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Yabar CA, Acuña M, Gazzo C, Salinas G, Cárdenas F, Valverde A, Romero S. New subtypes and genetic recombination in HIV type 1-infecting patients with highly active antiretroviral therapy in Peru (2008-2010). AIDS Res Hum Retroviruses 2012; 28:1712-22. [PMID: 22559065 DOI: 10.1089/aid.2012.0040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 subtype B is the most frequent strain in Peru. However, there is no available data about the genetic diversity of HIV-infected patients receiving highly active antiretroviral therapy (HAART) here. A group of 267 patients in the Peruvian National Treatment Program with virologic failure were tested for genotypic evidence of HIV drug resistance at the Instituto Nacional de Salud (INS) of Peru between March 2008 and December 2010. Viral RNA was extracted from plasma and the segments of the protease (PR) and reverse transcriptase (RT) genes were amplified by reverse transcriptase polymerase chain reaction (RT-PCR), purified, and fully sequenced. Consensus sequences were submitted to the HIVdb Genotypic Resistance Interpretation Algorithm Database from Stanford University, and then aligned using Clustal X v.2.0 to generate a phylogenetic tree using the maximum likelihood method. Intrasubtype and intersubtype recombination analyses were performed using the SCUEAL program (Subtype Classification by Evolutionary ALgo-rithms). A total of 245 samples (91%) were successfully genotyped. The analysis obtained from the HIVdb program showed 81.5% resistance cases (n=198). The phylogenetic analysis revealed that subtype B was predominant in the population (98.8%), except for new cases of A, C, and H subtypes (n=4). Of these cases, only subtype C was imported. Likewise, recombination analysis revealed nine intersubtype and 20 intrasubtype recombinant cases. This is the first report of the presence of HIV-1 subtypes C and H in Peru. The introduction of new subtypes and circulating recombinants forms can make it difficult to distinguish resistance profiles in patients and consequently affect future treatment strategies against HIV in this country.
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Affiliation(s)
| | - Maribel Acuña
- Laboratorio de VETS/VIH-SIDA, Instituto Nacional de Salud, Lima, Peru
| | - Cecilia Gazzo
- Laboratorio de VETS/VIH-SIDA, Instituto Nacional de Salud, Lima, Peru
| | - Gabriela Salinas
- Laboratorio de VETS/VIH-SIDA, Instituto Nacional de Salud, Lima, Peru
| | - Fanny Cárdenas
- Laboratorio de VETS/VIH-SIDA, Instituto Nacional de Salud, Lima, Peru
| | - Ada Valverde
- Laboratorio de VETS/VIH-SIDA, Instituto Nacional de Salud, Lima, Peru
| | - Soledad Romero
- Laboratorio de VETS/VIH-SIDA, Instituto Nacional de Salud, Lima, Peru
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Gräf T, Pinto AR. The increasing prevalence of HIV-1 subtype C in Southern Brazil and its dispersion through the continent. Virology 2012; 435:170-8. [PMID: 22999094 DOI: 10.1016/j.virol.2012.08.048] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 08/29/2012] [Accepted: 08/30/2012] [Indexed: 01/15/2023]
Abstract
The HIV-1 has evolved swiftly and the scenario of HIV-1 genetic diversity is constantly changing. In South America, recombinant forms of subtypes B, F1, and BF1 have historically driven the HIV-1 epidemic. In recent years, however, infection with subtype C has gained prominence as its prevalence increased in Southern Brazil as well as neighboring countries. Current studies point to a single introduction of closely related strains as the beginning of the Brazilian subtype C epidemic. However, the place of origin of these strains, date, and route of introduction are under continuous debate as well as the clinical outcomes of the emergence of subtype C. Therefore, this paper reviews the history of the HIV-1 subtype C in Brazil, particularly in the Southern region, covering its demographic and evolutionary history and the possible implications to the Brazilian AIDS epidemic as well as to neighboring countries.
