Detection of HIV-1 subtypes, recombinants, and dual infections in east Africa by a multi-region hybridization assay.
OBJECTIVE
To enable more rapid and efficient genotyping of HIV-1 in East Africa, where subtypes A, C, and D and their recombinants are co-circulating.


METHODS
Full-genome sequencing of HIV-1 provides complete discrimination of subtypes and recombinant forms but is costly and low-throughput compared to other genotyping approaches. Here we describe the development and evaluation of a Multi-region Hybridization Assay (MHA) for the efficient determination of HIV-1 subtypes A, C, D, recombinants, and dual infections.


METHODS
Five genome regions containing clustered mutations distinguishing subtypes A, C, and D were identified and used to design subtype-specific probes. DNA from primary peripheral blood mononuclear cells was used as template for real-time PCR using the fluorescent, subtype-specific probes.


RESULTS
A panel of 45 clinical samples from Uganda, Kenya, and Tanzania, previously characterized by full-genome sequencing and including 26 pure subtypes and 19 recombinant strains, was evaluated by MHA. The MHA provided 90% sensitivity and 98% specificity for the three subtypes, efficiently discriminated subtypes from recombinant forms, and detected several dual infections.


CONCLUSIONS
Accurate and efficient genotyping of HIV-1 strains in vaccine trial populations in East Africa, ascertainment of dual infections, and elucidation of the genesis of recombinant forms in individuals can be facilitated by the application of MHA.
Hoelscher
Michael
M
Department of Infectious Diseases and Tropical Medicine, Ludwig-Maximilians-University, Munich, Germany.
Dowling
William E
WE
Sanders-Buell
Eric
E
Carr
Jean K
JK
Harris
Matthew E
ME
Thomschke
Angelika
A
Robb
Merlin L
ML
Birx
Deborah L
DL
McCutchan
Francine E
FE
D000351:Africa, Eastern; D001483:Base Sequence; D015342:DNA Probes; D005838:Genotype; D015658:HIV Infections / Q000150:complications* / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D006801:Humans; D009693:Nucleic Acid Hybridization / Q000379:methods; D011995:Recombination, Genetic; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
D015342:DNA Probes