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Paulino-Ramírez R, López P, Mueses S, Cuevas P, Jabier M, Rivera-Amill V. Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20085503. [PMID: 37107785 PMCID: PMC10138544 DOI: 10.3390/ijerph20085503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/24/2023] [Accepted: 04/03/2023] [Indexed: 05/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that evolves over time, leading to new variants. In the current study, we assessed the genomic epidemiology of SARS-CoV-2 in the Dominican Republic. A total of 1149 SARS-CoV-2 complete genome nucleotide sequences from samples collected between March 2020 and mid-February 2022 in the Dominican Republic were obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database. Phylogenetic relationships and evolution rates were analyzed using the maximum likelihood method and the Bayesian Markov chain Monte Carlo (MCMC) approach. The genotyping details (lineages) were obtained using the Pangolin web application. In addition, the web tools Coronapp, and Genome Detective Viral Tools, among others, were used to monitor epidemiological characteristics. Our results show that the most frequent non-synonymous mutation over the study period was D614G. Of the 1149 samples, 870 (75.74%) were classified into 8 relevant variants according to Pangolin/Scorpio. The first Variants Being Monitored (VBM) were detected in December 2020. Meanwhile, in 2021, the variants of concern Delta and Omicron were identified. The mean mutation rate was estimated to be 1.5523 × 10-3 (95% HPD: 1.2358 × 10-3, 1.8635 × 10-3) nucleotide substitutions per site. We also report the emergence of an autochthonous SARS-CoV-2 lineage, B.1.575.2, that circulated from October 2021 to January 2022, in co-circulation with the variants of concern Delta and Omicron. The impact of B.1.575.2 in the Dominican Republic was minimal, but it then expanded rapidly in Spain. A better understanding of viral evolution and genomic surveillance data will help to inform strategies to mitigate the impact on public health.
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Affiliation(s)
- Robert Paulino-Ramírez
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
- Correspondence:
| | - Pablo López
- RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA (V.R.-A.)
| | - Sayira Mueses
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
| | - Paula Cuevas
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
| | - Maridania Jabier
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
- Servicio Nacional de Salud (SNS), Ministry of Health, Santo Domingo 10201, Dominican Republic
| | - Vanessa Rivera-Amill
- RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA (V.R.-A.)
- Basic Sciences Department, School of Medicine, Ponce Health Sciences University, Ponce, PR 00716-2348, USA
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Lebedev A, Pasechnik O, Ozhmegova E, Antonova A, Blokh A, Grezina L, Sandyreva T, Dementeva N, Kazennova E, Bobkova M. Prevalence and spatiotemporal dynamics of HIV-1 Circulating Recombinant Form 03_AB (CRF03_AB) in the Former Soviet Union countries. PLoS One 2020; 15:e0241269. [PMID: 33095842 PMCID: PMC7584246 DOI: 10.1371/journal.pone.0241269] [Citation(s) in RCA: 5] [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: 07/16/2020] [Accepted: 10/12/2020] [Indexed: 11/19/2022] Open
Abstract
Background HIV-1 circulating recombinant forms (CRFs) infections has been increasing in Former Soviet Union (FSU) countries in the recent decade. One is the CRF03_AB, which circulated in the region since late 1990s and probably became widespread in northwestern FSU countries. However, there is not much information provided about the dissemination of this recombinant. Here, we examine the prevalence, evolutionary dynamics and dispersion pattern of HIV-1 CRF03_AB recombinant. Methods We analyzed 32 independent studies and 151 HIV-1 CRF03_AB pol sequences isolated from different FSU countries over a period of 22 years. Pooled prevalence was estimated using a random effects model. Bayesian coalescent-based method was used to estimate the evolutionary, phylogeographic and demographic parameters. Results Our meta-analysis showed that the pooled prevalence of CRF03_AB infection in northwestern FSU region was 5.9% [95%CI: 4.1–7.8]. Lithuania (11.6%), Russia (5.9%) and Belarus (2.9%) were the most affected by CRF03_AB. We found that early region wide spread of HIV-1 CRF03_AB originated from one viral clade that arose in the city of Kaliningrad in 1992 [95%HPD: 1990–1995]. Fourteen migration route of this variant were found. The city of Kaliningrad is involved in most of these, confirming its leading role in CRF03_AB spread within FSU. Demographic reconstruction point to this is that CRF03_AB clade seems to have experienced an exponential growth until the mid-2000s and a decrease in recent years. Conclusion These data provide new insights into the molecular epidemiology of CRF03_AB as well as contributing to the fundamental understanding of HIV epidemic in FSU.
