<p>Computational analysis of naturally occurring resistance-associated substitutions in genes <em>NS3</em>, <em>NS5A</em>, and <em>NS5B</em> among 86 subtypes of hepatitis C virus worldwide</p>

Abstract

Background and objectiveDirect-acting antivirals (DAA) facing resistance continue to be used in some areas worldwide. Thus, identifying hepatitis C virus (HCV) genotypes/subtypes and loci with certain prevalent resistance-associated substitutions (RASs) deserves attention. We investigated the global and regional frequencies of naturally occurring RASs among all confirmed HCV subtypes (n=86) and explored co-occurring and mutually exclusive RAS pairs within and between genes NS3, NS5A, and NS5B.MethodsA total of 213,908 HCV sequences available as of July 10, 2019 were retrieved from the NCBI nucleotide database. After curation, 17,312 NS3, 8,478 NS5A, and 25,991 NS5B sequence fragments from DAA-naïve patients were screened for RASs. MEGA 6.0 was used to translate aligned nucleotide sequences into amino acid sequences, and RAS pairs were identified by hypergeometric analysis.ResultsRAS prevalence varied significantly among HCV subtypes. For example, D168E, highly resistanct to all protease inhibitors except voxilaprevir, was nearly absent in all subtypes except in 43.48% of GT5a sequences. RASs in NS3 exhibiting significantly different global distribution included Q80K in GT1a with the highest frequency in North America (54.49%), followed by in Europe (22.66%), Asia (6.98%), Oceania (6.62%), and South America (1.03%). The prevalence of NS3 S122G in GT1b was highest in Asia (26.6%) and lowest in Europe (2.64%). NS5A L28M, R30Q, and Y93H in GT1b, L31M in GT2b, and NS5B C316N in GT1b was most prevalent in Asia. A150V in GT3a, associated with sofosbuvir treatment failure, was most prevalent in Asia (44.09%), followed by Europe (31.19%), Oceania (24.29%), and North America (19.05%). Multiple mutually exclusive or co-occurring RAS pairs were identified, including Q80K+R155K and R155K+D168G in GT1a and L159F+C316N and R30Q (NS5A)+C316N (NS5B) in GT1b.ConclusionOur data may be of special relevance for those countries where highly effective antivirals might not be available. Considering the specific RASs prevalence will help the clinicians to make optimal treatment choices. The RASs pairs would benefit anti-HCV drug development.

Global evolutionary analysis of chronic hepatitis C patients revealed significant effect of baseline viral resistance, including novel non‐target sites, for DAA‐based treatment and retreatment outcome

“…We also found substitution A150V in the NS5B polymerase associated with treatment failure in GT3a patients as seen in a previous study 39 and indications that this mutation could also affect GT2b. The high prevalence of 150V in GT3a ranging from 19%–44% 40 at baseline could affect treatment with sofosbuvir/velpatasvir (Epclusa ® ) and sofosbuvir/velpatasvir/ voxilaprevir (Vosevi ® ), especially if NS5A RASs are also present.…”

Extended interaction networks with HCV protease NS3-4A substrates explain the lack of adaptive capability against protease inhibitors

“…By interference with critically balanced protease-peptide interactions, the second-site mutation rescues replicative fitness deficits of Asp 168 variants in infectious cell culture. The finding that NS3-Q41R, which itself is reported to confer resistance to macrocyclic PIs (19), has a fitnesscompensatory effect in Asp 168 variants is surprising, given the very low prevalence of variants harboring Q41R in PIexperienced patients (,0.1%) (20). Our findings highlight a previously unknown molecular mechanism for MAVS that potentially restricts virus evolution under PI pressure, providing a new paradigm for variant selection from HCVinfected cells.…”

Sofosbuvir plus ribavirin is tolerable and effective even in elderly patients 75-years-old and over

“…Furthermore, sofosbuvir-specific resistance-associated substitutions (RASs) were not tested for in this study. The prevalence of the naturally occurring RAS·S282T, as the only known variant conferring sofosbuvir resistance in vitro , is reportedly rare in genotype 2 (0.22%)[ 26 ]. However, RAS·A150V has recently been found to be associated with reduced response to treatment with sofosbuvir and ribavirin and has appeared in genotype 2a (13.8%) and genotype 2b (1.03%)[ 26 ].…”

“…The prevalence of the naturally occurring RAS·S282T, as the only known variant conferring sofosbuvir resistance in vitro , is reportedly rare in genotype 2 (0.22%)[ 26 ]. However, RAS·A150V has recently been found to be associated with reduced response to treatment with sofosbuvir and ribavirin and has appeared in genotype 2a (13.8%) and genotype 2b (1.03%)[ 26 ]. In addition, the naturally occurring nucleoside inhibitor-specific RASs (E237G, M289I/L, L320 F, and V321A/I) are also found in genotype 2[ 26 ].…”

“…However, RAS·A150V has recently been found to be associated with reduced response to treatment with sofosbuvir and ribavirin and has appeared in genotype 2a (13.8%) and genotype 2b (1.03%)[ 26 ]. In addition, the naturally occurring nucleoside inhibitor-specific RASs (E237G, M289I/L, L320 F, and V321A/I) are also found in genotype 2[ 26 ]. The influence of these preexisting RASs on SVR should be analyzed using a larger number of cases with treatment failure.…”