Universität zu Köln

Matsuda, Masakazu, Louvel, Severine, Sugiura, Wataru, Haas, Alexandra, Pfeifer, Nico, Yokomaku, Yoshiyuki, Iwatani, Yasumasa, Kaiser, Rolf and Klimkait, Thomas ORCID: 0000-0003-4945-6511 (2018). Performance Evaluation of a Genotypic Tropism Test Using HIV-1 CRF01_AE Isolates in Japan. Jpn. J. Infect. Dis., 71 (4). S. 264 - 267. TOKYO: NATL INST INFECTIOUS DISEASES. ISSN 1884-2836

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Abstract

Geno2Pheno (coreceptor), a genotypic tropism test, demonstrates excellent agreement with the phenotypic tropism test for subtype B and some other subtypes. However, potential X4-overcalling for CRF01_AE might occur with the present version. To confirm X4 overcalling for AE and to optimize the algorithm for use with AE, we compared the tropism of 22 AE samples by both genotypic and phenotypic methods. The env V3 region was analyzed by bulk sequencing, and tropism was evaluated using the Geno2Pheno algorithm. PhenXR, a phenotypic tropism test, was performed in parallel to determine chemokine receptor preferences. A high X4-overcalling for select samples and a low rate of R5-concordant samples (9.1%) were observed for AE with the current version of Geno2Pheno (coreceptor). On the other hand, the new version, namely, Geno2Pheno (Sanger), showed a high concordance rate of 81.8%, with PhenXR. Because majority of the samples were selected based on discrepancies in the genotypic tropism calls between the present version Geno2Pheno (coreceptor) (FPR < 10%) and the new version Geno2Pheno (Sanger) (X4-risk < 36), it remains to be determined whether the new version provides improved R5-calls for the AE sequences in general or only in this setting. Further clinical validation studies are warranted.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Matsuda, Masakazu UNSPECIFIED UNSPECIFIED UNSPECIFIED Louvel, Severine UNSPECIFIED UNSPECIFIED UNSPECIFIED Sugiura, Wataru UNSPECIFIED UNSPECIFIED UNSPECIFIED Haas, Alexandra UNSPECIFIED UNSPECIFIED UNSPECIFIED Pfeifer, Nico UNSPECIFIED UNSPECIFIED UNSPECIFIED Yokomaku, Yoshiyuki UNSPECIFIED UNSPECIFIED UNSPECIFIED Iwatani, Yasumasa UNSPECIFIED UNSPECIFIED UNSPECIFIED Kaiser, Rolf UNSPECIFIED UNSPECIFIED UNSPECIFIED Klimkait, Thomas UNSPECIFIED orcid.org/0000-0003-4945-6511 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-181236
DOI:	10.7883/yoken.JJID.2017.482
Journal or Publication Title:	Jpn. J. Infect. Dis.
Volume:	71
Number:	4
Page Range:	S. 264 - 267
Date:	2018
Publisher:	NATL INST INFECTIOUS DISEASES
Place of Publication:	TOKYO
ISSN:	1884-2836
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language CHEMOKINE RECEPTOR; RESISTANT HIV-1; MARAVIROC; CCR5; DRUG; ANTAGONIST; ASSAY Multiple languages Infectious Diseases Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/18123