Characterization of V3 sequence heterogeneity in subtype C human immunodeficiency virus type 1 isolates from Malawi: underrepresentation of X4 variants.
We have examined the nature of V3 sequence variability among subtype C human immunodeficiency virus type 1 (HIV-1) sequences from plasma-derived viral RNA present in infected men from Malawi. Sequence variability was assessed by direct sequence analysis of the V3 reverse transcription-PCR products, examination of virus populations by a subtype C V3-specific heteroduplex tracking assay (V3-HTA), and selected sequence analysis of molecular clones derived from the PCR products. Sequence variability in V3 among the subtype C viruses was not associated with the presence of basic amino acid substitutions. This observation is in contrast to that for subtype B HIV-1, where sequence variability is associated with such substitutions, and these substitutions are determinants of altered coreceptor usage. Evolutionary variants in subtype C V3 sequences, as defined by the V3-HTA, were not correlated with the CD4 level in the infected person, while such a correlation was found with subtype B V3 sequences. Viruses were isolated from a subset of the subjects; all isolates used CCR5 and not CXCR4 as a coreceptor, and none was able to grow in MT-2 cells, a hallmark of the syncytium-inducing phenotype that is correlated with CXCR4 usage. The overall sequence variability of the subtype C V3 region was no greater than that of the conserved regions of gp120. This limited sequence variability was also a feature of subtype B V3 sequences that do not carry the basic amino acid substitutions associated with altered coreceptor usage. Our results indicate that altered coreceptor usage is rare in subtype C HIV-1 isolates in sub-Saharan Africa and that sequence variability is not a feature of the V3 region of env in the absence of altered coreceptor usage.
Ping
L H
LH
UNC Center For AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Nelson
J A
JA
Hoffman
I F
IF
Schock
J
J
Lamers
S L
SL
Goodman
M
M
Vernazza
P
P
Kazembe
P
P
Maida
M
M
Zimba
D
D
Goodenow
M M
MM
Eron
J J
JJ
Fiscus
S A
SA
Cohen
M S
MS
Swanstrom
R
R
D001483:Base Sequence; D004279:DNA, Viral; D019143:Evolution, Molecular; D018740:Genetic Heterogeneity; D014644:Genetic Variation; D015699:HIV Envelope Protein gp120 / Q000235:genetics* / Q000378:metabolism; D006679:HIV Seropositivity / Q000821:virology*; D015497:HIV-1 / Q000235:genetics* / Q000254:growth & development / Q000302:isolation & purification / Q000378:metabolism; D006801:Humans; D008295:Malawi; D008969:Molecular Sequence Data; D009692:Nucleic Acid Heteroduplexes; D010446:Peptide Fragments / Q000235:genetics* / Q000378:metabolism; D012367:RNA, Viral / Q000097:blood; D019713:Receptors, CCR5 / Q000378:metabolism; D019718:Receptors, CXCR4 / Q000378:metabolism
D004279:DNA, Viral; D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D009692:Nucleic Acid Heteroduplexes; D010446:Peptide Fragments; D012367:RNA, Viral; D019713:Receptors, CCR5; D019718:Receptors, CXCR4