1
|
Moreno A, González C, Góndola J, Chavarría O, Ortiz A, Castillo J, Castillo Mewa J, Pascale JM, Martínez AA. HIV-1 Low-Frequency Variants Identified in Antiretroviral-Naïve Subjects with Virologic Failure after 12 Months of Follow-Up in Panama. Infect Dis Rep 2023; 15:436-444. [PMID: 37623048 PMCID: PMC10454674 DOI: 10.3390/idr15040044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 08/26/2023] Open
Abstract
Low-frequency mutations associated with drug resistance have been related to virologic failure in subjects with no history of pre-treatment and recent HIV diagnosis. In total, 78 antiretroviral treatment (ART)-naïve subjects with a recent HIV diagnosis were selected and followed by CD4+ T lymphocytes and viral load tests to detect virologic failure. We sequenced the basal samples retrospectively using next-generation sequencing (NGS), looking for low-frequency mutations that had not been detected before using the Sanger sequencing method (SSM) and describing the response to ART. Twenty-two subjects developed virologic failure (VF), and thirteen of them had at least one drug-resistance mutation associated with Reverse Transcriptase Inhibitors (RTI) and Protease Inhibitors (PIs) at frequency levels ≤ 1%, not detected previously in their basal genotyping test. No resistance mutations were observed to Integrase Strand Transfer Inhibitors (INSTIs). We identified a possible cause of VF in ART-naïve subjects with low-frequency mutations detected. To our knowledge, this is the first evaluation of pre-existing drug resistance for HIV-1 minority variants carried out on ART-naïve people living with HIV/AIDS (PLWHA) by analyzing the HIV-1 pol gene using NGS in the country.
Collapse
Affiliation(s)
- Ambar Moreno
- Department of Research in Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (A.M.)
| | - Claudia González
- Department of Research in Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (A.M.)
- Department of Microbiology and Immunology, University of Panama, Panama City 3366, Panama
| | - Jessica Góndola
- Department of Research in Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (A.M.)
| | - Oris Chavarría
- Department of Research in Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (A.M.)
| | - Alma Ortiz
- Department of Research in Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (A.M.)
| | - Jorge Castillo
- Department of Research in Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (A.M.)
| | - Juan Castillo Mewa
- Department of Research in Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (A.M.)
| | - Juan Miguel Pascale
- Department of Research in Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (A.M.)
- Department of Microbiology and Immunology, University of Panama, Panama City 3366, Panama
| | - Alexander Augusto Martínez
- Department of Research in Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (A.M.)
- Department of Microbiology and Immunology, University of Panama, Panama City 3366, Panama
| |
Collapse
|
2
|
Venkatachalam S, Murlidharan N, Krishnan SR, Ramakrishnan C, Setshedi M, Pandian R, Barh D, Tiwari S, Azevedo V, Sayed Y, Gromiha MM. Understanding Drug Resistance of Wild-Type and L38HL Insertion Mutant of HIV-1 C Protease to Saquinavir. Genes (Basel) 2023; 14:533. [PMID: 36833460 PMCID: PMC9957153 DOI: 10.3390/genes14020533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) is one of the most challenging infectious diseases to treat on a global scale. Understanding the mechanisms underlying the development of drug resistance is necessary for novel therapeutics. HIV subtype C is known to harbor mutations at critical positions of HIV aspartic protease compared to HIV subtype B, which affects the binding affinity. Recently, a novel double-insertion mutation at codon 38 (L38HL) was characterized in HIV subtype C protease, whose effects on the interaction with protease inhibitors are hitherto unknown. In this study, the potential of L38HL double-insertion in HIV subtype C protease to induce a drug resistance phenotype towards the protease inhibitor, Saquinavir (SQV), was probed using various computational techniques, such as molecular dynamics simulations, binding free energy calculations, local conformational changes and principal component analysis. The results indicate that the L38HL mutation exhibits an increase in flexibility at the hinge and flap regions with a decrease in the binding affinity of SQV in comparison with wild-type HIV protease C. Further, we observed a wide opening at the binding site in the L38HL variant due to an alteration in flap dynamics, leading to a decrease in interactions with the binding site of the mutant protease. It is supported by an altered direction of motion of flap residues in the L38HL variant compared with the wild-type. These results provide deep insights into understanding the potential drug resistance phenotype in infected individuals.
