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Iša P, Taboada B, García-López R, Boukadida C, Ramírez-González JE, Vázquez-Pérez JA, Hernández-Terán A, Romero-Espinoza JÁ, Muñoz-Medina JE, Grajales-Muñiz C, Rincón-Rubio A, Matías-Florentino M, Sanchez-Flores A, Mendieta-Condado E, Barrera-Badillo G, López S, Hernández-Rivas L, López-Martínez I, Ávila-Ríos S, Arias CF. Metagenomic analysis reveals differences in the co-occurrence and abundance of viral species in SARS-CoV-2 patients with different severity of disease. BMC Infect Dis 2022; 22:792. [PMID: 36261802 PMCID: PMC9580447 DOI: 10.1186/s12879-022-07783-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/06/2022] [Indexed: 11/22/2022] Open
Abstract
Background SARS-CoV-2 infections have a wide spectrum of clinical manifestations whose causes are not completely understood. Some human conditions predispose to severe outcome, like old age or the presence of comorbidities, but many other facets, including coinfections with other viruses, remain poorly characterized.
Methods In this study, the eukaryotic fraction of the respiratory virome of 120 COVID-19 patients was characterized through whole metagenomic sequencing. Results Genetic material from respiratory viruses was detected in 25% of all samples, whereas human viruses other than SARS-CoV-2 were found in 80% of them. Samples from hospitalized and deceased patients presented a higher prevalence of different viruses when compared to ambulatory individuals. Small circular DNA viruses from the Anneloviridae (Torque teno midi virus 8, TTV-like mini virus 19 and 26) and Cycloviridae families (Human associated cyclovirus 10), Human betaherpesvirus 6, were found to be significantly more abundant in samples from deceased and hospitalized patients compared to samples from ambulatory individuals. Similarly, Rotavirus A, Measles morbillivirus and Alphapapilomavirus 10 were significantly more prevalent in deceased patients compared to hospitalized and ambulatory individuals. Conclusions Results show the suitability of using metagenomics to characterize a broader peripheric virological landscape of the eukaryotic virome in SARS-CoV-2 infected patients with distinct disease outcomes. Identified prevalent viruses in hospitalized and deceased patients may prove important for the targeted exploration of coinfections that may impact prognosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07783-8.
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Affiliation(s)
- Pavel Iša
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | | | | | | | | | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Concepción Grajales-Muñiz
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Alma Rincón-Rubio
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Edgar Mendieta-Condado
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Ciudad de Mexico, Mexico
| | - Gisela Barrera-Badillo
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Ciudad de Mexico, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Lucía Hernández-Rivas
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Ciudad de Mexico, Mexico
| | - Irma López-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Ciudad de Mexico, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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2
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Avila-Rios S, García-Morales C, Reyes-Terán G, González-Rodríguez A, Matías-Florentino M, Mehta SR, Chaillon A. Phylodynamics of HIV in the Mexico City Metropolitan Region. J Virol 2022; 96:e0070822. [PMID: 35762759 PMCID: PMC9327710 DOI: 10.1128/jvi.00708-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/06/2022] [Indexed: 12/30/2022] Open
Abstract
Evolutionary analyses of viral sequences can provide insights into transmission dynamics, which in turn can optimize prevention interventions. Here, we characterized the dynamics of HIV transmission within the Mexico City metropolitan area. HIV pol sequences from persons recently diagnosed at the largest HIV clinic in Mexico City (between 2016 and 2021) were annotated with demographic/geographic metadata. A multistep phylogenetic approach was applied to identify putative transmission clades. A data set of publicly available sequences was used to assess international introductions. Clades were analyzed with a discrete phylogeographic model to evaluate the timing and intensity of HIV introductions and transmission dynamics among municipalities in the region. A total of 6,802 sequences across 96 municipalities (5,192 from Mexico City and 1,610 from the neighboring State of Mexico) were included (93.6% cisgender men, 5.0% cisgender women, and 1.3% transgender women); 3,971 of these sequences formed 1,206 clusters, involving 78 municipalities, including 89 clusters of ≥10 sequences. Discrete phylogeographic analysis revealed (i) 1,032 viral introductions into the region, over one-half of which were from the United States, and (ii) 354 migration events between municipalities with high support (adjusted Bayes factor of ≥3). The most frequent viral migrations occurred between northern municipalities within Mexico City, i.e., Cuauhtémoc to Iztapalapa (5.2% of events), Iztapalapa to Gustavo A. Madero (5.4%), and Gustavo A. Madero to Cuauhtémoc (6.5%). Our analysis illustrates the complexity of HIV transmission within the Mexico City metropolitan area but also identifies a spatially active transmission area involving a few municipalities in the north of the city, where targeted interventions could have a more pronounced effect on the entire regional epidemic. IMPORTANCE Phylogeographic investigation of the Mexico City HIV epidemic illustrates the complexity of HIV transmission in the region. An active transmission area involving a few municipalities in the north of the city, with transmission links throughout the region, is identified and could be a location where targeted interventions could have a more pronounced effect on the entire regional epidemic, compared with those dispersed in other manners.
