Global emergence of neuraminidase inhibitor-resistant influenza A(H1N1)pdm09 viruses with I223V and S247N mutations: implications for antiviral resistance monitoring
Authors: Rhoda Cheuk-Ying Leung, Jonathan Daniel Ip, Lin-Lei Chen, Wan-Mui Chan, Kelvin Kai-Wang To
Journal: The Lancet Microbe (2024)

Neuraminidase inhibitors (NAIs), such as oseltamivir and zanamivir, serve as the primary treatment for influenza virus infection. NAI-resistant influenza A(H1N1) strains were widespread during the 2008–09 influenza season, especially in Japan, where 100% of the strains were resistant to oseltamivir.1Baranovich T Saito R Suzuki Y et al.Emergence of H274Y oseltamivir-resistant A(H1N1) influenza viruses in Japan during the 2008–2009 season.J Clin Virol. 2010; 47: 23-28Google Scholar However, after the NAI-susceptible 2009 pandemic subtype (A[H1N1]pdm09) replaced the previous seasonal A(H1N1) subtype in 2009, the incidence of A(H1N1)pdm09 with reduced inhibition (10-fold to 100-fold) or highly reduced inhibition (>100-fold) was only approximately 1% in the 2019–20 influenza season.2Govorkova EA Takashita E Daniels RS et al.Global update on the susceptibilities of human influenza viruses to neuraminidase inhibitors and the cap-dependent endonuclease inhibitor baloxavir, 2018–2020.Antiviral Res. 2022; 200105281Google Scholar After a period of quiescence during the COVID-19 pandemic, the incidence of influenza has increased following the relaxation of physical distancing measures. In Hong Kong, the resurgence of the influenza virus occurred in 2023 following the relaxation of all COVID-19 restriction measures, with a peak in the spring, predominantly driven by A(H1N1)pdm09 in April, 2023.3Centre for Health ProtectionCOVID-19 & flu express. Local situation of COVID-19 activity (as of Dec 13, 2023).https://www.chp.gov.hk/files/pdf/covid_flux_week49_14_12_2023_eng.pdfDate accessed: December 18, 2023Google Scholar We have successfully sequenced the influenza neuraminidase gene in 92 individuals with A(H1N1) infection in Hong Kong in 2023. Among them, four individuals (4·35%) carried at least one mutation known to confer reduced susceptibility to the NAIs oseltamivir or zanamivir (appendix p 3).4Global Initiative on Sharing All Influenza Data (GISAID)FluServer Tool. Influenza surveillance. Preparing for the next wave.https://gisaid.org/database-features/flusurver-mutations-app/Date accessed: December 15, 2023Google Scholar Notably, three of ten (30%) A(H1N1)pdm09 strains collected in October, 2023, harboured both I223V and S247N mutations. To ascertain the global incidence of A(H1N1)pdm09 strains with I223V or S247N mutations, or a combination of both, we conducted a comprehensive analysis of A(H1N1)pdm09 strains available in the Global Initiative on Sharing All Influenza Data (GISAID) repository collected between January, 2016, and November, 2023 (appendix p 4). The incidence of strains with I223V or S247N mutations, or both, increased in the fall of 2023. The incidence of the I223V mutation increased from fewer than 1200 per 100 000 individuals before August, 2023, to 1250–4972 per 100 000 individuals between August and November, 2023, whereas that of the S247N mutation increased from fewer than 1200 per 100 000 individuals before September, 2023, to 1775–2500 per 100 000 individuals between September and October, 2023. None of the strains collected before July, 2023, harboured dual I223V/S247N mutations; however, since July, 2023, nine of 1023 strains (880 per 100 000 individuals) harboured dual I223V/S247N mutations, with the highest incidence in October, 2023 (five of 169 strains [2959 per 100 000 individuals]). Of the nine strains with dual I223V/S247N mutations, five were collected from Europe (two from the Netherlands and one each from Norway, Sweden, and France), and four were collected from Oman. Additionally, among these nine strains, three were clustered under clade 6B.1A.5a.2a, and the remaining six were clustered within clade 6B.1A.5a.2a.1 (appendix pp 1–2). Previous studies have shown that mutations at neuraminidase amino acid residue 223 