Performance of genotypic algorithms for predicting tropism for HIV-1 CRF01_AE recombinant.
- Soulie C Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France. Electronic address: cathia.soulie@aphp.fr.
- Morand-Joubert L Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Saint Antoine, Service de Virologie, Paris, France.
- Cottalorda J Laboratoire de Virologie, CHU, Nice, France.
- Charpentier C IAME, UMR 1137-Université Paris Diderot, Sorbonne Paris Cité, INSERM, AP-HP, Hôpital Bichat, Laboratoire de Virologie, Paris, France.
- Bellecave P CHU de Bordeaux, Laboratoire de Virologie, Univ. Bordeaux, CNRS UMR 5234, Bordeaux, France.
- Le Guen L Laboratoire de virologie, CHU, Nantes, France.
- Yerly S Laboratory of Virology, Geneva University Hospitals, Switzerland.
- Montes B Laboratoire de Virologie, CHU, Montpellier, France.
- Fafi-Kremer S Laboratoire de Virologie, CHU, Strasbourg, France.
- Dina J Laboratoire de virologie, CHU, Caen, France.
- Avettand-Fenoel V AP-HP, Laboratoire de Virologie, Hôpital Necker, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, EA7327, France.
- Amiel C AP-HP, Laboratoire de Virologie, Hôpital Tenon, Paris, France.
- Roussel C CHU, Amiens, France.
- Pallier C CHU Bicêtre, Paris, France.
- Zafilaza K Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France.
- Sayon S Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France.
- Signori-Schmuck A CHU, Grenoble, France.
- Mirand A CHU, Clermont-Ferrand, France.
- Trabaud MA Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.
- Berger S Laboratoire de Virologie, CHU de Nancy Brabois, EA 7300, Université de Lorraine, Faculté de Médecine, Vandoeuvre les Nancy, France.
- Calvez V Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France.
- Marcelin AG Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France.
- 2018-01-15
Published in:
- Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology. - 2018
CRF01_AE
Genotypic prediction
HIV tropism
Algorithms
CD4 Lymphocyte Count
False Positive Reactions
France
Genotype
Genotyping Techniques
HIV Envelope Protein gp120
HIV Infections
HIV-1
Humans
RNA, Viral
Switzerland
Viral Load
Viral Tropism
English
OBJECTIVES
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.
METHODS
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.
RESULTS
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.
CONCLUSION
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.
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.
METHODS
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.
RESULTS
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.
CONCLUSION
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.
- Language
-
- English
- Open access status
- green
- Identifiers
-
- DOI 10.1016/j.jcv.2017.12.014
- PMID 29331843
- Persistent URL
- https://sonar.ch/global/documents/46510
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