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Affiliation(s)
- Aleksey Lebedev
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
- * E-mail:
| | - Oksana Pasechnik
- Departments of Epidemiology, Omsk State Medical University, Omsk, Russia
| | - Ekaterina Ozhmegova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Anastasiia Antonova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Aleksey Blokh
- Departments of Epidemiology, Omsk State Medical University, Omsk, Russia
| | - Liliya Grezina
- Clinical Diagnostic Laboratory, Yamalo-Nenets Autonomous District Center for Prevention and Control of AIDS and Infectious Diseases, Noyabr'sk, Russia
| | - Tatiana Sandyreva
- Clinical Diagnostic Laboratory, Sverdlovsk Regional Center for Prevention and Control of AIDS and Infectious Diseases, Ekaterinburg, Russia
| | - Natalia Dementeva
- Clinical Diagnostic Laboratory, Saint-Petersburg Center for Prevention and Control of AIDS and Infectious Disease, Saint-Petersburg, Russia
| | - Elena Kazennova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Marina Bobkova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
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Mendoza Y, García-Morales C, Bello G, Garrido-Rodríguez D, Tapia-Trejo D, Pascale JM, Girón-Callejas AC, Mendizábal-Burastero R, Escobar-Urias IY, García-González BL, Navas-Castillo JS, Quintana-Galindo MC, Pinzón-Meza R, Mejía-Villatoro CR, Avila-Ríos S, Reyes-Terán G. Evolutionary history and spatiotemporal dynamics of the HIV-1 subtype B epidemic in Guatemala. PLoS One 2018; 13:e0203916. [PMID: 30212548 PMCID: PMC6136800 DOI: 10.1371/journal.pone.0203916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/30/2018] [Indexed: 11/22/2022] Open
Abstract
Different explanations exist on how HIV-1 subtype B spread in Central America, but the role of Guatemala, the Central American country with the highest number of people living with the virus, in this scenario is unknown. We investigated the evolutionary history and spatiotemporal dynamics of HIV-1 subtype B in Guatemala. A total of 1,047 HIV-1 subtype B pol sequences, from newly diagnosed ART-naïve, HIV-infected Guatemalan subjects enrolled between 2011 and 2013 were combined with published subtype B sequences from other Central American countries (n = 2,101) and with reference sequences representative of the BPANDEMIC and BCAR lineages from the United States (n = 465), France (n = 344) and the Caribbean (n = 238). Estimates of evolutionary, demographic, and phylogeographic parameters were obtained from sequence data using maximum likelihood and Bayesian coalescent-based methods. The majority of Guatemalan sequences (98.9%) belonged to the BPANDEMIC clade, and 75.2% of these sequences branched within 10 monophyletic clades: four also included sequences from other Central American countries (BCAM-I to BCAM-IV) and six were mostly (>99%) composed by Guatemalan sequences (BGU clades). Most clades mainly comprised sequences from heterosexual individuals. Bayesian coalescent-based analyses suggested that BGU clades originated during the 1990s and 2000s, whereas BCAM clades originated between the late 1970s and mid 1980s. The major hub of dissemination of all BGU, and of BCAM-II, and BCAM-IV clades was traced to the Department of Guatemala, while the root location of BCAM-I and BCAM-III was traced to Honduras. Most Guatemalan clades experienced initial phases of exponential growth (0.23 and 3.6 year-1), followed by recent growth declines. Our observations suggest that the Guatemalan HIV-1 subtype B epidemic is driven by dissemination of multiple BPANDEMIC founder viral strains, some restricted to Guatemala and others widely disseminated in the Central American region, with Guatemala City identified as a major hub of viral dissemination. Our results also suggest the existence of different sub-epidemics within Guatemala for which different targeted prevention efforts might be needed.