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Affiliation(s)
- Santiago Avila-Rios
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Claudia García-Morales
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Coordinating Commission of the National Institutes of Health and High Specialty Hospitals, Ministry of Health, Mexico City, Mexico
| | | | | | - Sanjay R. Mehta
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, San Diego, California, USA
- Veterans Affairs Health System, San Diego, California, USA
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, San Diego, California, USA
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3
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Zárate S, Taboada B, Muñoz-Medina JE, Iša P, Sanchez-Flores A, Boukadida C, Herrera-Estrella A, Selem Mojica N, Rosales-Rivera M, Gómez-Gil B, Salas-Lais AG, Santacruz-Tinoco CE, Montoya-Fuentes H, Alvarado-Yaah JE, Molina-Salinas GM, Espinoza-Ayala GE, Enciso-Moreno JA, Gutiérrez-Ríos RM, Loza A, Moreno-Contreras J, García-López R, Rivera-Gutierrez X, Comas-García A, Wong-Chew RM, Jiménez-Corona ME, del Angel RM, Vazquez-Perez JA, Matías-Florentino M, Pérez-García M, Ávila-Ríos S, Castelán-Sánchez HG, Delaye L, Martínez-Castilla LP, Escalera-Zamudio M, López S, Arias CF. The Alpha Variant (B.1.1.7) of SARS-CoV-2 Failed to Become Dominant in Mexico. Microbiol Spectr 2022; 10:e0224021. [PMID: 35389245 PMCID: PMC9045257 DOI: 10.1128/spectrum.02240-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/17/2022] [Indexed: 12/26/2022] Open
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, the emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in the United Kingdom in September 2020, was well documented in different areas of the world and became a global public health concern because of its increased transmissibility. The B.1.1.7 lineage was first detected in Mexico during December 2020, showing a slow progressive increase in its circulation frequency, which reached its maximum in May 2021 but never became predominant. In this work, we analyzed the patterns of diversity and distribution of this lineage in Mexico using phylogenetic and haplotype network analyses. Despite the reported increase in transmissibility of the B.1.1.7 lineage, in most Mexican states, it did not displace cocirculating lineages, such as B.1.1.519, which dominated the country from February to May 2021. Our results show that the states with the highest prevalence of B.1.1.7 were those at the Mexico-U.S. border. An apparent pattern of dispersion of this lineage from the northern states of Mexico toward the center or the southeast was observed in the largest transmission chains, indicating possible independent introduction events from the United States. However, other entry points cannot be excluded, as shown by multiple introduction events. Local transmission led to a few successful haplotypes with a localized distribution and specific mutations indicating sustained community transmission. IMPORTANCE The emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) throughout the world were due to its increased transmissibility. However, it did not displace cocirculating lineages in most of Mexico, particularly B.1.1.519, which dominated the country from February to May 2021. In this work, we analyzed the distribution of B.1.1.7 in Mexico using phylogenetic and haplotype network analyses. Our results show that the states with the highest prevalence of B.1.1.7 (around 30%) were those at the Mexico-U.S. border, which also exhibited the highest lineage diversity, indicating possible introduction events from the United States. Also, several haplotypes were identified with a localized distribution and specific mutations, indicating that sustained community transmission occurred in the country.
