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Rubio AE, Abraha A, Carpenter CA, Troyer RM, Reyes-Rodríguez ÁL, Salomon H, Arts EJ, Tebit DM. Similar replicative fitness is shared by the subtype B and unique BF recombinant HIV-1 isolates that dominate the epidemic in Argentina. PLoS One 2014; 9:e92084. [PMID: 24727861 PMCID: PMC3984079 DOI: 10.1371/journal.pone.0092084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 02/18/2014] [Indexed: 11/18/2022] Open
Abstract
The HIV-1 epidemic in South America is dominated by pure subtypes (mostly B and C) and more than 7 BF and BC recombinant forms. In Argentina, circulating recombinant forms (CRFs) comprised of subtypes B and F make up more than 50% of HIV infections. For this study, 28 HIV-1 primary isolates were obtained from patients in Buenos Aires, Argentina and initially classified into subtype B (n = 9, 32.1%), C (n = 1, 3.6%), and CRFs (n = 18, 64.3%) using partial pol and vpu-env sequences, which proved to be inconsistent and inaccurate for these phylogenetic analyses. Near full length genome sequences of these primary HIV-1 isolates revealed that nearly all intersubtype BF recombination sites were unique and countered previous "CRF" B/F classifications. The majority of these Argentinean HIV-1 isolates were CCR5-using but 4 had a dual/mixed tropism as predicted by both phenotypic and genotypic assays. Comparison of the replicative fitness of these BF primary HIV-1 isolates to circulating B, F, and C HIV-1 using pairwise competitions in peripheral blood mononuclear cells (PBMCs) indicated a similarity in fitness of these BF recombinants to subtypes B and F HIV-1 (of the same co-receptor usage) whereas subtype C HIV-1 was significantly less fit than all as previously reported. These results suggest that the multitude of BF HIV-1 strains present within the Argentinean population do not appear to have gained replicative fitness following recent B and F recombination events.
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Affiliation(s)
- Andrea E. Rubio
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Awet Abraha
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Crystal A. Carpenter
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Ryan M. Troyer
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Ángel L. Reyes-Rodríguez
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Horacio Salomon
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Eric J. Arts
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Denis M. Tebit
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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Corró G, Rocco CA, De Candia C, Catano G, Turk G, Mangano A, Aulicino PC, Bologna R, Sen L. Genetic and functional analysis of HIV type 1 nef gene derived from long-term nonprogressor children: association of attenuated variants with slow progression to pediatric AIDS. AIDS Res Hum Retroviruses 2012; 28:1617-26. [PMID: 22583022 DOI: 10.1089/aid.2012.0020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Among persons infected by HIV-1, the rate of progression to AIDS is multifactorial being affected by host and viral factors, including the HIV-encoded negative factor (Nef). Our aim was to define whether variations in the nef gene as well as its functions may be associated with slower HIV disease course in infected children. The proviral HIV-1 nef gene was cloned, sequenced, and compared in children with contrasting disease course: 10 long-term nonprogressors (LTNP) and six rapid progressor (RP). The CD4 and MHC-I down-modulation ability of nef alleles derived from LTNP and RP children was analyzed. We observed that only one of our 10 LTNP had a protective genetic background, and out of them, 40% had defective nef genes, carrying substitutions at the (AWLEAQ(56-61)) and the (Rxx(22-24)) domains, and that those alleles were unable of down-regulate CD4 and MHC-I. The emergence or presence of Nef L58V substitution was associated with viral attenuation, indicated by a reduction in HIV viral loads, a persistent preservation of CD4(+) T cell counts, and lack of AIDS-related symptoms. Our results demonstrate that HIV-1 perinatally infected children carrying functionally defective nef HIV-1 strains have prolonged asymptomatic phases without therapy, suggesting a relevant role of CD4 and MHC-I down-modulation Nef domains on in vivo HIV-1 pathogenesis and pediatric immunodeficiency outcome.
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Affiliation(s)
- Guillermo Corró
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Prof. Dr. Juan P. Garran,” Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Carlos A Rocco
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Prof. Dr. Juan P. Garran,” Buenos Aires, Argentina
| | - Cristian De Candia
- National Reference Center for AIDS, University of Buenos Aires, Buenos Aires, Argentina
| | - Gabriel Catano
- Veterans Administration Research Center for AIDS and HIV-1 Infection, South Texas Veterans Health Care System and Department of Medicine, University of Texas Health Science Care at San Antonio, San Antonio, Texas
| | - Gabriela Turk
- National Reference Center for AIDS, University of Buenos Aires, Buenos Aires, Argentina
| | - Andrea Mangano
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Prof. Dr. Juan P. Garran,” Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Paula C. Aulicino
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Prof. Dr. Juan P. Garran,” Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Rosa Bologna
- Servicio de Infectología, Hospital de Pediatría “Prof. Dr. Juan P. Garrahan,” Buenos Aires, Argentina
| | - Luisa Sen
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría “Prof. Dr. Juan P. Garran,” Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
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Saladini F, Foley BT, Rosi A, Vicenti I, Nannetti G, Meini G, Razzolini F, Zazzi M. Near full-length sequence analysis of HIV type 1 BF recombinants from Italy. AIDS Res Hum Retroviruses 2012; 28:299-303. [PMID: 21740272 DOI: 10.1089/aid.2011.0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recombination between HIV-1 subtypes B and F has generated several circulating and unique recombinant forms, particularly in Latin American areas. In Italy, subtype B is highly prevalent while subtype F is the most common pure non-B subtype. To investigate the recombination pattern in Italian BF recombinant viruses, we characterized full-length sequences derived from 15 adult patients, mostly Italian and infected by the heterosexual route. One of the BF mosaics was a CRF29, three sequences clustered with low bootstrap values with CRF39, CRF40, and CRF42. With the exception of the CRF29-like sequence, the other recombination patterns were unique, but two possible clusters were identified. Analysis of the gp120 V3 domain suggested a possible link with subtype F from Eastern Europe rather than from Latin America, favoring the hypothesis of local recombination between clade B and F viruses over that of import of BF recombinants from Latin America. HIV-1 subtypes B and F appear prone to generation of unique recombinants in Italy, warranting epidemiological surveillance and investigation of a possible clinical significance.
