title: Use of massive parallel pyrosequencing for near full-length characterization of a unique HIV Type 1 BF recombinant associated with a fatal primary infection.
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.
authors.affiliation: INMI L. Spallanzani, Rome, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Bruselles
authors.forename: Gabriella
authors.initials: G
authors.lastname: Rozera
authors.forename: Barbara
authors.initials: B
authors.lastname: Bartolini
authors.forename: Mattia
authors.initials: M
authors.lastname: Prosperi
authors.forename: Franca
authors.initials: F
authors.lastname: Del Nonno
authors.forename: Pasquale
authors.initials: P
authors.lastname: Narciso
authors.forename: Maria R
authors.initials: MR
authors.lastname: Capobianchi
authors.forename: Isabella
authors.initials: I
authors.lastname: Abbate
mesh_terms: D016000:Cluster Analysis; D017809:Fatal Outcome; D016679:Genome, Viral; D005838:Genotype; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007558:Italy; D008297:Male; D008969:Molecular Sequence Data; D015728:Receptors, HIV / Q000032:analysis; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D055815:Young Adult
chemical_list: D015728:Receptors, HIV