Secondary substitutions in the hemagglutinin and neuraminidase genes associated with neuraminidase inhibitor resistance are rare in the Influenza Resistance Information Study (IRIS)

Rueshandra Roosenhoff, Martin Schutten, Vaughan Reed, Barry Clinch, Anne van der Linden, Ron A. M. Fouchier, Pieter L. A. Fraaij*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

3 Citations (Scopus)
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Abstract

Amino acid substitutions in influenza virus neuraminidase (NA) that cause resistance to neuraminidase inhibitors (NAI) generally result in virus attenuation. However, influenza viruses may acquire secondary substitutions in the NA and hemagglutinin (HA) proteins that can restore viral fitness. To assess to which extent this happens, the emergence of NAI resistance substitutions and secondary – potentially compensatory – substitutions was quantified in influenza viruses of immunocompetent individuals included in the Influenza Resistance Information Study (IRIS; NCT00884117). Known resistance substitutions were detected by mutation specific RT-PCR in viruses of 57 of 1803 (3.2%) oseltamivir-treated individuals, including 39 individuals infected with A/H1N1pdm09 [H275Y] virus and 18 with A/H3N2 [R292K] virus. A total of fifteen and ten other amino acid substitutions were acquired in HA and NA respectively, of A/H1N1pdm09, A/H3N2 and influenza B viruses upon treatment with oseltamivir but none of these was associated with resistance to oseltamivir. All cultured viruses with the known resistance substitutions H275Y or R292K showed reduced susceptibility to oseltamivir in the NA-star assay. Upon next-generation sequencing, the vast majority of NAI resistant A/H1N1pdm09 and A/H3N2 viruses had no resistance-associated secondary substitutions at high frequency. Only in two A/H1N1pdm09 [H275Y] viruses, the potentially compensatory secondary substitutions HA-D52N and NA-R152K were detected. We conclude that the emergence of secondary substitutions that may restore viral fitness upon the emergence of known influenza virus NAI resistance substitutions was a rare event in this immunocompetent population.

Original languageEnglish
Article number105060
JournalAntiviral Research
Volume189
DOIs
Publication statusPublished - May 2021

Bibliographical note

Funding
The Influenza Resistance Information Study (IRIS) was sponsored and funded in full by F. Hoffmann-La Roche Ltd. The study was designed by the IRIS steering committee and F. Hoffmann-La Roche Ltd. Employees of F. Hoffmann-La Roche Ltd were involved in review of this manuscript. Final decisions on the analysis and interpretation of the data remained with Rueshandra Roosenhoff, Vaughan Reed, Barry Clinch, Ron A.M. Fouchier,Martin Schutten and Pieter Fraaij.

Research programs

  • EMC MM-04-54-08-A

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