Collapse
Affiliation(s)
- Sankaran Venkatachalam
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Nisha Murlidharan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Sowmya R. Krishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - C. Ramakrishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Mpho Setshedi
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Ramesh Pandian
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Debmalya Barh
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, West Bengal, India
| | - Sandeep Tiwari
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
- Institute of Biology, Federal University of Bahia, Salvador, BA 40110-909, Brazil
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA 40110-909, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| |
Collapse
|
3
|
Ventosa-Cubillo J, Pinzón R, González-Alba JM, Estripeaut D, Navarro ML, Holguín Á. Drug resistance in children and adolescents with HIV in Panama. J Antimicrob Chemother 2022; 78:423-435. [PMID: 36454248 PMCID: PMC9890268 DOI: 10.1093/jac/dkac407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
OBJECTIVES The inadequacy of resistance monitoring in Latin America leads to circulation of HIV strains with drug resistance mutations (DRMs), compromising ART effectiveness. This study describes the DRM prevalence in HIV-infected paediatric patients in Panama. METHODS During 2018-19, plasma was collected from 76 HIV-infected children/adolescents (5 ART-naive, 71 treated) in Panama for HIV-1 DRM pol analysis, predicted antiretroviral (ARV) susceptibility by Stanford, and HIV-1 variant phylogenetic characterization. RESULTS HIV-1 pol sequences were recovered from 67 (88.2%) of 76 children/adolescents (median age 12 years), carrying 65 subtype B, 1 subtype G and 1 unique recombinant URF_A1B. Five were ART-naive and 62 ART-treated under virological failure (viraemia >50 copies/mL) with previous exposure to NRTIs, (100%), NNRTIs (45.2%), PIs (95.2%) and integrase strand transfer inhibitors (INSTIs, 17.7%). Among the treated patients, 34 (54.8%) carried resistant strains, with major DRMs to one (40.3%), two (9.7%) or three (4.8%) ARV families. Most of them harboured DRMs to NRTIs (58.5%) or NNRTIs (39%), but also major DRMs to PIs (4.9%) and INSTIs (6.5%). We also found dual-class NRTI + NNRTI (12.2%) and NNRTI + PI (2.6%) resistance. Two naive subjects carried viruses with DRMs to NRTIs and NRTI + NNRTI, respectively. Sequenced viruses presented high/intermediate resistance mainly to emtricitabine/lamivudine (48.9% each) and efavirenz/nevirapine (33.3% each). Most participants were susceptible to PIs (91.3%) and INSTIs (88.1%). CONCLUSIONS The high DRM prevalence to NRTIs and NNRTIs observed among treated HIV-infected children/adolescents in Panama justifies the need for routine resistance monitoring for optimal rescue therapy selection in this vulnerable population.
Collapse
Affiliation(s)
- Judit Ventosa-Cubillo
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBERESP-ISCIII-RITIP-CoRISpe-PLANTAIDS-CYTED, Madrid, Spain
| | - Ramón Pinzón
- Hospital del Niño Doctor José Renán Esquivel, PLANTAIDS-CYTED, Panamá
| | - José María González-Alba
- Microbiology Department. Hospital Universitario Central de Asturias (HUCA) and Grupo de Investigación Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Dora Estripeaut
- Hospital del Niño Doctor José Renán Esquivel, PLANTAIDS-CYTED, Panamá,Sistema Nacional de Investigación, Secretaría Nacional de Ciencia, tecnología e Innovación, Panamá
| | - María Luisa Navarro
- Hospital Gregorio Marañón, IISGM, UCM, PLANTAIDS programa CYTED–CIBERINFEC-ISCIII, Madrid, Spain
| | | |
Collapse
|
4
|
de Azevedo SSD, Delatorre E, Gaido CM, Silva-de-Jesus C, Guimarães ML, Couto-Fernandez JC, Morgado MG. HIV-1 Diversity and Drug Resistance in Treatment-Naïve Children and Adolescents from Rio de Janeiro, Brazil. Viruses 2022; 14:v14081761. [PMID: 36016383 PMCID: PMC9413768 DOI: 10.3390/v14081761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 12/02/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) can be transmitted via parenteral, sexual, or vertical exposure routes. The number of HIV-1 cases detected yearly in children and adolescents in Brazil did not decrease over the last decade, representing ~5% of total cases described in the country. In recent years, the HIV-1 diversity and the prevalence of