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Affiliation(s)
- Yaxelis Mendoza
- Gorgas Memorial Institute for Health Studies, Panama City, Panama
- Department of Genetics and Molecular Biology, University of Panama, Panama City, Panama
| | - Claudia García-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Daniela Garrido-Rodríguez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Daniela Tapia-Trejo
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | | | | | | | | | | | | | | | | | | | - Santiago Avila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
- * E-mail: (GRT); (SAR)
| | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
- * E-mail: (GRT); (SAR)
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Chaillon A, Avila-Ríos S, Wertheim JO, Dennis A, García-Morales C, Tapia-Trejo D, Mejía-Villatoro C, Pascale JM, Porras-Cortés G, Quant-Durán CJ, Lorenzana I, Meza RI, Palou EY, Manzanero M, Cedillos RA, Reyes-Terán G, Mehta SR. Identification of major routes of HIV transmission throughout Mesoamerica. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2017; 54:98-107. [PMID: 28645708 PMCID: PMC5610625 DOI: 10.1016/j.meegid.2017.06.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 06/13/2017] [Accepted: 06/18/2017] [Indexed: 11/28/2022]
Abstract
BACKGROUND Migration and travel are major drivers of the spread of infectious diseases. Geographic proximity and a common language facilitate travel and migration in Mesoamerica, which in turn could affect the spread of HIV in the region. METHODS 6092 HIV-1 subtype B partial pol sequences sampled from unique antiretroviral treatment-naïve individuals from Mexico (40.7%), Guatemala (24.4%), Honduras (19%), Panama (8.2%), Nicaragua (5.5%), Belize (1.4%), and El Salvador (0.7%) between 2011 and 2016 were included. Phylogenetic and genetic network analyses were performed to infer putative relationships between HIV sequences. The demographic and geographic associations with clustering were analyzed and viral migration patterns were inferred using the Slatkin-Maddison approach on 100 iterations of random subsets of equal number of sequences per location. RESULTS A total of 1685/6088 (27.7%) of sequences linked with at least one other sequence, forming 603 putative transmission clusters (range: 2-89 individuals). Clustering individuals were significantly more likely to be younger (median age 29 vs 33years, p<0.01) and men-who-have-sex-with-men (40.4% vs 30.3%, p<0.01). Of the 603 clusters, 30 (5%) included sequences from multiple countries with commonly observed linkages between Mexican and Honduran sequences. Eight of the 603 clusters included >10 individuals, including two comprised exclusively of Guatemalans (52 and 89 individuals). Phylogenetic and migration analyses suggested that the Central and Southern regions of Mexico along with Belize were major sources of HIV throughout the region (p<0.01) with genetic flow southward from Mexico to the other nations of Mesoamerica. We also found evidence of significant viral migration within Mexico. CONCLUSION International clusters were infrequent, suggesting moderate migration between HIV epidemics of the different Mesoamerican countries. Nevertheless, we observed important sources of transnational HIV spread in the region, including Southern and Central Mexico and Belize.
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Affiliation(s)
| | - Santiago Avila-Ríos
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | | | - Ann Dennis
- University of North Carolina, Chapel Hill, NC, USA
| | - Claudia García-Morales
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Daniela Tapia-Trejo
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | | | - Juan M Pascale
- Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | | | | | - Ivette Lorenzana
- National Autonomous University of Honduras, Tegucigalpa, Honduras
| | - Rita I Meza
- Honduras National Reference HIV Laboratory, Tegucigalpa, Honduras
| | - Elsa Y Palou
- University School Hospital, Tegucigalpa, Honduras
| | | | | | - Gustavo Reyes-Terán
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico.
| | - Sanjay R Mehta
- University of California, San Diego, La Jolla, CA, USA; Veterans Affairs San Diego Healthcare System, San Diego, CA, USA.
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Eybpoosh S, Bahrampour A, Karamouzian M, Azadmanesh K, Jahanbakhsh F, Mostafavi E, Zolala F, Haghdoost AA. Spatio-Temporal History of HIV-1 CRF35_AD in Afghanistan and Iran. PLoS One 2016; 11:e0156499. [PMID: 27280293 PMCID: PMC4900578 DOI: 10.1371/journal.pone.0156499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/16/2016] [Indexed: 01/28/2023] Open
Abstract
HIV-1 Circulating Recombinant Form 35_AD (CRF35_AD) has an important position in the epidemiological profile of Afghanistan and Iran. Despite the presence of this clade in Afghanistan and Iran for over a decade, our understanding of its origin and dissemination patterns is limited. In this study, we performed a Bayesian phylogeographic analysis to reconstruct the spatio-temporal dispersion pattern of this clade using eligible CRF35_AD gag and pol sequences available in the Los Alamos HIV database (432 sequences available from Iran, 16 sequences available from Afghanistan, and a single CRF35_AD-like pol sequence available from USA). Bayesian Markov Chain Monte Carlo algorithm was implemented in BEAST v1.8.1. Between-country dispersion rates were tested with Bayesian stochastic search variable selection method and were considered significant where Bayes factor values were greater than three. The findings suggested that CRF35_AD sequences were genetically similar to parental sequences from Kenya and Uganda, and to a set of subtype A1 sequences available from Afghan refugees living in Pakistan. Our results also showed that across all phylogenies, Afghan and Iranian CRF35_AD sequences formed a monophyletic cluster (posterior clade credibility> 0.7). The divergence date of this cluster was estimated to be between 1990 and 1992. Within this cluster, a bidirectional dispersion of the virus was observed across Afghanistan and Iran. We could not clearly identify if Afghanistan or Iran first established or received this epidemic, as the root location of this cluster could not be robustly estimated. Three CRF35_AD sequences from Afghan refugees living in Pakistan nested among Afghan and Iranian CRF35_AD branches. However, the CRF35_AD-like sequence available from USA diverged independently from Kenyan subtype A1 sequences, suggesting it not to be a true CRF35_AD lineage. Potential factors contributing to viral exchange between Afghanistan and Iran could be injection drug networks and mass migration of Afghan refugees and labours to Iran, which calls for extensive preventive efforts.
