Genotypic inference of HIV-1 tropism using population-based sequencing of V3.
BACKGROUND
Prior to receiving a drug from CCR5-antagonist class in HIV therapy, a patient must undergo an HIV tropism test to confirm that his or her viral population uses the CCR5 coreceptor for cellular entry, and not an alternative coreceptor. One approach to tropism testing is to examine the sequence of the V3 region of the HIV envelope, which interacts with the coreceptor.


METHODS
Viral RNA is extracted from blood plasma. The V3 region is amplified in triplicate with nested reverse transcriptase-PCR. The amplifications are then sequenced and analyzed using the software, RE_Call. Sequences are then submitted to a bioinformatic algorithm such as geno2pheno to infer viral tropism from the V3 region. Sequences are inferred to be non-R5 if their geno2pheno false positive rate falls below 5.75%. If any one of the three sequences from a sample is inferred to be non-R5, the patient is unlikely to respond to a CCR5-antagonist.
Laboratory Program, BC Centre for Excellence in HIV/AIDS.
Rachel A
RA
McGovern
P Richard
PR
Harrigan
Luke C
LC
Swenson
D065100:CCR5 Receptor Antagonists; D005838:Genotype; D015658:HIV Infections / Q000097:blood / Q000188:drug therapy / Q000821:virology*; D015497:HIV-1 / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D006801:Humans; D012367:RNA, Viral / Q000097:blood / Q000235:genetics; D019713:Receptors, CCR5 / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction
D065100:CCR5 Receptor Antagonists; D012367:RNA, Viral; D019713:Receptors, CCR5
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