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Affiliation(s)
- Tiago Gräf
- Laboratório de Imunologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC, Brazil
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Cunha LKH, Kashima S, Amarante MFC, Haddad R, Rodrigues ES, Silva KLT, Lima TA, Castro DB, Brito FC, Almeida EG, Covas DT, Malheiro A. Distribution of human immunodeficiency virus type 1 subtypes in the State of Amazonas, Brazil, and subtype C identification. Braz J Med Biol Res 2012; 45:104-12. [PMID: 22249428 PMCID: PMC3854261 DOI: 10.1590/s0100-879x2012007500003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Accepted: 01/04/2012] [Indexed: 11/22/2022] Open
Abstract
Few studies have reported the molecular epidemiological characterization of HIV-1 in the Northern region of Brazil. The present study reports the molecular and epidemiological characterization of 31 HIV-1 isolates from blood donors from the State of Amazonas who donated blood between April 2006 and March 2007. Serum/plasma samples from all donors were screened for HIV antibodies by ELISA and the results confirmed by Western blot analysis. Genomic DNA was extracted from the buffy coat using the Super Quik-Gene-DNA Isolation kit. Nested PCR was performed on the env, gag, and pol regions of HIV-1 using the Gene Amp PCR System 9700. Sequencing reactions were performed using the inner PCR primers and the DYEnamic™ ET Dye Terminator Kit, and phylogenetic analysis was performed using the gag, pol, and env gene sequences. We collected samples from 31 blood donors who tested positive for HIV-1 in confirmatory experiments. The male:female ratio of blood donors was 3.4:1, and the mean age was 32.4 years (range: 19 to 61 years). Phylogenetic analysis showed that subtype B is the most prevalent among Northern Brazilian HIV-1-seropositive blood donors. One HIV-1 subtype C and one circulating recombinant form (CRF_BF) of HIV-1 were identified in the State of Amazonas. This is the first study showing the occurrence of a possible “homogenous” subtype C in this region of Brazil. This finding could contribute to a better characterization of the HIV-1 strains that circulate in the country. Key words: HIV-1; Subtypes; Phylogenetic analysis; Blood donors; Molecular and epidemiological characterization
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Affiliation(s)
- L K H Cunha
- Departamento de Parasitologia, Universidade Federal do Amazonas, Manaus, AM, Brasil
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Shen C, Craigo J, Ding M, Chen Y, Gupta P. Origin and dynamics of HIV-1 subtype C infection in India. PLoS One 2011; 6:e25956. [PMID: 22016790 PMCID: PMC3189977 DOI: 10.1371/journal.pone.0025956] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 09/14/2011] [Indexed: 11/24/2022] Open
Abstract
Objective To investigate the geographical origin and evolution dynamics of HIV-1 subtype C infection in India. Design Ninety HIV-1 subtype C env gp120 subtype C sequences from India were compared with 312 env gp120 reference subtype C sequences from 27 different countries obtained from Los Alamos HIV database. All the HIV-1 subtype C env gp120 sequences from India were used for the geographical origin analysis and 61 subtype C env gp120 sequences with known sampling year (from 1991 to 2008) were employed to determine the origin of HIV infection in India. Methods Phylogenetic analysis of HIV-1 env sequences was used to investigate the geographical origin and tMRCA of Indian HIV-1 subtype C. Evolutionary parameters including origin date and demographic growth patterns of Indian subtype C were estimated using a Bayesian coalescent-based approach under relaxed molecular clock models. Findings The majority of the analyzed Indian and South African HIV-1 subtype C sequences formed a single monophyletic cluster. The most recent common ancestor date was calculated to be 1975.56 (95% HPD, 1968.78–1981.52). Reconstruction of the effective population size revealed three phases of epidemic growth: an initial slow growth, followed by exponential growth, and then a plateau phase approaching present time. Stabilization of the epidemic growth phase correlated with the foundation of National AIDS Control Organization in India. Interpretation Indian subtype C originated from a single South African lineage in the middle of 1970s. The current study emphasizes not only the utility of HIV-1 sequence data for epidemiological studies but more notably highlights the effectiveness of community or government intervention strategies in controlling the trend of the epidemic.
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Affiliation(s)
- Chengli Shen
- Department of Infectious Diseases and Microbiology Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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Castillo J, Comegna M, Quijada W, Jauvin V, Pinson P, Masquelier B, Fleury H, Castro E. Surveillance of HIV type 1 drug resistance among naive patients from Venezuela. AIDS Res Hum Retroviruses 2009; 25:1329-33. [PMID: 19954301 DOI: 10.1089/aid.2009.0118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have studied 65 HIV-1-infected untreated patients recruited in Caracas, Venezuela with TCD4 counts > or =350/microl. The reverse transcriptase and protease sequences of the virus were sequenced, aligned with reference HIV-1 group M strains, and analyzed for drug resistance mutations. Most of the viruses were subtype B genotype in both the protease and RT genomic regions. Five of the 62 virus isolates successfully amplified showed evidence of recombination between protease and RT, with their protease region being non-B while their RT region was derived from subtype B. Four strains were found bearing resistance mutations either to NRTIs, NNRTIs, or PIs. The prevalence of HIV-1 isolates bearing resistance mutations was therefore above the 5% threshold of WHO.
