Performance of genotypic algorithms for predicting tropism for HIV-1 CRF01_AE recombinant

• Published in: Journal of clinical virology Vol. 99-100; pp. 57 - 60
• Main Authors: Soulie, C., Morand-Joubert, L., Cottalorda, J., Charpentier, C., Bellecave, P., Le Guen, L., Yerly, S., Montes, B., Fafi-Kremer, S., Dina, J., Avettand-Fenoel, V., Amiel, C., Roussel, C., Pallier, C., Zafilaza, K., Sayon, S., Signori-Schmuck, A., Mirand, A., Trabaud, M.A., Berger, S., Calvez, V., Marcelin, A.G.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01-02-2018; Elsevier
• Subjects: Algorithms; Bioinformatics; CD4 Lymphocyte Count; Computer Science; CRF01_AE; False Positive Reactions; France; Genotype; Genotypic prediction; Genotyping Techniques - methods; HIV Envelope Protein gp120 - genetics; HIV Infections - virology; HIV tropism; HIV-1 - classification; HIV-1 - genetics; HIV-1 - physiology; Humans; Life Sciences; Microbiology and Parasitology; RNA, Viral - blood; Switzerland; Viral Load; Viral Tropism; Virology; France; Switzerland; Genotypic prediction; CRF01_AE; HIV tropism; tropism; Genotypic prediction ANRS AC11 Resistance Study Group: Aix en Provence; HIV
• ISSN: 1386-6532; 1873-5967
• DOI: 10.1016/j.jcv.2017.12.014

•HIV tropism result can be slightly different according to the algorithm used.•In clinical practice, Geno2pheno FPR 5% could be used to predict CRF01_AE tropism.•Geno2Pheno are more conservative regarding the tropism than other genotypic rules.
There is no consensus about the performances of genotypic rules for predicting HIV-1 non-B subtype tropism. Three genotypic methods were compared for CRF01_AE HIV-1 tropism determination.
The V3 env region of 207 HIV-1 CRF01_AE and 178 B subtypes from 17 centers in France and 1 center in Switzerland was sequenced. Tropism was determined by Geno2Pheno algorithm with false positive rate (FPR) 5% or 10%, the 11/25 rule or the combined criteria of the 11/25, net charge rule and NXT/S mutations.
Overall, 72.5%, 59.4%, 86.0%, 90.8% of the 207 HIV-1 CRF01_AE were R5-tropic viruses determined by Geno2pheno FPR5%, Geno2pheno FPR10%, the combined criteria and the 11/25 rule, respectively. A concordance of 82.6% was observed between Geno2pheno FPR5% and the combined criteria for CRF01_AE. The results were nearly similar for the comparison between Geno2pheno FPR5% and the 11/25 rule. More mismatches were observed when Geno2pheno was used with the FPR10%. Neither HIV viral load, nor current or nadir CD4 was associated with the discordance rate between the different algorithms.
Geno2pheno predicted more X4-tropic viruses for this set of CRF01_AE sequences than the combined criteria or the 11/25 rule alone. For a conservative approach, Geno2pheno FPR5% seems to be a good compromise to predict CRF01_AE tropism.