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Volume 25, Number 10—October 2019

Susceptibility of Influenza A, B, C, and D Viruses to Baloxavir1

Vasiliy P. Mishin, Mira C. Patel, Anton Chesnokov, Juan De La Cruz, Ha T. Nguyen, Lori Lollis, Erin Hodges, Yunho Jang, John Barnes, Timothy Uyeki, Charles T. Davis, David E. Wentworth, and Larisa V. GubarevaComments to Author 
Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA (V.P. Mishin, M.C. Patel, A. Chesnokov, J. De La Cruz, H.T. Nguyen, L. Lollis, E. Hodges, Y. Jang, J. Barnes, T. Uyeki, C.T. Davis, D.E. Wentworth, L.V. Gubareva); Battelle Memorial Institute, Atlanta (M.C. Patel, J. De La Cruz, H.T. Nguyen, L. Lollis)

Cite This Article


Baloxavir showed broad-spectrum in vitro replication inhibition of 4 types of influenza viruses (90% effective concentration range 1.2–98.3 nmol/L); susceptibility pattern was influenza A ˃ B ˃ C ˃ D. This drug also inhibited influenza A viruses of avian and swine origin, including viruses that have pandemic potential and those resistant to neuraminidase inhibitors.

Influenza viruses are classified into 4 types: A, B, C, and D (1). Influenza A viruses infect a wide range of species and pose threats to human and animal health. Influenza A viruses belonging to 16 hemagglutinin and 9 neuraminidase subtypes have been identified in the natural reservoir (wild birds). Zoonotic infections with avian H5N1, H5N6, and H7N9 viruses are concerning because of their high fatality rates in humans and pandemic risk (2).

Swine are recognized as mixing vessels because influenza A viruses from multiple hosts can infect pigs and produce novel reassortants. Numerous subtypes of reassortant swine influenza A viruses are enzootic throughout North America and pose a threat to human health. For instance, H3N2 triple reassortant viruses caused a multistate outbreak affecting hundreds of persons in the United States during 2012, and a quadruple reassortant H1N1 virus caused the 2009 pandemic and now circulates as a seasonal virus (2,3).

Influenza B viruses are considered strictly human pathogens, although occasional outbreaks in aquatic mammals have been reported (1). Influenza C viruses are known to infect humans, pigs, camels, and dogs (1). Unlike influenza A and B viruses, influenza C viruses typically cause mild illness. However, in recent years, severe illness in children infected by influenza C virus has raised concerns over the lack of virus-specific therapeutics and vaccines (4). Recently discovered influenza D viruses were isolated from swine and bovines. No virologically confirmed human infections have been reported, but influenza D virus antibodies have been found in persons exposed to cattle (1). Evolutionarily, influenza C and D viruses are more closely related to each other than to influenza A or B viruses (1).

Antiviral drugs have been used to mitigate zoonotic virus outbreaks and are central to pandemic preparedness. However, therapeutic options remain limited and drug-resistant viruses can emerge after treatment, spontaneous mutation, or reassortment. Until recently, only matrix (M) 2 blockers and neuraminidase inhibitors (NAIs) were approved to control influenza. M2 blockers are effective only against influenza A viruses and are not recommended because of widespread resistance. NAIs are used for treatment of influenza A and B virus infections, but NAI-resistant viruses have emerged (5). NAI-resistant seasonal influenza H1N1 viruses circulated worldwide during late 2007 through early 2009 (6) and raised concerns over limited therapeutic options.

In 2014, favipiravir was licensed in Japan for restricted use in the event of a drug-resistant influenza pandemic (7). Favipiravir is a broad-spectrum antiviral drug that inhibits viral RNA polymerase, an enzyme recognized as an attractive target because of its critical role in virus replication and high degree of conservation (8). In 2018, another inhibitor of the viral RNA polymerase, baloxavir marboxil, was approved in Japan and the United States for treatment of influenza A and B virus infections (9). Its active metabolite, baloxavir acid, inhibits cap-dependent endonuclease activity of polymerase acidic (PA) protein (10). Amino acid substitutions at position 38 in the PA active site were recognized as the primary pathway to baloxavir resistance (11). PA substitutions at this and other positions have variable impact on resistance and are rarely found in nature (11,12). The purpose of this study was to determine the effectiveness of baloxavir against the 4 types of influenza viruses.

The Study

The active site of the PA protein (P3 in C and D viruses) is nearly identical in all 4 influenza virus types (1,8). Therefore, we hypothesized that baloxavir would inhibit replication of not only influenza A and B viruses but also influenza C and D viruses. First, we tested 2 viruses of each type by using a virus yield reduction assay. We used baloxavir acid (baloxavir) in experiments and included favipiravir as a control.

