.1097/01.qai.0000435602.73469.56] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Mendoza Y, Bello G, Castillo Mewa J, Martínez AA, González C, García-Morales C, Avila-Ríos S, Reyes-Terán G, Pascale JM. Molecular epidemiology of HIV-1 in Panama: origin of non-B subtypes in samples collected from 2007 to 2013. PLoS One 2014; 9:e85153. [PMID: 24454808 PMCID: PMC3890310 DOI: 10.1371/journal.pone.0085153] [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: 07/23/2013] [Accepted: 11/23/2013] [Indexed: 11/30/2022] Open
Abstract
Phylogenetic studies have suggested that the HIV-1 epidemic in the Americas is mainly dominated by HIV subtype B. However, countries of South America and the Caribbean have recently reported changes in their circulating HIV-1 genetic profiles. The aim of this study was to characterize the molecular profile of the HIV-1 epidemic in Panama by the analysis of 655 polymerase gene (pol) sequences that were obtained from HIV-infected Panamanians diagnosed between 1987 and 2013. Blood samples were collected from recently infected, antiretroviral drug-naïve and treatment-experienced subjects since mid-2007 to 2013. Viral RNA from plasma was extracted and sequences of HIV protease and reverse transcriptase genes were obtained. Bootscanning and phylogenetic methods were used for HIV subtyping and to trace the putative origin of non-B subtype strains. Our results showed that HIV-1 infections in Panama are dominated by subtype B (98.9%). The remaining 1.1% is represented by a diverse collection of recombinant variants including: three URFs_BC, one CRF20_BG, and one CRF28/29_BF, in addition to one subtype F1 and one subtype C, none of which were previously reported in Panama. The non-B subtype variants detected in Panama were probably introduced from Brazil (subtype F1 and CRF28/29_BF), Cuba (CRF20_BG), Dominican Republic (URFs_BC) and India (subtype C). Panama is the geographical vertex that connects the North with South America and the Caribbean through trade and cultural relations, which may explain the observed introductions of non-B subtype HIV-1 variants from both the Caribbean and South America into this Central American country.
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Affiliation(s)
- Yaxelis Mendoza
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur City, Andhra Pradesh, India
- Department of Genetics and Molecular Biology, University of Panama, Panama City, Panama
- INDICASAT-AIP, 219, City of Knowledge, Clayton, Panama City, Panama
- * E-mail:
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Juan Castillo Mewa
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | - Alexander A. Martínez
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur City, Andhra Pradesh, India
- INDICASAT-AIP, 219, City of Knowledge, Clayton, Panama City, Panama
| | - Claudia González
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | - Claudia García-Morales
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Santiago Avila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Juan M. Pascale
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City, Panama
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Yebra G, Delgado R, Pulido F, Rubio R, Galán JC, Moreno S, Holguín Á. Different trends of transmitted HIV-1 drug resistance in Madrid, Spain, among risk groups in the last decade. Arch Virol 2013; 159:1079-87. [PMID: 24297490 DOI: 10.1007/s00705-013-1933-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 11/20/2013] [Indexed: 11/30/2022]
Abstract
The presence of transmitted HIV drug resistance (TDR) threatens the efficacy of antiretroviral treatment. We aimed to assess the changes in TDR prevalence over the last decade in Madrid, Spain, to verify the role of the patients' risk groups in these changes. We analysed the trends of TDR between 2000 and 2011 in a cohort of 1,022 naïve HIV-infected patients in Madrid, Spain, whose pol sequences were available. They included, among others, 369 heterosexuals, 340 men who have sex with men (MSM), and 90 injection drug users (IDUs). TDR was reported following the WHO mutation list. The TDR rate in the whole cohort was 8.3 %, being the highest in MSM (9.1 %) and the lowest in IDUs (4.4 %). Over time, this rate decreased significantly (to 5.4 % in 2009-2011) since the period 2004-2006, when it peaked (10.7 %). Heterosexuals and IDUs showed similar trends, but in the 2009-2011 period, the TDR rate among MSM rebounded to 9.0 % (being absent among IDUs). TDR stabilized in the last years (2007-2011) for nucleoside reverse transcriptase inhibitors. The risk group also determined differences in the mutational profile, sex distribution, proportion of immigrants, and viral variants. In conclusion, the risk group caused different HIV sub-epidemics, determined by the patients' profiles. Despite the general decreasing trend in TDR, we observed a non-significant increase in TDR rate among MSM, a tendency that needs confirmation. Periodic TDR surveillance is important to prevent the widespread distribution of resistance, especially in MSM, given the growing HIV/AIDS epidemic in this high-risk population.
