Selection of appropriate HIV-1 genomic regions for single-strand conformation polymorphism analysis of the diversity, modification, and transmission of HIV-1 quasispecies.
Single-strand conformation polymorphism (SSCP) analysis is a useful tool for studying viral quasispecies. Four regions within the HIV-1 genome were studied by means of SSCP analysis with the aim of determining which regions were the most informative for the study of HIV-1 transmission or for detection of changes in HIV-1 quasispecies populations. Nested polymerase chain reaction (PCR) was used to amplify V1, V2, V3 of the env gene, and the p2 region in the gag gene. In total, 114 plasma specimens from 79 individuals were tested, including serial specimens from 10 mother-infant pairs that were provided by the Women and Infants Transmission Study (WITS). HIV-1 in specimens that were PCR-positive with primer pair SK38/SK39 showed different percentages of positive signals with primer pairs for the four regions: V1, 63%; V2, 83%; V3, 88%, and p2, 100%. HIV-1 sequences in the p2 target region displayed the greatest degree of polymorphism. Analysis of serial specimens showed that the V1 target region was the most variable of the four regions studied and was the most appropriate region for monitoring changes in quasispecies populations. Of the four regions studied, p2 was the most informative for the study of HIV transmission, as shown by analysis of samples from documented cases of mother to infant HIV-1 transmission.
Lin
H J
HJ
Division of Molecular Virology, Baylor College of Medicine, Houston, Texas 77030, USA.
Siwak
E B
EB
Lauder
I J
IJ
Hollinger
F B
FB
D005260:Female; D014644:Genetic Variation; D016679:Genome, Viral; D015658:HIV Infections / Q000635:transmission* / Q000821:virology; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D007231:Infant, Newborn; D018445:Infectious Disease Transmission, Vertical; D016133:Polymerase Chain Reaction; D018807:Polymorphism, Single-Stranded Conformational; D011247:Pregnancy