Baloxavir broadly inhibited virus replication of all 4 types (Table 1). On the basis of 90% effective concentration values determined at 48 hours postinfection, influenza A viruses were most susceptible to baloxavir and influenza D viruses least susceptible. Baloxavir susceptibility for influenza B viruses was ≈3-fold lower and that for influenza C viruses was ≈6-fold lower than that for influenza A viruses. Analysis of 34 P3 sequences of influenza D virus and 221 of influenza C virus (retrieved from GISAID,, and GenBank) showed that all influenza D viruses have valine at position 38, whereas influenza C viruses have isoleucine, similar to most influenza A and B viruses. Nevertheless, valine at 38 in influenza A and B viruses had little or no effect (<3-fold) on baloxavir susceptibility (1012). Favipiravir also showed inhibitory effects against all virus types, although much higher concentrations were required to achieve similar levels of reduction (Table 1).

Although the virus yield reduction assay has been used to assess baloxavir susceptibility of seasonal and avian viruses (10,13), other phenotypic assays, such as the focus-reduction assay (FRA) and the high-content imaging neutralization test (HINT), offer an improved throughput (12,14,15). Regardless of the assay used, baloxavir effective concentrations for influenza A viruses were similar (≈0.1–3 nmol/L) (10,1215). Unlike the FRA, HINT relies on single-cycle virus replication, which is achieved by withdrawing trypsin needed to activate infectivity of progeny virus. HINT eliminates variance caused by different replication kinetics. However, the FRA is optimal for testing highly pathogenic avian viruses because multicycle replication of these viruses is trypsin independent. We used 2 seasonal A(H1N1)pdm09 viruses, one of which contains the naturally occurring substitution PA-I38L, for reference purposes (12) (Table 2).

First, we tested 25 influenza viruses of avian origin, representing H5, H6, H7, H9, and H10 subtypes, by using FRA or HINT as described (12) (Table 2; Appendix Table 1). Most viruses were isolated from infected humans. Most viruses had markers of M2 resistance and some had NAI-resistance markers. Data showed that these diverse viruses were susceptible to baloxavir and had 50% effective concentration (EC50) values in a low nanomolar range (Table 2; Appendix Table 1). In the FRA, favipiravir EC50 values were much higher than those for baloxavir (Appendix Table 1). However, favipiravir did not produce a measurable antiviral effect by HINT because this drug requires several hours for activation in cells. Baloxavir susceptibility of 30 swine-origin viruses, representing different lineages and subtypes and collected over many years, demonstrated HINT EC50 values comparable to avian and seasonal influenza A viruses (Table 2; Appendix Table 2) (10,12,13).

It is prudent to analyze PA sequences of emerging influenza A viruses for markers previously associated with reduced baloxavir susceptibility (11,12). Among swine-origin viruses available for testing in this study, polymorphism PA-38I/M was detected in A/Iowa/33/2017 (H1N1)v. Virus populations with either PA-I38 or PA-I38M were recovered by biologic cloning and tested by using HINT. Substitution PA-I38M conferred 12-fold reduced baloxavir susceptibility, consistent with previous reports for PA-I38M–containing H3N2 viruses (11,12). Analysis of PA sequences from 2,485 H7N9 viruses (from GISAID and GenBank) showed 1 virus with PA-I38M, 2 with PA-E199G, and 1 with PA-A36V (11,12). The effect of these substitutions on baloxavir susceptibility for H7N9 viruses is currently unknown. Moreover, PA sequence of 1 swine influenza A virus showed PA-I38T, a marker associated with clinically relevant baloxavir resistance (11). None of these viruses were available for phenotypic testing.


Baloxavir displayed broad antiviral activity against diverse influenza viruses, including all 4 types and animal-origin influenza A viruses with pandemic potential. Our findings suggest that baloxavir might offer the first therapeutic option against influenza C virus infections. Further studies are needed to provide comprehensive assessment of baloxavir susceptibility by using a large panel of representative influenza C viruses. Ongoing monitoring of baloxavir susceptibility of emerging avian and swine influenza A viruses with pandemic potential is needed to inform clinical management and public health preparedness efforts.

Dr. Mishin is a biologist in the Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA. His primary research interests are influenza viruses, antiviral drugs, development and optimization of in vitro assays for monitoring drug susceptibility, and influenza antigenic characterization.



We thank Shionogi and Co., Ltd. (Osaka, Japan), for kindly providing baloxavir acid; the China Centers for Disease Control and Prevention and other partners from the World Health Organization Global Influenza Surveillance and Response System for providing influenza A viruses; Christine Warnes for providing influenza C virus isolates; Richard J. Webby for providing influenza D virus isolates; and the US Department of Agriculture, Agricultural Research Service and National Veterinary Services Laboratories, for providing viruses collected from birds and animals.

This study was supported by the Influenza Division, National Center for Immunization and Respiratory Diseases, CDC.



