Phylogenetic Analysis of Brazilian HIV Type 1 Subtype D Strains: Tracing the Origin of This Subtype in Brazil

Couto-Fernandez, José Carlos; Eyer-Silva, Walter de Araújo; Guimarães, Monick Lindenmeyer; Chequer-Fernandez, Saada L.; Grinsztejn, Beatriz; Delaporte, Eric; Peeters, Martine; Morgado, Mariza G.

doi:10.1089/aid.2006.22.207

Cited by 24 publications

(16 citation statements)

References 16 publications

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“…For instance, 60.2% of patients from Saquarema were born elsewhere, whereas the corresponding figures for Santo Antonio de Pádua and Miracema were 20.6% and 11.1%, respectively (p < 0.01). In agreement with our previous studies (Eyer-Silva & Morgado 2006), patients whose sequences fell within a cluster were significantly more likely to have a known epidemiologic relationship within the cohort and to always have lived in the studied city.…”

Section: Discussionsupporting

confidence: 92%

“…In spite of being a relatively conserved region of the HIV-1 genome, the polymerase gene has been shown to contain enough phylogenetic signal for subtyping analysis (Cornelissen et al 1997) and to allow studies of epidemiologic relationships between populations, groups and people (Hue et al 2004, Eyer-Silva & Morgado 2006. Sequences were deposited on the GenBank database under accession numbers DQ899721 through DQ899721 and EF042627 through EF042690.…”

Section: Patients Materials and Methodsmentioning

confidence: 99%

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Autochthonous horizontal transmission of a CRF02_AG strain revealed by a human immunodeficiency virus type 1 diversity survey in a small city in inner state of Rio de Janeiro, Southeast Brazil

Eyer-Silva

Morgado

2007

Mem. Inst. Oswaldo Cruz

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Key words: Brazil -CRF02_AG -human immunodeficiency virus type 1 -molecular epidemiology -transmission clustersThe extremely high genetic diversity of human immunodeficiency virus type 1 (HIV-1) has been successfully used to study the regional and global distribution of different viral groups and subtypes (Hu et al. 1996) and makes it possible to trace patterns of viral spread between populations, groups and people (Kuiken et al. 2000). Phylogenetic analysis allows classification of HIV-1 strains into three groups: M, N and O. The M (main) group, the widest spread, has been further subdivided into at least nine subtypes (A-D, F-H, J, and K) and 32 circulating recombinant forms (CRF), whereas a high diversity of unique intersubtype recombinant forms has also been demonstrated (Leitner et al. 2005). In Brazil, molecular analyses of HIV-1 nucleotide sequences have shown an epidemic driven mainly by three group M subtypes: B, C, and subsubtype F1 (heretofore designated subtype F1), as well as a myriad of unique BF1 intersubtype recombinants (Morgado et al. 1998, Tanuri et al. 1999, Vicente et al. 2000, Soares et al. 2003. Isolated cases of other subtypes, such as subtype D (Morgado et al. 1998, CoutoFernandez et al. 2006), subtype A (Caride et al. 2000, CRF02_AG (Pires et al. 2004, Couto-Fernandez et al. 2005), CRF28_BF and CRF29_BF (De Sa Filho et al. 2006 have also been reported.Phylogenetic analyses of HIV-1 nucleotide sequences are being increasingly used to better understand epidemiological patterns of viral spread. Such studies have proven to be invaluable to clarify the routes of viral transmission in community settings (Holmes et al. 1995, Brown et al. 1997, to establish (Ou et al. 1992, Blanchard et al. 1998 or rule out (Holmes et al. 1993, Jaffe et al. 1994) iatrogenic viral transmission, to study the pathways of viral spread among clusters of patients (Leitner et al. 1996, Robbins et al. 2002, to trace the geographic origin of recently introduced subtypes (Gao et al. 1996, Kato et al. 1999, Yu et al. 2001, CoutoFernandez et al. 2006, to infer the demographic history and date of origin of epidemic spread (Robbins et al. 2003, Bello et al. 2006, to investigate unusual forms of viral transmission (Goujon et al. 2000, Andreo et al. 2004, and has also found forensic applications (Albert et al. 1994, Banaschak et al. 2000, Metzker et al. 2002, Lemey et al. 2005. Phylogenetic analyses of HIV-1 sequences have also been used to provide evidence of a high incidence molecular profile, as evidenced by multiple transmission clusters, low level of sequence diversity and signature amino acid substitutions (Liitsola et al. 1998, Oelrichs et al. 2000, Shankarappa et al. 2001, Nguyen et al. 2002, and of an old and mature epidemic pattern, given the high sequence diversity and the absence of transmission clusters (Vidal et al. 2000, Trask et al. 2002.It is known that the AIDS epidemic in Brazil is spreading from the large urban centers towards small cities and the innermost parts of the country (Szwarcwald et al. 20...

