The analysis of near full-length genome sequences of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Chile, Venezuela and Spain reveals their relationship to diverse lineages of recombinant viruses related to CRF12_BF

Sierra, María; Thomson, Michael M.; Ríos, Maritza; Casado, Gema; Castro, Raúl Ojea-de; Delgado, Elena; Echevarría, Gloria; Muñoz, Mercedes; Colomina, Javier; Carmona, Rocı́o; Vega, Yolanda; Parga, Elena Vázquez-de; Medrano, Leandro; Pérez-Álvarez, Lucı́a; Contreras, Gerardo; Nájera, Rafael

doi:10.1016/j.meegid.2004.07.010

Cited by 60 publications

(49 citation statements)

References 26 publications

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“…The results of phylogenetic analysis of some of these samples were described previously [Thomson et al, 2001;Pérez-Alvarez et al, 2003]. Twelve viruses were characterized with full-length sequences from plasma RNA [Delgado et al, 2002;Casado et al, 2003;Sierra et al, 2005].…”

Section: Methodsmentioning

confidence: 99%

Isolation and biological characterization of HIV-1 BG intersubtype recombinants and other genetic forms circulating in Galicia, Spain

et al. 2006

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The biological characteristics of HIV-1 primary isolates of different recombinant forms (RFs) and non-B subtypes from Galicia, Spain, were investigated and the relationships between biological phenotype and evolution of infection were determined. Peripheral blood mononuclear cells (PBMCs) were obtained during the follow-up of 32 patients infected with HIV-1 non-subtype B genetic forms, characterized in partial sequences of pol (protease-reverse transcriptase) and env V3 region: 12 (37.5%) circulating RFs (CRFs), 9 (28.1%) unique RFs (URFs), and 11(34.4%) non-B subtypes. Primary isolates were obtained by coculture with donor PBMCs. Syncytium-inducing (SI) phenotype was examined in MT2 cell line and coreceptor use in GHOST and U87.CD4 cells. Fifty percent of tissue culture infective dose (TCID(50)) and viral phenotype based on V3 net charge and Geno2pheno(coreceptor) bioinformatic method were determined. Fifty-four HIV-1 primary isolates were obtained. CRF14_BG and BG URFs represented the largest group, being all SI/X4, independently of the CD4+ cell count, viral load, or the duration of infection. By contrast, 10 of 11 CRF02_AG viruses were NSI/R5. The prediction of co-receptor use was concordant with biological characterization in all NSI/R5 and in 23 of 26 SI/X4 isolates. The presence of SI/X4 or SI/X4,R5 isolates at early stages of the infection in addition to a decrease in CD4+ counts below 500 cells/microl between 2 and 6 years since diagnosis was observed in all patients infected with CRF14_BG and BG URFs. These data contrast with the usual progression in B subtype infections, in which SI/X4 viruses rarely predominate in the early years of HIV-1 infection.

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Section: Methodsmentioning

confidence: 99%

Isolation and biological characterization of HIV-1 BG intersubtype recombinants and other genetic forms circulating in Galicia, Spain

et al. 2006

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“…Primers used for PR-RT amplification were RP1-S and RP-1-A in RT-PCR and PR-O-S2b and RT-O-A in nested PCR (Table 1) and those used for amplification of the V3 region were described previously. 19 Near full-length genome (*9 kb) amplification in overlapping segments by RT-PCR and nested PCR and sequencing was done using a protocol similar to that described by us, 20,21 although some amplified fragments and their corresponding primers, all of which are listed in Table 1, were different. For amplification of the 3¢ semigenome, primers SG3-up and SG3-lo were used for RT-PCR.…”

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Short Communication: Molecular Epidemiology, Phylogeny, and Phylodynamics of CRF63_02A1, a Recently Originated HIV-1 Circulating Recombinant Form Spreading in Siberia

