Recombination is recognized as a primary force in human immunodeficiency virus type 1 (HIV-1) evolution, increasing viral diversity through reshuffling of genomic portions. The strand-switching activity of reverse transcriptase is required to complete HIV-1 replication and can occur randomly throughout the genome, leading to viral recombination. Some recombination hotspots have been identified and found to correlate with RNA structure or sequence features. The aim of this study was to evaluate the presence of recombination hotspots in the pol gene of HIV-1 and to assess their correlation with the underlying RNA structure. Analysis of the recombination pattern and breakpoint distribution in a group of unique recombinant forms (URFs) detected two recombination hotspots in the pol region. Two stable and conserved hairpins were consistently predicted corresponding to the identified hotspots using six different RNA-folding algorithms on the URF parental strains. These findings suggest that such hairpins may play a role in the higher recombination rates detected at these positions.

Recombination analysis and structure prediction show correlation between breakpoint clusters and RNA hairpins in the pol gene of human immunodeficiency virus type 1 unique recombinant forms / A. Galli, A. Lai, S. Corvasce, F. Saladini, C. Riva, L. Dehò, I. Caramma, M. Franzetti, L. Romano, M. Galli, M. Zazzi, C. Balotta. - In: JOURNAL OF GENERAL VIROLOGY. - ISSN 0022-1317. - 89:12(2008), pp. 3119-3125. [10.1099/vir.0.2008/003418-0]

Recombination analysis and structure prediction show correlation between breakpoint clusters and RNA hairpins in the pol gene of human immunodeficiency virus type 1 unique recombinant forms

A. Lai
Secondo
;
S. Corvasce;C. Riva;L. Dehò;I. Caramma;M. Franzetti;M. Galli;C. Balotta
2008

Abstract

Recombination is recognized as a primary force in human immunodeficiency virus type 1 (HIV-1) evolution, increasing viral diversity through reshuffling of genomic portions. The strand-switching activity of reverse transcriptase is required to complete HIV-1 replication and can occur randomly throughout the genome, leading to viral recombination. Some recombination hotspots have been identified and found to correlate with RNA structure or sequence features. The aim of this study was to evaluate the presence of recombination hotspots in the pol gene of HIV-1 and to assess their correlation with the underlying RNA structure. Analysis of the recombination pattern and breakpoint distribution in a group of unique recombinant forms (URFs) detected two recombination hotspots in the pol region. Two stable and conserved hairpins were consistently predicted corresponding to the identified hotspots using six different RNA-folding algorithms on the URF parental strains. These findings suggest that such hairpins may play a role in the higher recombination rates detected at these positions.
Secondary structure prediction; dynamics in-vivo; reverse transcription; retroviral recombination; strand transfer; intersubtype recombination; molecular epidemiology; HIV-1 variants; web server; hot-spots
Settore MED/17 - Malattie Infettive
Settore MED/42 - Igiene Generale e Applicata
Settore MED/07 - Microbiologia e Microbiologia Clinica
2008
Article (author)
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/53510
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