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Affiliation(s)
- Sana Eybpoosh
- Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Abbas Bahrampour
- Modeling in Health Research Centre, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Karamouzian
- Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
- School of Population and Public Health, Faculty of Medicine, University of British Colombia, Vancouver, BC, Canada
| | | | | | - Ehsan Mostafavi
- Epidemiology Department, Pasteur Institute of Iran, Tehran, Iran
- Emerging and Reemerging Infectious Diseases Research Centre, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
| | - Farzaneh Zolala
- Modeling in Health Research Centre, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Akbar Haghdoost
- Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
- * E-mail:
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Junqueira DM, Almeida SEDM. HIV-1 subtype B: Traces of a pandemic. Virology 2016; 495:173-84. [PMID: 27228177 DOI: 10.1016/j.virol.2016.05.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/01/2016] [Accepted: 05/03/2016] [Indexed: 11/18/2022]
Abstract
Human migration is a major process that shaped the origin and dissemination of HIV. Within HIV-1, subtype B (HIV-1B) is the most disseminated variant and it is assumed to be the causative agent in approximately 11% of all cases of HIV worldwide. Phylogenetic studies have revealed that HIV-1B emerged in Kinshasa (Africa) and was introduced into the Caribbean region via Haiti in or around 1966 by human migration. After localized dispersion, the virus was brought to the United States of America via homosexual/bisexual contact around 1969. Inside USA, the incidence of HIV-1B infection increased exponentially and it became established in the population, affecting not only homosexual individuals but also heterosexual individuals and injecting drug users. Soon after, the virus was disseminated and became established in other regions, including Europe, Asia, Latin America, and Australia. Recent studies suggest that, in addition to this pandemic clade, several lineages have emerged from Haiti and reached other Caribbean and Latin American countries via short-distance dissemination. Different subtype B genetic variants have also been detected in these epidemics. Four genetic variants have been described to date: subtype B', which mainly circulates in Thailand and other Asian countries; a specific variant mainly found in Trinidad and Tobago; the GPGS variant, which is primarily detected in Korea; and the GWGR variant, which is mainly detected in Brazil. This paper reviews the evolution of HIV-1B and its impact on the human population.
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Affiliation(s)
- Dennis Maletich Junqueira
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Avenida Ipiranga, 5400 - Jd Botânico, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Avenida Bento Gonçalves, 9800 - Agronomia, Porto Alegre, RS, Brazil; Centro Universitário Ritter dos Reis - UniRitter, Departamento de Ciências da Saúde, Avenida Orfanotrófio, 555 - Teresópolis, Porto Alegre, RS, Brazil.
| | - Sabrina Esteves de Matos Almeida
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Avenida Ipiranga, 5400 - Jd Botânico, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Avenida Bento Gonçalves, 9800 - Agronomia, Porto Alegre, RS, Brazil; Instituto de Ciências da Saúde, Universidade FEEVALE, Rodovia RS 239, 2755 - Vila Nova, Novo Hamburgo, RS, Brazil.
