HIV type 1 diversity and the reliability of the heteroduplex mobility assay.
We investigated HIV-1 diversity by means of heteroduplex mobility assay (HMA) genotyping. We studied 199 samples from patients originating from 26 countries and living in France. The HMA successfully genotyped 182 (91%) of these samples, as follows: 77 (42%) subtype A, 57 (31%) subtype B, 5 (3%) subtype C, 5 (3%) subtype D, 8 (4%) subtype E, 22 (12%) subtype F, 5 (3%) subtype G, and 3 (2%) subtype H. We were not able to genotype 12 samples by means of the HMA. These latter strains were sequenced, and phylogenetic analyses revealed that they were highly divergent subtype A-, D-, or G-related strains. Eight (of 12) subtype D strains were indeterminate by HMA, owing to the broad intrasubtype diversity, suggesting that new reference subtype D plasmids are required, as previously proposed. Thirty-seven strains belonging to the different subtypes were sequenced, and the results showed perfect concordance with the HMA results. Interlaboratory quality controls confirmed the reliability of the HMA for HIV-1 subtyping, despite the extensive viral variability. However, plasmid selection must be continuously revised to cover viral diversification.
Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Paris, France.
I
I
Loussert-Ajaka
E
E
Menu
C
C
Apetrei
M
M
Peeters
F
F
Damond
P
P
Mauclère
J
J
Eberle
C
C
Brengues
S
S
Saragosti
F
F
Barré-Sinoussi
F
F
Brun-Vézinet
F
F
Simon
D000595:Amino Acid Sequence; D001483:Base Sequence; D004279:DNA, Viral; D014644:Genetic Variation; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009692:Nucleic Acid Heteroduplexes; D010802:Phylogeny; D011786:Quality Control; D015203:Reproducibility of Results; D017421:Sequence Analysis; D017422:Sequence Analysis, DNA / Q000379:methods*; D017386:Sequence Homology, Amino Acid
D004279:DNA, Viral; D009692:Nucleic Acid Heteroduplexes