Correlation between rules-based interpretation and virtual phenotype interpretation of HIV-1 genotypes for predicting drug resistance in HIV-infected individuals

Journal of Virological Methods
Oscar GallegoVincent Soriano

Abstract

Drug resistance testing provides useful information for managing HIV-infected patients. Phenotyping could add complementary information to genotyping and occasionally be more useful, although is less available to clinicians. Large paired geno-pheno databases have allowed the prediction of phenotypes from genotypes. However, the accuracy of these virtual phenotypes (vPT) in a clinical setting has not been well assessed yet. We analyzed the concordance between vPT and interpreted genotype (GT) in 105 samples belonging to treatment-experienced HIV-infected patients. A high concordance was seen when examining both non-nucleoside reverse transcriptase inhibitors (NNRTI) and protease inhibitors (PI) (r = 0.95 either), while it was lower for nucleoside analogs (r = 0.79). The drugs with lower concordance were abacavir (71.1%), tenofovir (71.5%) and didanosine (71.9%). In 20% of specimens (21/105), the vPT did not provide results for all approved drugs. These were mainly samples with a high number of drug resistance mutations or rare genotypes, which seem to be underepresented in the VircoNET database. Overall, there is good correlation between vPT/GT, especially for PI and NNRTI. The inclusion of additional sequences in the VircoNET d...Continue Reading

References

Jan 25, 2002·AIDS·Cristina TuralUNKNOWN Havana Study Group
Mar 11, 2003·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Francesco MazzottaUNKNOWN Genotipo-Fenotipo di Resistenza (GenPheRex) Group of the Italian Management Standardizzato di Terapia Antiretrovirale (MASTE
Jun 7, 2003·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Nicolas A MargotMichael D Miller

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Citations

Sep 10, 2011·Journal of Chemical Information and Modeling·David W Wright, Peter V Coveney
May 9, 2008·AIDS Research and Human Retroviruses·Jeffrey A AndersonUNKNOWN AIDS Clinical Trials Group Study 359 Protocol Team
Nov 28, 2006·Enfermedades infecciosas y microbiología clínica·Ana Sáez-López, Jesús Agüero-Balbín
Feb 4, 2006·Journal of Hepatology·Tim ShawStephen Locarnini
Jan 4, 2007·Journal of Forensic Sciences·Cedric NeumannAndie Bromage-Griffiths
Oct 19, 2019·Epidemiology and Health·Yunsu ChoiMyeongsu Yoo
Jan 30, 2021·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Manisha GoyalBrian West

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