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Dyer RJ. Population Graphs and Landscape Genetics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054150] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rodney J. Dyer
- Department of Biology and Center for Environmental Studies, Virginia Commonwealth University, Richmond, Virginia 23284-2012;
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Murray GGR, Wang F, Harrison EM, Paterson GK, Mather AE, Harris SR, Holmes MA, Rambaut A, Welch JJ. The effect of genetic structure on molecular dating and tests for temporal signal. Methods Ecol Evol 2015; 7:80-89. [PMID: 27110344 PMCID: PMC4832290 DOI: 10.1111/2041-210x.12466] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/23/2015] [Indexed: 12/23/2022]
Abstract
‘Dated‐tip’ methods of molecular dating use DNA sequences sampled at different times, to estimate the age of their most recent common ancestor. Several tests of ‘temporal signal’ are available to determine whether data sets are suitable for such analysis. However, it remains unclear whether these tests are reliable. We investigate the performance of several tests of temporal signal, including some recently suggested modifications. We use simulated data (where the true evolutionary history is known), and whole genomes of methicillin‐resistant Staphylococcus aureus (to show how particular problems arise with real‐world data sets). We show that all of the standard tests of temporal signal are seriously misleading for data where temporal and genetic structures are confounded (i.e. where closely related sequences are more likely to have been sampled at similar times). This is not an artefact of genetic structure or tree shape per se, and can arise even when sequences have measurably evolved during the sampling period. More positively, we show that a ‘clustered permutation’ approach introduced by Duchêne et al. (Molecular Biology and Evolution, 32, 2015, 1895) can successfully correct for this artefact in all cases and introduce techniques for implementing this method with real data sets. The confounding of temporal and genetic structures may be difficult to avoid in practice, particularly for outbreaks of infectious disease, or when using ancient DNA. Therefore, we recommend the use of ‘clustered permutation’ for all analyses. The failure of the standard tests may explain why different methods of dating pathogen origins have reached such wildly different conclusions.
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Affiliation(s)
- Gemma G R Murray
- Department of Genetics University of Cambridge Downing Street Cambridge CB2 3EH UK
| | - Fang Wang
- Department of Genetics University of Cambridge Downing Street Cambridge CB2 3EH UK
| | - Ewan M Harrison
- Department of Veterinary Medicine University of Cambridge Madingley Road Cambridge CB3 0ES UK
| | - Gavin K Paterson
- Department of Veterinary Medicine University of Cambridge Madingley Road Cambridge CB3 0ESUK; School of Biological, Biomedical and Environmental Sciences University of Hull Cottingham Road Hull HU6 7RX UK
| | - Alison E Mather
- Department of Veterinary Medicine University of Cambridge Madingley Road Cambridge CB3 0ESUK; Wellcome Trust Sanger Institute Hinxton CB10 1SA UK
| | | | - Mark A Holmes
- Department of Veterinary Medicine University of Cambridge Madingley Road Cambridge CB3 0ES UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology University of Edinburgh King's Buildings Edinburgh EH9 3FL UK
| | - John J Welch
- Department of Genetics University of Cambridge Downing Street Cambridge CB2 3EH UK
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9
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Cabello M, Mendoza Y, Bello G. Spatiotemporal dynamics of dissemination of non-pandemic HIV-1 subtype B clades in the Caribbean region. PLoS One 2014; 9:e106045. [PMID: 25148215 PMCID: PMC4141835 DOI: 10.1371/journal.pone.0106045] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/29/2014] [Indexed: 11/18/2022] Open
Abstract
The Human immunodeficiency virus type-1 (HIV-1) epidemic in the Caribbean region is mostly driven by subtype B; but information about the pattern of viral spread in this geographic region is scarce and different studies point to quite divergent models of viral dissemination. In this study, we reconstructed the spatiotemporal and population dynamics of the HIV-1 subtype B epidemic in the Caribbean. A total of 1,806 HIV-1 subtype B pol sequences collected from 17 different Caribbean islands between 1996 and 2011 were analyzed together with sequences from the United States (n = 525) and France (n = 340) included as control. Maximum Likelihood phylogenetic analyses revealed that HIV-1 subtype B infections in the Caribbean are driven by dissemination of the pandemic clade (BPANDEMIC) responsible for most subtype B infections across the world, and older non-pandemic lineages (BCAR) characteristics of the Caribbean region. The non-pandemic BCAR strains account for >40% of HIV-1 infections in most Caribbean islands; with exception of Cuba and Puerto Rico. Bayesian phylogeographic analyses indicate that BCAR strains probably arose in the island of Hispaniola (Haiti/Dominican Republic) around the middle 1960s and were later disseminated to Trinidad and Tobago and to Jamaica between the late 1960s and the early 1970s. In the following years, the BCAR strains were also disseminated from Hispaniola and Trinidad and Tobago to other Lesser Antilles islands at multiple times. The BCAR clades circulating in Hispaniola, Jamaica and Trinidad and Tobago appear to have experienced an initial phase of exponential growth, with mean estimated growth rates of 0.35-0.45 year(-1), followed by a more recent stabilization since the middle 1990s. These results demonstrate that non-pandemic subtype B lineages have been widely disseminated through the Caribbean since the late 1960s and account for an important fraction of current HIV-1 infections in the region.
