Potential pandemic risk of circulating swine H1N2 influenza viruses

  1. Valerie Le Sage
  2. Nicole C. Rockey
  3. Kevin R. McCarthy
  4. Andrea J. French
  5. Meredith J. Shephard
  6. Ryan McBride
  7. Jennifer E. Jones
  8. Sydney G. Walter
  9. Joshua D. Doyle
  10. Lingqing Xu
  11. Dominique J. Barbeau
  12. Shengyang Wang
  13. Sheila A. Frizzell
  14. Lora H. Rigatti
  15. Michael M. Myerburg
  16. James C. Paulson
  17. Anita K. McElroy
  18. Tavis K. Anderson
  19. Amy L. Vincent Baker
  20. Seema S. Lakdawala

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Abstract

Influenza A viruses in swine have considerable genetic diversity and continue to pose a pandemic threat to humans. They were the source of the most recent influenza pandemic, and since 2010, novel swine viruses have spilled over into humans more than 400 times in the United States. Although these zoonotic infections generally result in mild illness with limited onward human transmission, the potential for sustained transmission of an emerging influenza virus between individuals due to lack of population level immunity is of great concern. Compiling the literature on pandemic threat assessment, we established a pipeline to characterize and triage influenza viruses for their pandemic risk and examined the pandemic potential of two widespread swine origin viruses. Our analysis revealed that a panel of human sera collected from healthy adults in 2020 has no cross-reactive neutralizing antibodies against an α-H1 clade strain but do against a γ-H1 clade strain. Swine H1N2 virus from the α-H1 clade (α-swH1N2) replicated efficiently in human airway cultures and exhibited phenotypic signatures similar to the human H1N1 pandemic strain from 2009 (H1N1pdm09). Furthermore, α-swH1N2 was capable of efficient airborne transmission to both naïve ferrets and ferrets with prior seasonal influenza immunity. Ferrets with H1N1pdm09 pre-existing immunity had reduced α-swH1N2 viral shedding from the upper respiratory tract and cleared the infection faster. Despite this, H1N1pdm09-immune ferrets that became infected via the air could still onward transmit α-swH1N2 with an efficiency of 50%. Taken together, these results indicate that this α-swH1N2 strain has a higher pandemic potential, but a moderate level of impact since there is reduced replication fitness in animals with prior immunity.

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    Summary

    This study provides a framework for assessing the pandemic potentials of swine influenza viruses and showcases it with two circulating swine flu viruses. Various in vitro assays examined their fitness within the human respiratory tract. Transmission potency was also investigated using ferrets for the ɑ-swH1N2 strain, which stood out with molecular features similar to the 2009 H1N1 strain. The in vivo experiments showed that the ɑ-swH1N2 strain has moderate pandemic potential yet is weaker than the 2009 H1N1 strain. 

    Since swine influenza viruses primarily cause zoonosis, proactive assessment of their pandemic potential using this work's benchmark can enable focused surveillance. The rigorous in vitro and in vivo results suggest that the ɑ-swH1N2 strain (Texas/A02245420/2020) has a moderate pandemic potential. However, it is unclear how moderate it is and what "moderate" exactly means. Below are comments to improve this aspect. 

    Major comments

    1. The in vitro experiments classified the ɑ-swH1N2 strain to the "Moderate pandemic risk" group and the γ-swH1N1 strain to the "Lower pandemic risk" group. Can this be related to or supported by any existing epidemiological or clinical data? Extended Data Figure 2 could represent zoonotic strains and compare their relatedness with the ɑ-swH1N2 or γ-swH1N1 strain. Alternatively, clinical severeness could be compared between zoonotic strains closer to either the ɑ-swH1N2 or γ-swH1N1 strain. 

    2. Can negative controls be added to experiments in Figure 2? The negative control could be one of the strains that have caused zoonosis but resulted in weak symptoms or limited transmission. The negative controls will help quantitatively evaluate the pandemic risk of the ɑ-swH1N2 strain. 

    3. Similarly, it would also be great if the ferret experiments had some standards. In Figures 3 and 4, how different are the ɑ-swH1N2's results from the previous results for the pandemic strains? Are the differences large enough to downgrade ɑ-swH1N2's pandemic risk to "moderate" level? 

    4. Can the authors provide examples belonging to the "lower," "moderate," and "higher" risk groups in Figure 1?

    5. How were the Texas/A02245420/2020 and Minnesota/A02245409/2020 chosen out of all swH1N2 and swH1N1 strains? The process could be added to Figure 1 as the first step, making the decision tree more general and comprehensive. 

    6. What was the logic behind the order, grouping, and particular cutoffs in Figure 1? This information will help peer researchers adapt the decision tree to their viruses of interest. Before reading the following sections, the numbers in Figure 1 seem a bit arbitrary.

    Minor comments

    1. In Figure 1, the current criterion for moving from Box 3 to Box 4 is "Yes to fewer than 2 questions," which is awkward, given that more "Yes" in Box 3 seems to indicate higher pandemic risk. It may be "Yes to greater than 1 question." On top of that, what were the rationales behind the stringency? For example, it could be "Yes to all questions."

    2. The γ-swH1N1 strain appears in a subset of in vitro assays without a clear description. Please mention the reason for this. 

    3. It would be great if biosafety levels for the ferret experiment were more detailed. Is the BSL-2 level safe enough? Is there no possibility of an emerging new reassorted virus during the experiment? Some studies have conducted ferret experiments at the BSL-3+ level elsewhere (Herft et al., 2010, 10.1126/science.1213362; Imai et al., 2010, 10.1038/nature10831).

    4. In Figures 3 and 4, some ferret experiments showed differences between replicates. Could you mention possible factors about this? 

    5. Based on the Extended Data Figure 3, can you find any other swine flu strains that show amino acid variations similar to the ɑ-swH1N2? They may also need caution for immune escape. The authors may include this in the Discussion section. 

    Competing interests

    The author declares that they have no competing interests.

  2. Version published to 10.1101/2024.01.05.574401v1 on bioRxiv