transmitted drug resistance mutations (TDRM) are moving toward a marked increase. In this study, we retrospectively evaluated the diversity of HIV-1 subtypes and the TDRM prevalence in 135 treatment-naïve HIV-1 vertically infected children and adolescents born in between 1993 and 2012. These children were assessed in either 2001–2007 or 2008–2012 when they were 0 to 17 years old. The individuals assessed in 2001–2007 (n = 38) had median CD4+ T cell counts of 1218 cells/mm3 (IQR: 738–2.084) and median HIV-1 plasma viral load of 4.18 log10 copies/mL (IQR: 3.88–4.08). The individuals (n = 97) evaluated in 2008–2012 showed median CD4+ T cell counts of 898.5 cells/mm3 (IQR: 591.3–1.821) and median HIV-1 plasma viral load of 4.69 log10 copies/mL (IQR: 4.26–5.33). A steady decrease in the median CD4 T+ cell counts was observed with age progression, as expected. The majority HIV-1 pol sequences (87%) were classified as pure HIV-1 subtypes (77% subtype B, 9% subtype F1 and 1.5% subtype C), while 13% of sequences were classified as recombinants (CRF45_cpx, n = 4; CRF28/29_BF1, n = 2; CRF02_AG, n = 1; CRF40_BF1, n = 1, CRF99_BF1, n = 1, URF_BF1, n = 8). The overall prevalence of TDRM was 14% (19/135), conferring resistance to the nucleoside reverse transcriptase inhibitors (NRTI, 13/135–9.6%), non-nucleoside reverse transcriptase inhibitors (NNRTI, 8/135–5.9%), and protease inhibitors (PI, 2/135–1.5%). The main TDRM observed for NNRTI was the K103N (n = 8), while the mutations T215I/Y/D/E (n = 7) and M184V (n = 4) were the main TDRM for NRTI. Only two TDRM were observed for PI in one individual each (M46I and V82A). Most TDRM were found in the HIV-1 subtype B (84%) sequences. This study reveals an HIV-1 epidemic with high diversity and moderate prevalence of TDRM in the pediatric population of Rio de Janeiro, indicating the existence of possible problems in the clinical management of prophylactic therapy to prevent mother-to-child transmission and future treatment options for the affected children.
Collapse
Affiliation(s)
- Suwellen Sardinha Dias de Azevedo
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
- Correspondence: or ; Tel.: +55-21-3865-8147; Fax: +55-21-3865-8173
| | - Edson Delatorre
- Centro de Ciências Exatas, Naturais e da Saúde, Departamento de Biologia—Universidade Federal do Espírito Santo—UFES, Espírito Santo 29500-000, Brazil
| | - Cibele Marina Gaido
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
| | - Carlos Silva-de-Jesus
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
| | | | - José Carlos Couto-Fernandez
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
| | - Mariza G. Morgado
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
| |
Collapse
|
5
|
Antiretroviral resistance, genotypic characterization and origin of Human Immunodeficiency Virus among the infected wives of Intravenous drug users in Manipur. Sci Rep 2018; 8:15183. [PMID: 30315192 PMCID: PMC6185977 DOI: 10.1038/s41598-018-33636-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 10/03/2018] [Indexed: 11/08/2022] Open
Abstract
Increasing incidence of drug resistance is ascertained to be the main obstacles in limiting the virus among the human immunodeficiency virus (HIV) infected individuals. This study investigates the drug resistance mutations (DRMs), genetic variants and origin of transmitted drug resistance of HIV-1 among the HIV-1 infected wives of intravenous drug users (IDUs) in Manipur. 44 HIV pol gene sequences were generated from 56 blood samples by viral gene amplification and sequencing. Sequences were then analysed for drug resistance, genetic variants and origin. The result revealed that among the treatment naive cases, 35.7% had Transmitted Drug Resistance Mutations (TDRMs) while among treatment experienced cases, 50% had Acquired Drug Resistant Mutations (ADRMs). These TDRMs and ADRMs conferred resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and/or protease inhibitors (PIs). Majority of the isolated HIV-1 sequences (77.3%) were subtype C while 9.1% was discordant subtype, 6.8% was subtype B, 4.5% was CRF_01AE and 2.3% was URF_BC. TDRM strains were found to be introduced from Myanmar, Vietnam and mainland India. This study also reveals the appearance of CRF_01AE for the first time in Manipur. The finding of this study indicates high prevalence of drug resistant mutations and complex molecular epidemiology in Manipur.
