1. Immunology and Inflammation
  2. Microbiology and Infectious Disease

A paucigranulocytic asthma host environment promotes the emergence of virulent influenza viral variants

  1. Katina D Hulme
  2. Anjana C Karawita
  3. Cassandra Pegg
  4. Myrna JM Bunte
  5. Helle Bielefeldt-Ohmann
  6. Conor J Bloxham
  7. Silvie Van den Hoecke
  8. Yin Xiang Setoh
  9. Bram Vrancken
  10. Monique Spronken
  11. Lauren E Steele
  12. Nathalie AJ Verzele
  13. Kyle R Upton
  14. Alexander A Khromykh
  15. Keng Yih Chew
  16. Maria Sukkar
  17. Simon Phipps
  18. Kirsty R Short  Is a corresponding author
  1. School of Chemistry and Molecular Biosciences, The University of Queensland, Australia
  2. Australian Infectious Diseases Research Centre, The University of Queensland, Australia
  3. School of Veterinary Science, The University of Queensland, Australia
  4. School of Biomedical Sciences, The University of Queensland, Australia
  5. VIB-UGent Center for Medical Biotechnology, Belgium
  6. Department of Biomedical Molecular Biology, Ghent University, Belgium
  7. Environmental Health Institute, National Environment Agency, Singapore
  8. KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Belgium
  9. Department of Viroscience, Erasmus MC, Netherlands
  10. Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Australia; Woolcock Institute of Medical Research, Sydney Medical School, University of Sydney, Australia
  11. QIMR Berghofer Medical Research Institute, Australia
https://doi.org/10.7554/eLife.61803
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Cite this article
  1. Katina D Hulme
  2. Anjana C Karawita
  3. Cassandra Pegg
  4. Myrna JM Bunte
  5. Helle Bielefeldt-Ohmann
  6. Conor J Bloxham
  7. Silvie Van den Hoecke
  8. Yin Xiang Setoh
  9. Bram Vrancken
  10. Monique Spronken
  11. Lauren E Steele
  12. Nathalie AJ Verzele
  13. Kyle R Upton
  14. Alexander A Khromykh
  15. Keng Yih Chew
  16. Maria Sukkar
  17. Simon Phipps
  18. Kirsty R Short
(2021)
A paucigranulocytic asthma host environment promotes the emergence of virulent influenza viral variants
eLife 10:e61803.
https://doi.org/10.7554/eLife.61803
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10 figures, 1 table and 4 additional files

Figures

Figure 1
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Pneumonia virus of mice (PVM)-infection (at 7 days of age and reinfection at 35 days of age) of RAGE-deficient mice induces the cardinal features of asthma.

(A) (Left) Percentage of airway epithelial cells (AECs) producing mucus was quantified by immunohistochemistry at 7 days post-reinfection (i.e. 42 days of age) from uninfected RAGE-deficient mice (non-asthmatic) and infected RAGE-deficient mice (asthmatic). (Right) Lung sections from non-asthmatic and asthmatic mice at 42 days of age were stained for smooth muscle actin by immunohistochemistry and the airway smooth muscle (ASM) area was calculated relative to the basement membrane (BM) length of small airways. (B) Cytokine levels in the lung of RAGE-deficient mice 7 days post-PVM or mock infection (i.e. 42 days of age). Statistical analysis was performed as described in Materials and methods with *p≤0.05. Data are pooled from at least two independent experiments and shown as mean ± SEM.

Figure 2
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RAGE-deficient asthmatic mice experience more severe influenza than non-asthmatic mice.

RAGE-deficient non-asthmatic and asthmatic mice were infected with 100 (PFU) of H1N1/Auck/09. Mock control groups received PBS only. (A) Percentage weight loss of influenza A virus (IAV) or mock infected mice. Weights are displayed as percentage of a mouse’s weight at the time of infection. Each data point represents mean ± SEM, with at least 17 mice per group. (B) Viral titres present in lung homogenate at 4 and 6 days post-infection (d.p.i.) in IAV and mock-infected mice. (C) Histopathology score of lung sections for vascular changes, bronchitis, interstitial inflammation, alveolar inflammation, pneumocyte hypertrophy, and pleuritis combined. (D) Cytokines in lung homogenate at 4 and 6 d.p.i. Data are normalised to Gapdh expression and fold change was calculated using the ΔΔCt method, expressed relative to mock infected mice. Statistical analysis was performed as described in Materials and methods with *p≤0.05, comparing non-asthmatic IAV to asthmatic IAV. Data are pooled from at least two independent experiments and shown as mean ± SEM (A–D), with a data point representing one mouse (B–D).

