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Shankarappa R, Mullins JI. Inferring viral population structures using heteroduplex mobility and DNA sequence analyses. J Virol Methods 2013; 194:169-77. [PMID: 23994080 DOI: 10.1016/j.jviromet.2013.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 08/08/2013] [Accepted: 08/09/2013] [Indexed: 11/19/2022]
Abstract
Heteroduplex mobility (HMA) and tracking assays (HTA) are used to assess genetic relationships between DNA molecules. While distinguishing relationships between clonal or nearly clonal molecules is relatively straightforward, inferring population structures is more complex. To address this issue, HIV-1 quasispecies with varying levels of diversity were studied using both HTA and DNA sequencing. Viral diversity estimates and the temporal features of virus evolution were found to be generally concordant between HTA and DNA sequencing. In addition, the distribution of pairwise differences and the rates of virus divergence were similar between the two methods. These findings support the use of HTA to characterize variant populations of DNA and strengthen previous inferences concerning the evolution of HIV-1 over the course of infection.
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Affiliation(s)
- Raj Shankarappa
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-8070, United States
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Guimarães ML, Velarde-Dunois KG, Segurondo D, Morgado MG. The HIV-1 epidemic in Bolivia is dominated by subtype B and CRF12_BF "family" strains. Virol J 2012; 9:19. [PMID: 22248191 PMCID: PMC3285048 DOI: 10.1186/1743-422x-9-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 01/16/2012] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Molecular epidemiological studies of HIV-1 in South America have revealed the occurrence of subtypes B, F1 and BF1 recombinants. Even so, little information concerning the HIV-1 molecular epidemiology in Bolivia is available. In this study we performed phylogenetic analyses from samples collected in Bolivia at two different points in time over a 10 year span. We analyzed these samples to estimate the trends in the HIV subtype and recombinant forms over time. MATERIALS AND METHODS Fifty one HIV-1 positive samples were collected in Bolivia over two distinct periods (1996 and 2005). These samples were genetically characterized based on partial pol protease/reverse transcriptase (pr/rt) and env regions. Alignment and neighbor-joining (NJ) phylogenetic analyses were established from partial env (n = 37) and all pol sequences using Mega 4. The remaining 14 env sequences from 1996 were previously characterized based on HMA-env (Heteroduplex mobility assay). The Simplot v.3.5.1 program was used to verify intragenic recombination, and SplitsTree 4.0 was employed to confirm the phylogenetic relationship of the BF1 recombinant samples. RESULTS Phylogenetic analysis of both env and pol regions confirmed the predominance of "pure" subtype B (72.5%) samples circulating in Bolivia and revealed a high prevalence of BF1 genotypes (27.5%). Eleven out of 14 BF1 recombinants displayed a mosaic structure identical or similar to that described for the CRF12_BF variant, one sample was classified as CRF17_BF, and two others were F1pol/Benv. No "pure" HIV-1 subtype F1 or B" variant of subtype B was detected in the present study. Of note, samples characterized as CRF12_BF-related were depicted only in 2005. CONCLUSION HIV-1 genetic diversity in Bolivia is mostly driven by subtype B followed by BF1 recombinant strains from the CRF12_BF "family". No significant temporal changes were detected between the mid-1990s and the mid-2000s for subtype B (76.2% vs 70.0%) or BF1 recombinant (23.8% vs 30.0%) samples from Bolivia.
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Affiliation(s)
- Monick L Guimarães
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil.
