title: Molecular characterization of a recombinant HIV type 1 isolate (A/G/E/?): unidentified regions may be derived from parental subtype E sequences.
abstract: Recombination is one of several factors contributing to the genetic diversity of HIV-1, which is divided into group M (itself comprising 11 subtypes, A-K) and two other groups named O and N. In the present study, the full-length genome of an HIV-1 isolate obtained from a Greek subject (GR17) infected in the Democratic Republic of the Congo (formerly Zaire) was analyzed to reveal a novel mosaic sequence composed of subtypes A, G, and E and regions of indeterminate classification. In particular, most of pol and tat/vpu, as well as the region encoding intracellular domain of gp41, did not cluster with any of the previously characterized HIV-1 subtypes. The clustering of the LTR of GR17 with subtype E was suggestive of a subtype E origin of the unclassified regions. However, the identification of distinct characteristics in the LTR, such as two functional NF-kappaB sites and a distinct TAR element, compared with those of circulating (A/E) recombinants, suggests that the partial subtype E sequences found in GR17 and the mosaic viruses (A/E) have not derived from each other. These results provide evidence that parental subtype E may have existed in the geographic area of Central Africa.
authors.affiliation: National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Greece.
authors.forename: D
authors.initials: D
authors.lastname: Paraskevis
authors.forename: M
authors.initials: M
authors.lastname: Magiorkinis
authors.forename: V
authors.initials: V
authors.lastname: Paparizos
authors.forename: G N
authors.initials: GN
authors.lastname: Pavlakis
authors.forename: A
authors.initials: A
authors.lastname: Hatzakis
mesh_terms: D000328:Adult; D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D015023:Democratic Republic of the Congo; D014644:Genetic Variation; D016679:Genome, Viral; D015658:HIV Infections / Q000821:virology*; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D009030:Mosaicism; D010802:Phylogeny; D011995:Recombination, Genetic; D012689:Sequence Homology, Nucleic Acid
chemical_list: D017931:DNA Primers; D004279:DNA, Viral