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Affiliation(s)
- Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Pavel Iša
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
| | - Nelly Selem Mojica
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia, México
| | - Mauricio Rosales-Rivera
- Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Unidad Mazatlám, Mazatlán, México
| | - Angel Gustavo Salas-Lais
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | - Héctor Montoya-Fuentes
- Centro de Investigación Biomedica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, México
| | - Julio Elias Alvarado-Yaah
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | | | - José Antonio Enciso-Moreno
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas, Zacatecas, México
| | - Rosa María Gutiérrez-Ríos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Antonio Loza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Joaquín Moreno-Contreras
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Xaira Rivera-Gutierrez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Andreu Comas-García
- Facultad de Medicna y Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Rosa María Wong-Chew
- Facultad de Medicina, Laboratorio de Investigación en Enfermedades Infecciosas, División de Investigación, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Rosa María del Angel
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav, Ciudad de México, México
| | - Joel Armando Vazquez-Perez
- Laboratorio de Biología Molecular de Enfermedades Emergentes y EPOC Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Marissa Pérez-García
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Hugo G. Castelán-Sánchez
- Programa de Investigadoras e investigadores por México Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Luis Delaye
- Departamento de Ingeniería Genética, Cinvestav Unidad Irapuato, Guanajuato, México
| | - León P. Martínez-Castilla
- Programa de Investigadoras e investigadores por México Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México, México
| | | | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
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4
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García-Morales C, Tapia-Trejo D, Matías-Florentino M, Quiroz-Morales VS, Dávila-Conn V, Beristain-Barreda Á, Cárdenas-Sandoval M, Becerril-Rodríguez M, Iracheta-Hernández P, Macías-González I, García-Mendiola R, Guzmán-Carmona A, Zarza-Sánchez E, Cruz RA, González-Rodríguez A, Reyes-Terán G, Ávila-Ríos S. HIV Pretreatment Drug Resistance Trends in Mexico City, 2017-2020. Pathogens 2021; 10:1587. [PMID: 34959542 PMCID: PMC8708254 DOI: 10.3390/pathogens10121587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 11/19/2022] Open
Abstract
In response to increasing pretreatment drug resistance (PDR), Mexico changed its national antiretroviral treatment (ART) policy, recommending and procuring second-generation integrase strand-transfer inhibitor (INSTI)-based regimens as preferred first-line options since 2019. We present a four-year observational study describing PDR trends across 2017-2020 at the largest HIV diagnosis and primary care center in Mexico City. A total of 6688 baseline protease-reverse transcriptase and 6709 integrase sequences were included. PDR to any drug class was 14.4% (95% CI, 13.6-15.3%). A significant increasing trend for efavirenz/nevirapine PDR was observed (10.3 to 13.6%, p = 0.02). No increase in PDR to second-generation INSTI was observed, remaining under 0.3% across the study period. PDR was strongly associated with prior exposure to ART (aOR: 2.9, 95% CI: 1.9-4.6, p < 0.0001). MSM had higher odds of PDR to efavirenz/nevirapine (aOR: 2.0, 95% CI: 1.0-3.7, p = 0.04), reflecting ongoing transmission of mutations such as K103NS and E138A. ART restarters showed higher representation of cisgender women and injectable drug users, higher age, and lower education level. PDR to dolutegravir/bictegravir remained low in Mexico City, although further surveillance is warranted given the short time of ART optimization. Our study identifies demographic characteristics of groups with higher risk of PDR and lost to follow-up, which may be useful to design differentiated interventions locally.
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Affiliation(s)
- Claudia García-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Daniela Tapia-Trejo
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Margarita Matías-Florentino
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Verónica Sonia Quiroz-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Vanessa Dávila-Conn
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Ángeles Beristain-Barreda
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Miroslava Cárdenas-Sandoval
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Manuel Becerril-Rodríguez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Patricia Iracheta-Hernández
- Condesa Specialised Clinic, General Benjamín Hill 24, Colonia Condesa, Mexico City 06140, Mexico; (P.I.-H.); (I.M.-G.); (A.G.-R.)
| | - Israel Macías-González
- Condesa Specialised Clinic, General Benjamín Hill 24, Colonia Condesa, Mexico City 06140, Mexico; (P.I.-H.); (I.M.-G.); (A.G.-R.)
| | - Rebecca García-Mendiola
- Condesa Iztapalapa Specialised Clinic, Combate de Celaya s/n, Colonia Unidad Habitacional Vicente Guerrero, Mexico City 09730, Mexico; (R.G.-M.); (A.G.-C.); (R.A.C.)
| | - Alejandro Guzmán-Carmona
- Condesa Iztapalapa Specialised Clinic, Combate de Celaya s/n, Colonia Unidad Habitacional Vicente Guerrero, Mexico City 09730, Mexico; (R.G.-M.); (A.G.-C.); (R.A.C.)
