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Moros ZC, Zambrano JL, Sulbaran Y, Loureiro CL, Marulanda E, Bracho F, D'Angelo P, Rodríguez L, Liprandi F, Rangel HR, Jaspe RC, Pujol FH. Dissemination of the Omicron Variant and Its Sub-Lineages among Residents and Travelers in Its First Year of Emergence in Venezuela. Viruses 2023; 15:1460. [PMID: 37515148 PMCID: PMC10385433 DOI: 10.3390/v15071460] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/13/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
The emergence of the SARS-CoV-2 Variant of Concern (VOC), Omicron, has been characterized by an explosive number of cases in almost every part of the world. The dissemination of different sub-lineages and recombinant genomes also led to several posterior waves in many countries. The circulation of this VOC and its major sub-lineages (BA.1 to BA.5) was monitored in community cases and in international travelers returning to Venezuela by a rapid partial sequencing method. The specific sub-lineage assignment was performed by complete genome sequencing. Epidemic waves of SARS-CoV-2 cases were observed among international travelers during 2022, a situation not seen before December 2021. The succession of the Omicron VOC sub-lineages BA.1 to BA.5 occurred sequentially, except for BA.3, which was almost not detected. However, the sub-lineages generally circulated two months earlier in international travelers than in community cases. The diversity of Omicron sub-lineages found in international travelers was related to the one found in the USA, consistent with the most frequent destination of international travel from Venezuela this year. These differences are compatible with the delay observed sometimes in Latin American countries in the circulation of the different lineages of the Omicron VOC. Once the sub-lineages were introduced in the country, community transmission was responsible for generating a characteristic distribution of them, with a predominance of sub-lineages not necessarily similar to the one observed in travelers or neighboring countries.
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Affiliation(s)
- Zoila C Moros
- Laboratorio de Virología Celular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
| | - José Luis Zambrano
- Laboratorio de Virología Celular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
| | - Yoneira Sulbaran
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
| | - Carmen L Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
| | | | - Francis Bracho
- Laboratorio de Biología Molecular CasaLab 2020, Caracas 1052, Venezuela
| | - Pierina D'Angelo
- Dirección de Diagnóstico y Vigilancia Epidemiológica, Instituto Nacional de Higiene "Rafael Rangel", Caracas 1053, Venezuela
| | - Lieska Rodríguez
- Dirección de Diagnóstico y Vigilancia Epidemiológica, Instituto Nacional de Higiene "Rafael Rangel", Caracas 1053, Venezuela
| | - Ferdinando Liprandi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
| | - Héctor R Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
| | - Rossana C Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
| | - Flor H Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
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D’Angelo P, Loureiro CL, Jaspe RC, Sulbaran YF, Rodríguez L, Alarcón V, García JM, Zambrano JL, Liprandi F, Rangel HR, Pujol FH. First Case of Monkeypox in Venezuela: Partial Complete Genome Sequence Allowed Its Grouping into the West African Clade II. Trop Med Infect Dis 2022; 8:tropicalmed8010002. [PMID: 36668909 PMCID: PMC9864145 DOI: 10.3390/tropicalmed8010002] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 12/24/2022] Open
Abstract
The ongoing epidemic of monkeypox virus (MPXV) infection has already reached more than 50,000 persons worldwide until the end of August 2022. We report the first case detected in Venezuela. The patient reported traveling from Spain and contact with friends tested positive for MPXV after his return. Partial complete genome phylogenetic analysis allowed to group the isolate within the clade II of MPXV, the major one circulating worldwide. No other case of MPXV has been detected until the end of August 2022 in the country, although the presence of undiagnosed cases due to the fear of stigmatization cannot be ruled out.
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Affiliation(s)
- Pierina D’Angelo
- Dirección de Diagnóstico y Vigilancia de Enfermedades Transmisibles, Instituto Nacional de Higiene “Rafael Rangel”, Caracas 1041, Venezuela
| | - Carmen L. Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
| | - Rossana C. Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
| | - Yoneira F. Sulbaran
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
| | - Lieska Rodríguez
- Dirección de Diagnóstico y Vigilancia de Enfermedades Transmisibles, Instituto Nacional de Higiene “Rafael Rangel”, Caracas 1041, Venezuela
| | - Víctor Alarcón
- Dirección de Diagnóstico y Vigilancia de Enfermedades Transmisibles, Instituto Nacional de Higiene “Rafael Rangel”, Caracas 1041, Venezuela
| | - José Manuel García
- Dirección General de Epidemiología, Ministerio del Poder Popular para la Salud, Caracas 1010, Venezuela
| | - José Luis Zambrano
- Laboratorio de Virología Celular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
| | - Ferdinando Liprandi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
| | - Héctor R. Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
| | - Flor H. Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela
- Correspondence: ; Tel.: +58-2125041623
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Jaspe RC, Sulbaran Y, Loureiro CL, Moros ZC, Marulanda E, Bracho F, Ramírez NA, Canonico Y, D'Angelo P, Rodríguez L, Castro J, Liprandi F, Rangel HR, Pujol FH. Detection of the Omicron variant of SARS-CoV-2 in international travelers returning to Venezuela. Travel Med Infect Dis 2022; 48:102326. [PMID: 35395405 PMCID: PMC8982480 DOI: 10.1016/j.tmaid.2022.102326] [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: 02/10/2022] [Revised: 03/31/2022] [Accepted: 04/02/2022] [Indexed: 12/02/2022]
Abstract
Background By the end of 2021, the SARS-CoV-2 Variant of Concern (VOC) Delta was predominant in most of the world. At the end of November, the Omicron variant was first detected in South Africa. This variant was immediately classified as VOC, due to the explosive increase of cases in South Africa, and the great number of mutations exhibited by this new lineage. Since then, Omicron VOC displaced Delta one in almost every country. Venezuela implemented in May 2021 molecular testing of all the passengers arriving at Venezuelan airports. Methods In this study, we analyzed the presence of variants of SARS-CoV-2 in those positive samples, by sequencing a small fragment of the Spike genomic region. Results The Omicron variant was found in passengers arriving to Venezuela from the beginning of December. Complete genome analysis confirmed the presence of the Omicron VOC. The detection of this VOC coincided with an unprecedented increase in the frequency of passengers with positive nucleic acid testing. Conclusions Genomic surveillance of samples for international travelers returning to Venezuela allowed us to rapidly detect the introduction of the Omicron variant in the country.
