Use of massive parallel pyrosequencing for near full-length characterization of a unique HIV type 1 BF recombinant associated with a fatal primary infection

Alessandro Bruselles, Gabriella Rozera, Barbara Bartolini, Mattia Prosperi, Franca Del Nonno, Pasquale Narciso, Maria R. Capobianchi, Isabella Abbate

Research output: Contribution to journalArticle

Abstract

Near full length genome characterization of a BF recombinant from a patient who died from multiorgan failure during HIV-1 seroconversion is reported. Massive parallel pyrosequencing was used with the shotgun approach. Intrahost genetic variability along the whole genome was calculated and coreceptor usage of viral quasispecies was predicted. A consensus sequence was established to perform subtype assignment, phylogenetic analysis, and recombination tests. The sequence clustered with two recently described BF unique recombinant forms from Brazil, consistent with the recombination pattern, yielding breakpoints located at the same positions, with the exception of the second env breakpoint. The actual prevalence of recombinant forms is probably underestimated if partial genomic regions are considered. Here the first full length BF recombinant from Italy is described, together with an evaluation of quasispecies heterogeneity. Our data provide evidence that next generation sequencing may provide a major contribution to HIV-1 molecular epidemiology and to the comprehension of intrapatient heterogeneity.

Original languageEnglish
Pages (from-to)937-942
Number of pages6
JournalAIDS Research and Human Retroviruses
Volume25
Issue number9
DOIs
Publication statusPublished - Sep 1 2009

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Genetic Recombination
HIV-1
Genome
HIV Seropositivity
Molecular Epidemiology
Consensus Sequence
Firearms
Infection
Italy
Brazil

ASJC Scopus subject areas

  • Immunology
  • Virology
  • Infectious Diseases

Cite this

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abstract = "Near full length genome characterization of a BF recombinant from a patient who died from multiorgan failure during HIV-1 seroconversion is reported. Massive parallel pyrosequencing was used with the shotgun approach. Intrahost genetic variability along the whole genome was calculated and coreceptor usage of viral quasispecies was predicted. A consensus sequence was established to perform subtype assignment, phylogenetic analysis, and recombination tests. The sequence clustered with two recently described BF unique recombinant forms from Brazil, consistent with the recombination pattern, yielding breakpoints located at the same positions, with the exception of the second env breakpoint. The actual prevalence of recombinant forms is probably underestimated if partial genomic regions are considered. Here the first full length BF recombinant from Italy is described, together with an evaluation of quasispecies heterogeneity. Our data provide evidence that next generation sequencing may provide a major contribution to HIV-1 molecular epidemiology and to the comprehension of intrapatient heterogeneity.",
author = "Alessandro Bruselles and Gabriella Rozera and Barbara Bartolini and Mattia Prosperi and {Del Nonno}, Franca and Pasquale Narciso and Capobianchi, {Maria R.} and Isabella Abbate",
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AU - Bruselles, Alessandro

AU - Rozera, Gabriella

AU - Bartolini, Barbara

AU - Prosperi, Mattia

AU - Del Nonno, Franca

AU - Narciso, Pasquale

AU - Capobianchi, Maria R.

AU - Abbate, Isabella

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