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Affiliation(s)
- Gonzalo Yebra
- HIV-1 Molecular Epidemiology Laboratory, Microbiology Department, Hospital Ramón y Cajal (IRYCIS) and CIBERESP, Ctra. Colmenar Viejo km. 9.100, 28034, Madrid, Spain
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Touloumi G, Pantazis N, Chaix ML, Bucher HC, Zangerle R, Kran AMB, Thiebaut R, Masquelier B, Kucherer C, Monforte AD, Meyer L, Porter K. Virologic and immunologic response to cART by HIV-1 subtype in the CASCADE collaboration. PLoS One 2013; 8:e71174. [PMID: 23936260 PMCID: PMC3728088 DOI: 10.1371/journal.pone.0071174] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 06/28/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND We aimed to compare rates of virologic response and CD4 changes after combination antiretroviral (cART) initiation in individuals infected with B and specific non-B HIV subtypes. METHODS Using CASCADE data we analyzed HIV-RNA and CD4 counts for persons infected ≥1996, ≥15 years of age. We used survival and longitudinal modeling to estimate probabilities of virologic response (confirmed HIV-RNA <500 c/ml), and failure (HIV-RNA>500 c/ml at 6 months or ≥1000 c/ml following response) and CD4 increase after cART initiation. RESULTS 2003 (1706 B, 142 CRF02_AG, 55 A, 53 C, 47 CRF01_AE) seroconverters were included in analysis. There was no evidence of subtype effect overall for response or failure (p = 0.075 and 0.317, respectively) although there was a suggestion that those infected with subtypes CRF01_AE and A responded sooner than those with subtype B infection [HR (95% CI):1.37 (1.01-1.86) and 1.29 (0.96-1.72), respectively]. Rates of CD4 increase were similar in all subtypes except subtype A, which tended to have lower initial, but faster long-term, increases. CONCLUSIONS Virologic and immunologic response to cART was similar across all studied subtypes but statistical power was limited by the rarity of some non-B subtypes. Current antiretroviral agents seem to have similar efficacy in subtype B and most widely encountered non-B infections in high-income countries.
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Rodríguez-Domínguez M, Puerta T, Menéndez B, González-Alba JM, Rodríguez C, Hellín T, Vera M, González-Sainz FJ, Clavo P, Villa M, Cantón R, Del Romero J, Galán JC. Clinical and epidemiological characterization of a lymphogranuloma venereum outbreak in Madrid, Spain: co-circulation of two variants. Clin Microbiol Infect 2013; 20:219-25. [PMID: 23730727 DOI: 10.1111/1469-0691.12256] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 04/04/2013] [Accepted: 04/23/2013] [Indexed: 11/28/2022]
Abstract
The lymphogranuloma venereum (LGV) outbreak described in the Netherlands in 2003, increased the interest in the genotyping of Chlamydia trachomatis. Although international surveillance programmes were implemented, these studies slowly decreased in the following years. Now data have revealed a new accumulation of LGV cases in those European countries with extended surveillance programmes. Between March 2009 and November 2011, a study was carried out to detect LGV cases in Madrid. The study was based on screening of C. trachomatis using commercial kits, followed by real-time pmpH-PCR discriminating LGV strains, and finally ompA gene was sequenced for phylogenetic reconstruction. Ninety-four LGV infections were identified. The number of cases increased from 10 to 30 and then to 54 during 2009-2011. Incidence of LGV was strongly associated with men who have sex with men; but in 2011, LGV cases were described in women and heterosexual men. Sixty-nine patients were also human immunodeficiency virus (HIV) positive, with detectable viral loads at the moment of LGV diagnosis, suggesting a high-risk of co-transmission. In fact, in four patients the diagnosis of HIV was simultaneous with LGV infection. The conventional treatment with doxycycline was prescribed in 75 patients, although in three patients the treatment failed. The sequencing of the ompA gene permitted identification of two independent transmission nodes. One constituted by 25 sequences identical to the L2b variant, and a second node including 37 sequences identical to L2. This epidemiological situation characterized by the co-circulation of two LGV variants has not been previously described, reinforcing the need for screening and genotyping of LGV strains.
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Affiliation(s)
- M Rodríguez-Domínguez
- Servicio de Microbiología and CIBER en Epidemiología y Salud Pública (CIBERESP), Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
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Phylogenetic inferences on HIV-1 transmission: implications for the design of prevention and treatment interventions. AIDS 2013; 27:1045-57. [PMID: 23902920 DOI: 10.1097/qad.0b013e32835cffd9] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Tramuto F, Maida CM, Bonura F, Perna AM, Vitale F. Dynamics and molecular evolution of HIV-1 strains in Sicily among antiretroviral naïve patients. INFECTION GENETICS AND EVOLUTION 2013; 16:290-7. [PMID: 23470353 DOI: 10.1016/j.meegid.2013.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 02/11/2013] [Accepted: 02/14/2013] [Indexed: 11/25/2022]
Abstract
HIV-1 subtype B is the most frequent strain in Sicily. To date, there is no available data about the genetic diversity of HIV-1 viral strains circulating in Sicily among antiretroviral (ARV) naïve subjects and the role of immigration as potential determinant of evolutionary dynamics of HIV-1 molecular epidemiology. For this purpose, HIV-1 polymerase (pol) sequences obtained from 155 ARV naïve individuals from 2004 to 2009 were phylogenetically analysed. The overall rate of HIV-1 non-B infections was 31.0% (n=48/155), increasing from 7.8% in 2004-2006 to 40.9% in 2009, and about one-third were identified as unique recombinant forms. CRF02_AG was the prevalent non-B clade (n=28/48, 58.3%), while subtype C-related strains were responsible for about 30% HIV-1 infections. Non-B viruses strictly associated with heterosexual transmission (85.4%) and were mostly found among immigrants (77.1%). Phylogenetic analysis of non-B sequences found in foreign-born subjects was geographically correlated to the respective country of origin. Moreover, the detection of non-B viral variants in the autochthonous population may support an increasing genetic diversity in Sicily as well as a local circulation of HIV strains also uncommon in our country. In Sicily, HIV-1 epidemic is still mostly attributable to the B subtype. Nevertheless, migration and population movements are progressively introducing novel HIV-1 subtypes causing a continuous increase of HIV-1 molecular dynamic at local level. Molecular surveillance is needed to monitor the genetic evolution of HIV-1 epidemic.