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Section: Discussionsupporting

confidence: 92%

Section: Patients Materials and Methodsmentioning

confidence: 99%

Autochthonous horizontal transmission of a CRF02_AG strain revealed by a human immunodeficiency virus type 1 diversity survey in a small city in inner state of Rio de Janeiro, Southeast Brazil

Eyer-Silva

Morgado

2007

Mem. Inst. Oswaldo Cruz

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“…Interestingly, although reported previously in Rio de Janeiro (Janini et al 1996, Couto-Fernandez et al 2006, subtype D was not identified in our study. Although the observed frequency of subtype F (9.3%) in our study was similar to other Southeastern states' observations, CoutoFernandez et al (2005) reported a lower frequency (4.9%) of subtype F among samples from Rio de Janeiro HIV patients.…”

Section: Discussioncontrasting

confidence: 87%

Human immunodeficiency virus type- 1 subtypes of infected patients in Espírito Santo, Brazil

Cabral

Cunha

Magalhaes

et al. 2006

Mem. Inst. Oswaldo Cruz

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Genetic variability of human immunodeficiency virus type - 1(HIV-1) is a potential threat for both diagnosis and treatment of HIV/AIDS, as well as the development of effective vaccines. Up to now, HIV subtypes circulating among HIV-positive patients in the state of Espírito Santo were not known. In the present study, blood samples from 100 therapy-naïve HIV-1 infected patients were collected and the HIV subtype was determined through the Heteroduplex Mobility Assay (HMA). Ninety-seven out of 100 studied samples were subtyped by HMA, 73 samples (75.2%) were from subtype B, 9 (9.3%) from subtype F, 3 (3.1%) from subtype C, 6 (6.2%) Benv/Fgag, and another 6 (6.2%) Fenv/Bgag, what suggests that recombinant viruses were present in the studied samples. Twenty-eight percent of the subtype B samples were represented by the Brazilian B" subtype, which were identified by RFLP with Fok I. Data presented here demonstrate that the epidemiological characteristics of the HIV epidemic in the state of Espírito Santo are similar to those from the other Southeastern states and helped to better understand the genetic polymorphism of HIV in Brazil

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“…4 Other Brazilian regions, except the south, show a similar pattern, with occasional detection of other non-B clades. [5][6][7][8][9] HIV diversity data from other countries in South America also suggest that HIV-1 B is the most frequent clade, with HIV-1 F1 and BF mosaics especially important in Argentina and Uruguay. 10,11 The southern States of Brazil, Rio Grande do Sul (RS, Site I) and Santa Catarina (SC, Site II), have a population of over 16 million inhabitants.…”

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confidence: 98%

HIV Type 1 Subtype C and CB Pol Recombinants Prevail at the Cities with the Highest AIDS Prevalence Rate in Brazil

Brígido

Nunes²,

Oliveira

et al. 2007

AIDS Research and Human Retroviruses

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HIV-1 B is predominant in Brazil, but HIV-1 C has increasingly been reported in the south of the country. However, many samples clustering with clade C are actually a recombinant, with a small B segment at RT (CRF31). Samples (209) from the three cities with the highest aids prevalence rate are analyzed. Partial polymerase sequences from HIV RNA made it possible to determine HIV clades and recombination patterns and to identify primary drug resistance mutations (DRMs). The incidence was estimated with a BED assay. HIV-1 C and CRF31 patterns were twice as frequent as clade B at all sites, but the proportion of C and CRF31 patterns was significantly different among sites. The incidence estimate for SC was 2.6 persons-years. Infection in recent or younger cases showed no association with clade C. Surveillance DRM was observed in 8.3% (95% CI 5-13), mostly to NNRTIs. Clade F pol genomes had significantly more primary DRM.

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Phylogenetic Analysis of Brazilian HIV Type 1 Subtype D Strains: Tracing the Origin of This Subtype in Brazil

Cited by 24 publications

References 16 publications

Autochthonous horizontal transmission of a CRF02_AG strain revealed by a human immunodeficiency virus type 1 diversity survey in a small city in inner state of Rio de Janeiro, Southeast Brazil

Autochthonous horizontal transmission of a CRF02_AG strain revealed by a human immunodeficiency virus type 1 diversity survey in a small city in inner state of Rio de Janeiro, Southeast Brazil

Human immunodeficiency virus type- 1 subtypes of infected patients in Espírito Santo, Brazil

HIV Type 1 Subtype C and CB Pol Recombinants Prevail at the Cities with the Highest AIDS Prevalence Rate in Brazil

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