PMID- 20637314
OWN - NLM
STAT- MEDLINE
DCOM- 20110318
LR  - 20101005
IS  - 1567-7257 (Electronic)
IS  - 1567-1348 (Linking)
VI  - 10
IP  - 8
DP  - 2010 Dec
TI  - An introduction to a novel population genetic approach for HIV characterization.
PG  - 1155-64
LID - 10.1016/j.meegid.2010.07.010 [doi]
AB  - The rapid evolution of the HIV genome is influenced in part by host selection 
      pressure, which may cause parallel evolution among strains under shared selection 
      pressures. To understand the mechanisms behind HIV-host immune escape across host 
      populations, researchers have compared signatures of positive selection pressure 
      on HIV codons across HIV subtypes and across phylogenetic groups of isolates 
      within major subtypes, all relying on a criterion of phylogenetic separation. The 
      HIV codon sites that retain diversity, evolve convergently among sets of hosts 
      (cohorts) and diverge between cohorts may be phylogenetically undiagnostic 
      (reveal little information about the relationship of the strains) and thus 
      undetectable on a tree. We propose a new approach to characterizing genetic 
      divergence among isolates using existing population genetic methods to better 
      understand HIV response to host selection pressures. The approach combines 
      population genetic statistical methods with codon analysis to identify putative 
      amino acid sites evolving convergently. To illustrate the approach, we compared 
      the C2-V3-C3 region of the envelope protein of HIV-1 clade B isolates between 
      Haiti and USA hosts. This region showed no phylogenetic separation between host 
      populations. Still, we identified codon sites in the C2-V3-C3 HIV-1 region that 
      may have evolved differently between the two host populations. The sites are 
      localized in human leukocyte antigen (HLA) class I binding epitopes, 
      N-glycosylation motifs or both and are limited to the C2 and C3 regions. Our 
      method provides a potential means to reveal candidate sites actively involved in 
      HIV-1 immune escape that would otherwise be missed if a requisite for 
      phylogenetic distinctiveness was made a priori. This strategy may prove to be a 
      helpful way to characterize HIV genetic variation among hosts with suspected 
      selection pressure differences, like progressors versus non-progressors.
CI  - Copyright (c) 2010 Elsevier B.V. All rights reserved.
FAU - Perez-Sweeney, Beatriz
AU  - Perez-Sweeney B
AD  - American Museum of Natural History, Sackler Institute for Comparative Genomics, 
      New York, NY, USA. bperez-sweeney@amnh.org
FAU - DeSalle, Rob
AU  - DeSalle R
FAU - Ho, John L
AU  - Ho JL
LA  - eng
GR  - 5R01 HL61960/HL/NHLBI NIH HHS/United States
GR  - D43 TW00018/TW/FIC NIH HHS/United States
GR  - D43 TW00018-S3/TW/FIC NIH HHS/United States
GR  - R01 HL61960S/HL/NHLBI NIH HHS/United States
GR  - R21 AI62332/AI/NIAID NIH HHS/United States
GR  - U2R TW006901/TW/FIC NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20100714
PL  - Netherlands
TA  - Infect Genet Evol
JT  - Infection, genetics and evolution : journal of molecular epidemiology and 
      evolutionary genetics in infectious diseases
JID - 101084138
RN  - 0 (Codon)
RN  - 0 (HIV Envelope Protein gp120)
RN  - 0 (HLA-A Antigens)
SB  - IM
MH  - Amino Acid Sequence
MH  - Codon
MH  - *Evolution, Molecular
MH  - *Genetic Variation
MH  - HIV Envelope Protein gp120/*chemistry/*genetics
MH  - HIV Infections/immunology/virology
MH  - HIV-1/chemistry/*genetics/immunology
MH  - HLA-A Antigens/immunology
MH  - Haiti
MH  - Humans
MH  - Immune Evasion
MH  - Phylogeny
MH  - *Selection, Genetic
MH  - United States
EDAT- 2010/07/20 06:00
MHDA- 2011/03/19 06:00
CRDT- 2010/07/20 06:00
PHST- 2010/04/15 00:00 [received]
PHST- 2010/07/06 00:00 [revised]
PHST- 2010/07/06 00:00 [accepted]
PHST- 2010/07/20 06:00 [entrez]
PHST- 2010/07/20 06:00 [pubmed]
PHST- 2011/03/19 06:00 [medline]
AID - S1567-1348(10)00198-X [pii]
AID - 10.1016/j.meegid.2010.07.010 [doi]
PST - ppublish
SO  - Infect Genet Evol. 2010 Dec;10(8):1155-64. doi: 10.1016/j.meegid.2010.07.010. 
      Epub 2010 Jul 14.