Figure 3 with 1 supplement
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Asthmatic hosts produced more diverse viral variants in PB1.

Influenza viral RNA isolated from the lung tissue of asthmatic (n = 27) and non-asthmatic (n = 25) mice was analysed for viral variants at 4 and 6 days post-infection (d.p.i). (A–H) Measurement of alpha diversity presented as Shannon entropy of viral mutations at a frequency above 1% by genome segment at the nucleotide level. Statistical analysis was performed as described in Materials and methods with *p≤0.05. Data are shown as mean ± SEM.

Figure 3—figure supplement 1
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Read depth of the eight Influenza genome segments from Ager-/- mice.

(A–H) Influenza viral RNA was isolated from the lung tissue of either asthmatic (n = 27) and non-asthmatic (n = 25) mice and analysed for viral variants. Each data point represents a sample. Statistical analysis was performed as described in Materials and methods. Data are shown as mean ± SEM.

Figure 4
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Asthmatic hosts produced more single nucleotide variants (SNVs) in the PB1 genome segment.

Influenza viral RNA isolated from the lung tissue of asthmatic (n = 27) and non-asthmatic (n = 25) mice was analysed for viral variants. Each data point represents the number of viral variants detected at that nucleotide position within the viral genome PB1 segment. bp: base pair.

Figure 5
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Increased replication of influenza A virus (IAV) was observed in samples derived from asthmatic hosts in vitro.

IAV isolated from asthmatic hosts replicates more quickly than non-asthmatic hosts in (A) Madin–Darby canine kidney (MDCK) cells, (B) Immortalized Mouse Mammary Epithelial Cells (iMMEC), and (C) adenocarcinomic human alveolar basal epithelial cells (A549 cells). Each cell type was infected with the indicated viruses at a multiplicity of infection (MOI) of 0.01 (n = 3 wells/virus/time point). Mock infected data not shown. Data were analysed using a one-way ANOVA with Holm–Sidak's multiple comparisons test and are represented as mean ± SEM. *p<0.05. Dashed line indicates the detection limit of the assay.

Figure 6
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Crystal structures of the mutations within PB1.

(A) Mutations C693Y and K691R. The molecule is displayed in surface view with cartoon representation of the protein backbone (PB1 magenta and PB2 sky blue). The α-helices are labelled and PB1 C693Y and K691R and PB2 K32 are shown as sticks in the respective colours of the subunits with the wild-type (WT) residues in pale yellow. (B) Mutations P651Q and S654N within the conserved β-hairpin (cartoon representation in pale green). The sites of mutations are shown as sticks with the WT residues in pale yellow.

Figure 7
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The PB1 C694Y and P651Q mutations showed increased polymerase activity compared to the wild type (WT).

Influenza RNA polymerase-driven activity is increased compared to WT in HEK 293 T cells transfected with either the C693Y or P651Q mutation in PB1. Data are pooled from four independent experiments (with five biological replicates per group, per experiment). Results are presented as a fold change relative to WT. Statistical significance was determined as described in the Materials and methods. Data shown as mean ± SEM. *p<0.05.

Figure 8
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Mice infected with asthmatic host-derived virus experience more severe influenza than mice infected with non-asthmatic host-derived virus.

C57BL/6 mice were infected with 2000 PFU of either asthmatic or non-asthmatic host-derived influenza A virus (IAV). (A) Percentage weight loss of mice following IAV infection. Weights are displayed as percentage of a mouse’s weight at the time of infection. Each data point represents mean ± SEM (n = 6 per group). (B) Percentage blood oxygen saturation of mice at 4 days post-infection (d.p.i.). (C) Viral titres present in lung homogenate at 4 d.p.i. in IAV-infected mice. (D) Viral mRNA detected by qPCR from murine lung homogenate at 4 d.p.i. Dashed line indicates the detection limit. (E) Cytokines in lung homogenate at 4 d.p.i. Data are normalised to Gapdh expression and fold change was calculated using the ΔΔCt method, expressed relative to samples infected with non-asthmatic-derived virus. Statistical analysis was performed as described in Materials and methods with *p≤0.05. Data are shown as mean ± SEM.

