Detection of a genetic footprint of the sofosbuvir resistance-associated substitution S282T after HCV treatment failure
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The major resistance-associated substitution for sofosbuvir (S282T) in HCV NS5B causes severe viral fitness costs and rapidly reverts back to prototype in the absence of selection pressure. Accordingly, resistance against sofosbuvir is rarely detected even in patients after treatment failure.
We report a case of a GT3a infected patient with viral breakthrough under SOF/DCV therapy. At the time of breakthrough the RAS S282T was predominant in NS5B and then rapidly disappeared during follow-up by week 12 after treatment. Interestingly, despite only serine was encoded in position 282 during follow-up, two distinct genetic pathways for reversion were detectable. In 31% of the quasispecies the original codon for serine was present whereas in the majority of the quasispecies an alternative codon was selected. This alternative codon usage was unique for all GT3a isolates from the HCV database and remained detectable as a genetic footprint for prior resistance selection at the RNA level for at least 6 months.
Comparative analyses of viral sequences at the codon level before and after DAA treatment may help to elucidate the patient’s history of resistance selection, which is particularly valuable for highly unfit substitutions that are detectable only for a short period of time. If such codon changes increase the risk of re-selection of resistance upon a second exposure to SOF remains to be addressed.
KeywordsSofosbuvir Daclatasvir Resistance Genotype 3a Breakthrough S282T MEDCOAT
Hepatitis C Virus
During the last few years, several directly acting antivirals (DAAs) became available for treatment of chronic hepatitis C, starting a new era of therapy of hepatitis C virus (HCV) infection. DAAs were typically optimized for inhibition of viral replication of HCV genotype 1a and 1b and are in most cases less active against genotype 3a. Currently, only a combination of the nucleoside analogue sofosbuvir (SOF) and one of the NS5A inhibitors Velpatasvir (VEL) or daclatasvir (DCV) are recommended for treatment of patients infected with HCV genotype 3a . Depending on the fibrosis stage, prior treatment experience and the duration of therapy, sustained viral response rates (SVR) between 63 and 96% have been reported [2, 3]. In clinical studies resistance-associated substitutions (RAS) were detected in the majority of patients who failed to achieve SVR (reviewed in [4, 5]). In Genotype 3a the most common NS5A-RAS are Y93H, A30K and L31I . In the ALLY-3 trial NS5A-Y93H RAS was present in 15 of 16 patients with relapse, whereas NS5B RASs associated with resistance to SOF (aa159, 282, or 321) were not detected . Up to date the major SOF resistance associated substitution S282T was only found in few patients with viral relapse [7, 8, 9].
Discussion and conclusions
We report here, to our knowledge, the first case of selection of the RAS S282T in a patient infected with genotype GT3a. Selection of the RAS was associated with a viral breakthrough detected at week 12, when the plasma drug levels were in a low therapeutic range. If the low plasma drug levels are a consequence of the MEDCOAT® coating of the tablets is unknown since no peer reviewed data on the pharmacokinetics are available. However, it has been described that co-medication with proton pump inhibitors (PI) during HCV-treatment is a risk factor for treatment failure . Accordingly, it seems plausible that the usage of MEDCOAT® might be a risk factor for treatment failure as well.
Although reversion of NS5A RAS has been described, in the majority (85–94%) of genotype 1 infected patients NS5A RAS persist in the viral population over years after treatment [13, 14, 15]. For genotype 3a no systematic analysis of the destiny of NS5A RAS after treatment failure is available. In line with previous reports the S282T substitution rapidly reverted back to prototype by week 12 after treatment . Interestingly, despite only serine was encoded in position 282 at that time, the codon usage had changed leaving a detectable genetic footprint of prior resistance selection that was unique for GT3a isolates. This genetic footprint of prior resistance selection remained detectable at the RNA level for at least 6 months, consistent with lower fitness costs compared to the original RAS. We conclude that comparative analyses of viral sequences at the codon level before and after DAA treatment may help to elucidate the patient’s history of resistance selection, which is particularly valuable for highly unfit RAS that are detectable only for a short period of time. If such codon changes increase the risk of re-selection of resistance upon a second exposure to SOF is unknown. The patient reported here was not re-treated until now, as no advanced fibrosis was yet detectable.
We thank Iris Herrmann and Jennifer Camdereli for excellent technical help.
This work was funded by DFG grant TI 323/4–1
Availability of data and materials
The datasets used and analyzed in the current study are available from the corresponding author on reasonable request.
Acquisition of data (AW, SF, NL, MO, RK, JT), study concept and design (DH, JT, HB), analysis and interpretation of data (AW, NL, JT, HB), drafting of the manuscript (AW, JT, HB) critical revision of the manuscript (AW, SF, NL, MO, RK, DH, JT,HB), study supervision (JT,DH,HB). All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Consent for publication
Obtained from the patient.
Ethics approval and consent to participate
Informed consent was obtained from the patient, and the study protocol was approved by the ethics committee of the Medical Faculty of the University of Düsseldorf (Ethic #2012048) in accordance with the guidelines of the Declaration of Helsinki.
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