are associated with an 11–28-fold increase in the half-maximal inhibitory concentration (IC50) for oseltamivir, whereas mutations at residue 247 are linked to a six-fold increase in the oseltamivir IC50, compared with the reference median IC50 values.2Govorkova EA Takashita E Daniels RS et al.Global update on the susceptibilities of human influenza viruses to neuraminidase inhibitors and the cap-dependent endonuclease inhibitor baloxavir, 2018–2020.Antiviral Res. 2022; 200105281Google Scholar,5Hurt AC Lee RT Leang SK et al.Increased detection in Australia and Singapore of a novel influenza A(H1N1)2009 variant with reduced oseltamivir and zanamivir sensitivity due to a S247N neuraminidase mutation.Euro Surveill. 2011; 1619884Google Scholar However, investigations into such associations for dual I223V/S247N mutations have not been reported. Therefore, in this study, we assessed the susceptibility of a strain with dual I223V/S247N mutation (HKU-231217-085) to neuraminidase inhibitors using a chemiluminescent neuraminidase inhibition assay (appendix p 7). The IC50 value for HKU-231217-085 was 10·63-fold higher (from 0·429 nM to 4·563 nM) against oseltamivir and 3·38-fold higher (from 0·924 nM to 3·120 nM) against zanamivir than the average IC50 value for the three A(H1N1) strains (HKU-231217-099/2023, HKU-231217-100/2023, and 415742/2009) without the dual mutation (appendix p 5). Hence, strains harbouring dual I223V/S247N mutations can be considered as having reduced inhibition, as per the WHO definition. In summary, the findings highlight the global emergence of NAI-resistant A(H1N1)pdm09 strains with dual I223V/S247N mutations. These results emphasise the importance of continual monitoring of antiviral resistance in influenza viruses. We declare no competing interests. RCYL and JDI contributed equally. Data are available upon reasonable request from the corresponding author. We acknowledge the authors from originating and submitting laboratories of the influenza virus genetic sequences, which were made available through GISAID and served as the foundation of this research (Supplementary Table S4). We also acknowledge Allen Chu and Brian Chan for their technical support. This work was funded by the Partnership Programme on Enhancing Laboratory Surveillance and Investigation of Emerging Infectious Diseases and Antimicrobial Resistance for Department of Health, HKSAR; and the National Key R&D Program of China (projects 2021YFC0866100 and 2023YFC3041600). We acknowledge funding received from private donors including Richard Yu and Carol Yu, Shaw Foundation Hong Kong, Michael Seak-Kan Tong, May Tam Mak Mei Yin, Lee Wan Keung Charity Foundation, Hong Kong Sanatorium & Hospital, Respiratory Viral Research Foundation Limited, Providence Foundation Limited (in memory of the late Lui Hac-Minh), Hui Ming, Hui Hoy and Chow Sin Lan Charity Fund, Chan Yin Chuen Memorial Charitable Foundation, Marina Man-Wai Lee, the Jessie & George Ho Charitable Foundation, Kai Chong Tong, Tse Kam Ming Laurence, Foo Oi Foundation, Betty Hing-Chu Lee, and Ping Cham So. The funders had no role in study design, data collection, data analysis, data interpretation, or writing of the report. The study has been approved by the Institutional Review Board of the University of Hong Kong, Hospital Authority, Hong Kong West Cluster (UW 13–372). Written informed consent was waived because specimens were analysed in an anonymous manner. KKWT conceptualised the study. RCYL, JDI, and KKWT established the study design. RCYL, JDI, LLC, WMC, and KKWT performed data collection, data analysis, and data interpretation. RCYL, JDI, and KKWT wrote the original draft and reviewed and edited the manuscript. The corresponding author had full access to all data in the study and had final responsibility for the decision to submit for publication. Editorial note: The Lancet Group takes a neutral position with respect to territorial claims in institutional affiliations. Download .pdf (.42 MB) Help with pdf files Supplementary appendix Download .xls (.04 MB) Help with xls files Supplementary Table S4