H1N1/H3N2 Influenza Variants With Reduced Susceptibility to Baloxavir

respiratory viruses
The PA-I38 mutations were noted frequently in influenza A/H3N2 viruses compared with A/H1N1pdm or influenza B viruses.

The cap-dependent endonuclease inhibitor baloxavir marboxil was approved by the United States Food and Drug Administration in 2018 for the treatment of acute uncomplicated influenza in patients aged >12 years.1 During clinical trials, investigators detected treatment-emergent amino acid substitutions at position 38 of the polymerase acidic (PA) protein in patients with the influenza A/H1N1 2009 pandemic (A/H1N1pdm) and A/H3N2 viruses who were treated with baloxavir.2 These mutations occurred in 2.2% and 9.7% of patients in phase 2 and phase 3 trials, respectively, and were found to confer reduced susceptibility to the drug.3

The PA-I38 mutations were noted frequently in influenza A/H3N2 viruses compared with A/H1N1pdm or influenza B viruses, and these variants commonly affected patients aged <12 years vs those aged 12 to 64 years.2 In addition, compared with the wild-type viruses, the mutant viruses were associated with prolonged virus shedding and a longer median time to symptom alleviation in patients receiving baloxavir.2

After these observations, Japanese researchers commenced nationwide monitoring of the susceptibility of influenza viruses to baloxavir. Their data for the 2018 to 2019 influenza season show that 1.5% of A/H1N1pdm and 9.5% A/H3N2 viruses possessed a PA-I38 substitution.2 Of note, in the United States, no cases of reduced susceptibility to baloxavir were reported in a Centers for Disease Control and Prevention update on January 18, 2020.4

Other findings demonstrated that “replication of recombinant influenza A/H1N1 and A/H3N2 viruses expressing the I38T substitution in their PA protein in the background of the A/WSN/33 (H1N1) or A/Victoria/2/75 (H3N2) strains was greatly attenuated in cell culture relative to their [baloxavir]-sensitive counterparts, suggesting that the reduction in replicative fitness of influenza A viruses is caused by the I38T mutation,” according to a paper published in January 2020 in Nature Microbiology.5 “However, the effect of this substitution on the viral fitness of clinical isolates from patients and on viral fitness in vivo is unknown. Furthermore, it remains unclear whether the emergence of this mutation is related to adverse clinical outcomes.”

To elucidate these points, researchers at the University of Tokyo, the University of Wisconsin, and the Icahn School of Medicine at Mount Sinai examined the in vitro and in vivo properties of influenza A/H1N1pdm and A/H3N2 viruses carrying the PA-138T mutation in isolates from Japanese patients before and after baloxavir treatment. Selected results are highlighted here:5

  • In 38 patients infected with the influenza A virus, variants possessing PA-I38T, PA-I38T/N/S, PA-I38T/S, and/or PA-I38M substitutions were detected in the posttreatment samples of 22.7% and 25.0% of patients with A/H1N1 and A/H3N2 viruses, respectively.
  • Two cases from another sample illustrate the transmissibility of the PA-138T variants. The pretreatment clinical sample of an 11-year-old boy (patient GR125) treated with baloxavir contained A/H3N2 viruses encoding PA-138. One week after the onset of illness in this patient, his 3-year-old sister developed influenza-like symptoms, and her pretreatment clinical sample contained A/H3N2 variants carrying the PA-138T mutation. Sequencing analysis of the pretreatment isolates recovered from samples from the children revealed no nucleotide differences in any of the 8 gene segments, with the exception of a difference at residue 113 within the codon of amino acid residue 38 of PA.
  • Results of other studies show that the the I38T mutation was not detected in A/H3N2 isolates before the availability of baloxavir. “Taken together, these epidemiological and virological data indicate that person-to-person transmission of PA-I38T variants occurred within this family.” In alignment with data from the 2018 to 2019 influenza season in Japan, these observations “also demonstrate that seasonal influenza A viruses that possess an I38T mutation in their PA, conferring reduced susceptibility to [baloxavir], can emerge during treatment with this drug and that such variants seem to be transmissible from person to person.”
  • The study also assessed the susceptibility of PA-I38T variant isolates to baloxavir in 4 patients (2 with A/H1N1pdm and 2 with A/H3N2). In each of these variants, baloxavir susceptibility was reduced by more than 107-fold, 67-fold, 233-fold, and 71-fold, respectively, compared with the pretreatment wild-type viruses.
  • Results of additional in vitro analyses indicated that the PA-138T mutation has a detrimental effect on the replication fitness of A/H1NIpdm viruses (which was shown to improve via compensatory mutation), while no such effect on the fitness of A/H3N2 viruses was noted.