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Affiliation(s)
- Rossana C Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Yoneira Sulbaran
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Carmen L Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Zoila C Moros
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | | | - Francis Bracho
- Laboratorio de Biología Molecular Casa Lab 2020, Caracas, Venezuela
| | - Nieves A Ramírez
- Laboratorio de Biología Molecular Tu Buen Doctor, Caracas, Venezuela
| | - Yeilis Canonico
- Laboratorio de Biología Molecular Tu Buen Doctor, Caracas, Venezuela
| | - Pierina D'Angelo
- Instituto Nacional de Higiene "Rafael Rangel", Caracas, Miranda, Venezuela
| | - Lieska Rodríguez
- Instituto Nacional de Higiene "Rafael Rangel", Caracas, Miranda, Venezuela
| | | | - Ferdinando Liprandi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Héctor R Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Flor H Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela.
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Jaspe RC, Zambrano JL, Hidalgo M, Sulbarán Y, Loureiro CL, Moros ZC, Garzaro DJ, Liprandi F, Rangel HR, Pujol FH. Detection of the Omicron variant of SARS-CoV-2 by restriction analysis targeting the mutations K417N and N440K of the spike protein. Investigación Clínica 2022. [DOI: 10.54817/ic.v63n1a08] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
By the end of 2021, the Omicron variant of concern (VOC) emerges in South Africa. This variant caused immediate concern, due to the explosive increase in cases associated with it and the large number of mutations it exhibits. In this study, the restriction sites that allow detecting the mutations K417N and N440K in the Spike gene are described. This analysis allows us to propose a rapid method for the identification of cases infected with the Omicron variant. We show that the proposed methodology can contribute to provide more information on the prevalence and rapid detection of cases of this new VOC.
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Affiliation(s)
- Rossana C Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - José Luis Zambrano
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Mariana Hidalgo
- Laboratorio de Inmunoparasitología, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Yoneira Sulbarán
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Carmen L Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Zoila C Moros
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Domingo J Garzaro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Ferdinando Liprandi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Héctor R Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Flor H Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
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Jaspe RC, Loureiro CL, Sulbaran Y, Moros ZC, D'Angelo P, Rodríguez L, Zambrano JL, Hidalgo M, Vizzi E, Alarcón V, Aguilar M, Garzaro DJ, Rangel HR, Pujol FH. Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Infect Genet Evol 2021; 96:105147. [PMID: 34800714 PMCID: PMC8596652 DOI: 10.1016/j.meegid.2021.105147] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/22/2021] [Accepted: 11/15/2021] [Indexed: 12/24/2022]
Abstract
In less than two years since SARS-CoV-2 emerged, the new coronavirus responsible for COVID-19, has accumulated a great number of mutations. Many of these mutations are located in the Spike protein and some of them confer to the virus higher transmissibility or partial resistance to antibody mediated neutralization. Viral variants with such confirmed abilities are designated by WHO as Variants of Concern (VOCs). The aim of this study was to monitor the introduction of variants and VOCs in Venezuela. A small fragment of the viral genome was sequenced for the detection of the most relevant mutations found in VOCs. This approach allowed the detection of Gamma VOC. Its presence was confirmed by complete genome sequencing. The Gamma VOC was detected in Venezuela since January 2021, and in March 2021 was predominant in the East and Central side of the country, representing more than 95% of cases sequenced in all the country in April–May 2021. In addition to the Gamma VOC, other isolates carrying the mutation E484K were also detected. The frequency of this mutation has been increasing worldwide, as shown in a survey of sequences carrying E484K mutation in GISAID, and was detected in Venezuela in many probable cases of reinfection. Complete genome sequencing of these cases allowed us to identify E484K mutation in association with Gamma VOC and other lineages. In conclusion, the strategy adopted in this study is suitable for genomic surveillance of variants for countries lacking robust genome sequencing capacities. In the period studied, Gamma VOC seems to have rapidly become the dominant variant throughout the country.
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Affiliation(s)
- Rossana C Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Carmen L Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Yoneira Sulbaran
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Zoila C Moros
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Pierina D'Angelo
- Instituto Nacional de Higiene "Rafael Rangel", Caracas, Miranda, Venezuela
| | - Lieska Rodríguez
- Instituto Nacional de Higiene "Rafael Rangel", Caracas, Miranda, Venezuela
| | - José Luis Zambrano
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Mariana Hidalgo
- Laboratorio de Inmunoparasitología, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Esmeralda Vizzi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Víctor Alarcón
- Instituto Nacional de Higiene "Rafael Rangel", Caracas, Miranda, Venezuela
| | - Marwan Aguilar
- Instituto Nacional de Higiene "Rafael Rangel", Caracas, Miranda, Venezuela
| | - Domingo J Garzaro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | | | - Héctor R Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Flor H Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela.
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Loureiro CL, Jaspe RC, D´Angelo P, Zambrano JL, Rodriguez L, Alarcon V, Delgado M, Aguilar M, Garzaro D, Rangel HR, Pujol FH. SARS-CoV-2 genetic diversity in Venezuela: Predominance of D614G variants and analysis of one outbreak. PLoS One 2021; 16:e0247196. [PMID: 33606828 PMCID: PMC7895374 DOI: 10.1371/journal.pone.0247196] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 10/10/2020] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
SARS-CoV-2 is the new coronavirus responsible for COVID-19 disease. The first two cases of COVID-19 were detected in Venezuela on March 13, 2020. The aim of this study was the genetic characterization of Venezuelan SARS-CoV-2 isolates. A total of 7 full SARS-CoV-2 genome sequences were obtained by Sanger sequencing, from patients of different regions of Venezuela, mainly from the beginning of the epidemic. Ten out of 11 isolates (6 complete genomes and 4 partial spike genomic regions) belonged to lineage B, bearing the D614G mutation in the Spike protein. Isolates from the first outbreak that occurred in the Margarita Island harbored an in-frame deletion in its sequence, without amino acids 83–85 of the NSP1 of the ORF1. The search for deletions in 48,635 sequences showed that the NSP1 gene exhibit the highest frequency of deletions along the whole genome. Structural analysis suggests a change in the N-terminal domain with the presence of this deletion. In contrast, isolates circulating later in this island lacked the deletion, suggesting new introductions to the island after this first outbreak. In conclusion, a high diversity of SARS-CoV-2 isolates were found circulating in Venezuela, with predominance of the D614G mutation. The first small outbreak in Margarita Island seemed to be associated with a strain carrying a small deletion in the NSP1 protein, but these isolates do not seem to be responsible for the larger outbreak which started in July.
