title: An outbreak of HIV-1 BC recombinants in Southern Italy.
abstract: BACKGROUND
  In Western Europe, a previously subtype B HIV-1 restricted area, BC recombinants have been rarely reported.
  
  
  OBJECTIVE
  To describe an outbreak of HIV-1 BC recombinants in southern Italy.
  
  
  METHODS
  We analyzed pol (protease/reverse transcriptase) sequences from 135 newly diagnosed HIV-1-infected patients during the years 2009-2011. For phylogenetic relationships, sequences were aligned to the most recent reference data set from the Los Alamos database using BioEdit (version 7.1.3). The resulting alignment was analyzed with the Phylip package (version 3.67) building a neighbor-joining tree based on the Kimura two-parameter substitution model. The reliability of the tree topology was assessed through bootstrapping using 1000 replicates. The recombination pattern was characterized using SimPlot 3.5.1 and SplitsTree 4.
  
  
  RESULTS
  At phylogenetic analysis, 22 (16.2%) isolates whose sequences were not unequivocally assigned to a pure subtype or known CRF, formed a distinct monophyletic clade (100% of bootstrap value). For these isolates, the recombination analysis identified a BC mosaic pattern with two breakpoints at positions 2778±5 and 3162±8 (HXB2 numbering) which differed from those of known BC CRFs. All patients from whom these sequences were derived were highly educated youth Italians, 91% males and 82% MSM. Sequences of pol integrase, gp120 and gp41 from these same patients were classified as C subtype.
  
  
  CONCLUSIONS
  This outbreak which further reflects the increasing heterogeneity of HIV epidemic in our country is the first report of an Italian outbreak of a BC recombinant, possibly a novel candidate CRF.
authors.affiliation: Clinic of Infectious Diseases, University of Bari, Bari, Italy. laura.monno@uniba.it
authors.forename: Laura
authors.initials: L
authors.lastname: Monno
authors.forename: Gaetano
authors.initials: G
authors.lastname: Brindicci
authors.forename: Alessia
authors.initials: A
authors.lastname: Lai
authors.forename: Grazia
authors.initials: G
authors.lastname: Punzi
authors.forename: Maurantonio
authors.initials: M
authors.lastname: Altamura
authors.forename: Francesco Roberto
authors.initials: FR
authors.lastname: Simonetti
authors.forename: Nicoletta
authors.initials: N
authors.lastname: Ladisa
authors.forename: Annalisa
authors.initials: A
authors.lastname: Saracino
authors.forename: Claudia
authors.initials: C
authors.lastname: Balotta
authors.forename: Gioacchino
authors.initials: G
authors.lastname: Angarano
mesh_terms: D000293:Adolescent; D000328:Adult; D016000:Cluster Analysis; D004196:Disease Outbreaks; D005260:Female; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D007558:Italy / Q000453:epidemiology; D008297:Male; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D055815:Young Adult; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D054302:pol Gene Products, Human Immunodeficiency Virus