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Affiliation(s)
- Francesco Saladini
- Section of Microbiology, Department of Biotechnology, University of Siena, Siena, Italy
| | - Brian T. Foley
- HIV Databases, T-6, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Andrea Rosi
- Section of Microbiology, Department of Biotechnology, University of Siena, Siena, Italy
| | - Ilaria Vicenti
- Section of Microbiology, Department of Biotechnology, University of Siena, Siena, Italy
| | - Giulio Nannetti
- Section of Microbiology, Department of Biotechnology, University of Siena, Siena, Italy
| | - Genny Meini
- Section of Microbiology, Department of Biotechnology, University of Siena, Siena, Italy
| | - Francesca Razzolini
- Section of Microbiology, Department of Biotechnology, University of Siena, Siena, Italy
| | - Maurizio Zazzi
- Section of Microbiology, Department of Biotechnology, University of Siena, Siena, Italy
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The Use of Bioinformatics for Studying HIV Evolutionary and Epidemiological History in South America. AIDS Res Treat 2011; 2011:154945. [PMID: 22162803 PMCID: PMC3226295 DOI: 10.1155/2011/154945] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 08/19/2011] [Indexed: 12/03/2022] Open
Abstract
The South American human immunodeficiency virus type 1 (HIV-1) epidemic is driven by several subtypes (B, C, and F1) and circulating and unique recombinant forms derived from those subtypes. Those variants are heterogeneously distributed around the continent in a country-specific manner. Despite some inconsistencies mainly derived from sampling biases and analytical constrains, most of studies carried out in the area agreed in pointing out specificities in the evolutionary dynamics of the circulating HIV-1 lineages. In this paper, we covered the theoretical basis, and the application of bioinformatics methods to reconstruct the HIV spatial-temporal dynamics, unveiling relevant information to understand the origin, geographical dissemination and the current molecular scenario of the HIV epidemic in the continent, particularly in the countries of Southern Cone.
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Mónaco DC, Rodríguez AM, Pascutti MF, Carobene M, Falivene J, Gómez A, Maeto C, Turk G, Nájera JL, Esteban M, Gherardi MM. T-cell immune responses against Env from CRF12_BF and subtype B HIV-1 show high clade-specificity that can be overridden by multiclade immunizations. PLoS One 2011; 6:e17185. [PMID: 21364754 PMCID: PMC3041790 DOI: 10.1371/journal.pone.0017185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Indexed: 11/28/2022] Open
Abstract
Background The extreme genetic diversity of the human immunodeficiency virus type 1 (HIV-1) poses a daunting challenge to the generation of an effective AIDS vaccine. In Argentina, the epidemic is characterized by the high prevalence of infections caused by subtype B and BF variants. The aim of this study was to characterize in mice the immunogenic and antigenic properties of the Env protein from CRF12_BF in comparison with clade B, employing prime-boost schemes with the combination of recombinant DNA and vaccinia virus (VV) vectors. Methodology/Principal Findings As determined by ELISPOT from splenocytes of animals immunized with either EnvBF or EnvB antigens, the majority of the cellular responses to Env were found to be clade-specific. A detailed peptide mapping of the responses reveal that when there is cross-reactivity, there are no amino acid changes in the peptide sequence or were minimal and located at the peptide ends. In those cases, analysis of T cell polifunctionality and affinity indicated no differences with respect to the cellular responses found against the original homologous sequence. Significantly, application of a mixed immunization combining both clades (B and BF) induced a broader cellular response, in which the majority of the peptides targeted after the single clade vaccinations generated a positive response. In this group we could also find significant cellular and humoral responses against the whole gp120 protein from subtype B. Conclusions/Significance This work has characterized for the first time the immunogenic peptides of certain EnvBF regions, involved in T cell responses. It provides evidence that to improve immune responses to HIV there is a need to combine Env antigens from different clades, highlighting the convenience of the inclusion of BF antigens in future vaccines for geographic regions where these HIV variants circulate.
