Global update on the susceptibilities of influenza viruses to neuraminidase inhibitors and the cap-dependent endonuclease inhibitor baloxavir, 2020–2023

Fig. 1. Influenza viruses collected and assessed for NAI susceptibility during the 2020–2021, 2021–2022 and 2022–2023 periods by the WHO CCs. For each period viruses were collected from patients at week 21 through week 20 of the following year. (A) The number of viruses collected by year and week of specimen collection and virus type/subtype or lineage for specimens assessed in the three consecutive periods. Typically, week 21 to week 39 of a year covers the Southern Hemisphere influenza season, while week 40 of a year to week 20 of the following year covers the Northern Hemisphere influenza season. (B) The number of viruses assessed for susceptibility to the four NAIs using NA inhibition assays and/or sequence-based analysis by WHO Region for the three consecutive periods. For 2021–2022 and 2022–2023, two reassortant A(H1N2) viruses were counted among the A(H3N2) viruses because of assessment of N2 NA for NAI susceptibility but these are not shown on the graph.

Fig. 2. Comparison of NAI susceptibility surveillance over 11 periods for phenotypic and/or sequence-based analysis data generated by WHO CCs. (A) Number of viruses tested. For the 2012–2018 periods testing was reported based on NA inhibition assays only. For the subsequent five periods, results of assessment by NA inhibition assays and/or sequence-based analysis were included. (B) The proportion of viruses showing RI/HRI by one or more NAIs over the 2012–2023 periods. Data were compiled from the global studies of viruses analyzed by WHO CCs during the 2012–2013 (Meijer et al., 2014), 2013–2014 (Takashita et al., 2015), 2014–2015 (Hurt et al., 2016), 2015–2016 (Gubareva et al., 2017), 2016–2017 (Lackenby et al., 2018), 2017–2018 (Takashita et al., 2020b), 2018–2020 (Govorkova et al., 2022), and 2020–2023 (current study) periods. For 2021–2022 and 2022–2023, reassortant A(H1N2) viruses were counted among the A(H3N2) viruses because of assessment of N2 NA for NAI susceptibility. Based on sequence-based analysis, viruses were considered RI or HRI when the NA contained an amino acid substitution for which the NA marker table posted on the WHO website and/or current testing data showed an…

Fig. 3. Column-scatter plots of log-transformed 50% inhibitory concentration (IC50) fold-change values for NAIs. Overall, 1447/2015, 5287/9899 and 10558/19030 viruses assessed for NAI susceptibility were tested phenotypically for one or more NAIs for 2020–2021, 2021–2022 and 2022–2023 periods, respectively. Data are presented by virus subtype or lineage [(A) A(H1N1)pdm09; (B) A(H3N2); and (C) B/Victoria-lineage] with NAI (labelled on the x-axis: oseltamivir, zanamivir, peramivir, and laninamivir) and log-transformed IC50 fold-changes compared to the period median on the y-axis. The boxes indicate the 25th–75th percentiles, and the whiskers stretch to the lowest and highest values within 1.5 times the interquartile region (IQR) value from both the 25th and 75th percentile values, respectively (Tukey's definition). The y-axes have been split into three compartments according to the thresholds recommended by the WHO-AVWG for NI (<10-fold for type A viruses; <5-fold for type B viruses), RI (10- to 100-fold for type A viruses; 5- to 50-fold for type B viruses), and HRI (>100-fold for type A viruses; >50-fold for type B viruses). NA amino acid substitutions are shown for viruses displaying RI…

Fig. 4. Influenza viruses collected and assessed for baloxavir susceptibility during the 2020–2021, 2021–2022 and 2022–2023 periods by the WHO CCs. For each period viruses were collected from patients at week 21 through week 20 of the following year. (A) The number of viruses collected by year and week of specimen collection and virus type/subtype or lineage for specimens assessed in the three consecutive periods. Typically, week 21 to week 39 of a year covers the Southern Hemisphere influenza season, while week 40 of a year to week 20 of the following year covers the Northern Hemisphere influenza season. (B) The number of viruses assessed for susceptibility to baloxavir using phenotypic assays and/or sequence-based analysis, by WHO Region for the three consecutive periods. One A(H1N2) virus was included in the baloxavir susceptibility assessment but are not shown in the graph.

Fig. 5. Comparison of baloxavir susceptibility surveillance over six periods for phenotypic and/or sequence-based analysis data generated by WHO CCs. (A) Number of viruses tested. For the 2017–2018 period, baloxavir susceptibility assessment was reported based on sequence-based analysis only. For the 2018–2023 periods, results of phenotypic testing by cell culture-based assays and/or sequence-based analysis were included. (B) The proportion of viruses showing RS to baloxavir over the 2017–2023 periods. Data were compiled from the global studies of viruses during the 2017–2018 (Takashita et al., 2020b), 2018–2020 (Govorkova et al., 2022) and 2020–2023 (current study) periods. For 2017–2018, data from all PA sequences available from public sequence databases; for 2018–2020, data from all PA sequences available from public databases and phenotypic testing data from WHO CCs; for 2020–2023, data from all PA sequences and phenotypic testing data generated by WHO CCs. Viruses characterized by sequence-based analysis were considered RS when the PA contained amino acid substitutions for which the WHO website and/or current testing data showed an >3-fold EC50 fold-change compared to baloxavir…

Fig. 6. Column-scatter plots of log-transformed 50% effective concentration (EC50) fold-change values for baloxavir. The phenotypic susceptibility of influenza viruses to baloxavir was tested by cell culture–based assays, focus-reduction assay (FRA), high-content imaging neutralization test (HINT), or influenza replication inhibition neuraminidase-based assay (IRINA). Overall, 126/1244, 766/6516, and 1054/11172 viruses assessed for baloxavir susceptibility were tested phenotypically for the 2020–2021, 2021–2022 and 2022–2023 periods, respectively. Data are presented by virus subtype or lineage [labelled on the x-axis: A(H1N1)pdm09; A(H3N2); and B/Victoria-lineage] and log-transformed EC50 fold changes compared to the period median on the y-axis. The boxes and whiskers are as defined in Fig. 3. An arbitrary cut-off of >3-fold increase in the EC50 of a test virus compared to period median EC50 was used for reporting viruses with RS to baloxavir. PA amino acid substitutions are shown for viruses displaying a RS phenotype that have been sequenced. Of seven A(H3N2) and eleven B/Victoria-lineage viruses showing an RS phenotype, the PA sequences did not show known markers associated with RS to…