Figure 9
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Asthmatic host-derived virus shows consolidation of PB1 viral variants population across parent and daughter.

C57BL/6 mice were infected with 6 days post-infection (d.p.i.) murine lung homogenate from either non-asthmatic or asthmatic hosts. Multiple dimension scaling (MDS) analysis of the PB1 gene in (A) non-asthmatic-derived virus and (B) asthmatic-derived virus (each data point represents an individual haplotype). Data is representative of six samples per group. Parent: virus derived from either asthmatic or non-asthmatic Ager-/- host. Daughter: virus isolated from C57BL/6 mice lung following infection with host-derived virus.

Author response image 1
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Asthmatic day 6 samples show a positive relationship between weight loss and measures of viral diversity in the PB1.

Influenza viral RNA isolated from the lung tissue of asthmatic (n=27) and non-asthmatic (n=25) mice was analysed for viral variants. Weight-loss as a function of (A) Shannon entropy of PB1 genome segment and of (B) SNVs detected in the PB genome segment. Viral titre (PFU/mL) as a function of (C) Shannon entropy of PB1 genome segment and of (D) SNVs detected in the PB genome segment. Samples with a Shannon Entropy value of 0 were excluded. A simple linear regression was fit, and statistical significance was determined using Prism. * p ≤ 0.05.

Tables

Table 1
Frequency of exclusive non-synonymous viral mutations detected in PB1 at 4 and 6 days post-influenza A virus (IAV) inoculation and their frequency in clinical samples.
Non-asthmaticAsthmaticClinical samples (n = 51 per group)
Day 4 (n* = 13)Day 6 (n = 12)Day 4 (n = 13)Day 6 (n = 14)Non-asthmaticAsthmaticp-Value‡
M1I50%†0%0%
M1L17%0%0%
D2H14%0%0%
N77I14%0%0%
P74A14%0%0%
E75D29%0%0%
E75V14%0%0%
D76A14%0%0%
D76H14%0%0%
N77V14%0%0%
E78G14%0%0%
S80H14%0%0%
I205M14%0%0%
I248V14%0%0%
M616I14%0%0%
R621P14%0%0%
C625S14%0%0%
A652P14%0%0%
S654N14%4%18%0.0514
Y657H14%0%0%
N671H17%R670S14%0%0%
 R672P15%0%0%
S673A17%0%0%
I682F15%0%0%
D685E15%0%0%
D685H14%0%0%
M688I14%0%0%
Y689D21%0%0%
Y689R14%0%0%
Q690S15%0%0%
K691R15%4%16%0.092
C692S14%0%0%
C693N14%0%0%
N694R14%0%0%
L695I15%0%0%
R727T14%0%0%

  1. *n = Total number of mouse samples.

    †Percentage of mice with identified mutation.

  2. ‡Statistical comparisons were made using a two-sided fisher’s exact test.

Additional files

Supplementary file 1

Forward and reverse primers used for qPCR.

https://cdn.elifesciences.org/articles/61803/elife-61803-supp1-v1.docx
Supplementary file 2

Non-synonymous viral mutations detected in PB1 at 4 and 6 days post-influenza A virus (IAV) inoculation.

https://cdn.elifesciences.org/articles/61803/elife-61803-supp2-v1.docx
Supplementary file 3

Workflow used to reconstruct haplotypes.

https://cdn.elifesciences.org/articles/61803/elife-61803-supp3-v1.png
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https://cdn.elifesciences.org/articles/61803/elife-61803-transrepform-v1.docx

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  1. Katina D Hulme
  2. Anjana C Karawita
  3. Cassandra Pegg
  4. Myrna JM Bunte
  5. Helle Bielefeldt-Ohmann
  6. Conor J Bloxham
  7. Silvie Van den Hoecke
  8. Yin Xiang Setoh
  9. Bram Vrancken
  10. Monique Spronken
  11. Lauren E Steele
  12. Nathalie AJ Verzele
  13. Kyle R Upton
  14. Alexander A Khromykh
  15. Keng Yih Chew
  16. Maria Sukkar
  17. Simon Phipps
  18. Kirsty R Short
(2021)
A paucigranulocytic asthma host environment promotes the emergence of virulent influenza viral variants
eLife 10:e61803.
https://doi.org/10.7554/eLife.61803