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Affiliation(s)
- Daniela C. Mónaco
- Centro Nacional de Referencia para el SIDA, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ana M. Rodríguez
- Centro Nacional de Referencia para el SIDA, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María F. Pascutti
- Centro Nacional de Referencia para el SIDA, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mauricio Carobene
- Centro Nacional de Referencia para el SIDA, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juliana Falivene
- Centro Nacional de Referencia para el SIDA, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alejandro Gómez
- Centro Nacional de Referencia para el SIDA, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cynthia Maeto
- Centro Nacional de Referencia para el SIDA, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gabriela Turk
- Centro Nacional de Referencia para el SIDA, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - José L. Nájera
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma, Madrid, Spain
| | - Mariano Esteban
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma, Madrid, Spain
| | - M. Magdalena Gherardi
- Centro Nacional de Referencia para el SIDA, Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail:
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Tebit DM, Arts EJ. Tracking a century of global expansion and evolution of HIV to drive understanding and to combat disease. THE LANCET. INFECTIOUS DISEASES 2011; 11:45-56. [PMID: 21126914 DOI: 10.1016/s1473-3099(10)70186-9] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Aulicino PC, Bello G, Guimaraes ML, Ruchansky D, Rocco C, Mangano A, Morgado MG, Sen L. Longitudinal analysis of HIV-1 BF1 recombinant strains in vertically infected children from Argentina reveals a decrease in CRF12_BF pol gene mosaic patterns and high diversity of BF unique recombinant forms. INFECTION GENETICS AND EVOLUTION 2010; 11:349-57. [PMID: 21130901 DOI: 10.1016/j.meegid.2010.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 11/02/2010] [Accepted: 11/18/2010] [Indexed: 11/27/2022]
Abstract
The HIV-1 epidemic associated to BF1 recombinants in South America is both complex and intriguing, with an underestimated diversity of recombinant structures. Our aim was to explore the characteristics and temporal dynamics of the HIV-1 BF1 epidemic in Argentina, through the study of 172 HIV-1 pol BF1 recombinant sequences obtained from HIV-1 vertically infected patients born from 1986 to 2008. Recombination patterns were characterized by bootscanning, subtype signature analysis, and phylogenetic approaches. Proportion of sequences sharing common ancestry and recombination breakpoints with the Circulating Recombinant Form (CRF) CRF12_BF was compared against sequences with a non-CRF12_BF pattern in three study periods, and by fitting the data to a logistic model. Twenty-eight HIV-1 pol BF1 mosaic structures were identified, including four of the seven South-American CRF_BF-like patterns. However, common ancestry of these sequences with reference CRF strains only confirmed the presence of CRF12_BF (51.1%) and CRF17_BF (1.2%) among the Argentine BF pol sequences. Most non-CRF_BF-like recombinant patterns shared at least one common recombination breakpoint with CRF12_BF. The number of transmissions caused by CRF12_BF viruses decreased in a linear way over time, from 69% in the period 1986-1993 to 46% in 2001-2008. In conclusion, the diversity of HIV-1 pol BF1 recombinant structures in Argentina is much more complex than previously described, with at least two CRFs_BF and 26 BF1 unique recombinant forms. For the first time, we provide evidence of a decrease in the proportion of CRF12_BF viruses transmitted from mother-to-child since the start of the epidemic to the present time in Argentina.
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Affiliation(s)
- Paula C Aulicino
- Laboratorio de Biología Celular y Retrovirus-CONICET, Hospital de Pediatría J.P. Garrahan, Buenos Aires, Argentina.
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8
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De Candia C, Espada C, Duette G, Ghiglione Y, Turk G, Salomón H, Carobene M. Viral replication is enhanced by an HIV-1 intersubtype recombination-derived Vpu protein. Virol J 2010; 7:259. [PMID: 20920359 PMCID: PMC2967538 DOI: 10.1186/1743-422x-7-259] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/04/2010] [Indexed: 01/02/2023] Open
Abstract
Background Multiple HIV-1 intersubtype recombinants have been identified in human populations. Previous studies from our lab group have shown that the epidemic in Argentina is characterized by the high prevalence of a circulating recombinant form, CRF12_BF, and many related BF recombinant forms. In these genomic structures a recombination breakpoint frequently involved the vpu coding region. Due to the scarce knowledge of Vpu participation in the virion release process and its impact on pathogenesis and of the functional capacities of intersubtype recombinant Vpu proteins, the aim of this work was to perform a comparative analysis on virion release capacity and relative replication capacity among viral variants harboring either a BF recombinant Vpu or a subtype B Vpu. Results Our results showed that BF recombinant Vpu was associated to an increased viral particles production when compared to WT B variant in tetherin-expressing cell lines. This observation was tested in the context of a competition assay between the above mentioned variants. The results showed that the replication of the BF Vpu-harboring variant was more efficient in cell cultures than subtype B, reaching a higher frequency in the viral population in a short period of time. Conclusion This study showed that as a result of intersubtype recombination, a structurally re-organized HIV-1 Vpu has an improved in vitro capacity of enhancing viral replication, and provides evidence of the changes occurring in this protein function that could play an important role in the successful spread of intersubtype recombinant variants.
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Affiliation(s)
- Cristian De Candia
- National Reference Center for AIDS, Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
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9
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Ambrosioni J, Andreani G, Acuipil C, Barral R, Rabinovich R, Martinez Peralta L. Comparative reactivity of serum samples from Argentinean HIV-infected patients with V3 peptides from subtype B or BF recombinants. Arch Virol 2010; 155:2029-34. [PMID: 20835735 DOI: 10.1007/s00705-010-0785-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 07/30/2010] [Indexed: 11/28/2022]
Abstract
To analyze humoral cross-reactivity to V3 peptides from subtype B and BF recombinant forms, plasma samples from 50 HIV-1-infected patients were characterized by sequencing fragments of the env and pol genes. An in-house EIA was performed using peptides corresponding to the 15 central amino acids of the V3 loop of gp120 from subtypes B (MN, SF2) and F1 and a consensus peptide from Argentinean BF recombinants. No differences were found with respect to the infecting subtype, but significant differences were found among the peptides. Reactivity was higher against the MN and BF peptides in both groups infected with subtype B (n = 28) and BF (n = 22) recombinants than against subtype F1 and SF2 peptides.