| | - Eduardo Zarza-Sánchez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
| | - Raúl Adrián Cruz
- Condesa Iztapalapa Specialised Clinic, Combate de Celaya s/n, Colonia Unidad Habitacional Vicente Guerrero, Mexico City 09730, Mexico; (R.G.-M.); (A.G.-C.); (R.A.C.)
| | - Andrea González-Rodríguez
- Condesa Specialised Clinic, General Benjamín Hill 24, Colonia Condesa, Mexico City 06140, Mexico; (P.I.-H.); (I.M.-G.); (A.G.-R.)
| | - Gustavo Reyes-Terán
- Coordinating Commission of the National Institutes of Health and High Specialty Hospitals, Periférico Sur 4809, Colonia Arenal de Tepepan, Mexico City 14610, Mexico;
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, Mexico City 14080, Mexico; (C.G.-M.); (D.T.-T.); (M.M.-F.); (V.S.Q.-M.); (V.D.-C.); (Á.B.-B.); (M.C.-S.); (M.B.-R.); (E.Z.-S.)
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5
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Taboada B, Zárate S, Iša P, Boukadida C, Vazquez-Perez JA, Muñoz-Medina JE, Ramírez-González JE, Comas-García A, Grajales-Muñiz C, Rincón-Rubio A, Matías-Florentino M, Sanchez-Flores A, Mendieta-Condado E, Verleyen J, Barrera-Badillo G, Hernández-Rivas L, Mejía-Nepomuceno F, Martínez-Orozco JA, Becerril-Vargas E, López S, López-Martínez I, Ávila-Ríos S, Arias CF. Genetic Analysis of SARS-CoV-2 Variants in Mexico during the First Year of the COVID-19 Pandemic. Viruses 2021; 13:2161. [PMID: 34834967 PMCID: PMC8622467 DOI: 10.3390/v13112161] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/09/2021] [Accepted: 10/19/2021] [Indexed: 12/21/2022] Open
Abstract
During the first year of the SARS-CoV-2 pandemic in Mexico, more than two million people were infected. In this study, we analyzed full genome sequences from 27 February 2020 to 28 February 2021 to characterize the geographical and temporal distribution of SARS-CoV-2 lineages and identify the most common circulating lineages during this period. We defined six different geographical regions with particular dynamics of lineage circulation. The Northeast and Northwest regions were the ones that exhibited the highest lineage diversity, while the Central south and South/Southeast regions presented less diversity with predominance of a certain lineage. Additionally, by late February 2021, lineage B.1.1.519 represented more than 89% of all circulating lineages in the country.
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Affiliation(s)
- Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (B.T.); (P.I.); (S.L.)
| | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico;
| | - Pavel Iša
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (B.T.); (P.I.); (S.L.)
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (C.B.); (A.R.-R.); (M.M.-F.); (S.Á.-R.)
| | - Joel Armando Vazquez-Perez
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.V.-P.); (F.M.-N.); (J.A.M.-O.); (E.B.-V.)
| | - José Esteban Muñoz-Medina
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico;
| | - José Ernesto Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City 01480, Mexico; (J.E.R.-G.); (E.M.-C.); (G.B.-B.); (L.H.-R.); (I.L.-M.)
| | - Andreu Comas-García
- Facultad de Medicina y Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78120, Mexico;
| | - Concepción Grajales-Muñiz
- Coordinación de Control Técnico de Insumos, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico;
| | - Alma Rincón-Rubio
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (C.B.); (A.R.-R.); (M.M.-F.); (S.Á.-R.)
| | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (C.B.); (A.R.-R.); (M.M.-F.); (S.Á.-R.)
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (A.S.-F.); (J.V.)
| | - Edgar Mendieta-Condado
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City 01480, Mexico; (J.E.R.-G.); (E.M.-C.); (G.B.-B.); (L.H.-R.); (I.L.-M.)
| | - Jerome Verleyen
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (A.S.-F.); (J.V.)
| | - Gisela Barrera-Badillo
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City 01480, Mexico; (J.E.R.-G.); (E.M.-C.); (G.B.-B.); (L.H.-R.); (I.L.-M.)
| | - Lucía Hernández-Rivas
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City 01480, Mexico; (J.E.R.-G.); (E.M.-C.); (G.B.-B.); (L.H.-R.); (I.L.-M.)
| | - Fidencio Mejía-Nepomuceno
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.V.-P.); (F.M.-N.); (J.A.M.-O.); (E.B.-V.)
| | - José Arturo Martínez-Orozco
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.V.-P.); (F.M.-N.); (J.A.M.-O.); (E.B.-V.)
| | - Eduardo Becerril-Vargas
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.V.-P.); (F.M.-N.); (J.A.M.-O.); (E.B.-V.)