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Affiliation(s)
- Carmen L. Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Rossana C. Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Pierina D´Angelo
- Instituto Nacional de Higiene “Rafael Rangel”, Caracas, Miranda, Venezuela
| | - José L. Zambrano
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Lieska Rodriguez
- Instituto Nacional de Higiene “Rafael Rangel”, Caracas, Miranda, Venezuela
| | - Víctor Alarcon
- Instituto Nacional de Higiene “Rafael Rangel”, Caracas, Miranda, Venezuela
| | - Mariangel Delgado
- Unidad Unidad de Microscopia Electrónica y Confocal, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Marwan Aguilar
- Instituto Nacional de Higiene “Rafael Rangel”, Caracas, Miranda, Venezuela
| | - Domingo Garzaro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Héctor R. Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Flor H. Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
- * E-mail:
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Chemin I, Pujol FH, Scholtès C, Loureiro CL, Amirache F, Levrero M, Zoulim F, Pérez-Vargas J, Cosset FL. Preliminary Evidence for Hepatitis Delta Virus Exposure in Patients Who Are Apparently Not Infected With Hepatitis B Virus. Hepatology 2021; 73:861-864. [PMID: 32628280 PMCID: PMC7898870 DOI: 10.1002/hep.31453] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Isabelle Chemin
- Cancer Research Center of LyonUMR Inserm 1052 - CNRS 5286 mixte CLB - UCBL1LyonFrance
| | - Flor H Pujol
- Laboratorio de Virología MolecularCMBC, IVIC, Apdo 20632CaracasVenezuela
| | - Caroline Scholtès
- Cancer Research Center of LyonUMR Inserm 1052 - CNRS 5286 mixte CLB - UCBL1LyonFrance.,Laboratoire de VirologieGroupement Hospitalier NordInstitut des Agents Infectieux, CBN, Hospices Civil de LyonLyonFrance
| | - Carmen L Loureiro
- Laboratorio de Virología MolecularCMBC, IVIC, Apdo 20632CaracasVenezuela
| | - Fouzia Amirache
- CIRI, Centre International de Recherche en Infectiologie, Team EVIRUniv Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de LyonLyonFrance
| | - Massimo Levrero
- Cancer Research Center of LyonUMR Inserm 1052 - CNRS 5286 mixte CLB - UCBL1LyonFrance.,Department of HepatologyHôpital de la Croix RousseHospices Civil de LyonLyonFrance
| | - Fabien Zoulim
- Cancer Research Center of LyonUMR Inserm 1052 - CNRS 5286 mixte CLB - UCBL1LyonFrance.,Department of HepatologyHôpital de la Croix RousseHospices Civil de LyonLyonFrance
| | - Jimena Pérez-Vargas
- CIRI, Centre International de Recherche en Infectiologie, Team EVIRUniv Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de LyonLyonFrance
| | - François-Loïc Cosset
- CIRI, Centre International de Recherche en Infectiologie, Team EVIRUniv Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de LyonLyonFrance
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Jaspe RC, Loureiro CL, Chemin I, Pujol FH. Mutation pattern and methylation susceptibility of Hepatitis B virus American genotypes. Clin Res Hepatol Gastroenterol 2020; 44:973-976. [PMID: 32814675 DOI: 10.1016/j.clinre.2020.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 02/07/2023]
Affiliation(s)
- Rossana C Jaspe
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, 1020A Caracas, Venezuela
| | - Carmen L Loureiro
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, 1020A Caracas, Venezuela
| | - Isabelle Chemin
- INSERM U1052, CNRS 5286, Univ Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69000 Lyon, France
| | - Flor H Pujol
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, 1020A Caracas, Venezuela.
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Pujol F, Jaspe RC, Loureiro CL, Chemin I. Hepatitis B virus American genotypes: Pathogenic variants ? Clin Res Hepatol Gastroenterol 2020; 44:825-835. [PMID: 32553521 DOI: 10.1016/j.clinre.2020.04.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/19/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023]
Abstract
Hepatitis B virus (HBV) chronic infection is responsible for almost 900.000 deaths each year, due to cirrhosis or hepatocellular carcinoma (HCC). Ten HBV genotypes have been described (A-J). HBV genotype F and H circulate in America. HBV genotypes have been further classified in subgenotypes. There is a strong correlation between the genetic admixture of the American continent and the frequency of genotypes F or H: a high frequency of these genotypes is found in countries with a population with a higher ratio of Amerindian to African genetic admixture. The frequency of occult HBV infection in Amerindian communities from Latin America seems to be higher than the one found in other HBV-infected groups, but its association with American genotypes is unknown. There is growing evidence that some genotypes might be associated with a faster evolution to HCC. In particular, HBV genotype F has been implicated in a frequent and rapid progression to HCC. However, HBV genotype H has been associated to a less severe progression of disease. This study reviews the diversity and frequency of autochthonous HBV variants in the Americas and evaluates their association to severe progression of disease. Although no significant differences were found in the methylation pattern between different genotypes and subgenotypes of the American types, basal core promoter mutations might be more frequent in some subgenotypes, such as F1b and F2, than in other American subgenotypes or genotype H. F1b and probably F2 may be associated with a severe presentation of liver disease as opposed to a more benign course for subgenotype F4 and genotype H. Thus, preliminary evidence suggests that not all of the American variants are associated with a rapid progression to HCC.
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Affiliation(s)
- Flor Pujol
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, Caracas 1020A, Venezuela.
| | - Rossana C Jaspe
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, Caracas 1020A, Venezuela
| | - Carmen L Loureiro
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, Caracas 1020A, Venezuela
| | - Isabelle Chemin
- INSERM U1052, CNRS 5286, Université de Lyon, Université Claude Bernard Lyon 1, centre Léon Bérard, centre de recherche en cancérologie de Lyon, 69000, Lyon, France
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Loureiro CL, Jaspe RC, Pujol FH. Variation in Hepatitis C Virus Subtype Distribution during 20 Years in Venezuela. Intervirology 2019; 62:191-197. [PMID: 31865350 DOI: 10.1159/000505065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/24/2019] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Hepatitis C virus (HCV) infection is a public health problem and a major cause of chronic hepatitis. This virus exhibits a great genetic variability, with 8 genotypes and numerous subtypes. The aim of this study was to evaluate the fluctuations of HCV subtypes during 2 decades in Venezuela. METHODS HCV genotypes were determined by direct sequencing of the 5'-noncoding region in 392 isolates circulating in patients attended during the years 2014-2015. HCV subtype assignment was confirmed in a subset of samples (n = 24) by partial sequencing of the NS5B region. The genotype distribution was compared with the one observed in a previous study of patients followed up during the years 1994-1996 and 2005-2006. RESULTS Some variation was observed in the HCV genotype distribution over these 20 years. HCV genotype 1b prevalence was reduced significantly from 1994-1995 to 2004-2005, as previously described, and then remained constant. During the last 10 years, a significant decrease of HCV subtype 2b (36/237 in 2005-2006 vs. 24/392 in 2014-2015, p < 0.001) was observed. Patients infected with HCV G2acj were significantly older than the ones infected with G1 (53 vs. 47 years, p = 0.004), and male sex was significantly more prevalent among G3a-infected patients compared to the other ones (71 vs. 47%, p = 0.047). CONCLUSIONS Fluctuations in HCV subtype distribution have been observed over 2 decades in Venezuela. Different major mode of transmission and susceptibility to the available HCV treatment during each period might be playing a role in the observed fluctuations in HCV subtype distribution.