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Affiliation(s)
- J Ambrosioni
- National Reference Center for AIDS, Microbiology Department, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
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10
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Bello G, Aulicino PC, Ruchansky D, Guimarães ML, Lopez-Galindez C, Casado C, Chiparelli H, Rocco C, Mangano A, Sen L, Morgado MG. Phylodynamics of HIV-1 circulating recombinant forms 12_BF and 38_BF in Argentina and Uruguay. Retrovirology 2010; 7:22. [PMID: 20307282 PMCID: PMC2854103 DOI: 10.1186/1742-4690-7-22] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 03/22/2010] [Indexed: 11/10/2022] Open
Abstract
Background Although HIV-1 CRF12_BF and CRF38_BF are two epidemiologically important recombinant lineages circulating in Argentina and Uruguay, little is known about their population dynamics. Methods A total of 120 "CRF12_BF-like" and 20 "CRF38_BF-like" pol recombinant sequences collected in Argentina and Uruguay from 1997 to 2009 were subjected to phylogenetic and Bayesian coalescent-based analyses to estimate evolutionary and demographic parameters. Results Phylogenetic analyses revealed that CRF12_BF viruses from Argentina and Uruguay constitute a single epidemic with multiple genetic exchanges among countries; whereas circulation of the CRF38_BF seems to be confined to Uruguay. The mean estimated substitution rate of CRF12_BF at pol gene (2.5 × 10-3 substitutions/site/year) was similar to that previously described for subtype B. According to our estimates, CRF12_BF and CRF38_BF originated at 1983 (1978-1988) and 1986 (1981-1990), respectively. After their emergence, the CRF12_BF and CRF38_BF epidemics seem to have experienced a period of rapid expansion with initial growth rates of around 1.2 year-1 and 0.9 year-1, respectively. Later, the rate of spread of these CRFs_BF seems to have slowed down since the mid-1990s. Conclusions Our results suggest that CRF12_BF and CRF38_BF viruses were generated during the 1980s, shortly after the estimated introduction of subtype F1 in South America (~1975-1980). After an initial phase of fast exponential expansion, the rate of spread of both CRFs_BF epidemics seems to have slowed down, thereby following a demographic pattern that resembles those previously reported for the HIV-1 epidemics in Brazil, USA, and Western Europe.
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Affiliation(s)
- Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil.
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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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12
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Characterization of DNA and MVA vectors expressing Nef from HIV-1 CRF12_BF revealed high immune specificity with low cross-reactivity against subtype B. Virus Res 2009; 146:1-12. [PMID: 19715734 DOI: 10.1016/j.virusres.2009.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 08/06/2009] [Accepted: 08/20/2009] [Indexed: 11/20/2022]
Abstract
The HIV epidemic in Argentina is characterized by the high prevalence of infections caused by subtype B and BF variants. In this study, the Nef protein was used as a tool to study the impact of HIV-1 BF variants in the design of future vaccines. DNA and MVA vectors expressing Nef of the CRF12_BF recombinant form of HIV-1 were generated and characterized. After the administration of single DNAprime/MVAboost immunization schedules in Balb/c mice we found that NefBF delivered from these vectors generated a response of high specificity with low cross-reactivity against subtype B. But, when a more potent response was induced after 3 priming DNA doses and a booster with MVA virus, cross-reactivity against NefB was detected, although of lower magnitude than the NefBF specific. These results will be pivotal for vaccines designs in our region, indicating that antigens from these viral variants must be considered for a future vaccine.
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13
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Ceballos A, Andreani G, Ripamonti C, Dilernia D, Mendez R, Rabinovich RD, Cárdenas PC, Zala C, Cahn P, Scarlatti G, Peralta LM. Lack of viral selection in human immunodeficiency virus type 1 mother-to-child transmission with primary infection during late pregnancy and/or breastfeeding. J Gen Virol 2009; 89:2773-2782. [PMID: 18931075 DOI: 10.1099/vir.0.83697-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mother-to-child transmission (MTCT) of human immunodeficiency virus type 1 (HIV-1) as described for women with an established infection is, in most cases, associated with the transmission of few maternal variants. This study analysed virus variability in four cases of maternal primary infection occurring during pregnancy and/or breastfeeding. Estimated time of seroconversion was at 4 months of pregnancy for one woman (early seroconversion) and during the last months of pregnancy and/or breastfeeding for the remaining three (late seroconversion). The C2V3 envelope region was analysed in samples of mother-child pairs by molecular cloning and sequencing. Comparisons of nucleotide and amino acid sequences as well as phylogenetic analysis were performed. The results showed low variability in the virus population of both mother and child. Maximum-likelihood analysis showed that, in the early pregnancy seroconversion case, a minor viral variant with further evolution in the child was transmitted, which could indicate a selection event in MTCT or a stochastic event, whereas in the late seroconversion cases, the mother's and child's sequences were intermingled, which is compatible with the transmission of multiple viral variants from the mother's major population. These results could be explained by the less pronounced selective pressure exerted by the immune system in the early stages of the mother's infection, which could play a role in MTCT of HIV-1.