Shcherbakova

Shalamova²,

Delgado³

et al. 2014

AIDS Research and Human Retroviruses

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The HIV-1 epidemic in Russia is dominated by the former Soviet Union subtype A (A FSU ) variant, but other genetic forms are circulating in the country. One is the recently described CRF63_02A1, derived from recombination between a CRF02_AG variant circulating in Central Asia and A FSU , which has spread in the Novosibirsk region, Siberia. Here we phylogenetically analyze pol and env segments from 24 HIV-1 samples from the Novosibirsk region collected in 2013, with characterization of three new near full-length genome CRF63_02A1 sequences, and estimate the time of the most recent common ancestor (tMRCA) and the demographic growth of CRF63_02A1 using a Bayesian method. The analyses revealed that CRF63_02A1 is highly predominant in the Novosibirsk region (81.2% in pol sequences) and is transmitted both among injecting drug users and by heterosexual contact. Similarity searches with database sequences combined with phylogenetic analyses show that CRF63_02A1 is circulating in East Kazakhstan and the Eastern area of Russia bordering China. The analyses of near full-length genome sequences show that its mosaic structure is more complex than reported, with 18 breakpoints. The tMRCA of CRF63_02A1 was estimated around 2006, with exponential growth in 2008-2009 and subsequent stabilization. These results provide new insights into the molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1.

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“…In addition, other sequences showed BF1 mosaics within the individual pol or env region. Since BF recombinants have been previously reported in Latin America, [5][6][7][8][9][10][11] we were interested in analyzing BF mosaic forms circulating in Italy.…”

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Near Full-Length Sequence Analysis of HIV Type 1 BF Recombinants from Italy

Saladini

Foley

Rosi

et al. 2012

AIDS Research and Human Retroviruses

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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.H uman immunodeficiency virus type 1 (HIV-1) is characterized by an extremely broad genetic diversity, caused by high mutation and recombination rates. Currently, HIV-1 group M (''Major''), which is responsible of the worldwide pandemic, is divided into pure subtypes A-D, F-H, J, and K (with subtypes A and F further subdivided into subsubtypes A1-A4 and F1-F2, respectively) as well as 48 circulating recombinant forms (CRFs) of varying epidemiological significance, and untold numbers of unique recombinants that are not known to have spread to many patients. Subtype B has long been predominant in Western European countries but the prevalence of non-B strains has been increasing significantly in past years as a consequence of recent migration waves from Africa, Eastern Europe, and South America.1 Continuous surveillance of HIV-1 molecular epidemiology plays a critical role in the understanding of genetic diversity of HIV-1 and for research purposes such as vaccine development. In clinical practice, pol-based subtype assignment is usually accomplished as a by-product of genotypic antiretroviral resistance testing.A homebrew HIV-1 genotyping assay has been established and offered as a public health service at the HIV Monitoring Laboratory (HML), Department of Molecular Biology, University of Siena, Italy since 1995. 2 The laboratory has been serving a number of clinics for analysis of drug resistance mutations accumulating around 10,000 protease and reverse transcriptase sequences from more than 4000 patients. In addition, some hundred partial gag and env sequences have been obtained for research studies. A recent survey on the whole HIV-1 sequence database at the HML revealed 85% of subtype B sequences and 15% of non-B subtypes, mainly CRF02_AG, F1, C, and A1, based on the pol region.3 In some cases, assignments of subtype based on the pol and env regions were not in agreement. 4 These discrepan...

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The analysis of near full-length genome sequences of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Chile, Venezuela and Spain reveals their relationship to diverse lineages of recombinant viruses related to CRF12_BF

Cited by 60 publications

References 26 publications

Isolation and biological characterization of HIV-1 BG intersubtype recombinants and other genetic forms circulating in Galicia, Spain

Isolation and biological characterization of HIV-1 BG intersubtype recombinants and other genetic forms circulating in Galicia, Spain

Short Communication: Molecular Epidemiology, Phylogeny, and Phylodynamics of CRF63_02A1, a Recently Originated HIV-1 Circulating Recombinant Form Spreading in Siberia

Near Full-Length Sequence Analysis of HIV Type 1 BF Recombinants from Italy

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