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (B.T.); (P.I.); (S.L.)
| | - Irma López-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City 01480, Mexico; (J.E.R.-G.); (E.M.-C.); (G.B.-B.); (L.H.-R.); (I.L.-M.)
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (C.B.); (A.R.-R.); (M.M.-F.); (S.Á.-R.)
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (B.T.); (P.I.); (S.L.)
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Rodríguez-Maldonado AP, Vázquez-Pérez JA, Cedro-Tanda A, Taboada B, Boukadida C, Wong-Arámbula C, Nuñez-García TE, Cruz-Ortiz N, Barrera-Badillo G, Hernández-Rivas L, López-Martínez I, Mendoza-Vargas A, Reyes-Grajeda JP, Alcaraz N, Peñaloza-Figueroa F, Gonzalez-Barrera D, Rangel-DeLeon D, Herrera-Montalvo LA, Mejía-Nepomuceno F, Hernández-Terán A, Mújica-Sánchez M, Becerril-Vargas E, Martínez-Orozco JA, Pérez-Padilla R, Salas-Hernández J, Sanchez-Flores A, Isa P, Matías-Florentino M, Ávila-Ríos S, Muñoz-Medina JE, Grajales-Muñiz C, Salas-Lais AG, Santos Coy-Arechavaleta A, Hidalgo-Miranda A, Arias CF, Ramírez-González JE. Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. Arch Virol 2021; 166:3173-3177. [PMID: 34448936 PMCID: PMC8390838 DOI: 10.1007/s00705-021-05208-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/27/2021] [Indexed: 11/28/2022]
Abstract
SARS-CoV-2 variants emerged in late 2020, and at least three variants of concern (B.1.1.7, B.1.351, and P1) have been reported by WHO. These variants have several substitutions in the spike protein that affect receptor binding; they exhibit increased transmissibility and may be associated with reduced vaccine effectiveness. In the present work, we report the identification of a potential variant of interest, harboring the mutations T478K, P681H, and T732A in the spike protein, within the newly named lineage B.1.1.519, that rapidly outcompeted the preexisting variants in Mexico and has been the dominant virus in the country during the first trimester of 2021.
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Affiliation(s)
- Abril Paulina Rodríguez-Maldonado
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | | | | | - Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico
| | - Claudia Wong-Arámbula
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Tatiana Ernestina Nuñez-García
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Natividad Cruz-Ortiz
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Gisela Barrera-Badillo
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Lucía Hernández-Rivas
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Irma López-Martínez
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | | | | | - Nicolas Alcaraz
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | | | | | | | | | | | | | | | | | | | | | - Alejandro Sanchez-Flores
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Pavel Isa
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico
| | | | | | | | | | | | - Carlos F Arias
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico.
| | - José Ernesto Ramírez-González
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico.