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Affiliation(s)
- Ana Ceballos
- National Reference Center for AIDS, Department of Microbiology, University of Buenos Aires School of Medicine, Buenos Aires, Argentina
| | - Guadalupe Andreani
- National Reference Center for AIDS, Department of Microbiology, University of Buenos Aires School of Medicine, Buenos Aires, Argentina
| | - Chiara Ripamonti
- Viral Evolution and Transmission Unit, DIBIT - San Raffaele Scientific Institute, Milan, Italy
| | - Dario Dilernia
- National Reference Center for AIDS, Department of Microbiology, University of Buenos Aires School of Medicine, Buenos Aires, Argentina
| | - Ramiro Mendez
- National Reference Center for AIDS, Department of Microbiology, University of Buenos Aires School of Medicine, Buenos Aires, Argentina
| | - Roberto D Rabinovich
- National Reference Center for AIDS, Department of Microbiology, University of Buenos Aires School of Medicine, Buenos Aires, Argentina
| | | | - Carlos Zala
- Hospital Juan Fernández, Buenos Aires, Argentina
| | - Pedro Cahn
- Hospital Juan Fernández, Buenos Aires, Argentina
| | - Gabriella Scarlatti
- Viral Evolution and Transmission Unit, DIBIT - San Raffaele Scientific Institute, Milan, Italy
| | - Liliana Martínez Peralta
- National Reference Center for AIDS, Department of Microbiology, University of Buenos Aires School of Medicine, Buenos Aires, Argentina
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14
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Magnitude, breadth, and functional profile of T-cell responses during human immunodeficiency virus primary infection with B and BF viral variants. J Virol 2008; 82:2853-66. [PMID: 18184702 DOI: 10.1128/jvi.02260-07] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The molecular pattern of the human immunodeficiency virus (HIV) epidemic in Argentina provides an appropriate scenario to study cellular immune responses in patients with non-clade B infection. We aimed to map T-cell responses in patients infected with BF recombinant variants and compare them with those of clade B patients. Sixteen recently infected patients were enrolled and grouped by viral subtype. Nef-specific responses were evaluated with a peptide matrix-based gamma interferon (IFN-gamma) enzyme-linked immunospot (ELISPOT) assay using B and BF overlapping peptides. Cross-clade and clade-specific responses were found. A correlation between B versus BF Nef-specific responses was identified. Detailed analysis at the single-peptide level revealed that BF patients show a narrower response but greater magnitude. Nef immunodominant responses agreed with previous publications, although the B loop was targeted at an unexpectedly high frequency. The putative HLA allele(s) restricting each positive response was determined. Single-peptide level screening with two different peptide sets uncovered discordant responses (mostly caused by peptide offsetting) and allowed detection of increased breadth. Positive responses identified by ELISPOT assay were further studied by intracellular cytokine staining. These were almost exclusively mediated by CD8 T cells. Characterization of concordant responses revealed that cells show distinct functional profiles, depending on the peptide presented. Last, quality (in terms of polyfunctionality) of T cells was associated with better viral replication containment. Overall, interclade differences in the frequency of epitopes recognized, structural domains targeted, and magnitude of responses were identified. Screening T-cell responses with multiple sets increased sensitivity. Further support for the notion of polyfunctional CD8(+) T-cell requirement to better control viral replication is also provided.
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Aulicino PC, Bello G, Rocco C, Romero H, Mangano A, Morgado MG, Sen L. Description of the first full-length HIV type 1 subtype F1 strain in Argentina: implications for the origin and dispersion of this subtype in South America. AIDS Res Hum Retroviruses 2007; 23:1176-82. [PMID: 17961101 DOI: 10.1089/aid.2007.0038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 subtype F1 in South America is mainly found as part of diverse BF1 recombinant forms and only five full-length "pure" F1 strains from Brazil were characterized to date. In the present study we describe the first near full-length sequence of a nonrecombinant F1 HIV-1 strain from Argentina, and explore the epidemiological history of this subtype in South America. Three separate phylogenetic analyses were carried out: with all available F1 full-length sequences, with concatenated F1 sequences contained in F1 and BF1 strains, and with partial F1 env sequences derived from worldwide strains. All analyses were consistent in showing a local origin of the newly reported Argentine subtype F1 strain, and a common ancestry of the South American subtype F1 sequences, present either in pure or recombinant genomes. By coalescent analysis, the onset date of the HIV-1 subtype F1 epidemic in South America was estimated to be around the late 1970s. The results indicate for the first time that nonrecombinant F1 HIV-1 strains are present in Argentina, and suggest that the subtype F1 epidemic in South America was initiated by the introduction of a very small group of genetically related viruses during late 1970s.
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Affiliation(s)
- Paula C. Aulicino
- Laboratorio de Biología Celular y Retrovirus-CONICET, Hospital de Pediatría “J. P. Garrahan,” Buenos Aires, Argentina
| | - Gonzalo Bello
- Laboratory of AIDS and Molecular Immunology, Department of Immunology, Instituto Oswaldo Cruz–Fiocruz, Rio de Janeiro, Brazil
| | - Carlos Rocco
- Laboratorio de Biología Celular y Retrovirus-CONICET, Hospital de Pediatría “J. P. Garrahan,” Buenos Aires, Argentina
| | - Héctor Romero
- Laboratorio de Organización y Evolución del Genoma, Sección Biomatemáticas, Facultad de Ciencias, Universidad de la República, Uruguay
| | - Andrea Mangano
- Laboratorio de Biología Celular y Retrovirus-CONICET, Hospital de Pediatría “J. P. Garrahan,” Buenos Aires, Argentina
| | - Mariza G. Morgado
- Laboratory of AIDS and Molecular Immunology, Department of Immunology, Instituto Oswaldo Cruz–Fiocruz, Rio de Janeiro, Brazil
| | - Luisa Sen
- Laboratorio de Biología Celular y Retrovirus-CONICET, Hospital de Pediatría “J. P. Garrahan,” Buenos Aires, Argentina
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16
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Schvachsa N, Turk G, Burgard M, Dilernia D, Carobene M, Pippo M, Gómez-Carrillo M, Rouzioux C, Salomon H. Examination of real-time PCR for HIV-1 RNA and DNA quantitation in patients infected with HIV-1 BF intersubtype recombinant variants. J Virol Methods 2006; 140:222-7. [PMID: 17166599 DOI: 10.1016/j.jviromet.2006.11.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Revised: 10/30/2006] [Accepted: 11/08/2006] [Indexed: 02/08/2023]
Abstract
The impact of HIV-1 genetic diversity on the performance of laboratory testing is an issue that has to be monitored continuously. An "in-house" real-time PCR assay was developed by the Agence Nationale de Recherche sur le SIDA (ANRS) in France for viral load (VL) quantitation based on the amplification of the HIV-1 long terminal repeat (LTR) region. This technology has not been used in Argentina yet and considering the HIV-1 diversity in the country, a comparative analysis of this assay was undertaken versus the Versant HIV-1 RNA 3.0 Assay (b-DNA). The performance was assessed on 30 drug-naïve HIV-1 infected patients who were characterized previously by phylogenetic analysis of the pol and vpu gene. The results showed that there is a significant linear correlation between values of transformed viral load logarithms measured by both, bDNA and real-time PCR assay and that this assay can be used to quantify viral load in samples from BF-infected patients with the same accuracy and reliability as for B subtype samples. The use of "in-house" real-time PCR to measure DNA in PBMCs correlated strongly with the HIV-1 RNA levels in all specimens.
