In vitro dynamics of HIV-1 BF intersubtype recombinants genomic regions involved in the regulation of gene expression

Carobene, Mauricio; Rodrígues, Christian Fernando Ariel Rodríguez; Candia, Cristian Ariel de; Turk, Gabriela; Salomón, Horacio

doi:10.1186/1743-422x-6-107

Cited by 8 publications

(7 citation statements)

References 34 publications

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“…It has also been suggested that the HIV-1 epidemic could be evolving toward a more complex epidemiological landscape (18). Recombination seems to be very important in the evolution of HIV-1 (42), since it can provide a biological advantage versus parental viruses (28), promoting biological adaptation and enhancing fitness (6). It can also facilitate drug resistance and may allow superinfecting HIV-1 strains to evade preexisting immune responses (32).…”

Section: One Of 10 Hiv-1-infections In Spain Could Represent Recombinmentioning

confidence: 99%

Most HIV Type 1 Non-B Infections in the Spanish Cohort of Antiretroviral Treatment-Naïve HIV-Infected Patients (CoRIS) Are Due to Recombinant Viruses

et al. 2012

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HIV-1 group M is classified into 9 subtypes, as well as recombinants favored by coinfection and superinfection events with different variants. Although HIV-1 subtype B is predominant in Europe, intersubtype recombinants are increasing in prevalence and complexity. In this study, phylogenetic analyses of pol sequences were performed to detect the HIV-1 circulating and unique recombinant forms (CRFs and URFs, respectively) in a Spanish cohort of antiretroviral treatment-naïve HIV-infected patients included in the Research Network on HIV/AIDS (CoRIS). Bootscanning and other methods were used to define complex recombinants not assigned to any subtype or CRF. A total of 670 available HIV-1 pol sequences from different patients were collected, of which 588 (87.8%) were assigned to HIV-1 subtype B and 82 (12.2%) to HIV-1 non-B variants. Recombinants caused the majority (71.9%) of HIV-1 non-B infections and were found in 8.8% of CoRIS patients. Eleven URFs (accounting for 13.4% of HIV-1 non-B infections), presenting complex mosaic patterns, were detected. Among them, 10 harbored subtype B fragments. Four of the 11 URFs were found in Spanish natives. A cluster of three B/CRF02_AG recombinants was detected. We conclude that complex variants, including unique recombinant forms, are being introduced into Spain through both immigrants and natives. An increase in the frequency of mosaic viruses, reflecting the increasing heterogeneity of the HIV epidemic in our country, is expected.

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Section: One Of 10 Hiv-1-infections In Spain Could Represent Recombinmentioning

confidence: 99%

Most HIV Type 1 Non-B Infections in the Spanish Cohort of Antiretroviral Treatment-Naïve HIV-Infected Patients (CoRIS) Are Due to Recombinant Viruses

et al. 2012

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“…This result is very important since recombination may shift the virulence of DENV. One could speculate if this shift may increase or diminish the virulence, like has happened in other RNA viruses, such as poliovirus [ 36 , 37 ] influenza virus [ 38 ] and the HIV virus [ 39 ]. A dramatic example is the loss of the attenuated phenotype of the poliovirus vaccine by recombination, resulting in the generation of new phenotypes that produce the acute paralytic disease.…”

Section: Discussionmentioning

confidence: 99%

Multiple recombinants in two dengue virus, serotype-2 isolates from patients from Oaxaca, Mexico

et al. 2009

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BackgroundDengue (DEN) is a serious cause of mortality and morbidity in the world including Mexico, where the infection is endemic. One of the states with the highest rate of dengue cases is Oaxaca. The cause of DEN is a positive-sense RNA virus, the dengue virus (DENV) that evolves rapidly increasing its variability due to the absence of a repair mechanism that leads to approximately one mutational event per genome replication; which results in enhancement of viral adaptation, including the escape from host immune responses. Additionally, recombination may play a role in driving the evolution of DENV, which may potentially affect virulence and cause host tropism changes. Recombination in DENV has not been described in Mexican strains, neither has been described the relevance in virus evolution in an endemic state such as Oaxaca where the four serotypes of DENV are circulating.ResultsTo study whether there are isolates from Oaxaca having recombination, we obtained the sequence of 6 different isolates of DENV-2 Asian/American genotype from the outbreak 2005-6, one clone of the C(91)-prM-E-NS1(2400) structural genes, and 10 clones of the E gene from the isolate MEX_OAX_1656_05. Evidence of recombination was found by using different methods along with two softwares: RDP3 and GARD. The Oaxaca MEX_OAX_1656_05 and MEX_OAX_1038_05 isolates sequenced in this study were recombinant viruses that incorporate the genome sequence from the Cosmopolitan genotype. Furthermore, the clone of the E gene namely MEX_OAX_165607_05 from this study was also recombinant, incorporating genome sequence from the American genotype.ConclusionsThis is the first report of recombination in DENV-2 in Mexico. Given such a recombinant activity new genomic combinations were produced, this could play a significant role in the DENV evolution and must be considered as a potentially important mechanism generating genetic variation in this virus with serious implications for the vaccines and drugs formulation as occurs for other viruses like poliovirus, influenza and HIV.

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“…17 In general, the prevalence of BF, as well as other mosaic structures is probably underestimated due to large-scale partial genotyping of clinical samples for antiretroviral resistance testing. Along with the upcoming availability of effective technologies for large-scale sequencing, information on full-length HIV genomes is expected to expand providing an accurate picture of virus diversification in different areas over time.…”

Section: Aids Research and Human Retrovirusesmentioning

confidence: 99%

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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In vitro dynamics of HIV-1 BF intersubtype recombinants genomic regions involved in the regulation of gene expression

Cited by 8 publications

References 34 publications

Most HIV Type 1 Non-B Infections in the Spanish Cohort of Antiretroviral Treatment-Naïve HIV-Infected Patients (CoRIS) Are Due to Recombinant Viruses

Most HIV Type 1 Non-B Infections in the Spanish Cohort of Antiretroviral Treatment-Naïve HIV-Infected Patients (CoRIS) Are Due to Recombinant Viruses

Multiple recombinants in two dengue virus, serotype-2 isolates from patients from Oaxaca, Mexico

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

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