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.
UNC Center For AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
L H
LH
Ping
J A
JA
Nelson
I F
IF
Hoffman
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J
Schock
S L
SL
Lamers
M
M
Goodman
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Vernazza
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P
Kazembe
M
M
Maida
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Zimba
M M
MM
Goodenow
J J
JJ
Eron
S A
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Fiscus
M S
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Cohen
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Swanstrom
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