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Rubio EV, Candia P, Lattes K. Transmisión vertical de VIH y sida: realidad epidemiológica del Cono Sur. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s0304-5013(09)72331-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Stefani MMA, Pereira GAS, Lins JAB, Alcantara KC, Silveira AA, Viegas AA, Maya NC, Mussi AH. Molecular screening shows extensive HIV-1 genetic diversity in Central West Brazil. J Clin Virol 2007; 39:205-9. [PMID: 17537671 DOI: 10.1016/j.jcv.2007.04.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Revised: 04/11/2007] [Accepted: 04/14/2007] [Indexed: 12/01/2022]
Abstract
BACKGROUND Information is limited about HIV-1 subtypes circulating in less populated Brazilian areas where the AIDS epidemic is expanding, such as in the Central West region. OBJECTIVE To describe HIV-1 subtypes in patients from the States of Goias, Mato Grosso do Sul and Mato Grosso in Central West Brazil. STUDY DESIGN Heteroduplex mobility analysis of nested-PCR products from env (primers: ED5/ED12, ES7/ES8) and gag regions (primers: H1P202/H1G777, H1Gag1584/g17) of 406 HIV-1 isolates from Goias (n=271), Mato Grosso do Sul (n=85) and Mato Grosso (n=50) collected from 2001 to 2004. RESULTS Median age of patients was 26 years (1-79 range), 68.7% (279/406) females, 69.9% (269/385) sexual exposure, 14.3% parenteral risk, 15.8% vertical cases. Overall 69.9% (284/406) of HIV-1 subtypes were concordant B(env)/B(gag), 1.7% F(env)/F(gag) and 1% C(env)/C(gag). Discordant HIV-1 isolates were 14.5% (59/406), mainly B(env)/F(gag) and F(env)/B(gag) (49/59); five were B(env)/D(gag), four B(env)/C(gag) and one C(env)/D(gag). B/B and discordant B/F isolates were detected among all risk categories and among children and adults. CONCLUSION Extensive genetic diversity of HIV-1 was observed in Central West Brazil. Continued molecular studies should monitor the changing dynamics of HIV-1 over time especially in areas where the epidemic is growing.
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Affiliation(s)
- Mariane M A Stefani
- Tropical Pathology and Public Health Institute, Federal University of Goias, Rua Delenda Rezende de Melo s/n, Setor Universitario, 74.605-050 Goiania, Goias, Brazil.
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Bastos FI, Hacker MA. Pesquisas brasileiras biomédicas e epidemiológicas face às metas da UNGASS. Rev Saude Publica 2006; 40 Suppl:31-41. [PMID: 16729157 DOI: 10.1590/s0034-89102006000800006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
O foco do estudo é a resposta brasileira em Ciência, Tecnologia e Inovação às metas formuladas no documento da UNGASS. Foram analisados os itens 70-73 que integram o documento Draft Declaration of Commitment for the UNGASS on HIV/AIDS, 2001, que definem metas para a Ciência, Tecnologia e Inovação em HIV/Aids. Os principais tópicos listados nesses itens foram operacionalizados sob a forma de "palavras-chave", de modo a orientar buscas sistemáticas nos bancos de dados padrão em biomedicina, incluindo ainda o Web of Science, nas suas subdivisões referentes às ciências naturais e sociais. O sucesso da pesquisa brasileira no âmbito da caracterização e isolamento do HIV-1 é inegável. Estudos vacinais fases II/III têm sido desenvolvidos no Rio de Janeiro, Belo Horizonte e São Paulo. O monitoramento da resistência primária teve estudos empíricos desenvolvidos em populações específicas, por meio da "Rede Brasileira em Monitoramento da Resistência do HIV". No âmbito do monitoramento da resistência secundária, destacaram-se iniciativas como a Rede Nacional de Genotipagem. Dois sistemas nacionais, o Sistema de Informações de Mortalidade e o Sistema de Informações de Agravos de Notificação - Aids e alguns estudos de maior abrangência têm dado origem a trabalhos sobre tendências da epidemia. A produção de medicamentos genéricos de qualidade e sua distribuição gratuita aos pacientes foram destacadas. O Brasil tem implementado uma resposta consistente e diversificada no âmbito do HIV/Aids, com estudos referentes ao desenvolvimento de vacinas, novos medicamentos e monitoramento da epidemia.