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Affiliation(s)
- N Schvachsa
- National Reference Center for AIDS, School of Medicine, University of Buenos Aires, Paraguay 2155 Piso 11, C1121ABG, Buenos Aires, Argentina
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17
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Aulicino PC, Holmes EC, Rocco C, Mangano A, Sen L. Extremely rapid spread of human immunodeficiency virus type 1 BF recombinants in Argentina. J Virol 2006; 81:427-9. [PMID: 17050594 PMCID: PMC1797267 DOI: 10.1128/jvi.01403-06] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The epidemic of human immunodeficiency virus type 1 (HIV-1) in Argentina is distinctive in that many infections are caused by subtype BF recombinant viruses. To determine their demographic history, we estimated the evolutionary rate, mode of population growth, and age of genetic diversity among 40 BF vpu sequences. This revealed one of the highest substitution rates reported for HIV-1, at 10.793 x 10(-3) substitutions per site per year, and a very rapid rate of population growth, with an initial mean epidemic doubling time of 3.72 months. This rapid population growth is compatible with an elevated fitness for subtype BF compared to that for "pure" B and F viruses.
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Affiliation(s)
- Paula C Aulicino
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría Garrahan, Combate de los Pozos 1881, (1245) Capital Federal, Argentina
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18
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Moncany MLJ, Dalet K, Courtois PRR. Identification of conserved lentiviral sequences as landmarks of genomic flexibility. C R Biol 2006; 329:751-64. [PMID: 17027636 PMCID: PMC7172886 DOI: 10.1016/j.crvi.2006.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 06/29/2006] [Accepted: 07/05/2006] [Indexed: 11/25/2022]
Abstract
Considering that recombinations produce quasispecies in lentivirus spreading, we identified and localized highly conserved sequences that may play an important role in viral ontology. Comparison of entire genomes, including 237 human, simian and non-primate mammal lentiviruses and 103 negative control viruses, led to identify 28 Conserved Lentiviral Sequences (CLSs). They were located mainly in the structural genes forming hot spots particularly in the gag and pol genes and to a lesser extent in LTRs and regulatory genes. The CLS pattern was the same throughout the different HIV-1 subtypes, except for some HIV-1-O strains. Only CLS 3 and 4 were detected in both negative control HTLV-1 oncornaviruses and D-particle-forming simian viruses, which are not immunodeficiency inducers and display a genetic stability. CLSs divided the virus genomes into domains allowing us to distinguish sequence families leading to the notion of ‘species self’ besides that of ‘lentiviral self’. Most of acutely localized CLSs in HIV-1s (82%) corresponded to wide recombination segments being currently reported. To cite this article: M.L.J. Moncany et al., C. R. Biologies 329 (2006).
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Affiliation(s)
- Maurice L J Moncany
- Laboratoire de biologie cellulaire et moléculaire, UFR de sciences, Université de La Rochelle, av. Michel-Crépeau, 17042 La Rochelle cedex 1, France.
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19
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Turk G, Carobene M, Monczor A, Rubio AE, Gómez-Carrillo M, Salomón H. Higher transactivation activity associated with LTR and Tat elements from HIV-1 BF intersubtype recombinant variants. Retrovirology 2006; 3:14. [PMID: 16483381 PMCID: PMC1402313 DOI: 10.1186/1742-4690-3-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Accepted: 02/16/2006] [Indexed: 01/02/2023] Open
Abstract
Background HIV-1 is characterized by its rapid genetic evolution and high diversity as a consequence of its error-prone reverse transcriptase and genetic recombination. This latter mechanism is responsible for the creation of circulating recombinant forms (CRFs) found in nature. Previous studies from our lab group have shown that the epidemic in Argentina is characterized by one highly prevalent circulating recombinant form, CRF12_BF, and many related BF recombinant forms. Since transcriptional transactivation of the HIV-1 long terminal repeat (LTR) promoter element requires the essential viral Tat protein, since these genetic structures underwent recombination in variants widely spread in South America, the aim of this work was to study transcriptional activity associated with the recombinant LTR and Tat elements. Results Differential transcriptional activity was measured for the BF recombinant LTR/Tat complex that is present in widely spread viral variants was demonstrated. This analysis demonstrated a higher activity for the BF complex when compared to its B subtype counterpart. Conclusion This study indicates structural and functional consequences of recombination events within the LTR promoter and Tat transactivator protein of a naturally occurring HIV-1 recombinant form.
