Genomic Analysis of Influenza A and B Viruses Carrying Baloxavir Resistance-Associated Substitutions Serially Passaged in Human Epithelial Cells

Overview

Journal Viruses

Publisher MDPI

Specialty Microbiology

Date 2023 Dec 23

PMID 38140689

Authors

Brady T Hickerson

Bruce K Huang

Svetlana N Petrovskaya

Natalia A Ilyushina

Affiliations

Soon will be listed here.

Abstract

Baloxavir marboxil (baloxavir) is an FDA-approved inhibitor of the influenza virus polymerase acidic (PA) protein. Here, we used next-generation sequencing to compare the genomic mutational profiles of IAV H1N1 and H3N2, and IBV wild type (WT) and mutants (MUT) viruses carrying baloxavir resistance-associated substitutions (H1N1-PA I38L, I38T, and E199D; H3N2-PA I38T; and IBV-PA I38T) during passaging in normal human bronchial epithelial (NHBE) cells. We determined the ratio of nonsynonymous to synonymous nucleotide mutations (d/d) and identified the location and type of amino acid (AA) substitutions that occurred at a frequency of ≥30%. We observed that IAV H1N1 WT and MUT viruses remained relatively stable during passaging. While the mutational profiles for IAV H1N1 I38L, I38T, and E199D, and IBV I38T MUTs were relatively similar after each passage compared to the respective WTs, the mutational profile of the IAV H3N2 I38T MUT was significantly different for most genes compared to H3N2 WT. Our work provides insight into how baloxavir resistance-associated substitutions may impact influenza virus evolution in natural settings. Further characterization of the potentially adaptive mutations identified in this study is needed.

References

Hoffmann E, Neumann G, Kawaoka Y, HOBOM G, Webster R . A DNA transfection system for generation of influenza A virus from eight plasmids. Proc Natl Acad Sci U S A. 2000; 97(11):6108-13. PMC: 18566. DOI: 10.1073/pnas.100133697. View

Barbezange C, Jones L, Blanc H, Isakov O, Celniker G, Enouf V . Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing. Front Microbiol. 2018; 9:2596. PMC: 6220372. DOI: 10.3389/fmicb.2018.02596. View

Swierczynska M, Mirowska-Guzel D, Pindelska E . Antiviral Drugs in Influenza. Int J Environ Res Public Health. 2022; 19(5). PMC: 8910682. DOI: 10.3390/ijerph19053018. View

Ilyushina N, Lugovtsev V, Samsonova A, Sheikh F, Bovin N, Donnelly R . Generation and characterization of interferon-lambda 1-resistant H1N1 influenza A viruses. PLoS One. 2017; 12(7):e0181999. PMC: 5531537. DOI: 10.1371/journal.pone.0181999. View

Nobusawa E, Sato K . Comparison of the mutation rates of human influenza A and B viruses. J Virol. 2006; 80(7):3675-8. PMC: 1440390. DOI: 10.1128/JVI.80.7.3675-3678.2006. View

Ince W, Smith F, ORear J, Thomson M . Treatment-Emergent Influenza Virus Polymerase Acidic Substitutions Independent of Those at I38 Associated With Reduced Baloxavir Susceptibility and Virus Rebound in Trials of Baloxavir Marboxil. J Infect Dis. 2020; 222(6):957-961. DOI: 10.1093/infdis/jiaa164. View

Checkmahomed L, Mhamdi Z, Carbonneau J, Venable M, Baz M, Abed Y . Impact of the Baloxavir-Resistant Polymerase Acid I38T Substitution on the Fitness of Contemporary Influenza A(H1N1)pdm09 and A(H3N2) Strains. J Infect Dis. 2019; 221(1):63-70. PMC: 6910874. DOI: 10.1093/infdis/jiz418. View

Koszalka P, Tilmanis D, Roe M, Vijaykrishna D, Hurt A . Baloxavir marboxil susceptibility of influenza viruses from the Asia-Pacific, 2012-2018. Antiviral Res. 2019; 164:91-96. DOI: 10.1016/j.antiviral.2019.02.007. View

Takizawa N, Momose F . A novel E198K substitution in the PA gene of influenza A virus with reduced susceptibility to baloxavir acid. Arch Virol. 2022; 167(7):1565-1570. PMC: 9069958. DOI: 10.1007/s00705-022-05456-0. View

10.

Noshi T, Kitano M, Taniguchi K, Yamamoto A, Omoto S, Baba K . In vitro characterization of baloxavir acid, a first-in-class cap-dependent endonuclease inhibitor of the influenza virus polymerase PA subunit. Antiviral Res. 2018; 160:109-117. DOI: 10.1016/j.antiviral.2018.10.008. View

11.

Dawood F, Iuliano A, Reed C, Meltzer M, Shay D, Cheng P . Estimated global mortality associated with the first 12 months of 2009 pandemic influenza A H1N1 virus circulation: a modelling study. Lancet Infect Dis. 2012; 12(9):687-95. DOI: 10.1016/S1473-3099(12)70121-4. View

12.

Liu Q, Liu Y, Yang J, Huang X, Han K, Zhao D . Two Genetically Similar H9N2 Influenza A Viruses Show Different Pathogenicity in Mice. Front Microbiol. 2016; 7:1737. PMC: 5096341. DOI: 10.3389/fmicb.2016.01737. View

13.

Vahey M, Fletcher D . Low-Fidelity Assembly of Influenza A Virus Promotes Escape from Host Cells. Cell. 2019; 176(3):678. PMC: 6498858. DOI: 10.1016/j.cell.2019.01.009. View

14.

Suzuki H, Saito R, Masuda H, Oshitani H, Sato M, Sato I . Emergence of amantadine-resistant influenza A viruses: epidemiological study. J Infect Chemother. 2003; 9(3):195-200. DOI: 10.1007/s10156-003-0262-6. View

15.

Hurt A, Holien J, Parker M, Kelso A, Barr I . Zanamivir-resistant influenza viruses with a novel neuraminidase mutation. J Virol. 2009; 83(20):10366-73. PMC: 2753113. DOI: 10.1128/JVI.01200-09. View

16.

Kim J, Lee I, Park S, Bae J, Yoo K, Cheong H . Phylogenetic relationships of the HA and NA genes between vaccine and seasonal influenza A(H3N2) strains in Korea. PLoS One. 2017; 12(3):e0172059. PMC: 5336230. DOI: 10.1371/journal.pone.0172059. View

17.

Roosenhoff R, Schutten M, Reed V, Clinch B, van der Linden A, Fouchier R . Secondary substitutions in the hemagglutinin and neuraminidase genes associated with neuraminidase inhibitor resistance are rare in the Influenza Resistance Information Study (IRIS). Antiviral Res. 2021; 189:105060. DOI: 10.1016/j.antiviral.2021.105060. View

18.

Pascua P, Jones J, Webby R, Govorkova E . Effect of E23G/K, F36V, N37T, E119D, and E199G polymerase acidic protein substitutions on the replication and baloxavir susceptibility of influenza B viruses. Antiviral Res. 2022; 208:105455. DOI: 10.1016/j.antiviral.2022.105455. View

19.

Smyk J, Szydlowska N, Szulc W, Majewska A . Evolution of Influenza Viruses-Drug Resistance, Treatment Options, and Prospects. Int J Mol Sci. 2022; 23(20). PMC: 9602850. DOI: 10.3390/ijms232012244. View

20.

Abed Y, Baz M, Boivin G . Impact of neuraminidase mutations conferring influenza resistance to neuraminidase inhibitors in the N1 and N2 genetic backgrounds. Antivir Ther. 2007; 11(8):971-6. View