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Affiliation(s)
- Francisco Inácio Bastos
- Departamento de Informações em Saúde, Centro de Informação Científica e Tecnológica, Fundação Oswaldo Cruz, 21040-900 Rio de Janeiro, RJ, Brazil.
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Brígido LFM, Franco HM, Custódio RM, Oliveira CAF, P Ferreira JL, Eira M, Bergel F, Araújo F, Carvalheiro JR, Rodrigues R. Molecular characteristics of HIV type 1 circulating in São Paulo, Brazil. AIDS Res Hum Retroviruses 2005; 21:673-82. [PMID: 16060840 DOI: 10.1089/aid.2005.21.673] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Partial sequences of HIV-1 polymerase from 185 patients, 141 ARV experienced and 44 naive, of gag (p24) and env (C2V3) from a subset of naive cases were evaluated in São Paulo, Brazil. Antiretroviral resistance mutations were detected in 4% of 26 recently (<2 years) infected patients. Polymorphisms at the protease gene were common both in contemporary and pre-HAART era isolates, some significantly associated with the viral clade. HIV-1 clade B was preponderant, in 79%, with 11% clade F and one case of HIV-1 C. Recently infected women had a significantly higher proportion of non-B clade HIV-1. A mosaic pol was observed in 9%, all B/F except for one G mosaic. A CRF-12-BF structure, observed in 20% of B/F pol mosaics, provides evidence for an epidemic relationship in the major South American metropolitan areas.
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Affiliation(s)
- Luis F M Brígido
- Retrovirus Laboratory, Virology Service, Adolfo Lutz Institute, São Paulo, Brazil
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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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Castro E, Echeverría G, Deibis L, González de Salmen B, Dos Santos Moreira A, Guimarães ML, Bastos FI, Morgado MG. Molecular epidemiology of HIV-1 in Venezuela: high prevalence of HIV-1 subtype B and identification of a B/F recombinant infection. J Acquir Immune Defic Syndr 2003; 32:338-44. [PMID: 12626896 DOI: 10.1097/00126334-200303010-00015] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The authors assessed HIV-1 variability in two distinct areas of Venezuela (the capital Caracas and Margarita Island) through the analysis of blood specimens and clinical and epidemiologic data of 72 persons. Proviral DNA was evaluated through heteroduplex mobility assay (HMA) based on the envelope region. Additionally, FOK I restriction enzyme digestion assay was performed in all subtype B ED31/33 amplified products to check the presence of the typical Brazilian subtype B GWGR variant. Sequencing and phylogenetic analysis for C2-V3 region of gp120 was performed in selected cases. The vast majority of samples were found to belong to subtype B, with a North American/European RFLP profile. An F subtype HIV-1 based on the region was identified for the first time in Venezuela. Genetic analyses of the protease and reverse transcriptase fragments of this sample depicted a recombinant B/F genetic profile. The discrimination capacity of HIV-1 subtypes using the primer set ED3/14-ED31/33 among the Caracas samples was found to be higher than for those from Margarita Island. The authors' results point to relevant differences between the samples of continental and Caribbean regions of Venezuela, requiring further evaluation of larger samples.
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Affiliation(s)
- Erika Castro
- Department of Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
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Morgado MG, Guimarães ML, Galvão-Castro B. HIV-1 polymorphism: a challenge for vaccine development - a review. Mem Inst Oswaldo Cruz 2002; 97:143-50. [PMID: 12016434 DOI: 10.1590/s0074-02762002000200001] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The perspective for the development of anti-HIV/AIDS vaccines became a target sought by several research groups and pharmaceutical companies. However, the complex virus biology in addition to a striking genetic variability and the limited understanding of the immunological correlates of protection have made this an enormous scientific challenge not overcome so far. In this review we presented an updating of HIV-1 subtypes and recombinant viruses circulating in South American countries, focusing mainly on Brazil, as one of the challenges for HIV vaccine development. Moreover, we discussed the importance of stimulating developing countries to participate in the process of vaccine evaluation, not only testing vaccines according to already defined protocols, but also working together with them, in order to take into consideration their local information on virus diversity and host genetic background relevant for the vaccine development and testing, as well as including local virus based reagents to evaluate the immunogenicity of the candidate vaccines.
