title: Molecular characterization of the HIV-1 gag nucleocapsid gene associated with vertical transmission.
abstract: BACKGROUND
  The human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) plays a pivotal role in the viral lifecycle: including encapsulating the viral genome, aiding in strand transfer during reverse transcription, and packaging two copies of the viral genome into progeny virions. Another gag gene product, p6, plays an integral role in successful viral budding from the plasma membrane and inclusion of the accessory protein Vpr within newly budding virions. In this study, we have characterized the gag NC and p6 genes from six mother-infant pairs following vertical transmission by performing phylogenetic analysis and by analyzing the degree of genetic diversity, evolutionary dynamics, and conservation of functional domains.
  
  
  RESULTS
  Phylogenetic analysis of 168 gag NC and p6 genes sequences revealed six separate subtrees that corresponded to each mother-infant pair, suggesting that epidemiologically linked individuals were closer to each other than epidemiologically unlinked individuals. A high frequency (92.8%) of intact open reading frames of NC and p6 with patient and pair specific sequence motifs were conserved in mother-infant pairs' sequences. Nucleotide and amino acid distances showed a lower degree of viral heterogeneity, and a low degree of estimates of genetic diversity was also found in NC and p6 sequences. The NC and p6 sequences from both mothers and infants were found to be under positive selection pressure. The two important functional motifs within NC, the zinc-finger motifs, were highly conserved in most of the sequences, as were the gag p6 Vpr binding, AIP1 and late binding domains. Several CTL recognition epitopes identified within the NC and p6 genes were found to be mostly conserved in 6 mother-infant pairs' sequences.
  
  
  CONCLUSIONS
  These data suggest that the gag NC and p6 open reading frames and functional domains were conserved in mother-infant pairs' sequences following vertical transmission, which confirms the critical role of these gene products in the viral lifecycle.
authors.affiliation: Department of Microbiology and Immunology, College of Medicine, The University of Arizona Health Sciences Center, Tucson, Arizona, USA. bwellen1@u.arizona.edu
authors.forename: Brian P
authors.initials: BP
authors.lastname: Wellensiek
authors.forename: Vasudha
authors.initials: V
authors.lastname: Sundaravaradan
authors.forename: Rajesh
authors.initials: R
authors.lastname: Ramakrishnan
authors.forename: Nafees
authors.initials: N
authors.lastname: Ahmad
mesh_terms: D000163:Acquired Immunodeficiency Syndrome / Q000235:genetics* / Q000517:prevention & control / Q000635:transmission; D001483:Base Sequence; D003001:Cloning, Molecular; D017931:DNA Primers; D004279:DNA, Viral / Q000235:genetics; D005260:Female; D015683:Gene Products, gag / Q000145:classification / Q000235:genetics*; D016679:Genome, Viral; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D007231:Infant, Newborn; D018445:Infectious Disease Transmission, Vertical / Q000517:prevention & control; D019590:Nucleocapsid Proteins / Q000145:classification / Q000235:genetics*; D016366:Open Reading Frames; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011247:Pregnancy; D011251:Pregnancy Complications, Infectious / Q000517:prevention & control / Q000821:virology; D016335:Zinc Fingers / Q000235:genetics
chemical_list: D017931:DNA Primers; D004279:DNA, Viral; D015683:Gene Products, gag; D019590:Nucleocapsid Proteins