Polymorphisms and resistance mutations of hepatitis C virus on sequences in the European hepatitis C virus database.
OBJECTIVE
To evaluate the occurrence of resistant mutations in treatment-naïve hepatitis C virus (HCV) sequences deposited in the European hepatitis C virus database (euHCVdb).


METHODS
The sequences were downloaded from the euHCVdb (https://euhcvdb.ibcp.fr/euHCVdb/). The search was performed for full-length NS3 protease, NS5A and NS5B polymerase sequences of HCV, separated by genotypes 1a, 1b, 2a, 2b and 3a, and resulted in 798 NS3, 708 NS5A and 535 NS5B sequences from HCV genotypes 1a, 1b, 2a, 2b and 3a, after the exclusion of sequences containing errors and/or gaps or incomplete sequences, and sequences from patients previously treated with direct antiviral agents (DAA). The sequence alignment was performed with MEGA 6.06 MAC and the resulting protein sequences were then analyzed using the BioEdit 7.2.5. for mutations associated with resistance. Only positions that have been described as being associated with failure in treatment inin vivostudies, and/or as conferring a more than 2-fold change in replication in comparison to the wildtype reference strain inin vitrophenotypic assays were included in the analysis.


RESULTS
The Q80K variant in theNS3gene was the most prevalent mutation, being found in 44.66% of subtype 1a and 0.25% of subtype 1b. Other frequent mutations observed in more than 2% of the NS3 sequences were: I170V (3.21%) in genotype 1a, and Y56F (15.93%), V132I (23.28%) and I170V (65.20%) in genotype 1b. For the NS5A, 2.21% of the genotype 1a sequences have the P58S mutation, 5.95% of genotype 1b sequences have the R30Q mutation, 15.79% of subtypes 2a sequences have the Q30R mutation, 23.08% of subtype 2b sequences have a L31M mutation, and in subtype 3a sequences, 23.08% have the M31L resistant variants. For the NS5B, the V321L RAV was identified in 0.60% of genotype 1a and in 0.32% of genotype 1b sequences, and the N142T variant was observed in 0.32% of subtype 1b sequences. The C316Y, S556G, D559N RAV were identified in 0.33%, 7.82% and 0.32% of genotype 1b sequences, respectively, and were not observed in other genotypes.


CONCLUSIONS
HCV mutants resistant to DAAs are found in low frequency, nevertheless they could be selected and therapy could fail due resistance substitutions in HCV genome.
Dimas Alexandre Kliemann, Cristiane Valle Tovo, Ana Beatriz Gorini da Veiga, Angelo Alves de Mattos, Graduate Program in Medicine: Hepatology - Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS 90050-170, Brazil.
Dimas Alexandre
DA
Kliemann
Dimas Alexandre Kliemann, Cristiane Valle Tovo, Ana Beatriz Gorini da Veiga, Angelo Alves de Mattos, Graduate Program in Medicine: Hepatology - Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS 90050-170, Brazil.
Cristiane Valle
CV
Tovo
Dimas Alexandre Kliemann, Cristiane Valle Tovo, Ana Beatriz Gorini da Veiga, Angelo Alves de Mattos, Graduate Program in Medicine: Hepatology - Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS 90050-170, Brazil.
Ana Beatriz Gorini
AB
da Veiga
Dimas Alexandre Kliemann, Cristiane Valle Tovo, Ana Beatriz Gorini da Veiga, Angelo Alves de Mattos, Graduate Program in Medicine: Hepatology - Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS 90050-170, Brazil.
Angelo Alves
AA
de Mattos
Dimas Alexandre Kliemann, Cristiane Valle Tovo, Ana Beatriz Gorini da Veiga, Angelo Alves de Mattos, Graduate Program in Medicine: Hepatology - Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS 90050-170, Brazil.
Charles
C
Wood
D024882:Drug Resistance, Viral / Q000235:genetics*; D005260:Female; D016174:Hepacivirus / Q000235:genetics*; D006801:Humans; D008297:Male; D009154:Mutation; D011110:Polymorphism, Genetic; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases; D012324:RNA-Dependent RNA Polymerase
D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase
Direct antiviral agents; Drug resistance; Hepatitis C virus resistance; Polymorphisms; Quasispecies