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Matías-Florentino M, Chaillon A, Ávila-Ríos S, Mehta SR, Paz-Juárez HE, Becerril-Rodríguez MA, del Arenal-Sánchez SJ, Piñeirúa-Menéndez A, Ruiz V, Iracheta-Hernández P, Macías-González I, Tena-Sánchez J, Badial-Hernández F, González-Rodríguez A, Reyes-Terán G. Pretreatment HIV drug resistance spread within transmission clusters in Mexico City. J Antimicrob Chemother 2020; 75:656-667. [PMID: 31819984 PMCID: PMC7021100 DOI: 10.1093/jac/dkz502] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/28/2019] [Accepted: 11/05/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Pretreatment HIV drug resistance (HIVDR) to NNRTIs has consistently increased in Mexico City during the last decade. OBJECTIVES To infer the HIV genetic transmission network in Mexico City to describe the dynamics of the local HIV epidemic and spread of HIVDR. PATIENTS AND METHODS HIV pol sequences were obtained by next-generation sequencing from 2447 individuals before initiation of ART at the largest HIV clinic in Mexico City (April 2016 to June 2018). Pretreatment HIVDR was estimated using the Stanford algorithm at a Sanger-like threshold (≥20%). Genetic networks were inferred with HIV-TRACE, establishing putative transmission links with genetic distances <1.5%. We examined demographic associations among linked individuals with shared drug resistance mutations (DRMs) using a ≥ 2% threshold to include low-frequency variants. RESULTS Pretreatment HIVDR reached 14.8% (95% CI 13.4%-16.2%) in the cohort overall and 9.6% (8.5%-10.8%) to NNRTIs. Putative links with at least one other sequence were found for 963/2447 (39%) sequences, forming 326 clusters (2-20 individuals). The inferred network was assortative by age and municipality (P < 0.001). Clustering individuals were younger [adjusted OR (aOR) per year = 0.96, 95% CI 0.95-0.97, P < 0.001] and less likely to include women (aOR = 0.46, 95% CI 0.28-0.75, P = 0.002). Among clustering individuals, 175/963 (18%) shared DRMs (involving 66 clusters), of which 66/175 (38%) shared K103N/S (24 clusters). Eight municipalities (out of 75) harboured 65% of persons sharing DRMs. Among all persons sharing DRMs, those sharing K103N were younger (aOR = 0.93, 95% CI 0.88-0.98, P = 0.003). CONCLUSIONS Our analyses suggest age- and geographically associated transmission of DRMs within the HIV genetic network in Mexico City, warranting continuous monitoring and focused interventions.
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Affiliation(s)
- Margarita Matías-Florentino
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Antoine Chaillon
- University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Sanjay R Mehta
- University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA
| | - Héctor E Paz-Juárez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Manuel A Becerril-Rodríguez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Silvia J del Arenal-Sánchez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Alicia Piñeirúa-Menéndez
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Verónica Ruiz
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Patricia Iracheta-Hernández
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Israel Macías-González
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Jehovani Tena-Sánchez
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Florentino Badial-Hernández
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Andrea González-Rodríguez
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
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Cortés-Rubio CN, Salgado-Montes de Oca G, Prado-Galbarro FJ, Matías-Florentino M, Murakami-Ogasawara A, Kuri-Cervantes L, Carranco-Arenas AP, Ormsby CE, Cortés-Rubio IK, Reyes-Terán G, Ávila-Ríos S. Longitudinal variation in human immunodeficiency virus long terminal repeat methylation in individuals on suppressive antiretroviral therapy. Clin Epigenetics 2019; 11:134. [PMID: 31519219 PMCID: PMC6743183 DOI: 10.1186/s13148-019-0735-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/30/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Persistence of latent, replication-competent provirus in CD4+ T cells of human immunodeficiency virus (HIV)-infected individuals on antiretroviral treatment (ART) is the main obstacle for virus eradication. Methylation of the proviral 5' long terminal repeat (LTR) promoter region has been proposed as a possible mechanism contributing to HIV latency; however, conflicting observations exist regarding its relevance. We assessed 5'-LTR methylation profiles in total CD4+ T cells from blood of 12 participants on short-term ART (30 months) followed up for 2 years, and a cross-sectional group of participants with long-term ART (6-15 years), using next generation sequencing. We then looked for associations between specific 5'-LTR methylation patterns and baseline and follow-up clinical characteristics. RESULTS 5'-LTR methylation was observed in all participants and behaved dynamically. The number of 5'-LTR variants found per sample ranged from 1 to 13, with median sequencing depth of 16270× (IQR 4107×-46760×). An overall significant 5'-LTR methylation increase was observed at month 42 compared to month 30 (median CpG Methylation Index: 74.7% vs. 0%, p = 0.025). This methylation increase was evident in a subset of participants (methylation increase group), while the rest maintained fairly high and constant methylation (constant methylation group). Persons in the methylation increase group were younger, had higher CD4+ T cell gain, larger CD8% decrease, and larger CD4/CD8 ratio change after 48 months on ART (all p < 0.001). Using principal component analysis, the constant methylation and methylation increase groups showed low evidence of separation along time (factor 2: p = 0.04). Variance was largely explained (21%) by age, CD4+/CD8+ T cell change, and CD4+ T cell subpopulation proportions. Persons with long-term ART showed overall high methylation (median CpG Methylation Index: 78%; IQR 71-87%). No differences were observed in residual plasma viral load or proviral load comparing individuals on short-term (both at 30 or 42 months) and long-term ART. CONCLUSIONS Our study shows evidence that HIV 5'-LTR methylation in total CD4+ T cells is dynamic along time and that it can follow different temporal patterns that are associated with a combination of baseline and follow-up clinical characteristics. These observations may account for differences observed between previous contrasting studies.
