Using NS5B Sequencing for Hepatitis C Virus Genotyping Reveals Discordances with Commercial Platforms.
We aimed to evaluate the correct assignment of HCV genotypes by three commercial methods-Trugene HCV genotyping kit (Siemens), VERSANT HCV Genotype 2.0 assay (Siemens), and Real-Time HCV genotype II (Abbott)-compared to NS5B sequencing. We studied 327 clinical samples that carried representative HCV genotypes of the most frequent geno/subtypes in Spain. After commercial genotyping, the sequencing of a 367 bp fragment in the NS5B gene was used to assign genotypes. Major discrepancies were defined, e.g. differences in the assigned genotype by one of the three methods and NS5B sequencing, including misclassification of subtypes 1a and 1b. Minor discrepancies were considered when differences at subtype levels, other than 1a and 1b, were observed. The overall discordance with the reference method was 34% for Trugene and 15% for VERSANT HCV2.0. The Abbott assay correctly identified all 1a and 1b subtypes, but did not subtype all the 2, 3, 4 and 5 (34%) genotypes. Major discordances were found in 16% of cases for Trugene HCV, and the majority were 1b- to 1a-related discordances; major discordances were found for VERSANT HCV 2.0 in 6% of cases, which were all but one 1b to 1a cases. These results indicated that the Trugene assay especially, and to a lesser extent, Versant HCV 2.0, can fail to differentiate HCV subtypes 1a and 1b, and lead to critical errors in clinical practice for correctly using directly acting antiviral agents.
Servicio de Microbiología, Complejo Hospitalario Universitario Granada-Hospital San Cecilio, Instituto de Investigación Biosanitaria IBS, Granada, Spain.
Natalia
N
Chueca
Departamento de Microbiología y Parasitología USC, Servicio de Microbiología Hospital Conxo-CHUS Santiago de Compostela, A Coruña, Spain.
Isidro
I
Rivadulla
Servicio de Microbiología, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
Rubén
R
Lovatti
Servicio de Microbiología, Clínica Universidad de Navarra, Navarra Institute for Health Research (IdiSNA), Pamplona, Spain.
Gabriel
G
Reina
Servicio de Microbiología, Hospital la Princesa, Madrid, Spain.
Ana
A
Blanco
Servicio de Microbiología, Complejo Hospitalario Universitario Granada-Hospital San Cecilio, Instituto de Investigación Biosanitaria IBS, Granada, Spain.
Jose Angel
JA
Fernandez-Caballero
Servicio de Microbiología, Hospital la Princesa, Madrid, Spain.
Laura
L
Cardeñoso
Servicio de Microbiología, Complejo Hospitalario Universitario Granada, Hospital Virgen de las Nieves, Granada, Spain.
Javier
J
Rodriguez-Granjer
Servicio de Microbiología, Clínica Universidad de Navarra, Navarra Institute for Health Research (IdiSNA), Pamplona, Spain.
Miriam
M
Fernandez-Alonso
Departamento de Microbiología y Parasitología USC, Servicio de Microbiología Hospital Conxo-CHUS Santiago de Compostela, A Coruña, Spain.
Antonio
A
Aguilera
Servicio de Microbiología, Complejo Hospitalario Universitario Granada-Hospital San Cecilio, Instituto de Investigación Biosanitaria IBS, Granada, Spain.
Marta
M
Alvarez
Servicio de Microbiología, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
Juan Carlos
JC
Galán
Servicio de Microbiología, Complejo Hospitalario Universitario Granada-Hospital San Cecilio, Instituto de Investigación Biosanitaria IBS, Granada, Spain.
Federico
F
García
D060005:Genotyping Techniques / Q000379:methods*; D016174:Hepacivirus / Q000235:genetics*; D006801:Humans; D017422:Sequence Analysis, DNA; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D012324:RNA-Dependent RNA Polymerase
D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase