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Coinfection by influenza A virus and respiratory syncytial virus produces hybrid virus particles

Nature Microbiology volume 7, pages 1879–1890 (2022)Cite this article

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Abstract

Interactions between respiratory viruses during infection affect transmission dynamics and clinical outcomes. To identify and characterize virus–virus interactions at the cellular level, we coinfected human lung cells with influenza A virus (IAV) and respiratory syncytial virus (RSV). Super-resolution microscopy, live-cell imaging, scanning electron microscopy and cryo-electron tomography revealed extracellular and membrane-associated filamentous structures consistent with hybrid viral particles (HVPs). We found that HVPs harbour surface glycoproteins and ribonucleoproteins of IAV and RSV. HVPs use the RSV fusion glycoprotein to evade anti-IAV neutralizing antibodies and infect and spread among cells lacking IAV receptors. Finally, we show that IAV and RSV coinfection in primary cells of the bronchial epithelium results in viral proteins from both viruses co-localizing at the apical cell surface. Our observations define a previously unknown interaction between respiratory viruses that might affect virus pathogenesis by expanding virus tropism and enabling immune evasion.

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Fig. 1: Replication kinetics and cellular infection during IAV and RSV coinfections.
Fig. 2: Filaments containing both IAV and RSV proteins extend from coinfected cells.
Fig. 3: Hybrid viral particles contain IAV- and RSV-like structural regions.
Fig. 4: Hybrid viruses enable IAV infection in sialic acid-depleted cells.
Fig. 5: Hybrid viral particles enable spread of IAV in a refractory cell population.
Fig. 6: Coinfection occurs in primary cells.

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Data availability

Representative tomograms of the chimeric virus particles described in this paper have been deposited in the Electron Microscopy Data Bank (www.ebi.ac.uk/emdb) under accession codes EMD-13228 and EMD-13229. Source data are provided with this paper.

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Acknowledgements

This work was supported by grants from the Medical Research Council of the United Kingdom (MC_UU_12014/9 to P.R.M., MR/N013166/1 to J.H., MR/R502327/1 to D.M.G., MC_UU_12014/7 to S.V., and MC_UU_12014/7 to D.B.). The Scottish Centre for Macromolecular Imaging is funded by the Medical Research Council of the United Kingdom (MC_PC_17135) and the Scottish Funding Council (H17007).

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Authors and Affiliations

  1. MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK

    Joanne Haney, Swetha Vijayakrishnan, Kieran Dee, Daniel Max Goldfarb, Stephen D. Carter, David Bhella & Pablo R. Murcia

  2. Scottish Centre for Macromolecular Imaging, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK

    James Streetley, Mairi Clarke & David Bhella

  3. Glasgow Imaging Facility, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, UK

    Margaret Mullin

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Contributions

Author contributions are based on the CRediT taxonomy (https://casrai.org/credit/). J.H.: investigation, methodology, formal analysis, visualization, writing—original draft. S.V.: investigation, data curation, formal analysis, resources, methodology, validation, visualization, supervision, writing—original draft. J.S.: investigation, writing—review and editing. K.D.: investigation, writing—review and editing. D.M.G.: investigation, writing—review and editing. M.C.: investigation, writing—review and editing. M.M.: investigation, methodology, writing—review and editing. S.D.C.: formal analysis, writing—review and editing. D.B.: resources, funding acquisition, writing—review and editing. P.R.M.: conceptualization, methodology, validation, data curation, supervision, funding acquisition, project administration, writing—original draft.

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Correspondence to Pablo R. Murcia.

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Extended data

Extended Data Fig. 1 HA and F are expressed in discrete patches along the length of filaments, with HA predominantly at the distal end.