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Affiliation(s)
- Gabriela Turk
- National Reference Center for AIDS, Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
| | - Mauricio Carobene
- National Reference Center for AIDS, Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
| | - Ana Monczor
- National Reference Center for AIDS, Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
| | - Andrea Elena Rubio
- National Reference Center for AIDS, Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
| | - Manuel Gómez-Carrillo
- National Reference Center for AIDS, Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
| | - Horacio Salomón
- National Reference Center for AIDS, Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
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20
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De Sá Filho DJ, Sucupira MCA, Caseiro MM, Casiero MM, Sabino EC, Diaz RS, Janini LM. Identification of two HIV type 1 circulating recombinant forms in Brazil. AIDS Res Hum Retroviruses 2006; 22:1-13. [PMID: 16438639 DOI: 10.1089/aid.2006.22.1] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recombination is an important way to generate genetic diversity. Accumulation of HIV-1 full-length genomes in databases demonstrated that recombination is pervasive in viral strains collected globally. Recombinant forms achieving epidemiological relevance are termed circulating recombinant forms (CRFs). CRF12_BF was up to now the only CRF described in South America. The objective was to identify the first CRF in Brazil conducting full genome analysis of samples sharing the same partial genome recombinant structure. Ten samples obtained from individuals residing in Santos, Brazil, sharing the same recombination pattern based on partial genome sequence data, were selected from a larger group to undergo full length genome analysis. Near full length genomes were assembled from overlapping fragments. Mosaic genomes were evaluated by Bootscan, alignment inspection, and phylogenetic analysis using neighbor joining and maximum likelihood. Full genomes were also analyzed by split decomposition. We were able to identify five mosaic genomes. Two of these structures were represented by at least three samples derived from epidemiologically unlinked individuals. These structures were named CRF28_BF and CRF29_BF and are the second and third CRFs composed exclusively by subtypes B and F as well as the second and third CRFs encountered in South America. Other recombinant forms studied here resembled CRF28_BF and CRF29_BF. Our results suggest that a diverse population of related recombinants, including CRFs may play an important part in the Brazilian and South American epidemic.
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21
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Aulicino PC, Kopka J, Mangano AM, Rocco C, Iacono M, Bologna R, Sen L. Circulation of novel HIV type 1 A, B/C, and F subtypes in Argentina. AIDS Res Hum Retroviruses 2005; 21:158-64. [PMID: 15725755 DOI: 10.1089/aid.2005.21.158] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Argentine HIV-1 epidemic is considered to be represented mainly by subtype B and diverse B/F recombinants, with apparent absence of pure subtype F. In this study we describe three novel HIV-1 variants isolated from four infants born in different and distant provinces of Argentina. Partial analysis of different gene fragments spanning 18.5-40.8% of the HIV-1 complete genome revealed two subtype A HIV-1 strains in siblings, a B/C recombinant with a novel mosaic structure, and a putative subtype F. Characteristic patterns of genomic and amino acid sequences of the newly reported subtype F isolate suggest a closer genetic relationship to Argentine B/F recombinants than any other subtype F strain described so far, while the A and B/C subtypes found correspond to unusual genotypes in Argentina. Understanding the origin, diversity, and spread of HIV-1 strains worldwide will be necessary for the development of an effective vaccine approach.
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Affiliation(s)
- Paula C Aulicino
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
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22
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Quarleri JF, Rubio A, Carobene M, Turk G, Vignoles M, Harrigan RP, Montaner JSG, Salomón H, Gómez-Carrillo M. HIV type 1 BF recombinant strains exhibit different pol gene mosaic patterns: descriptive analysis from 284 patients under treatment failure. AIDS Res Hum Retroviruses 2004; 20:1100-7. [PMID: 15585101 DOI: 10.1089/aid.2004.20.1100] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Different complex structures of the pol gene have been identified in 284 HIV-1 B/F recombinant sequences obtained from a group of 587 patients under treatment failure from Argentina. To analyze the mosaic structures of these viral sequences and to determine their phylogenetic relationship, the 284 partial pol gene sequences of BF recombinant viruses were amplified by RT-PCR and sequenced. Intersubtype breakpoints were analyzed by bootscanning. Phylogenetic relationships were determined by means of neighbor-joining trees. The analysis of the sequences showed multiple phylogenetic topologies clustering within intersubtype BF reference sequences. At least three different mosaic patterns were found compared to previously described BF-type viruses with unequal distribution in the studied population. The analysis also showed that HIV-1 BF recombinant viruses with diverse mosaic structures are phylogenetically related in their F segments and in selected B fragments with the F1 subtype and with BF recombinant viruses from Brazil, respectively, suggesting a common recombinant ancestor. No association was observed between the prevalence of each mosaic pattern and the frequency of major drug-resistance mutations in PR and RT.
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Affiliation(s)
- Jorge F Quarleri
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, 1121 Buenos Aires, Argentina.
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23
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Reggeti F, Bienzle D. Feline immunodeficiency virus subtypes A, B and C and intersubtype recombinants in Ontario, Canada. J Gen Virol 2004; 85:1843-1852. [PMID: 15218168 DOI: 10.1099/vir.0.19743-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Knowledge of the geographical distribution of feline immunodeficiency virus (FIV) subtypes is important for understanding different disease courses and for vaccine design. Intersubtype recombination may develop in areas where more than one subtype is prevalent and has the potential to create new transmittable variants with novel pathogenic properties. In this study, 40 FIV-positive DNA samples were classified by sequence analysis of the LTR-gag region. Phylogenetic analysis indicated that 32 Canadian FIV isolates clustered with previously identified subtypes A, B and C and that subtype A was most frequent in Ontario. Four strains with inconsistent clade assignment were further analysed by sequencing of the env-LTR regions. Comparisons of phylogenetic trees constructed from the two different regions of the genome and analysis of similarities to reference sequences yielded classification of three samples as A/B and one as A/C intersubtype recombinants. Although the A/B recombinant samples were obtained from unrelated cats in geographically disparate regions, a common breakpoint was consistently identified within gag. In addition, there was no evidence of co-infection with parental strains of subtypes A and B as indicated by PCR-based limiting dilution assays, although these assays allowed for the identification of two different recombinant viruses co-existing in one sample. Both sequences contained the same breakpoint. These findings suggested that a new circulating recombinant FIV may be enzootic in Ontario.