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Affiliation(s)
- Julio Castillo
- Department of Internal Medicine, Vargas Hospital, Central University of Venezuela, Caracas, Venezuela
| | - Mario Comegna
- Department of Infectious Diseases, Vargas Hospital, Central University of Venezuela, Caracas, Venezuela
| | - Wilmary Quijada
- Department of Internal Medicine, Vargas Hospital, Central University of Venezuela, Caracas, Venezuela
| | - Valérie Jauvin
- Laboratoire de Virologie EA 2968, Université de Bordeaux, Bordeaux, France
| | - Patricia Pinson
- Laboratoire de Virologie EA 2968, Université de Bordeaux, Bordeaux, France
| | - Bernard Masquelier
- Laboratoire de Virologie EA 2968, Université de Bordeaux, Bordeaux, France
| | - Hervé Fleury
- Laboratoire de Virologie EA 2968, Université de Bordeaux, Bordeaux, France
| | - Erika Castro
- Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
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Jones LR, Dilernia DA, Manrique JM, Moretti F, Salomón H, Gomez-Carrillo M. In-depth analysis of the origins of HIV type 1 subtype C in South America. AIDS Res Hum Retroviruses 2009; 25:951-9. [PMID: 19842791 DOI: 10.1089/aid.2008.0293] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The South American HIV-1 epidemic is characterized by the co-circulation of subtype B and BF recombinant variants. Together with the B and BF genotypes, HIV-1 subtype C (HIV-1C), F1, and several other recombinants have been reported. The epidemiological significance and immune correlates of these "non-B-non-BF" strains circulating in South America are still uncertain and therefore are increasingly attracting the interest of the scientific community. In this study, the South American HIV-1C epidemic was studied using new technologies for the phylogenetic analysis of large datasets. Our results indicate that there is a major clade encompassing most of the South American HIV-1C strains. These analyses also agreed that some strains do not group inside this major clade, suggesting that there could be HIV-1C sequences of different origins circulating in South America. Others have proposed different hypotheses about the origins of HIV-1C strains from South America. This study shows that an exact single origin cannot be determined, a fact that could be attributed to sampling problems, phylogenetic uncertainty, and the shortage of historical and epidemiological data. Currently, the reported data indicate that HIV-1C strains were introduced in Brazil and afterward spread to other regions of South America. By using character optimization on the obtained phylogenetic trees, we observed that Argentina could also be a point in which the HIV-1C epidemic entered South America.
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Affiliation(s)
- Leandro R. Jones
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
- Estación de Fotobiología Playa Unión-CONICET, Playa Unión, Chubut, Argentina
| | - Darío A. Dilernia
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Julieta M. Manrique
- Cátedra de Química Analítica Instrumental, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Franco Moretti
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Horacio Salomón
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Manuel Gomez-Carrillo
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
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Machado LF, Ishak MO, Vallinoto AC, Lemos JAR, Azevedo VN, Moreira MR, Souza MI, Fernandes LM, Souza LL, Ishak R. Molecular epidemiology of HIV type 1 in northern Brazil: identification of subtypes C and D and the introduction of CRF02_AG in the Amazon region of Brazil. AIDS Res Hum Retroviruses 2009; 25:961-6. [PMID: 19795985 DOI: 10.1089/aid.2009.0027] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The molecular epidemiology of HIV-1 strains circulating in Belem-PA and Macapa-AP, in the Northern region of Brazil, is described using sequences of the C2V3 segment of the env and the pro gene of HIV-1 from patients of the Reference Unit for Special Infectious and Parasitary Diseases (URE-DIPE) in Belem-PA and the Central Laboratory (LACEN) in Macapa-AP. Subtype B was the most frequently found in relation to pro (88.3%) in Belem and in Macapa (97.1%) and env (88.3% in Belem and 100% in Macapa). Subtype F was also described in Belem (9.3% pro and 8.3% env) and Macapa (2.8% pro). Subtype D was described for the first time in the Northern region of the country as well as the recent entry of CRF02_AG. Furthermore, several possible recombinant forms among the various subtypes were found in both cities. The results support the hypothesis that HIV-1 infection is associated with the epidemic of the virus in the Southeast region of the country and that the city of Belem is the most important route for HIV-1 entry in the Northern region of Brazil.