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Affiliation(s)
- Carmen L Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Rossana C Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela,
| | - Flor H Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
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Puche ML, Kay-Valero S, Michelli P, Oropeza MD, Loureiro CL, Devesa M, Dagher L, Pujol FH. Genetic diversity of hepatitis B virus and mutations associated to hepatocellular carcinoma in patients from Venezuela, with different stages of liver disease. Invest Clin 2016; 57:38-46. [PMID: 27382800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Globally, about 50% of liver cancer originates as a result of long term infection with hepatitis B virus (HBV), and some genotypes and mutations have been associated with an increased severity of infection. The aim of this study was to evaluate the genetic diversity of HBV in patients from Venezuela, with chronic infection, cirrhosis and hepatocellular carcinoma (HCC) and to compare the occurrence of mutations in all patient groups. Samples from patients with different pathologies of the liver, associated with HBV infection, were collected. The HBV S region was analyzed for genotype determination and, when available, the whole genome sequence was examined for mutations analysis. Genotype F was the most common genotype (87%). While the HBV subgenotype F3 was the most frequent genotype in the whole group of samples (44%), the subgenotype F2 predominated in HCC patients (56%). Mutations were more common in HCC and cirrhosis cases (p=0.01). The A1762T mutation was significantly associated with the advanced stage of liver disease (p=0.008). Additionally, mutations were more common in early stages of liver disease in HBV subgenotype F2-infected patients, and a significant association between this subgenotype and the emergence of T 1753C, A1762T, A1762T/G1764A (p=0.04) and C1773T (p=0.001) mutations in chronic patients was found, when compared to the HBV subgenotype F3. By comparing F2 with all other HBV subgenotypes, a positive association for the three basal core promoter (BCP) mutants (A1762T, A1762T/G1764A p=0.01, G1764A p=0.04) was found. These results suggest that the HBV subgenotype F2 might be associated to more severe forms of liver disease in comparison with the HBV subgenotype F3.
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Rangel HR, Bello G, Villalba JA, Sulbaran YF, Garzaro D, Maes M, Loureiro CL, de Waard JH, Pujol FH. The Evolving HIV-1 Epidemic in Warao Amerindians Is Dominated by an Extremely High Frequency of CXCR4-Utilizing Strains. AIDS Res Hum Retroviruses 2015; 31:1265-8. [PMID: 26414846 DOI: 10.1089/aid.2015.0155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We previously reported a high prevalence of HIV-1 infection in Warao Amerindians from Venezuela due to the rapid spread of a single B subtype strain. In this study we evaluated the coreceptor use of the HIV-1 strains infecting this Amerindian community. Sequences of the HIV-1 V3 loop from 56 plasma samples were genotyped for coreceptor use. An extremely high frequency of CXCR4 strains was found among HIV-1-infecting Waraos (47/49, 96%), compared to HIV-1 strains infecting the non-Amerindian Venezuelan population (35/79, 44%, p < 0.00001). Evolutionary analysis showed that a significant number of infections occurred between 1 and 12 months before collection and that a great proportion (50-70%) of HIV-1 transmissions occurred within the very early phase of infection (≤12 months). This is consistent with an initial infection dominated by an X4 strain or a very rapid selection of X4 variants after infection. This Amerindian population also exhibits the highest prevalence of tuberculosis in Venezuela, being synergistically bad prognostic factors for the evolution of morbidity and mortality in this vulnerable population.
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Affiliation(s)
- Héctor R. Rangel
- Laboratorio de Virología Molecular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Gonzalo Bello
- Laboratorio de AIDS e Inmunología Molecular Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Julian A. Villalba
- Laboratorio de Tuberculosis, Instituto de Biomedicina, Caracas, Venezuela
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Yoneira F. Sulbaran
- Laboratorio de Virología Molecular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Domingo Garzaro
- Laboratorio de Virología Molecular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Mailis Maes
- Laboratorio de Tuberculosis, Instituto de Biomedicina, Caracas, Venezuela
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Carmen L. Loureiro
- Laboratorio de Virología Molecular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | | | - Flor H. Pujol
- Laboratorio de Virología Molecular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
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Jaspe RC, Sulbarán YF, Loureiro CL, Martínez N, Devesa M, Rodríguez Y, Torres JR, Rangel HR, Pujol FH. Genetic diversity of hepatitis B virus and hepatitis C virus in human immunodeficiency virus type 1-co-infected patients from Venezuela. J Med Microbiol 2014; 63:1099-1104. [PMID: 24895404 DOI: 10.1099/jmm.0.067496-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The aim of this study was to evaluate the prevalence and genetic diversity of hepatitis B virus (HBV) and hepatitis C virus (HCV) in human immunodeficiency virus type 1 (HIV-1)-co-infected Venezuelan patients. The prevalence of HBV and HCV markers of infection in HIV-1 patients was 14% for anti-hepatitis B core antigen, 3% for hepatitis B surface antigen and 0.7% for anti-HCV, respectively. HBV prevalence was higher than HCV, as expected for a country where sexual intercourse, not intravenous drug use, is the main mode of HIV-1 transmission. The HCV genotype distribution in HIV-1-co-infected patients was similar to that obtained in HCV-mono-infected patients, but genotype 1a was more frequent in HIV-1-infected patients. The HBV genotype distribution exhibited differences between mono-infected and HIV-1-co-infected individuals. HBV F3 was the most common subgenotype in both groups, followed by F1b in HIV-1 co-infection and F2 in HBV mono-infection. In addition, genotype G (single infection) was found in an HIV-1-co-infected individual. A high prevalence of occult HBV infection was detected in HIV-1-co-infected naïve patients (18%), with F2 being the most common genotype (75%). To the best of our knowledge, these results correspond to the first description of frequency and molecular characterization of HBV and HCV in HIV-1 Venezuelan patients.
