Abstract：
:HIV drug resistance (DR) testing using Sanger sequencing (SS) is limited by the inability of the method to identify low abundance drug resistance variants. The application of tagged pooled pyrosequencing (TPP) for HIV DR surveillance is described and the results compared with SS. HIV(+) serum specimens were genotyped using both SS and TPP. Surveillance drug resistance mutations were identified using SS and TPP consensus reads at multiple mixed base identification thresholds (MBITs). Drug resistance patterns were highly concordant between SS and TPP when the MBIT was set at 20%. DR mutations were detected in 7.1% of the subjects, with 1.6% of individuals harboring resistance to NRTI, 3.3% NNRTI and 2.7% PI. Analyzing the TPP reads for each subject confirmed that drug resistance mutations with frequencies <20% were inconsistently detected by SS. Conversely, low abundance drug resistant variants were easily identified using TPP with mixed base identification threshold set at low value. In conclusion, at considerable savings when compared to commercial assays, TPP produces HIV DR profiles that are concordant with those from SS, furthermore, these same data can be used to identify low abundance drug resistant variants.
journal_name
J Virol Methodsjournal_title
Journal of virological methodsauthors
Ji H,Liang B,Li Y,Van Domselaar G,Graham M,Tyler S,Merks H,Sandstrom P,Brooks Jdoi
10.1016/j.jviromet.2012.10.018subject
Has Abstractpub_date
2013-02-01 00:00:00pages
314-20issue
2eissn
0166-0934issn
1879-0984pii
S0166-0934(12)00382-5journal_volume
187pub_type
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