Multicountry Spread of Influenza A(H1N1)pdm09 Viruses with Reduced Oseltamivir Inhibition, May 2023-February 2024

Abstract

Since May 2023, a novel combination of neuraminidase mutations, I223V + S247N, has been detected in influenza A(H1N1)pdm09 viruses collected in countries spanning 5 continents, mostly in Europe (67/101). The viruses belong to 2 phylogenetically distinct groups and display ≈13-fold reduced inhibition by oseltamivir while retaining normal susceptibility to other antiviral drugs.

Keywords: H1N1; Influenza; United States; antimicrobial resistance; antiviral; baloxavir; influenza A(H1N1)pdm09; neuraminidase inhibitors; oseltamivir; pH1N1; phenotypic testing; reduced inhibition; substitution; viruses.

Figure 1

Detection of influenza A(H1N1)pdm09 viruses with dual NA-I223V + S247N substitutions through NA inhibitors susceptibility surveillance conducted by the Centers for Disease Control and Prevention and analysis of available sequences (GISAID EpiFlu, https://www.gisaid.org, accessed March 11, 2024), May 2023–February 2024. A total of 15,003 NA sequences of pH1N1 viruses (duplicate sequences excluded: 2,039 from Centers for Disease Control and Prevention and the remaining 12,964 from GISAID EpiFlu) were analyzed to screen for amino acid substitutions at residues 223 and 247. A) Introduction of single substitution (I223V or S247N) or dual substitutions (I223V + S247N) across NA subclades of pH1N1 viruses circulating during May 2023–February 2024. Amino acid signatures of NA subclades are shown in comparison to A/Wisconsin/67/2022, the Northern Hemisphere 2023–2024 vaccine cell prototype virus for the pH1N1 component. Vaccine viruses, A/Wisconsin/67/2022 and A/Victoria/4897/2022 (Northern Hemisphere 2023–2024 vaccine egg prototype virus), represented NA subclades C.5.2 and C.5.1.1, respectively. C.5.3 was the subclade most abundantly sequenced (41.3% frequency), followed by other minor subclades: C.5 (25.4%), C.5.2 (16.5%), C.4 (7.5%), C.5.1.1 (5.2%), and others (4.1%). Most viruses with single S247N substitution belonged to dominant NA subclade C.5.3 and minor subclade C.5. Conversely, most viruses with single I223V substitution and all viruses with dual I223V + S247N substitutions belonged to NA subclade C.5.3. B) Spatiotemporal distribution of dual mutant viruses. Dual mutants were divided into 2 groups based on their NA sequence difference. Group 1 shared additional substitution R257K not found in group 2. The small group 1 had 9 dual mutants, and the large group 2 had 92 dual mutants. The first dual mutant belonging to group 2 was collected in Canada at the end of May 2023, and most dual mutants were collected between September 2023 and February 2024. Two dual mutant viruses collected in Australia also contained NA-H275Y. NA, neuraminidase.

Figure 2

Tanglegram showing influenza A(H1N1)pdm09 phylogenies for NA gene (left) and HA gene (right) from susceptibility surveillance conducted by the Centers for Disease Control and Prevention and analysis of available sequences (GISAID EpiFlu, https://www.gisaid.org, accessed March 11, 2024), May 2023–February 2024. The NA-HA tangle tree was constructed by using Nextclade (8) and visualized by Auspice (https://auspice.us). NA phylogenetic tree is zoomed to show only subclade C.5.3 with 2 groups of dual I223V + S247N mutants. All dual mutant viruses shared >6 NA amino acid substitutions (V13I, S200N, I223V, S247N, L339S, S366N) compared with vaccine prototype virus A/Wisconsin/67/2022. Group 1 shared an additional substitution R257K not observed in group 2. Tree tips colored in blue indicate viruses with wild type amino acids at residues 223 and 247 (i.e., I223 and S247); green shows single I223V mutants; and orange shows dual mutants. Small group 1 with 9 dual mutants and large group 2 with 92 dual mutants are indicated. The NA sequence and corresponding HA of each virus are connected by lines. Group 1 dual mutants have HA 5a.2a_C.1. Only 2 group 2 dual mutants (A/British Columbia/PHL1108/2023 collected in May 2023 and A/France/IDF-RELAB-IPP24993/2023 collected in October 2023) have HA 5a.2a_C.1; remaining group 2 dual mutants shared HA 5a.2a.1_C.1.1.1. HA 5a.2a_C.1 is represented by A/Sydney/5/2021, the Southern Hemisphere 2023 vaccine egg/cell prototype virus. HA 5a.2a.1_C.1.1.1 is represented by A/Victoria/4897/2022, the Northern Hemisphere 2023–2024 vaccine egg prototype virus. The Northern Hemisphere 2023–2024 vaccine cell prototype virus, A/Wisconsin/67/2022, represents HA 5a.2a.1_C.1.1. HA, hemagglutinin; NA, neuraminidase.