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Affiliation(s)
- Rossana C Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Apdo 20632, Caracas 1020-A, Venezuela
| | - Yoneira F Sulbarán
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Apdo 20632, Caracas 1020-A, Venezuela
| | - Carmen L Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Apdo 20632, Caracas 1020-A, Venezuela
| | - Nahir Martínez
- Sección de Infectología, Instituto de Medicina Tropical, UCV, Caracas, Venezuela
| | - Marisol Devesa
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Apdo 20632, Caracas 1020-A, Venezuela
| | - Yesseima Rodríguez
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Apdo 20632, Caracas 1020-A, Venezuela
| | - Jaime R Torres
- Sección de Infectología, Instituto de Medicina Tropical, UCV, Caracas, Venezuela
| | - Héctor R Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Apdo 20632, Caracas 1020-A, Venezuela
| | - Flor H Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Apdo 20632, Caracas 1020-A, Venezuela
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Pujol FH, Mejías E, Loureiro CL, Ludert JE, Liprandi F, Pernalete JM. Infection with transfusion-transmitted virus (TTV) in humans and other primates in Venezuela. Annals of Tropical Medicine & Parasitology 2013; 99:173-80. [PMID: 15814036 DOI: 10.1179/136485905x24193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Tranfusion-transmitted virus (TTV), a single-stranded circular DNA virus that chronically infects humans and other animals, displays a high degree of genetic diversity and was originally thought to be associated with hepatitis. The prevalences of TTV infection among different populations of humans and non-human primates from Venezuela have now been evaluated, using serum samples and three different detection tests. All three tests were PCR-based, one involving a hemi-nested PCR and primers based on the N22 open-reading-frame-1 region (N22-PCR), another employing 55 cycles with primers from the more conserved untranslated region (UTR-PCR), and the other using a hemi-nested PCR with primers from the same region (HUTR-PCR). The overall prevalences of human infection appeared much higher with the HUTR-PCR (52%) than with the N22-PCR (13%) or the UTR-PCR (5%). When the products amplified by N22-PCR from 28 human isolates of TTV were sequenced, only two genotypes of the virus were detected. The non-human sera tested came from primates kept in a zoo in north-western Venezuela. TTV DNA was detected, by HUTR-PCR, in both of the chimpanzee sera tested but not in any of the sera from the 11 New-World primates or the other 12 Old-World primates that were investigated. The results, particularly those of the HUTR-PCR, indicate that TTV infection is common in Venezuela, especially in populations, such as many Amerindian groups, who live under poor sanitary conditions. Although TTV infection may be relatively rare among non-human primates from the New World, this will have to be investigated further, using many more samples collected throughout the Americas.
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Affiliation(s)
- F H Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Apartado 21827, Caracas 1020-A, Venezuela.
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Jaspe RC, Sulbarán YF, Sulbarán MZ, Loureiro CL, Rangel HR, Pujol FH. Prevalence of amino acid mutations in hepatitis C virus core and NS5B regions among Venezuelan viral isolates and comparison with worldwide isolates. Virol J 2012; 9:214. [PMID: 22995142 PMCID: PMC3511240 DOI: 10.1186/1743-422x-9-214] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [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: 04/30/2012] [Accepted: 09/18/2012] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Recent reports show that R70Q and L/C91M amino acid substitutions in the core from different hepatitis C virus (HCV) genotypes have been associated with variable responses to interferon (IFN) and ribavirin (RBV) therapy, as well to an increase of hepatocellular carcinoma (HCC) risk, liver steatosis and insulin resistance (IR). Mutations in NS5B have also been associated to IFN, RBV, nucleoside and non-nucleoside inhibitors drug resistance. The prevalence of these mutations was studied in HCV RNA samples from chronically HCV-infected drug-naïve patients. METHODS After amplification of core and NS5B region by nested-PCR, 12 substitutions were analyzed in 266 Venezuelan HCV isolates subtype 1a, 1b, 2a, 2c, 2b, 2j (a subtype frequently found in Venezuela) and 3a (n = 127 and n = 228 for core and NS5B respectively), and compared to isolates from other countries (n = 355 and n = 646 for core and NS5B respectively). RESULTS R70Q and L/C91M core substitutions were present exclusively in HCV G1b. Both substitutions were more frequent in American isolates compared to Asian ones (69% versus 26%, p < 0.001 and 75% versus 45%, p < 0.001 respectively). In Venezuelan isolates NS5B D310N substitution was detected mainly in G3a (100%) and G1a (13%), this later with a significantly higher prevalence than in Brazilian isolates (p = 0.03). The NS5B mutations related to IFN/RBV treatment D244N was mainly found in G3a, and Q309R was present in all genotypes, except G2. Resistance to new NS5B inhibitors (C316N) was only detected in 18% of G1b, with a significantly lower prevalence than in Asian isolates, where this polymorphism was surprisingly frequent (p < 0.001). CONCLUSIONS Genotypical, geographical and regional differences were found in the prevalence of substitutions in HCV core and NS5B proteins. The substitutions found in the Venezuelan G2j type were similar to that found in G2a and G2c isolates. Our results suggest a high prevalence of the R70Q and L/C91M mutations of core protein for G1b and D310N substitution of NS5B protein for the G3a. C316N polymorphism related with resistance to new NS5B inhibitors was only found in G1b. Some of these mutations could be associated with a worse prognosis of the disease in HCV infected patients.
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Affiliation(s)
- Rossana C Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Apdo 20632, Caracas 1020-A, Venezuela
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Cardona NE, Loureiro CL, Garzaro DJ, Duarte MC, García DM, Pacheco MC, Chemin I, Pujol FH. Unusual presentation of hepatitis B serological markers in an Amerindian community of Venezuela with a majority of occult cases. Virol J 2011; 8:527. [PMID: 22152023 PMCID: PMC3253065 DOI: 10.1186/1743-422x-8-527] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [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: 09/02/2011] [Accepted: 12/09/2011] [Indexed: 12/18/2022] Open
Abstract
Background Occult hepatitis B infection (OBI) is characterized by the presence of hepatitis B virus (HBV) DNA in the absence of HBsAg in the serum of patients. The aim of this study was to characterize HBV infection among a Piaroa community, an Amerindian group which exhibits significant evidence of exposure to HBV but relatively low presence of HBsAg, and to explore the presence of OBI in this population. Results Of 150 sera, with 17% anti-HBc and 1.3% HBsAg prevalence, 70 were tested for the presence of HBV DNA. From these, 25 (36%) were found positive for HBV DNA by PCR in the core region. Two of these 25 sera were HBsAg positive, indicating an overt infection. Of the remaining 68 sera tested, 23 exhibited OBI. Of these, 13 were HBV DNA out of 25 anti-HBc positive (52%) and 10 HBV DNA positive, out of 43 anti-HBc negative (23%), with a statistical significance of p = 0.03. Viral DNA and HBsAg were present intermittently in follow up sera of 13 individuals. Sequence analysis in the core region of the amplified DNA products showed that all the strains belonged to HBV genotype F3. The OBI isolates displayed 96-100% nucleotide identity between them. One isolate exhibited the co-circulation of a wild type variant with a variant with a premature stop codon at the core protein, and a variant exhibiting a deletion of 28 amino acids. Conclusions The frequency of OBI found in this Amerindian group warrants further studies in other communities exhibiting different degrees of HBV exposure.
