Genotypic Analysis of Human Immunodeficiency Virus Type 1envV3 Loop Sequences: Bioinformatics Prediction of Coreceptor Usage Among 28 Infected Mother–Infant Pairs in a Drug-Naive Population

Abstract

We sought to predict virus coreceptor utilization using a simple bioinformatics method based on genotypic analysis of human immunodeficiency virus types 1 (HIV-1) env V3 loop sequences of 28 infected but drug-naive women during pregnancy and their infected infants and to better understand coreceptor usage in vertical transmission dynamics. The HIV-1 env V3 loop was sequenced from plasma samples and analyzed for viral coreceptor usage and subtype in a cohort of HIV-1-infected pregnant women. Predicted maternal frequencies of the X4, R5X4, and R5 genotypes were 7%, 11%, and 82%, respectively. Antenatal plasma viral load was higher, with a mean log(10) (SD) of 4.8 (1.6) and 3.6 (1.2) for women with the X4 and R5 genotypes, respectively, p = 0.078. Amino acid substitution from the conserved V3 loop crown motif GPGQ to GPGR and lymphadenopathy were associated with the X4 genotype, p = 0.031 and 0.043, respectively. The maternal viral coreceptor genotype was generally preserved in vertical transmission and was predictive of the newborn's viral genotype. Infants born to mothers with X4 genotypes were more likely to have lower birth weights relative to those born to mothers with the R5 genotype, with a mean weight (SD) of 2870 (±332) and 3069 (±300) g, respectively. These data show that at least in HIV-1 subtype C, R5 coreceptor usage is the most predominant genotype, which is generally preserved following vertical transmission and is associated with the V3 GPGQ crown motif. Therefore, antiretroviral-naive pregnant women and their infants can benefit from ARV combination therapies that include R5 entry inhibitors following prediction of their coreceptor genotype using simple bioinformatics methods.

Phylogenetic Analysis of Human Immunodeficiency Virus Type 1 Subtype C Env gp120 Sequences Among Four Drug-Naive Families Following Subsequent Heterosexual and Vertical Transmissions

“…Sexually transmitted infection (STI) screening, nucleic acid extraction, polymerase chain reaction (PCR) amplification, cloning, and DNA sequencing methods for the HIV-1 env gp120 C2-V5 region were done as previously described and so was HIV-1 subtype determination. 35 Briefly, the primary PCR amplified an approximately 800-base pair (bp) fragment spanning the C2 and V5 region of the envelope, positions 6948-7537 in the HIV-HXB2 genome while the secondary PCR amplified an approximately 650-bp env gene fragment.…”

HIV-1 subtype C envelope C2V5 characteristics; associations with markers of disease progression among 6 slowing progressing pediatric patients

“…The first available HIV-1 positive sample was genotyped for the second siblings at about 15±3 months. CD4 counts, viral load determination, nucleic acid extraction, PCR amplification, cloning and DNA sequencing methods for the HIV-1 env gp120 C2V5 region were done as previously described and so was subtype determination [23].…”

HIV-1 Env gp120 C2V5 Potential N-Linked Glycosylation Site(s) (PNGs) Variations and Amino Acid Length Polymorphisms among Infected Family Members

“…In cases of second siblings the first available HIV-1 positive samples were genotyped and sampling time was at about 15 ± 3 months of age. Nucleic acid extraction, PCR amplification, cloning and DNA sequencing methods for the HIV-1 env gp120 C2V5 region were done as previously described and so was HIV-1 subtype determination [28].…”