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Affiliation(s)
- F Reggeti
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - D Bienzle
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada, N1G 2W1
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Gómez-Carrillo M, Quarleri JF, Rubio AE, Carobene MG, Dilernia D, Carr JK, Salomón H. Drug resistance testing provides evidence of the globalization of HIV type 1: a new circulating recombinant form. AIDS Res Hum Retroviruses 2004; 20:885-8. [PMID: 15320992 DOI: 10.1089/0889222041725172] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To monitor HIV-1 diversity in Argentina, a phylogenetic-based analysis of HIV-1 partial pol sequences obtained for resistance testing in 587 treatment failure patients was performed in Buenos Aires city between 2001 and 2003. HIV-1 RNA was isolated from plasma samples and partial pol fragments amplified by RT-PCR. Sequences were obtained by automated sequencing. Phylogenetic analysis was performed and recombination patterns characterized. A total of 299 sequences grouped into clade B (50.94%) and 284 were B/F recombinants (48.38%). Four sequences were grouped into clades A, C, and F (0.68%). The clade C sample, 96105, was found to be a BC recombinant and samples 103396 and 104575 showed the same mosaic pattern with Kisii5009 from Kenya and 97KR004 from Korea, previously described as A2D recombinants. With the presence of two full-length genomes, one from Kenya and one from Korea, and now two partial genomes from Argentina, this recombinant is designated CRF16_A2D. Its presence on three continents shows that CRF16_A2D has a global distribution.
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Affiliation(s)
- Manuel Gómez-Carrillo
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, C1121ABG Buenos Aires, Argentina.
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25
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Espinosa A, Vignoles M, Carrillo MG, Sheppard H, Donovan R, Peralta LM, Rossi D, Radulich G, Salomón H, Weissenbacher M. Intersubtype BF Recombinants of HIV-1 in a Population of Injecting Drug Users in Argentina. J Acquir Immune Defic Syndr 2004; 36:630-6. [PMID: 15097307 DOI: 10.1097/00126334-200405010-00012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The presence of recombinant intersubtypes of HIV-1 in Argentina has been reported since the mid-1990s. In this study, sequences of a region of the gag, pol, and vpu genes of HIV-1 were analyzed in samples of 21 injection drug users (IDUs) residing in the suburbs of the city of Buenos Aires. Genomic characterization and identification of recombination sites were made comparing the 3 regions with reference isolation sequences of subtypes B, F, C, A, and B/F recombinants: CRF12_BF and non-CRF12_BF sequences. Subtype assignment of the analyzed segments was phylogenetically confirmed. All the samples turned out to be BF recombinants in at least 1 of the 3 studied genes. Twelve samples (57%) had the same pattern as the Argentinean CRF12_BF, whereas in the rest, the pattern differed in at least 1 of the 3 genes. The relation of these fragments to the CRF12_BF was phylogenetically verified. These results indicate the predominance of BF recombinants and the presence of a high percentage of sequences closely related to the CRF12_BF in the IDU population in Argentina and suggest a possible association between viral variants and the transmission route.
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Affiliation(s)
- Alex Espinosa
- Viral and Rickettsial Disease Laboratory, California Department of Health Services, Richmond, CA, USA
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Hierholzer J, Montano S, Hoelscher M, Negrete M, Hierholzer M, Avila MM, Carrillo MG, Russi JC, Vinoles J, Alava A, Acosta ME, Gianella A, Andrade R, Sanchez JL, Carrion G, Sanchez JL, Russell K, Robb M, Birx D, McCutchan F, Carr JK. Molecular Epidemiology of HIV Type 1 in Ecuador, Peru, Bolivia, Uruguay, and Argentina. AIDS Res Hum Retroviruses 2002; 18:1339-50. [PMID: 12487805 DOI: 10.1089/088922202320935410] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Surveillance for HIV infection among people at increased risk was conducted in five countries in South America. Seroprevalence studies were conducted in more than 36,000 people in Ecuador, Peru, Boliva, Uruguay, and Argentina, along with genetic analysis of the HIV-1 strains. In all countries, the prevalence of HIV-1 among men who have sex with men (MSM) was high (3-30%), whereas the prevalence among female commercial sex workers (FCSMs) was low (0.3-6%). By envelope heteroduplex mobility assay, subtype B predominated in MSM communities and in FCSWs in Ecuador, Bolivia, and Peru. A new genetic screening assay, the multiregion hybridization assay for subtypes B and F (MHA-bf), was developed to improve large-scale genetic screening in South America. MHA-bf can screen four regions of the genome for subtype B or subtype F, and thus can detect most recombinants. The sensitivity of MHA-bf when applied to a panel of pure subtypes and CRF12_BF was 100%, and 88% of unique recombinants were also detected as recombinant. Using MHA-bf, more than 80% of samples from Ecuador, Peru, and Bolivia were classified as pure subtype B, whereas in Uruguay and Argentina this proportion was only 30 to 40%. BF recombinants were the most prevalent form of HIV-1 in Uruguay and Argentina. Subtype B is the most common subtype in countries lacking injecting drug use (IDU) epidemics, whereas BF recombinants are more common in countries where extensive IDU epidemics have been documented, suggesting the ontogeny of recombinant strains in particular risk groups in South America.
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Affiliation(s)
- Jesse Hierholzer
- U.S. Military HIV Research Program, Henry M. Jackson Foundation, Rockville, Maryland 20850, USA
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