Genotypic Prediction of Co-receptor Tropism of HIV-1 Subtypes A and C.

Abstract

Antiretroviral treatment of Human Immunodeficiency Virus type-1 (HIV-1) infections with CCR5-antagonists requires the co-receptor usage prediction of viral strains. Currently available tools are mostly designed based on subtype B strains and thus are in general not applicable to non-B subtypes. However, HIV-1 infections caused by subtype B only account for approximately 11% of infections worldwide. We evaluated the performance of several sequence-based algorithms for co-receptor usage prediction employed on subtype A V3 sequences including circulating recombinant forms (CRFs) and subtype C strains. We further analysed sequence profiles of gp120 regions of subtype A, B and C to explore functional relationships to entry phenotypes. Our analyses clearly demonstrate that state-of-the-art algorithms are not useful for predicting co-receptor tropism of subtype A and its CRFs. Sequence profile analysis of gp120 revealed molecular variability in subtype A viruses. Especially, the V2 loop region could be associated with co-receptor tropism, which might indicate a unique pattern that determines co-receptor tropism in subtype A strains compared to subtype B and C strains. Thus, our study demonstrates that there is a need for the development of novel algorithms facilitating tropism prediction of HIV-1 subtype A to improve effective antiretroviral treatment in patients.

DOI: 10.1038/srep24883

Extracted Key Phrases

6 Figures and Tables

05020162017
Citations per Year

Citation Velocity: 17

Averaging 17 citations per year over the last 2 years.

Learn more about how we calculate this metric in our FAQ.

Cite this paper

@article{Riemenschneider2016GenotypicPO, title={Genotypic Prediction of Co-receptor Tropism of HIV-1 Subtypes A and C.}, author={Mona Riemenschneider and Kieran Y Cashin and Bettina Budeus and Saleta Sierra and Elham Shirvani-Dastgerdi and Saeed Bayanolhagh and Rolf Kaiser and Paul R. Gorry and Dominik Heider}, journal={Scientific reports}, year={2016}, volume={6}, pages={24883} }