Subtype Classification by Polymerase and Gag Genes of HIV-1 Iranian Sequences Registered in the NCBI GenBank

Author(s): Behzad Dehghani, Zahra Hasanshahi, Tayebeh Hashempour*, Parvin Afsar Kazerooni*

Journal Name: Current Proteomics

Volume 18 , Issue 2 , 2021


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Graphical Abstract:


Abstract:

Background: The rate of Human Immunodeficiency Virus type 1 (HIV-1) infection in Iran has increased dramatically in the last few years.

Objective: The aim of this study was to investigate the HIV subtype amongst all Iranian HIV sequences, using 8 websites.

Methods: In this study, 637 sequences of polymerase, and gag genes of HIV-1 were obtained from NCBI. HIV-1 subtyping was done, using 8 reliable software.

Results: The final results of the 8 online tools indicated that the majority of sequences were HIV-1 subtype CRF35 AD. However, it appeared that in some genes, a few programs could not determine specific subtypes and in some cases they described different subtypes.

Conclusion: Considering the CRF35 AD diagram, it was clear that integrase was not an appropriate region to define this subtype. Also the full length of gag gene should be used for subtyping. For CRF1, AE envelop gene is a reliable region to define this subtype. Stanford software was used to determine the drug resistance prevalence and in 5.7% of the sequences, drug resistance mutations were found.

Keywords: HIV, subtyping, bioinformatics, Iran, CRF35 AD, drug resistance.

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VOLUME: 18
ISSUE: 2
Year: 2021
Published on: 10 May, 2020
Page: [153 - 161]
Pages: 9
DOI: 10.2174/1570164617999200510233018
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