Poster Presentation 12th Australasian Virology Society Meeting 2024

Multiple neuraminidase gene mutations in serial samples from an immunocompromised influenza A(H3N2) infected patient treated with oseltamivir (#169)

Saira Hussain 1 2 , Christina Guo 3 , Yi-Mo Deng 1 , Nikita Deshpande 1 , Natalie Spirason 1 , Presa Chanthalavanh 1 , Olivia Lay 1 , Clyde Dapat 1 , Heidi Peck 1 , Kanta Subbarao 1 2 , Bradley Gardiner 3 4 , Ian Barr 1 2
  1. WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
  2. Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, Australia
  3. Department of Infectious Diseases, Alfred Health, Melbourne, VIC, Australia
  4. School of Translational Medicine, Monash University, Melbourne, VIC, Australia

Introduction

Neuraminidase (NA) inhibitors (NAI) are the main antiviral medications used for influenza worldwide. NAI resistance rates for seasonal influenza viruses have remained low (<0.7%) in recent years, especially in A(H3N2) subtype viruses.  

Methods

A 30-year-old man with cystic fibrosis was infected with influenza A(H3N2) 14 days after living related kidney transplantation. He received several courses of oseltamivir over the next 10 weeks but had persistent symptoms and was unable to clear the virus. Several nose/throat swabs collected over 14 weeks were sent to the WHO Collaborating Centre for Reference and Research on Influenza for antiviral resistance testing. Samples were subjected to whole genome sequencing (WGS) and available virus isolates were tested for NAI susceptibility to oseltamivir, zanamivir, peramivir and laninamivir by the 2′-(4-Methylumbelliferyl)-α-D-N-acetylneuraminic acid (MUNANA) substrate phenotypic assay.

Results

The clinical samples showed variable Cycle threshold values (Ct 10-32) for influenza A over the 14 weeks that samples were taken. WGS of the clinical samples revealed that the patient had acquired a range of changes in the NA gene in several samples over the course of the infection that conferred highly reduced inhibition (HRI) to oseltamivir. These included NA-R292K and NA-E119V substitutions, and a deletion at 245-248 residues. These results were confirmed by the phenotypic assay (IC50 values were 103- to 166-fold higher than the median value). Following these results, treatment with zanamivir was initiated and the influenza infection was cleared.

Conclusions

This is a rare case of oseltamivir resistance in an influenza A(H3N2) virus caused by a variety of mutations in the NA, all leading to HRI to oseltamivir, occurring in a highly immunocompromised patient shortly after kidney transplant. Early detection of drug resistance and alternative treatments such as zanamivir, peramivir and baloxavir (a polymerase inhibitor) are most likely to improve clinical outcomes.