Collapse
|
6
|
Valenzuela-Ponce H, Alva-Hernández S, Garrido-Rodríguez D, Soto-Nava M, García-Téllez T, Escamilla-Gómez T, García-Morales C, Quiroz-Morales VS, Tapia-Trejo D, Del Arenal-Sánchez S, Prado-Galbarro FJ, Hernández-Juan R, Rodríguez-Aguirre E, Murakami-Ogasawara A, Mejía-Villatoro C, Escobar-Urias IY, Pinzón-Meza R, Pascale JM, Zaldivar Y, Porras-Cortés G, Quant-Durán C, Lorenzana I, Meza RI, Palou EY, Manzanero M, Cedillos RA, Aláez C, Brockman MA, Harrigan PR, Brumme CJ, Brumme ZL, Ávila-Ríos S, Reyes-Terán G. Novel HLA class I associations with HIV-1 control in a unique genetically admixed population. Sci Rep 2018; 8:6111. [PMID: 29666450 PMCID: PMC5904102 DOI: 10.1038/s41598-018-23849-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/21/2018] [Indexed: 12/26/2022] Open
Abstract
Associations between HLA class I alleles and HIV progression in populations exhibiting Amerindian and Caucasian genetic admixture remain understudied. Using univariable and multivariable analyses we evaluated HLA associations with five HIV clinical parameters in 3,213 HIV clade B-infected, ART-naïve individuals from Mexico and Central America (MEX/CAM cohort). A Canadian cohort (HOMER, n = 1622) was used for comparison. As expected, HLA allele frequencies in MEX/CAM and HOMER differed markedly. In MEX/CAM, 13 HLA-A, 24 HLA-B, and 14 HLA-C alleles were significantly associated with at least one clinical parameter. These included previously described protective (e.g. B*27:05, B*57:01/02/03 and B*58:01) and risk (e.g. B*35:02) alleles, as well as novel ones (e.g. A*03:01, B*15:39 and B*39:02 identified as protective, and A*68:03/05, B*15:30, B*35:12/14, B*39:01/06, B*39:05~C*07:02, and B*40:01~C*03:04 identified as risk). Interestingly, both protective (e.g. B*39:02) and risk (e.g. B*39:01/05/06) subtypes were identified within the common and genetically diverse HLA-B*39 allele group, characteristic to Amerindian populations. While HLA-HIV associations identified in MEX and CAM separately were similar overall (Spearman's rho = 0.33, p = 0.03), region-specific associations were also noted. The identification of both canonical and novel HLA/HIV associations provides a first step towards improved understanding of HIV immune control among unique and understudied Mestizo populations.
Collapse
Affiliation(s)
- Humberto Valenzuela-Ponce
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Selma Alva-Hernández
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Daniela Garrido-Rodríguez
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Maribel Soto-Nava
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Thalía García-Téllez
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico.,Institut Pasteur, Unité HIV, Inflammation and Persistence, Paris, France
| | - Tania Escamilla-Gómez
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Claudia García-Morales
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | | | - Daniela Tapia-Trejo
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Silvia Del Arenal-Sánchez
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | | | - Ramón Hernández-Juan
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Edna Rodríguez-Aguirre
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Akio Murakami-Ogasawara
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | | | | | | | | | - Yamitzel Zaldivar
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | | | | | - Ivette Lorenzana
- Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Rita I Meza
- Honduras HIV National Laboratory, Tegucigalpa, Honduras
| | - Elsa Y Palou
- Hospital Escuela Universitario, Tegucigalpa, Honduras
| | | | | | - Carmen Aláez
- National Institute of Genomic Medicine, Translational Medicine Laboratory, Mexico City, Mexico
| | - Mark A Brockman
- Simon Fraser University, Faculty of Health Sciences, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | | | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Zabrina L Brumme
- Simon Fraser University, Faculty of Health Sciences, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Santiago Ávila-Ríos
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico.