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Affiliation(s)
- Nathalia E Cardona
- Servicio Autónomo: Centro Amazónico para la Investigación y Control de enfermedades Tropicales, Simón Bolívar CAICET, Puerto Ayacucho, Venezuela
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Sulbarán MZ, Di Lello FA, Sulbarán Y, Cosson C, Loureiro CL, Rangel HR, Cantaloube JF, Campos RH, Moratorio G, Cristina J, Pujol FH. Genetic history of hepatitis C virus in Venezuela: high diversity and long time of evolution of HCV genotype 2. PLoS One 2010; 5:e14315. [PMID: 21179440 PMCID: PMC3001475 DOI: 10.1371/journal.pone.0014315] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 11/19/2010] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The subtype diversity of the hepatitis C virus (HCV) genotypes is unknown in Venezuela. METHODOLOGY/PRINCIPAL FINDINGS Partial sequencing of the NS5B region was performed in 310 isolates circulating in patients from 1995 to 2007. In the samples collected between 2005 and 2007, HCV genotype 1 (G1) was the most common genotype (63%), composed as expected of mainly G1a and G1b. G2 was the second most common genotype (33%), being G2a almost absent and G2j the most frequent subtype. Sequence analysis of the core region confirmed the subtype assignment performed within the NS5b region in 63 isolates. The complete genome sequence of G2j was obtained. G2j has been described in France, Canada and Burkina Fasso, but it was not found in Martinique, where several subtypes of G2 circulate in the general population. Bayesian coalescence analysis indicated a most recent common ancestor (MRCA) of G2j around 1785, before the introduction of G1b (1869) and G1a (1922). While HCV G1a and G1b experienced a growth reduction since 1990, coincident with the time when blood testing was implemented in Venezuela, HCV G2j did not seem to reach growth equilibrium during this period. CONCLUSIONS/SIGNIFICANCE Assuming the introduction of G2j from Africa during the slave trade, the high frequency of G2j found in Venezuela could suggest: 1- the introduction of African ethnic groups different from the ones introduced to Martinique or 2- the occurrence of a founder effect. This study represents an in-depth analysis of the subtype diversity of HCV in Venezuela, which is still unexplored in the Americas and deserves further studies.
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Affiliation(s)
| | - Federico A. Di Lello
- Cátedra de Virología de la Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Yoneira Sulbarán
- Laboratorio de Virología Molecular, CMBC, IVIC, Caracas, Venezuela
| | - Clarisa Cosson
- Laboratorio de Virología Molecular, CMBC, IVIC, Caracas, Venezuela
| | | | - Héctor R. Rangel
- Laboratorio de Virología Molecular, CMBC, IVIC, Caracas, Venezuela
| | - Jean F. Cantaloube
- Unité Emergence et Co-évolution virale, Etablissement Français du Sang Alpes-Méditerranée, Marseille, France
| | - Rodolfo H. Campos
- Cátedra de Virología de la Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gonzalo Moratorio
- Departamento de Técnicas Nucleares Aplicadas, Facultad de Ciencias, Centro de Investigaciones Nucleares, Universidad de la República, Montevideo, Uruguay
- Unidad de Biofísica de Proteínas, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Juan Cristina
- Departamento de Técnicas Nucleares Aplicadas, Facultad de Ciencias, Centro de Investigaciones Nucleares, Universidad de la República, Montevideo, Uruguay
| | - Flor H. Pujol
- Laboratorio de Virología Molecular, CMBC, IVIC, Caracas, Venezuela
- * E-mail:
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Devesa M, Loureiro CL, Rivas Y, Monsalve F, Cardona N, Duarte MC, Poblete F, Gutierrez MF, Botto C, Pujol FH. Subgenotype diversity of hepatitis B virus American genotype F in Amerindians from Venezuela and the general population of Colombia. J Med Virol 2008; 80:20-6. [PMID: 18041024 DOI: 10.1002/jmv.21024] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The objective of this study was the evaluation of the genetic diversity found in HBV circulating among Venezuelan Amerindians and the general population in Colombia. Phylogenetic analysis of the S region in 194 isolates showed that genotype F is highly predominant in Colombia and Venezuela. This might be related to the genetic background of the population. F3 is the main subgenotype which circulates in both countries. Phylogenetic analysis of 61 complete genome sequences of HBV American genotypes confirms the presence of two genotypes F and H, and 4 F subgenotypes. In Venezuela, subgenotypes F1, F2, and F3 circulate in East and West Amerindians, while only F3 was found among South Amerindians. Japreira community derived from Yucpa Amerindians around 150 years ago. However, several Japreira HBV sequences were forming a clade that can be classified as subgenotype 2b, differing from Yucpa sequences that belong mainly to subgenotype F3. The apparent absence of correlation between the phylogenetic groupings of HBV isolates with the ethnical origin in aboriginal populations might be suggesting a recent origin of HBV American subgenotypes, or a genetic drift effect.
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Affiliation(s)
- M Devesa
- Laboratorio de Virología Molecular, CMBC, IVIC, Caracas, Venezuela
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Abstract
BACKGROUND Changes in hepatitis C virus (HCV) genotype distribution with time have been reported in several countries. GOALS To explore eventual changes in HCV genotype distribution in Venezuela over a 10 years period. STUDY HCV genotype was determined by direct sequencing of the 5' noncoding region, in 236 isolates circulating in patients treated during years 2005 to 2006. Genotype distribution was compared with the one observed in 43 patients followed during years 1994 to 1996. RESULTS The prevalence HCV genotype 1 and 2 was 70% and 26%, respectively, in patients followed during years 1994 to 1996. The frequency of genotype 2 was significantly increased to 41% (P=0.04) in patients treated during years 2005 to 2006. A significant reduction in HCV genotype 1b prevalence (48% to 27%, P=0.01) was also observed after this 10 years period, whereas the prevalence of HCV genotype 1a did not change over time (22% vs. 27%, NS). Transfusion was more significantly associated with infection with HCV genotype 1b than with other genotypes (52% vs. 20%, P=0.002). CONCLUSIONS HCV subtype 1b seems to have been displaced by HCV genotype 2 in a relatively short period, without increase in the frequency of genotype 3. The low frequency of HCV genotype 3 in Venezuela might be due to the fact that intravenous drug use in Venezuela is less common than in other countries. The implementation of anti-HCV testing in blood banks since 1994 in Venezuela, might have contributed to the reduction in the frequency HCV genotype 1b infection.