(a) Magnified view of cell associated filaments (full image shown in Fig. 2A) show filaments with distinct patches of IAV HA (magenta) and RSV F (green) glycoproteins along the length of the filaments. (b) White arrows and filament numbering correspond to fluorescence intensity profiles displayed in (c). Minimal colocalisation was observed in the fluorescence intensity profiles (c) for IAV HA (magenta line) and RSV F (green line) signal along filaments numbered 1–15. IAV (filament 3, magenta star) and RSV (filament 7, green star) filaments were also identified among dual positive filaments.

Source data

Extended Data Fig. 2 Scanning electron microscopy shows clear differences between IAV and RSV virion structure.

Scanning electron micrographs of IAV, RSV, coinfected or mock infected cells imaged at 1000x (top row), 10,000x (middle row) and 20,000x (bottom row), region of magnification is denoted by the white box. Scale bars represent 10 µm at 1000x and 1 µm at 10,000x and 20,000x magnification. Micrographs representative of n = 2 biologically independent experiments.

Extended Data Fig. 3 Coinfection generates RSV filaments that are pseudotyped with IAV envelope proteins.

(a) Tomogram shows a pseudotyped RSV filament, indicated by red ‘PV’ label, near to RSV filaments, one example indicated by blue ‘RSV’ label. Scale bar indicates 200 nm. (b) Magnified cross-section of end of pseudotyped filament, showing RSV RNP contained within virion. (c) Surface of psuedotyped filament shows irregular arrangement of glycoproteins, with many displaying characteristic triangular shape of HA trimers, shown in magnified inset image. (d) Magnified cross-section of end of RSV filament, showing RSV RNP contained within virion and ultra-structure consistent with the pseudotyped virion. (e) Surface of the RSV filament shows helical arrangement of glycoproteins, with ring-shaped density of glycoproteins highlighted in magnified insert. Scale bars in panels (c-e) indicate 50 nm. Micrographs shown in (a-e) representative of n = 3 biologically independent experiments.

Extended Data Fig. 4 Further examples of hybrid particles.

(a and b) show two z-positions through the same hybrid particle, which also displays pseudotyping in RSV-like region. (a) IAV-like regions extend from the top of the filament and ring-shaped densities corresponding to RSV genome, indicated by green arrows and highlighted in magnified inset image, are present within the virion. (b) The surface of the virion is covered in glycoproteins that are consistent in shape and arrangement with IAV glycoproteins, highlighted in magnified inset. Scale bars indicate 200 nm. (c) Tomogram shows a further example of a hybrid particle with two IAV-like regions which are joined to the RSV-like region by a continuous membrane. Black and green arrows indicate IAV and RSV RNP respectively, contained with in their associated structural regions. Scale bar indicates 200 nm. There is a clear shared lumen which continues between RSV and IAV regions, highlighted within magnified inset which corresponds to region marked by white dashed box. Scale bar indicates 50 nm. Micrographs shown in (a-c) representative of n = 3 biologically independent experiments.

Extended Data Fig. 5 Inter-spike distance measurements reveal that pseudotyped viruses are decorated with IAV glycoproteins.

To determine the glycoprotein arrangement on pseudotyped viruses, inter-spike distances were measured between glycoprotein pairs. Representative examples are shown for IAV (a), RSV (b) and pseudotyped virions (c) with red lines indicating example distances measured. Pink, green and blue dashed lines indicate the edges of IAV, RSV and psuedotyped filaments respectively. Scale bars indicate 200 nm. (d) Tomography data was collected from n = 2 biologically independent experiments. Control measurements were collected from 11 tomograms for IAV (measurements n = 326) and 11 tomograms for RSV (measurements n = 236). Measurements of pseudotyped virions were collected from 4 individual tomograms (n = 50 measurements per tomogram). Average inter-spike distances were 8.71 nm for IAV, 12.9 nm for RSV and a range of 8.31–9.56 nm for pseudotypes. Statistical significance was determined by two tailed unpaired t-test analysis, **** p < 0.0001. Box plot shows interquartile range (25th percentile, median, 75th percentile), whiskers represent minimum and maximum values and black points represent outliers.

Source data

Extended Data Fig. 6 Hybrid viral particles evade neutralizing antibodies against IAV, but not RSV.

Virus harvested from coinfection or single infections was pre-incubated with serum targeting IAV HA, RSV F or a serum-free control, and then used to infect A549 cells. Infections were fixed and immunostained at 12 hpi and the number of IAV infected cells was quantified using an automated image-based cell counter. The same virus stocks were back titrated to determine infectious viral input. (a) Back titration of IAV in single infection (magenta bars) or coinfection (teal bars) by IAV plaque assay. (b) Back titration of RSV in single infection (green bars) or coinfection (dark blue bars) by RSV plaque assay. (c) Neutralisation of IAV by polyclonal antisera targeting IAV HA when virus was harvested from the supernatant or cell pellet fractions of a single IAV infection (magenta bars) or a coinfection (teal bars). Neutralisation was calculated as a percentage of IAV infected cells in the wells containing serum compared to matched serum-free controls. (d) Neutralisation of RSV by Palivizumab (targeting RSV F) when virus was harvested from the supernatant or cell pellet fractions of a single RSV infection (green bars) or a coinfection (dark blue bars). Neutralisation calculated as a percentage of RSV infected cells in the wells containing serum compared to matched serum-free controls. Data shown in (a-d) was collected from n = 3 independent experiments and statistical significance calculated by two tailed Mann Whitney test, ns indicates p > 0.05. Bars represent mean and data points represent biological replicates.

Source data

Extended Data Fig. 7 Supporting data for neuraminidase experiment.

(a) Schematic demonstrating experimental design. (b) NA-treated and untreated cells stained with Maackia Amurensis Lectin II (MAL II) in yellow (top row) and Erythrina Cristagalli Lectin (ECL) in cyan (bottom row). Scale bar represents 20 µm. Images representative of n = 2 biologically independent experiments. (c) Viral input in pfu/ml of IAV as determined by back-titration of inoculum for NA-experiment by IAV plaque assay. (d) Ratio of RSV entry into NA-treated cells versus control cells when harvested from single infection (green bars) or mixed infection (blue bars). RSV entry to NA-treated cells was calculated as a percentage of the RSV-positive cell count in the matched untreated control. (e) Ratio of virus entry of IAV only or RSV only (red bars) into NA-treated over control cells, compared to entry of IAV pre-mixed with RSV or RSV pre-mixed with IAV into NA-treated over control cells (blue bars). Data shown in (c-e) was collected from n = 2 (c) or 3 (d-e) independent experiments and statistical significance calculated by two tailed Mann Whitney test, ns indicates p > 0.05. Bars represent mean and data points represent biological replicates.

Source data

Supplementary information

Supplementary Information

Description of IAV and RSV particles, Supplementary Figs. 1–3 and references

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Supplementary Video 1

Video showing serial sections through the z-axis of a tomogram of a hybrid particle with a multiple IAV region, formed during coinfection of IAV and RSV (corresponding image shown in Fig. 3). Glycoproteins and RNPs of both IAV and RSV are labelled and denoted by arrows.

Supplementary Video 2

Video showing serial sections through the z-axis of a tomogram of hybrid particle with IAV and RSV regions with an adjoining region with a clear lumen (corresponding image shown in Extended Data Fig. 4c). Glycoproteins and RNPs of both IAV and RSV are labelled and denoted by arrows.

Supplementary Video 3

Video showing serial sections through a tomogram of a pseudotyped viral filament generated during IAV and RSV coinfection (corresponding image shown in Extended Data Fig. 3). Glycoproteins and RNPs are labelled and denoted by arrows.

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Haney, J., Vijayakrishnan, S., Streetley, J. et al. Coinfection by influenza A virus and respiratory syncytial virus produces hybrid virus particles. Nat Microbiol 7, 1879–1890 (2022). https://doi.org/10.1038/s41564-022-01242-5

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