title: Difficulties in classifying a/g recombinants: methodological problems or genetic variability?
abstract: Thirty pol gene plasma-derived sequences clustering with the circulating recombinant form (CRF) 02_AG (IbNG) (bootstrap 100%) were evaluated to analyze the genomic composition. Subtype assignment was also phylogenetically confirmed by C2-V3 region analysis for 18/21 sequences evaluated. Thereafter, we compared the genomic recombination of the CRF02_AG/IbNG prototype as predicted by bootscanning and Jumping HMMER software (jpHMM) to that of our strains. With these methods, 27% and 50%, respectively, of our clinical sequences demonstrated the same pol structure as the prototype CRF02_A/G-IbNG. However, in subtrees built for each segment predicted by jpHMM (with a bootstrap value of more than 75%), all fragments clustered with IbNG and were distinct from A and G clades. Overall, our sequences resulted in true members of CRF02_AG-IbNG, which, however, appeared to be a subtype phylogenetically separate from A or G, at least with regard to the pol gene.
authors.affiliation: Clinic of Infectious Diseases, University of Bari, Bari, Italy.
authors.forename: Gaetano
authors.initials: G
authors.lastname: Brindicci
authors.forename: Grazia
authors.initials: G
authors.lastname: Punzi
authors.forename: Antonella
authors.initials: A
authors.lastname: Lagioia
authors.forename: Sergio
authors.initials: S
authors.lastname: Lo Caputo
authors.forename: Nicoletta
authors.initials: N
authors.lastname: Ladisa
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Di Nicuolo
authors.forename: Annalisa
authors.initials: A
authors.lastname: Saracino
authors.forename: Gioacchino
authors.initials: G
authors.lastname: Angarano
authors.forename: Laura
authors.initials: L
authors.lastname: Monno
mesh_terms: D000328:Adult; D044383:Black People / Q000208:ethnology; D002675:Child, Preschool; D004641:Emigration and Immigration; D005260:Female; D015752:Genes, env / Q000235:genetics; D015751:Genes, pol / Q000235:genetics*; D006678:HIV / Q000145:classification / Q000235:genetics*; D015658:HIV Infections / Q000453:epidemiology / Q000235:genetics*; D006801:Humans; D007558:Italy / Q000453:epidemiology; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D016865:Reassortant Viruses / Q000145:classification / Q000235:genetics*; D012725:Sexual Behavior