Universität zu Köln

Riemenschneider, Mona, Cashin, Kieran Y., Budeus, Bettina ORCID: 0000-0002-9313-8636, Sierra, Saleta, Shirvani-Dastgerdi, Elham, Bayanolhagh, Saeed, Kaiser, Rolf, Gorry, Paul R. and Heider, Dominik ORCID: 0000-0002-3108-8311 (2016). Genotypic Prediction of Co-receptor Tropism of HIV-1 Subtypes A and C. Sci Rep, 6. LONDON: NATURE PUBLISHING GROUP. ISSN 2045-2322

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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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Riemenschneider, Mona UNSPECIFIED UNSPECIFIED UNSPECIFIED Cashin, Kieran Y. UNSPECIFIED UNSPECIFIED UNSPECIFIED Budeus, Bettina UNSPECIFIED orcid.org/0000-0002-9313-8636 UNSPECIFIED Sierra, Saleta UNSPECIFIED UNSPECIFIED UNSPECIFIED Shirvani-Dastgerdi, Elham UNSPECIFIED UNSPECIFIED UNSPECIFIED Bayanolhagh, Saeed UNSPECIFIED UNSPECIFIED UNSPECIFIED Kaiser, Rolf UNSPECIFIED UNSPECIFIED UNSPECIFIED Gorry, Paul R. UNSPECIFIED UNSPECIFIED UNSPECIFIED Heider, Dominik UNSPECIFIED orcid.org/0000-0002-3108-8311 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-278231
DOI:	10.1038/srep24883
Journal or Publication Title:	Sci Rep
Volume:	6
Date:	2016
Publisher:	NATURE PUBLISHING GROUP
Place of Publication:	LONDON
ISSN:	2045-2322
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language IMMUNODEFICIENCY-VIRUS TYPE-1; AMINO-ACID CHANGES; SEQUENCE ALIGNMENT; V3 LOOP; IDENTIFICATION; GP120; CXCR4; USAGE; RESISTANCE; RECEPTOR Multiple languages Multidisciplinary Sciences Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/27823