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Affiliation(s)
- F Tramuto
- Department of Sciences for Health Promotion G. D'Alessandro - Hygiene Section, University of Palermo, Palermo, Italy.
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Touloumi G, Pantazis N, Pillay D, Paraskevis D, Chaix ML, Bucher HC, Kücherer C, Zangerle R, Kran AMB, Porter K. Impact of HIV-1 subtype on CD4 count at HIV seroconversion, rate of decline, and viral load set point in European seroconverter cohorts. Clin Infect Dis 2013; 56:888-97. [PMID: 23223594 DOI: 10.1093/cid/cis1000] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) subtype may influence disease progression. We compared CD4 lymphocyte cell count levels at seroconversion, decline rates and viral load set point in individuals infected with different HIV-1 subtypes. METHODS We used data from the Concerted Action on SeroConversion to AIDS and Death in Europe (CASCADE) collaboration, restricted to those infected since 1996, aged ≥15 years, and applied mixed effects models for CD4 cell count decline and median regression for viral load set point (mean level 6-24 months from seroconversion). RESULTS The analysis included 3364 seroconverters with known HIV-1 subtypes. Compared with subtype B, CD4 at seroconversion was significantly higher for subtype CRF01 and lower for subtype C. Subsequent CD4 decline was significantly slower for subtypes A and CRF02 and marginally slower for subtype C compared with B. Mean CD4 loss at 2 years of seroconversion for white men exposed through sex between men, aged 30-39 years, having seroconverted since 2006, enrolled within 6 months of seroconversion, and without acute infection was 88, 142, 100, 130, 103, and 167 cells/µL for subtypes A, B, C, CRF01_AE, CRF02_AG, and G, respectively. In adjusted analysis, median viral load set point and time to clinical AIDS/death did not differ significantly by subtype, although all subtypes, except C, tended to have lower levels compared with B. CONCLUSIONS HIV-1 subtype significantly influences seroconversion CD4 cell levels and decline rates but not viral load set point. These findings may be helpful to HIV-positive individuals and their attending physicians in understanding disease progression.
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Affiliation(s)
- Giota Touloumi
- Department of Hygiene, Epidemiology and Medical Statistics, Athens University Medical School, Greece.
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Yebra G, Holguín Á, Pillay D, Hué S. Phylogenetic and demographic characterization of HIV-1 transmission in Madrid, Spain. INFECTION GENETICS AND EVOLUTION 2013; 14:232-9. [DOI: 10.1016/j.meegid.2012.12.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 12/10/2012] [Accepted: 12/12/2012] [Indexed: 11/26/2022]
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Most HIV type 1 non-B infections in the Spanish cohort of antiretroviral treatment-naïve HIV-infected patients (CoRIS) are due to recombinant viruses. J Clin Microbiol 2011; 50:407-13. [PMID: 22162552 DOI: 10.1128/jcm.05798-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
HIV-1 group M is classified into 9 subtypes, as well as recombinants favored by coinfection and superinfection events with different variants. Although HIV-1 subtype B is predominant in Europe, intersubtype recombinants are increasing in prevalence and complexity. In this study, phylogenetic analyses of pol sequences were performed to detect the HIV-1 circulating and unique recombinant forms (CRFs and URFs, respectively) in a Spanish cohort of antiretroviral treatment-naïve HIV-infected patients included in the Research Network on HIV/AIDS (CoRIS). Bootscanning and other methods were used to define complex recombinants not assigned to any subtype or CRF. A total of 670 available HIV-1 pol sequences from different patients were collected, of which 588 (87.8%) were assigned to HIV-1 subtype B and 82 (12.2%) to HIV-1 non-B variants. Recombinants caused the majority (71.9%) of HIV-1 non-B infections and were found in 8.8% of CoRIS patients. Eleven URFs (accounting for 13.4% of HIV-1 non-B infections), presenting complex mosaic patterns, were detected. Among them, 10 harbored subtype B fragments. Four of the 11 URFs were found in Spanish natives. A cluster of three B/CRF02_AG recombinants was detected. We conclude that complex variants, including unique recombinant forms, are being introduced into Spain through both immigrants and natives. An increase in the frequency of mosaic viruses, reflecting the increasing heterogeneity of the HIV epidemic in our country, is expected.
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