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Affiliation(s)
- M G Morgado
- Laboratório de AIDS e Imunologia Molecular, Departamento de Imunologia, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, 21045-900, Brasil.
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Thomson MM, Delgado E, Herrero I, Villahermosa ML, Vázquez-de Parga E, Cuevas MT, Carmona R, Medrano L, Pérez-Álvarez L, Cuevas L, Nájera R. Diversity of mosaic structures and common ancestry of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Argentina revealed by analysis of near full-length genome sequences. J Gen Virol 2002; 83:107-119. [PMID: 11752707 DOI: 10.1099/0022-1317-83-1-107] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The findings that BF intersubtype recombinant human immunodeficiency type 1 viruses (HIV-1) with coincident breakpoints in pol are circulating widely in Argentina and that non-recombinant F subtype viruses have failed to be detected in this country were reported recently. To analyse the mosaic structures of these viruses and to determine their phylogenetic relationship, near full-length proviral genomes of eight of these recombinant viruses were amplified by PCR and sequenced. Intersubtype breakpoints were analysed by bootscanning and examining the signature nucleotides. Phylogenetic relationships were determined with neighbour-joining trees. Five viruses, each with predominantly subtype F genomes, exhibited mosaic structures that were highly similar. Two intersubtype breakpoints were shared by all viruses and seven by the majority. Of the consensus breakpoints, all nine were present in two viruses, which exhibited identical recombinant structures, and four to eight breakpoints were present in the remaining viruses. Phylogenetic analysis of partial sequences supported both a common ancestry, at least in part of their genomes, for all recombinant viruses and the phylogenetic relationship of F subtype segments with F subtype viruses from Brazil. A common ancestry of the recombinants was supported also by the presence of shared signature amino acids and nucleotides, either unreported or highly unusual in F and B subtype viruses. These results indicate that HIV-1 BF recombinant viruses with diverse mosaic structures, including a circulating recombinant form (which are widespread in Argentina) derive from a common recombinant ancestor and that F subtype segments of these recombinants are related phylogenetically to the F subtype viruses from Brazil.
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MESH Headings
- Argentina
- Base Sequence
- DNA, Viral
- Female
- Gene Products, gag/genetics
- Gene Products, gag/physiology
- Gene Products, rev/genetics
- Gene Products, rev/physiology
- Genetic Variation
- Genome, Viral
- HIV Antigens/genetics
- HIV Antigens/physiology
- HIV Envelope Protein gp41/genetics
- HIV Envelope Protein gp41/physiology
- HIV Infections/virology
- HIV Reverse Transcriptase/genetics
- HIV Reverse Transcriptase/physiology
- HIV-1/classification
- HIV-1/genetics
- Human Immunodeficiency Virus Proteins
- Humans
- Male
- Molecular Sequence Data
- Mosaicism
- Phylogeny
- Protein Structure, Tertiary
- Recombination, Genetic
- Sequence Analysis, Protein
- Sequence Analysis, RNA
- Viral Proteins
- Viral Regulatory and Accessory Proteins/genetics
- Viral Regulatory and Accessory Proteins/physiology
- gag Gene Products, Human Immunodeficiency Virus
- rev Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- Michael M Thomson
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Elena Delgado
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Isabel Herrero
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - María Luisa Villahermosa
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Elena Vázquez-de Parga
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - María Teresa Cuevas
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Rocío Carmona
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Leandro Medrano
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Lucía Pérez-Álvarez
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Laureano Cuevas
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Rafael Nájera
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
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