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Simply, what distinguished the virus collected from the brother before treatment and the virus collected from the sister later was a single mutation, implying that the virus acquired resistance during treatment, and the resistant infection was subsequently transmitted from brother to sister. The concern about this stems from the fact that baloxavir has roughly 40% of the antiviral market in Japan, where 23% of patients carried drug-resistant mutations after treatment.6

Baloxavir was approved by the FDA partially as a response to sporadic resistance to oseltamivir. The results of a study published in Eurosurveillance demonstrated that during the 2016/2017 and 2017/2018 influenza seasons in the United States, there was minimal evidence of resistance to baloxavir.7 Researchers postulated that this may be the result of the drug being less commonly prescribed in the United States compared with Japan. Of note, H1N1 or H3N2 that develops resistance to baloxavir with treatment subsequently responds to other antiviral medications.6

“In summary, our data suggest that influenza A/H1N1pdm and A/H3N2 viruses circulating in humans can rapidly acquire an I38T mutation in their PA, which confers reduced susceptibility to [baloxavir], without a loss of viral fitness,” the study authors concluded.5 Their findings highlight the possibility that the widespread use of baloxavir could lead to the circulation of these variants. “The proper use of this drug and continued close monitoring for the emergence or prevalence of seasonal influenza A virus PA-I38T variants is extremely important.”


1. US Food and Drug Administration. FDA approves new drug to treat influenza.  https://www.fda.gov/news-events/press-announcements/fda-approves-new-drug-treat-influenza. October 24, 2018. Accessed on January 24, 2020.

2. Takashita E, Ichikawa M, Morita H, et al. Human-to-human transmission of influenza A(H3N2) virus with reduced susceptibility to baloxavir, Japan, February 2019. Emerg Infect Dis. 2019;25(11):2108-2111.

3. Hayden FG, Sugaya N, Hirotsu N, et al. Baloxavir marboxil for uncomplicated influenza in adults and adolescents. N Engl J Med. 2018;379(10):913-923.

4. Centers for Disease Control and Prevention. Weekly US influenza surveillance report. https://www.cdc.gov/flu/weekly/weeklyarchives2019-2020/Week03.htm. January 18, 2020. Accessed on January 24, 2020.

5. Imai M, Yamashita M, Sakai-Tagawa Y, et al. Influenza A variants with reduced susceptibility to baloxavir isolated from Japanese patients are fit and transmit through respiratory droplets. Nat Microbiol. 2020;5(1):27-33.

6. Streenhuysen J. New Roche flu drug can drive resistance in influenza viruses: researchers. Reuters. https://www.reuters.com/article/us-roche-hldg-flu-resistance/new-roche-flu-drug-can-drive-resistance-in-influenza-viruses-researchers-idUSKBN1XZ27J. Published November 25, 2019. Accessed February 12, 2019.

7. Schnirring L. Experts on watch for resistance to new flu drug. Center for Infectious Disease Research and Policy. http://www.cidrap.umn.edu/news-perspective/2019/01/experts-watch-resistance-new-flu-drug. Published January 18, 2019. Accessed February 12, 2020.