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Affiliation(s)
- César N. Cortés-Rubio
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Gonzalo Salgado-Montes de Oca
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | | | - Margarita Matías-Florentino
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Akio Murakami-Ogasawara
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Leticia Kuri-Cervantes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Ana P. Carranco-Arenas
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Christopher E. Ormsby
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | | | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Tlalpan 4502, 14080 Mexico City, Mexico
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9
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Ávila-Ríos S, García-Morales C, Matías-Florentino M, Romero-Mora KA, Tapia-Trejo D, Quiroz-Morales VS, Reyes-Gopar H, Ji H, Sandstrom P, Casillas-Rodríguez J, Sierra-Madero J, León-Juárez EA, Valenzuela-Lara M, Magis-Rodríguez C, Uribe-Zuñiga P, Reyes-Terán G. Pretreatment HIV-drug resistance in Mexico and its impact on the effectiveness of first-line antiretroviral therapy: a nationally representative 2015 WHO survey. Lancet HIV 2016; 3:e579-e591. [PMID: 27658867 DOI: 10.1016/s2352-3018(16)30119-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/10/2016] [Accepted: 08/04/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND WHO has developed a global HIV-drug resistance surveillance strategy, including assessment of pretreatment HIV-drug resistance. We aimed to do a nationally representative survey of pretreatment HIV-drug resistance in Mexico using WHO-recommended methods. METHODS Among 161 Ministry of Health antiretroviral therapy (ART) clinics in Mexico, the largest, including 90% of ART initiators within the Ministry of Health (66 in total), were eligible for the survey. We used a probability-proportional-to-size design method to sample 25 clinics throughout the country. Consecutive ART-naive patients with HIV about to initiate treatment were invited to participate in the survey; individuals with previous exposure to ART were excluded. We assessed pretreatment HIV-drug resistance by Sanger sequencing and next-generation sequencing of viruses from plasma specimens from eligible participants with Stanford University HIV Drug Resistance Database methods. We obtained follow-up data for a median of 9·4 months (range 6-12) after enrolment. We investigated possible relations between demographic variables and pretreatment drug resistance with univariate and multivariate logistic regression. FINDINGS Between Feb 3 and July 30, 2015, we screened 288 patients in 25 clinics, from whom 264 provided successfully sequenced viruses with no evidence of current exposure to antiretroviral drugs. With the Sanger method, of these 264 participants, 41 (15·5%, 95% CI 11·4-20·5) had pretreatment resistance to any antiretroviral drug and 28 (10·6%, 7·2-15·0) had pretreatment resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs). At least low-level pretreatment resistance (Stanford penalty score ≥15) was noted in 13 (4 · 9%) of participants to efavirenz and in 23 (8·7%) to the combination tenofovir plus emtricitabine plus efavirenz. With next-generation sequencing, of 264 participants, 38 (14·4%, 95% CI 10·4-19·2) had pretreatment resistance to any antiretroviral drug and 26 (9·8%, 6·5-14·1) had pretreatment resistance to NNRTIs. After median follow-up of 8 months (IQR 6·5-9·4, range 5-11) after ART initiation, 97 (72%) of 135 NNRTI initiators achieved viral suppression (<50 copies per mL) compared with ten (40%) of 25 individuals who started with protease inhibitor-based regimens (p=0·0045). After multivariate regression considering pretreatment resistance and initial ART regimen as composite variables, people starting NNRTIs with pretreatment drug resistance achieved significantly lower viral suppression (odds ratio 0·24, 95% CI 0·07-0·74; p=0·014) than patients without NNRTI resistance. INTERPRETATION High levels of pretreatment drug resistance were noted in Mexico, and NNRTI pretreatment drug resistance significantly reduced the effectiveness of first-line ART regimens based on these drugs. Baseline HIV-drug resistance testing for initial ART follow-up and decision making should be considered. FUNDING The Mexican Government and Consejo Nacional de Ciencia y Tecnología.
