Determining the mutation bias of favipiravir in influenza virus using next-generation sequencing

Daniel H. Goldhill, Pinky Langat, Hongyao Xie, Monica Galiano, Shahjahan Miah, Paul Kellam, Maria Zambon, Angie Lackenby, Wendy S. Barclay*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

42 Citations (Scopus)


Favipiravir is a broad-spectrum antiviral drug that may be used to treat influenza. Previous research has identified that favipiravir likely acts as a mutagen, but the precise mutation bias that favipiravir induces in influenza virus RNAs has not been described. Here, we use next-generation sequencing (NGS) with barcoding of individual RNA molecules to accurately and quantitatively detect favipiravir-induced mutations and to sample orders of magnitude more mutations than would be possible through Sanger sequencing. We demonstrate that favipiravir causes mutations and show that favipiravir primarily acts as a guanine analogue and secondarily as an adenine analogue resulting in the accumulation of transition mutations. We also use a standard NGS pipeline to show that the mutagenic effect of favipiravir can be measured by whole-genome sequencing of virus. IMPORTANCE New antiviral drugs are needed as a first line of defense in the event of a novel influenza pandemic. Favipiravir is a broad-spectrum antiviral which is effective against influenza. The exact mechanism of how favipiravir works to inhibit influenza is still unclear. We used next-generation sequencing (NGS) to demonstrate that favipiravir causes mutations in influenza RNA. The greater depth of NGS sequence information over traditional sequencing methods allowed us to precisely determine the bias of particular mutations caused by favipiravir. NGS can also be used in a standard diagnostic pipeline to show that favipiravir is acting on the virus by revealing the mutation bias pattern typical to the drug. Our work will aid in testing whether viruses are resistant to favipiravir and may help demonstrate the effect of favipiravir on viruses in a clinical setting. This will be important if favipiravir is used during a future influenza pandemic.

Original languageEnglish
Article numbere01217-18
JournalJournal of Virology
Issue number2
Publication statusPublished - 1 Jan 2019

Bibliographical note

Funding Information:
This study was supported by the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Respiratory Infections at Imperial College in partnership with PHE. P.L., P.K., and W.S.B. were supported by Wellcome Trust Grant 200187/Z/15/Z.

Publisher Copyright:
Copyright © 2019 Goldhill et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.


  • Favipiravir
  • Influenza
  • Mutation bias
  • Next-generation sequencing
  • Primer ID


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