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Abstract
The evaluation of position specific scoring matrix (PSSM) for genotypic prediction of co-receptor switching in HIV-1 isolates circulating in Iran
Shirvani E.1, Sarrami-Forooshani R.1, Nategh R.2, Haji-Abdolbaghi M.3, Mohraz M.3, Gomari H.1, Doosti A.1, Barkhordari F.1, Adeli A.1, Mahboudi F.1
Objectives: HIV-1 Coreceptor Switching is one of the most important genotypic demonstrations of the virus that accurse following some mutations in one of the variable regions of the env part of the viral genome (v3 loop). In this study we evaluated position specific scoring matrix or PSSM reliability as one of the bioinformatics tools which have been offered to be suitable replacement for cell culture methods in predicting of coreceptor usage in HIV-1 isolates.
Methods: A 461 base pair fragment of env nucleotides containing the entire V3 loop was amplified using a nested – PCR protocol. The amplified fragments then were cloned into the PGEM-T easy vector (promega) and amplified in E.coli Top10F´. 6-12 env clones were obtained from each amplified sample and subjected to automated sequencing in both directions. Sequences were aligned, manually edited, adjusted and translated into amino acids. Predictions of the HIV-1 coreceptor usage from the amino acid sequences of the third variable loop (V3) of the envelope gene were determined by the WebPSSM
Results: Most of the sequence´s scores were lower than the cut-off for R5 strains. The rest of sequences had scores clearly above the cut-off score of X4 strains and a few ones show scores between these two cut-off values.
Conclusions: In our study a new bioinformatics tool predicted all Iranian isolates to utilize CCR5 coreceptor. However some of the sequences belong to subtypes A, B also contained clones representing viruses with the potential to utilize the CXCR4 coreceptor .Some viral isolates predicted to be CCR-5 tropic had quasi-species with PSSM scores distributed over a wide range, suggesting ongoing coreceptor switch. The achieved scores then compare with clinical data including CD4 counts and viral load.
4th IAS Conference on HIV Pathogenesis, Treatment and Prevention
Abstract no.
MOPEA048
Suggested Citation
"ShirvaniE., et al.
The evaluation of position specific scoring matrix (PSSM) for genotypic prediction of co-receptor switching in HIV-1 isolates circulating in Iran.
Poster exhibition:
4th IAS Conference on HIV Pathogenesis, Treatment and Prevention:
Abstract no.
MOPEA048"
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