| | - Gustavo Reyes-Terán
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico.
| | | |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Mendoza Y, Castillo Mewa J, Martínez AA, Zaldívar Y, Sosa N, Arteaga G, Armién B, Bautista CT, García-Morales C, Tapia-Trejo D, Ávila-Ríos S, Reyes-Terán G, Bello G, Pascale JM. HIV-1 Antiretroviral Drug Resistance Mutations in Treatment Naïve and Experienced Panamanian Subjects: Impact on National Use of EFV-Based Schemes. PLoS One 2016; 11:e0154317. [PMID: 27119150 PMCID: PMC4847863 DOI: 10.1371/journal.pone.0154317] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 04/12/2016] [Indexed: 11/29/2022] Open
Abstract
The use of antiretroviral therapy in HIV infected subjects prevents AIDS-related illness and delayed occurrence of death. In Panama, rollout of ART started in 1999 and national coverage has reached 62.8% since then. The objective of this study was to determine the level and patterns of acquired drug resistance mutations of clinical relevance (ADR-CRM) and surveillance drug resistance mutations (SDRMs) from 717 HIV-1 pol gene sequences obtained from 467 ARV drug-experienced and 250 ARV drug-naïve HIV-1 subtypes B infected subjects during 2007–2013, respectively. The overall prevalence of SDRM and of ADR-CRM during the study period was 9.2% and 87.6%, respectively. The majority of subjects with ADR-CRM had a pattern of mutations that confer resistance to at least two classes of ARV inhibitors. The non-nucleoside reverse transcriptase inhibitor (NNRTI) mutations K103N and P225H were more prevalent in both ARV drug-naïve and ARV drug-experienced subjects. The nucleoside reverse transcriptase inhibitor (NRTI) mutation M184V was more frequent in ARV drug-experienced individuals, while T215YFrev and M41L were more frequent in ARV drug-naïve subjects. Prevalence of mutations associated to protease inhibitors (PI) was lower than 4.1% in both types of subjects. Therefore, there is a high level of resistance (>73%) to Efavirenz/Nevirapine, Lamivudine and Azidothymidine in ARV drug-experienced subjects, and an intermediate to high level of resistance (5–10%) to Efavirenz/Nevirapine in ARV drug-naïve subjects. During the study period, we observed an increasing trend in the prevalence of ADR-CRM in subjects under first-line schemes, but not significant changes in the prevalence of SDRM. These results reinforce the paramount importance of a national surveillance system of ADR-CRM and SDRM for national management policies of subjects living with HIV.
Collapse
Affiliation(s)
- Yaxelis Mendoza
- Direction of Research and Technological Development, Gorgas Memorial Institute for Health Studies, Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur City, India
- Department of Genetics and Molecular Biology, School of Biology, University of Panama, Panama City, Panama
- Institute for Scientific Research and High Technology Services of Panama, Panama City, Panama
| | - Juan Castillo Mewa
- Direction of Research and Technological Development, Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | - Alexander A. Martínez
- Direction of Research and Technological Development, Gorgas Memorial Institute for Health Studies, Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur City, India
- Institute for Scientific Research and High Technology Services of Panama, Panama City, Panama
| | - Yamitzel Zaldívar
- Direction of Research and Technological Development, Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | - Néstor Sosa
- Direction of Research and Technological Development, Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | - Griselda Arteaga
- Department of Microbiology, School of Medicine, University of Panama, Panama City, Panama
| | - Blas Armién
- Direction of Research and Technological Development, Gorgas Memorial Institute for Health Studies, Panama City, Panama
- Facultad de Ciencias de la Salud, Universidad Interamericana de Panamá, Panama City, Panama
| | - Christian T. Bautista
- Direction of Research and Technological Development, Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | - Claudia García-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases (Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias), Mexico City, Mexico
| | - Daniela Tapia-Trejo
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases (Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias), Mexico City, Mexico
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases (Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias), Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases (Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias), Mexico City, Mexico
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Juan M. Pascale
- Direction of Research and Technological Development, Gorgas Memorial Institute for Health Studies, Panama City, Panama
- Department of Microbiology, School of Medicine, University of Panama, Panama City, Panama
- * E-mail:
| |
Collapse
|
9
|
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.
Collapse
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:
| |
Collapse
|