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Affiliation(s)
- Marina Cabello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - 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, City of Knowledge, Clayton, Panama City, Panama
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
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10
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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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Mendoza Y, Martínez AA, Castillo Mewa J, González C, García-Morales C, Avila-Ríos S, Reyes-Terán G, Armién B, Pascale JM, Bello G. Human immunodeficiency virus type 1 (HIV-1) subtype B epidemic in Panama is mainly driven by dissemination of country-specific clades. PLoS One 2014; 9:e95360. [PMID: 24748274 PMCID: PMC3991702 DOI: 10.1371/journal.pone.0095360] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 03/25/2014] [Indexed: 11/25/2022] Open
Abstract
The Human immunodeficiency virus type-1 (HIV-1) subtype B is the most predominant clade in Central America; but information about the evolutionary history of this virus in this geographic region is scarce. In this study, we reconstructed the spatiotemporal and population dynamics of the HIV-1 subtype B epidemic in Panama. A total of 761 HIV-1 subtype B pol sequences obtained in Panama between 2004 and 2013 were combined with subtype B pol sequences from the Americas and Europe. Maximum Likelihood phylogenetic analyses revealed that HIV-1 subtype B infections in Panama derived from the dissemination of multiple founder viruses. Most Panamanian subtype B viruses (94.5%) belong to the pandemic viral strain proposed as originated in the US, whereas others (5.5%) were intermixed among non-pandemic Caribbean strains. The bulk (76.6%) of subtype B sequences from Panama grouped within 12 country-specific clades that were not detected in other Central American countries. Bayesian coalescent-based analyses suggest that most Panamanian clades probably originated between the early 1970s and the early 1980s. The root location of major Panamanian clades was traced to the most densely populated districts of Panama province. Major Panamanian clades appear to have experienced one or two periods of exponential growth of variable duration between the 1970s and the 2000s, with median growth rates from 0.2 to 0.4 year−1. Thus, the HIV-1 subtype B epidemic in Panama is driven by the expansion of local viral strains that were introduced from the Caribbean and other American countries at an early stage of the AIDS pandemic.
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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, City of Knowledge, Clayton, 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, City of Knowledge, Clayton, Panama City, Panama
| | - Juan Castillo Mewa
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, 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
| | - Blas Armién
- Department of Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | - Juan M. Pascale
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
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Abubakar YF, Meng Z, Zhang X, Xu J. Multiple independent introductions of HIV-1 CRF01_AE identified in China: what are the implications for prevention? PLoS One 2013; 8:e80487. [PMID: 24282546 PMCID: PMC3839914 DOI: 10.1371/journal.pone.0080487] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 10/11/2013] [Indexed: 11/19/2022] Open
Abstract
Background HIV-1 CRF01_AE accounts for an important fraction of HIV infections in Asia including China, but little is known about the phylogenetic and evolutionary history of this CRF (circulating recombinant form). In the current study, we collected a large number of 1,957 CRF01_AE gag p17 sequences with known sampling year (1990-2010) from 5 global regions representing 15 countries to better understand the phylogenetic relationships and epidemic history of CRF01_AE strains in China. Methodology/Principal Findings CRF01_AE gag p17 sequences were retrieved from public databases to explore phylogenetic relationships and phylogeographic dynamics of CRF01_AE in Asia by using maximum-likelihood phylogenetics and Bayesian coalescent-based analyses. We found close phylogenetic relationships between sequences from Thailand, Vietnam and China. Moreover, at least 5 independent introductions and 5 independent autochthonous clades of CRF01_AE, which descended from Thailand or Vietnam were identified in China from 1991 through 2003. Conclusion/Significance The current study not only defines the migration of CRF01_AE clades to/in Asia, but also demonstrates the criticalness of identifying the circulating strains in the population for the development of vaccine and microbicides.
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Affiliation(s)
- Yassir F. Abubakar
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health at Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhefeng Meng
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health at Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health at Shanghai Medical College, Fudan University, Shanghai, China
- State Key Laboratory of Infectious Disease Control and Prevention (CDC), Beijing, China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health at Shanghai Medical College, Fudan University, Shanghai, China
- State Key Laboratory of Infectious Disease Control and Prevention (CDC), Beijing, China
- * E-mail:
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