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Affiliation(s)
- Flor H Pujol
- Laboratorio de Virología Molecular, CMBC, IVIC, Caracas, Venezuela
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Loureiro CL, Alonso R, Pacheco BA, Uzcátegui MG, Villegas L, León G, De Saéz A, Liprandi F, López JL, Pujol FH. High prevalence of GB virus C/hepatitis G virus genotype 3 among autochthonous Venezuelan populations. J Med Virol 2002; 68:357-62. [PMID: 12226822 DOI: 10.1002/jmv.10211] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
GB virus C or hepatitis G virus (GBV-C/HGV) is highly prevalent among population groups at risk of parenterally transmitted viral agents, but it has also a worldwide distribution in other non-risk population groups. GBV-C/HGV RNA and antibodies against its envelope protein (anti-E2 Abs) were found in 3/86 (3%) and 7/89 (8%) of biomedical science personnel (BSP), in 31/453 (7%) and 37/200 (19%) of blood donors (BD), and in 6/64 (9%) and 26/59 (44%) of hemodialysis patients (HD) from Caracas, Venezuela. A significant gradient of GBV-C/HGV exposure (anti-E2 Abs and/or GBV-C/HGV RNA) was found between BSP (lowest prevalence), BD, and HD (P < 0.001). GBV-C/HGV RNA and anti-E2 Abs were also found in 2/69 (2.9%) and 2/44 (4.5%) of individuals from a rural community, in 9/162 (5.5%) and 2/40 (5%) of West Amerindians, and in 14/56 (25%) and 4/53 (7.5%) of South Amerindians. Socioeconomic and cultural factors may have contributed to the relatively high risk of exposure to GBV-C/HGV in BD and Amerindians. Whereas GBV-C/HGV genotypes 1 (n = 1), 2 (n = 6), and 3 (n = 22) were present in Venezuela, only the Asiatic genotype 3 was found infecting Amerindians and rural populations (n = 16). Genotype assignment based on the 5' noncoding region of the GBV- C/HGV genome was corroborated in some isolates by genetic analysis of the E2 region. This report confirms the circulation of the Asiatic genotype of GBV-C/HGV among Amerindians, suggesting an old origin of GBV-C/HGV. This might be associated with the apparently low pathogenesis of this virus.
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MESH Headings
- Adolescent
- Adult
- Aged
- Child
- Child, Preschool
- Female
- Flaviviridae Infections/epidemiology
- Flaviviridae Infections/transmission
- Flaviviridae Infections/virology
- GB virus C/genetics
- Genotype
- Hepatitis Antibodies/blood
- Hepatitis, Viral, Human/epidemiology
- Hepatitis, Viral, Human/transmission
- Hepatitis, Viral, Human/virology
- Humans
- Indians, South American
- Male
- Middle Aged
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction
- Prevalence
- RNA, Viral/blood
- Rural Population
- Sequence Analysis, DNA
- Urban Population
- Venezuela/epidemiology
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Affiliation(s)
- Carmen L Loureiro
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, IVIC, Caracas, Venezuela
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21
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Quintero A, Uzcátegui N, Loureiro CL, Villegas L, Illarramendi X, Guevara ME, Ludert JE, Blitz L, Liprandi F, Pujol FH. Hepatitis delta virus genotypes I and III circulate associated with hepatitis B virus genotype F In Venezuela. J Med Virol 2001; 64:356-9. [PMID: 11424126 DOI: 10.1002/jmv.1058] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The genotypes of hepatitis B (HBV) and delta (HDV) viruses circulating among Venezuelan Amerindian populations, where these viruses are endemic, were determined by sequencing of PCR amplified products from HBsAg positive sera. HDV genotype I (n = 7, 6 from West Amerindians), and III (n = 5, 4 from South Amerindians), were found. Only one HDV genotype I isolate was associated with HBV genotype D, 4 HDV genotype I and 2 HDV genotype III infected individuals were co-infected with HBV genotype F. The failure to detect the South American HDV genotype III in West Amerindians might be related to the outbreak of fulminant hepatitis with high mortality rate occurred between 1979 and 1982, probably affecting more the Amerindians infected with HDV genotype III. These results suggest the circulation of HDV genotype I among Amerindians, probably introduced through European immigrations, and that this HDV genotype is able to replicate in association with HBV genotype F.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Biomarkers/analysis
- Biomarkers/blood
- DNA, Viral/analysis
- DNA, Viral/blood
- Genotype
- Hepatitis Antibodies/analysis
- Hepatitis Antibodies/blood
- Hepatitis Antibodies/immunology
- Hepatitis B/blood
- Hepatitis B/virology
- Hepatitis B Surface Antigens/analysis
- Hepatitis B Surface Antigens/blood
- Hepatitis B virus/genetics
- Hepatitis B virus/isolation & purification
- Hepatitis D/blood
- Hepatitis D/complications
- Hepatitis D/epidemiology
- Hepatitis D/genetics
- Hepatitis D/virology
- Hepatitis D, Chronic/blood
- Hepatitis D, Chronic/complications
- Hepatitis D, Chronic/epidemiology
- Hepatitis D, Chronic/virology
- Hepatitis Delta Virus/genetics
- Hepatitis Delta Virus/isolation & purification
- Humans
- Indians, South American/classification
- Indians, South American/genetics
- Phylogeny
- Polymerase Chain Reaction
- RNA, Viral/analysis
- RNA, Viral/blood
- Sequence Alignment
- Venezuela/epidemiology
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Affiliation(s)
- A Quintero
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, IVIC, Caracas, Venezyçuela
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22
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Aguilar MS, Cosson C, Loureiro CL, Devesa M, Martínez J, Villegas L, Flores J, Ludert JE, Alarcón de Noya B, Noya O, Liprandi F, Pujol FH. Prevalence of infection with hepatitis C virus in Venezuela, as assessed with an immuno-assay based on synthetic peptides. Ann Trop Med Parasitol 2001; 95:187-95. [PMID: 11299125 DOI: 1080/00034980120042944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Information on infection with hepatitis C virus (HCV) in South America is scarce. The seroprevalences of antibodies to HCV among urban, rural and Amerindian populations from Venezuela, and the genotypes of the HCV isolates recovered, were therefore determined. A total of 2592 sera were tested with an immuno-assay which was developed in-house and based on synthetic peptides. Each reactive sample was then re-tested, using other enzyme immuno-assays and a reverse-transcription, nested PCR, and any sample confirmed positive (in any test) was considered HCV-positive. Genotypes were determined by analysis of RFLP. Overall, 39 (1.5%) of the samples were found HCV positive. The results of the immuno-assays indicated that the seroprevalence of HCV markers among the Amerindians investigated (23/1082, or 2.1%) was significantly higher than that among the other subjects (16/1510, or 1.1%; P = 0.02). No such difference was observed in the numbers of subjects confirmed positive by PCR, however (6/1082 v. 10/1510), and some of the anti-HCV reactivity observed among Amerindians may have been the result of cross-reactivity with parasitic infections. The relative low prevalence of active HCV infection (16/2582, or 0.6%) and the HCV genotypes observed (mainly genotype 1) are in agreement with the results of previous studies indicating that HCV is not autochthonous to South America. However, it is clear that the virus may now be found even in isolated Amerindian populations. The in-house, synthetic-peptide-based immuno-assay seems to be a valuable tool for epidemiological studies.