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Affiliation(s)
- Luiz F.A. Machado
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - Marluísa O.G. Ishak
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - Antonio C.R. Vallinoto
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - José Alexandre R. Lemos
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
- Laboratory of Molecular Biology, State Blood Bank, Para, Brazil
| | - Vania N. Azevedo
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | | | - Maria I.M. Souza
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - Luciana M. Fernandes
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - Lia L.B. Souza
- Reference Unit for Special Infectious and Parasitary Diseases, Brazil
| | - Ricardo Ishak
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
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Rangel HR, Garzaro D, Gutiérrez CR, Vásquez L, Guillen G, Torres JR, Pujol FH. HIV diversity in Venezuela: predominance of HIV type 1 subtype B and genomic characterization of non-B variants. AIDS Res Hum Retroviruses 2009; 25:347-50. [PMID: 19327054 DOI: 10.1089/aid.2008.0241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The aim of this study was the analysis of human immunodeficiency virus (HIV) diversity in Venezuela, and the characterization of variants other than subtype B. A total of 425 HIV isolates, collected between 2003 and 2008, were analyzed. The sequence of at least one genomic region (Pol, Env, Vif, or Nef ) was available for all of them and at least two genomic regions were analyzed in 46% of them. From the 425 HIV isolates analyzed, 421 (99.1%) were classified as HIV-1 subtype B. The four non-subtype B isolates correspond to one subtype C, one recombinant AG, and two HIV-2 isolates. This study shows that HIV-1 subtype B is still highly predominant in Venezuela. Whereas some sporadic cases of other HIV types can be found, they do not seem to have disseminated to the present.
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Affiliation(s)
- Héctor R. Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Domingo Garzaro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | | | | | - Genni Guillen
- Escuela de Bioanálisis, Universidad de Oriente, Núcleo Sucre, Cumaná, Venezuela
| | - Jaime R. Torres
- Sección de Infectología, Instituto de Medicina Tropical, UCV, 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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Abstract
OBJECTIVE Our aim was to investigate the monophyletic status of the HIV-1C that circulates in South America and its phylogenetic relationships with other HIV-1C populations around the world in order to shed light on its the geographic origins as well as the place of introduction in the continent. METHODS Fifty-one sequences from South America and 46 from non-South American countries, including samples from Africa and Asia, were obtained from the Los Alamos National Laboratory. The data analyzed corresponded to the entire protease and two-thirds of the polymerase domain from the reverse transcriptase. Phylogenetic analyses using maximum likelihood and Bayesian inference were performed in Phylogenetic Analysis Using Parsymony, PHYlogenetic inferences using Maximum Likelihood, and MrBayes. RESULTS Samples from South America formed a monophyletic group independent of the method used. The bootstrap support of South American HIV-1C was higher than 60% in maximum likelihood trees and its posterior probability was 99% in the Bayesian analysis. These results indicate the monophyletic nature of the South American HIV-1C. Moreover, in all trees estimated, a sequence from Kenya was the most closely related to the South American clade, followed by two from Ethiopia. All South American sequences from countries other than Brazil showed closer phylogenetic relatedness to Brazilian samples, indicating that HIV-1C was introduced in South America in Brazil. CONCLUSION Our results indicate that the entry of HIV-1C in South America occurred in a single episode or in multiples episodes of genetically related viruses, possibly from an eastern African country. HIV-1C was then disseminated to the remaining South American countries from Brazil.
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Bouchard M, Masquelier B, Moreno M, Deibis L, De Pérez GE, Fleury H, Castro E. HIV type 1 drug resistance among naive patients from Venezuela. AIDS Res Hum Retroviruses 2007; 23:482-5. [PMID: 17411383 DOI: 10.1089/aid.2006.0219] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this study, we characterize proviral DNA of 20 HIV-1 asymptomatic antiretroviral-naive patients from Venezuela in env, gag, and pol genes regions. Results from both env/gag HMA subtyping and phylogenetic analysis of pol partial sequences led to the description of clade B in all cases. Nevertheless, the high prevalence of polymorphisms was particularly evident among the protease sequences. A 10% prevalence of major resistance mutations to RTIs was found. Our data also suggested that the protease polymorphisms I62T and V77T could be considered as molecular markers of the subtype B local epidemic. In addition, we show how proviral DNA can be used as a reliable tool to follow trends of resistance mutation transmission.
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Affiliation(s)
- Morella Bouchard
- Immunology Institute, Central University of Venezuela, Caracas, Venezuela
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