  1. Asha  K, Kumar  B. Emerging influenza D virus threat: what we know so far! J Clin Med. 2019;8:E192. DOIPubMedGoogle Scholar
  2. Uyeki  TM, Katz  JM, Jernigan  DB. Novel influenza A viruses and pandemic threats. Lancet. 2017;389:21724. DOIPubMedGoogle Scholar
  3. Garten  RJ, Davis  CT, Russell  CA, Shu  B, Lindstrom  S, Balish  A, et al. Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science. 2009;325:197201. DOIPubMedGoogle Scholar
  4. Njouom  R, Monamele  GC, Ermetal  B, Tchatchouang  S, Moyo-Tetang  S, McCauley  JW, et al. Detection of influenza C virus infection among hospitalized patients, Cameroon. Emerg Infect Dis. 2019;25:6079. DOIPubMedGoogle Scholar
  5. Hu  Y, Lu  S, Song  Z, Wang  W, Hao  P, Li  J, et al. Association between adverse clinical outcome in human disease caused by novel influenza A H7N9 virus and sustained viral shedding and emergence of antiviral resistance. Lancet. 2013;381:22739. DOIPubMedGoogle Scholar
  6. Hurt  AC. The epidemiology and spread of drug resistant human influenza viruses. Curr Opin Virol. 2014;8:229. DOIPubMedGoogle Scholar
  7. Furuta  Y, Komeno  T, Nakamura  T. Favipiravir (T-705), a broad spectrum inhibitor of viral RNA polymerase. Proc Jpn Acad, Ser B, Phys Biol Sci. 2017;93:44963. DOIPubMedGoogle Scholar
  8. DuBois  RM, Slavish  PJ, Baughman  BM, Yun  MK, Bao  J, Webby  RJ, et al. Structural and biochemical basis for development of influenza virus inhibitors targeting the PA endonuclease. PLoS Pathog. 2012;8:e1002830. DOIPubMedGoogle Scholar
  9. Hayden  FG, Sugaya  N, Hirotsu  N, Lee  N, de Jong  MD, Hurt  AC, et al.; Baloxavir Marboxil Investigators Group. Baloxavir marboxil for uncomplicated influenza in adults and adolescents. N Engl J Med. 2018;379:91323. DOIPubMedGoogle Scholar
  10. Noshi  T, Kitano  M, Taniguchi  K, Yamamoto  A, Omoto  S, Baba  K, et al. In vitro characterization of baloxavir acid, a first-in-class cap-dependent endonuclease inhibitor of the influenza virus polymerase PA subunit. Antiviral Res. 2018;160:10917. DOIPubMedGoogle Scholar
  11. Omoto  S, Speranzini  V, Hashimoto  T, Noshi  T, Yamaguchi  H, Kawai  M, et al. Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Sci Rep. 2018;8:9633. DOIPubMedGoogle Scholar
  12. Gubareva  LV, Mishin  VP, Patel  MC, Chesnokov  A, Nguyen  HT, De La Cruz  J, et al. Assessing baloxavir susceptibility of influenza viruses circulating in the United States during the 2016/17 and 2017/18 seasons. Euro Surveill. 2019;24:24. DOIPubMedGoogle Scholar
  13. Taniguchi  K, Ando  Y, Nobori  H, Toba  S, Noshi  T, Kobayashi  M, et al. Inhibition of avian-origin influenza A(H7N9) virus by the novel cap-dependent endonuclease inhibitor baloxavir marboxil. Sci Rep. 2019;9:3466. DOIPubMedGoogle Scholar
  14. Koszalka  P, Tilmanis  D, Roe  M, Vijaykrishna  D, Hurt  AC. Baloxavir marboxil susceptibility of influenza viruses from the Asia-Pacific, 2012-2018. Antiviral Res. 2019;164:916. DOIPubMedGoogle Scholar
  15. Takashita  E, Morita  H, Ogawa  R, Nakamura  K, Fujisaki  S, Shirakura  M, et al. Susceptibility of influenza viruses to the novel cap-dependent endonuclease inhibitor baloxavir marboxil. Front Microbiol. 2018;9:3026. DOIPubMedGoogle Scholar




Cite This Article

DOI: 10.3201/eid2510.190607

Original Publication Date: July 09, 2019

1Preliminary results from this study were presented at the 6th International Society for Influenza and Other Respiratory Virus Diseases Antiviral Group Conference; November 13–15, 2018; Rockville, Maryland, USA.

Table of Contents – Volume 25, Number 10—October 2019

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Please use the form below to submit correspondence to the authors or contact them at the following address:

Larisa V. Gubareva, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Mailstop H17-5, Atlanta, GA 30329-4027, USA

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Page created: September 17, 2019
Page updated: September 17, 2019
Page reviewed: September 17, 2019
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.