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Affiliation(s)
- Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Claudia García-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Margarita Matías-Florentino
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Karla A Romero-Mora
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Daniela Tapia-Trejo
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Verónica S Quiroz-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Helena Reyes-Gopar
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico
| | - Hezhao Ji
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB, Canada
| | | | - Juan Sierra-Madero
- National Institute of Medical Sciences and Nutrition Salvador Zubirán, Colonia Sección XVI, Mexico City, Mexico
| | - Eddie A León-Juárez
- National Centre for HIV/AIDS Prevention and Control, Colonia Anzures, Mexico City, Mexico
| | | | - Carlos Magis-Rodríguez
- National Centre for HIV/AIDS Prevention and Control, Colonia Anzures, Mexico City, Mexico
| | - Patricia Uribe-Zuñiga
- National Centre for HIV/AIDS Prevention and Control, Colonia Anzures, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Mexico City, Mexico.
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Mejía-López H, Santacruz-Valdés C, Matías-Florentino M. [Genetic characterization of adenovirus isolated from follicular conjunctivitis and epidemic keratoconjunctivitis in a group of Mexican patients]. Arch Soc Esp Oftalmol 2008; 83:161-7. [PMID: 18311674 DOI: 10.4321/s0365-66912008000300006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To determine the adenovirus serotype in Mexican patients with folicular conjunctivitis and keratoconjunctivitis. METHODS Adenovirus-specific PCR was used to analyze sample scrapings from the inferior fornix of patients with follicular conjunctivitis and clinical suspicion of adenovirus from January 2005 to December 2006. Identification of the serotype was made by automated sequencing. The nucleotide sequences obtained were compared with the reported sequences in GenBank. Descriptive statistical analyses were performed on the results. RESULTS Of the 77 samples with clinical data of follicular conjunctivitis that were analyzed, 43 (56%) presented adenovirus. The sequencing of each positive sample allowed the identification of Ad1, Ad2, Ad3 and Ad8; the sequences of the serotype were identical those reported in GenBank with accession numbers: AF 534906 and AY 224420 for a sequence of the gene coding for the filament of Ad1 and Ad2 respectively, and AY 854180 and DQ 149614 for a sequence of the gene that codes for the Hexon protein of Ad3 and Ad8 respectively. From the statistical analysis it was possible to determine that a preferential seasonality of the serotype does not exist. CONCLUSION In this work the Ad1, Ad2 and Ad3 serotypes were identified in patients with clinical diagnosis of follicular conjunctivitis in 2005. Ad2 was the predominant serotype. Ad8 was also detected in an outbreak of epidemic keratoconjunctivitis. From an epidemiological point of view, no serotype found seems to have a preferred seasonality.
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Affiliation(s)
- H Mejía-López
- Instituto de Oftalmología Conde de Valenciana, Unidad de Investigación, México DF, Mexico.
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Mejía-López H, Matías-Florentino M, Vélez-Montoya R. [Identification of adenovirus associated with conjunctivitis by molecular methodology]. Arch Soc Esp Oftalmol 2006; 81:375-82. [PMID: 16888690 DOI: 10.4321/s0365-66912006000700005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To identify adenovirus in patients with conjunctivitis by molecular methods such as the Polymerase Chain Reaction (PCR) and DNA sequencing. METHODS Samples of scrapings from the inferior fornix of 51 patients (39 diagnosed with Follicular Conjunctivitis and 12 diagnosed with Vernal Conjunctivitis) were processed by generic PCR to identify adenovirus. All the samples that were PCR positive were cultured on VERO cells for virus isolation, with this being demonstrated by immunofluorescence. For the identification of the isolated serotype, the multiplex PCR was utilized and DNA automated sequencing was employed to identify the genetic variants. RESULTS Twenty-eight of the individuals diagnosed with Follicular Conjunctivitis and six of those diagnosed with Vernal Conjunctivitis, had positive results to adenovirus (67%). The cultures in VERO cells allowed the isolation of eight samples. Only three of the isolated viruses (one Ad1 and two Ad2) were identified by the multiplex PCR used to identify the subgenus C adenovirus. An Ad1 genetic variant was identified by automated sequencing while the Ad2 serotypes were identical to the ones reported by Genbank. CONCLUSIONS The Polymerase Chain Reaction and DNA sequencing are useful tools to identify and characterize microorganisms responsible for diseases such as conjunctivitis caused by adenoviruses.
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Affiliation(s)
- H Mejía-López
- Instituto de Oftalmología Conde de Valenciana, Unidad de Investigación, México D.F., México
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