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Affiliation(s)
- M S Aguilar
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Apartado 21827, Caracas 1020-A, Venezuela
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23
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Gutiérrez C, León G, Loureiro CL, Uzcátegui N, Liprandi F, Pujol FH. Hepatitis B virus DNA in blood samples positive for antibodies to core antigen and negative for surface antigen. Clin Diagn Lab Immunol 1999; 6:768-70. [PMID: 10473534 PMCID: PMC95771 DOI: 10.1128/cdli.6.5.768-770.1999] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Anti-hepatitis B core antigen (HBcAg)-positive hepatitis B surface antigen (HBsAg)-negative plasma samples from blood donors were tested by nested PCR. DNA positivity was more significantly associated with high levels of anti-HBcAg than with low levels of anti-HBsAg antibodies. Analysis of a dilution of anti-HBcAg antibodies might result in a more rational exclusion of anti-HBcAg-positive HBsAg-negative samples, reducing the number of donations discarded and enabling more countries to incorporate anti-HBcAg testing.
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Affiliation(s)
- C Gutiérrez
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Cellular, Instituto Venezolano de Investigaciones Científicas, Apartado 21827, Caracas 1020-A, Venezuela
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24
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Abstract
Hepatitis C virus (HCV) genotypes were determined in hemodialysis patients with a high prevalence and incidence of infection. A change of HCV genotype was observed in 6/14 follow-up samples analyzed 13 and 21 months later. The appearance and disappearance of HCV genotypes may be due to either genotype-specific intermittent viremic status or viral interference.
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Affiliation(s)
- F H Pujol
- Laboratorio de Biología de Virus, CMBC, IVIC, Caracas, Venezuela
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25
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Pujol FH, Vásquez G, Rojas AM, Fuenmayor ME, Loureiro CL, Pérez-Schael I, Estes MK, Liprandi F. Norwalk virus infection in Venezuela. Ann Trop Med Parasitol 1998; 92:205-11. [PMID: 9625917] [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] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The presence of antibodies against Norwalk virus (NV) was studied in sera from different Venezuelan populations, using an enzyme immuno-assay (EIA) based on recombinant NV protein. Antibodies to NV were found in 47%-53% of urban subjects from Caracas, 83% of rural subjects from the west of the country, and 73%-93% of Amerindian subjects. The prevalences found in the rural and Amerindian groups were significantly higher than that in the urban group. Although about 50% of the children studied were seropositive for NV by the age of 5 years, only four (0.4%) of 1120 faecal samples from children with diarrhoea which were tested for the presence of NV antigen by sandwich EIA were found positive. An increase of at least 4-fold in the titre of anti-NV IgA was found in three (5%) of 61 pairs of sera taken during and 1 month after an acute episode of diarrhoea not due to rotavirus. NV was therefore not a predominant aetiological cause of gastro-enteritis in young children in Venezuela between 1993 and 1995, although it can be the cause of diarrhoea in infants.
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Affiliation(s)
- F H Pujol
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Cientificas, Caracas, Venezuela
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26
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Pujol FH, Khudyakov YE, Devesa M, Cong ME, Loureiro CL, Blitz L, Capriles F, Beker S, Liprandi F, Fields HA. Hepatitis G virus infection in Amerindians and other Venezuelan high-risk groups. J Clin Microbiol 1998; 36:470-4. [PMID: 9466761 PMCID: PMC104562 DOI: 10.1128/jcm.36.2.470-474.1998] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/1997] [Accepted: 11/19/1997] [Indexed: 02/06/2023] Open
Abstract
Recently, a new virus related to flaviviruses, the hepatitis G virus (HGV), or GBV-C virus, was discovered as a putative blood-borne human pathogen. HGV RNA (NS5 region) was amplified by reverse transcription-nested PCR in the sera of 6 of 64 (9%) hemodialysis patients; 2 of 80 (2.5%) West Yukpa Amerindians, a population with a high rate of HBV infection but negative for HCV infection; and 1 patient with an acute episode of non-A, non-B, non-C hepatitis (NABCH). The patterns of single-strand conformation polymorphism of the amplified products were unique among different specimens and similar on follow-up for hemodialysis patients. All patients tested remained HGV RNA positive 1 and 2 years later, without major sequence variation, except for the NABCH patient, for whom a double infection and an apparent clearance of the original dominant variant was observed after 2 years. The sequences of the NS5 amplified products demonstrated 85 to 90% identity with other reported HGV sequences.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- Flaviviridae/genetics
- Flaviviridae/isolation & purification
- Hepatitis C/diagnosis
- Hepatitis E/diagnosis
- Hepatitis, Viral, Human/blood
- Hepatitis, Viral, Human/diagnosis
- Hepatitis, Viral, Human/epidemiology
- Humans
- Indians, South American
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- Polymorphism, Single-Stranded Conformational
- RNA, Viral/blood
- RNA, Viral/genetics
- RNA, Viral/isolation & purification
- Renal Dialysis/adverse effects
- Sequence Analysis, RNA
- Venezuela/epidemiology
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Affiliation(s)
- F H Pujol
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Caracas, Venezuela.
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27
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Pujol FH, Loureiro CL, Devesa M, Blitz L, Parra K, Beker S, Liprandi F. Determination of genotypes of hepatitis C virus in Venezuela by restriction fragment length polymorphism. J Clin Microbiol 1997; 35:1870-2. [PMID: 9196212 PMCID: PMC229860 DOI: 10.1128/jcm.35.7.1870-1872.1997] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Hepatitis C virus genotypes in Venezuela were analyzed by restriction fragment length polymorphism in the 5' noncoding region. The absence of BstUI digestion was found to be a useful marker for genotype 2 specimens. From 122 serum samples, 66, 20, and 2.5% were classified as genotypes 1, 2, and 3, respectively; 0.8% were classified as genotype 4; and 10% appeared to be mixed infections.
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Affiliation(s)
- F H Pujol
- Laboratorio Biología de Virus, CMBC, IVIC, Caracas, Venezuela.
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