Quantitative structural analysis of influenza virus by cryo-electron tomography and convolutional neural networks

Influenza viruses pose severe public health threats globally. Influenza viruses are extensively pleomorphic, in shape, size, and organization of viral proteins. Analysis of influenza morphology and ultrastructure can help elucidate viral structure-function relationships and aid in therapeutics and vaccine development. While cryo-electron tomography (cryoET) can depict the 3D organization of pleomorphic influenza, the low signalto-noise ratio inherent to cryoET and viral heterogeneity have precluded detailed characterization of influenza viruses. In this report, we leveraged convolutional neural networks and cryoET to characterize the morphological architecture of the A/Puerto Rico/8/34 (H1N1) influenza strain. Our pipeline improved the throughput of cryoET analysis and accurately identified viral components within tomograms. Using this approach, we successfully characterized influenza morphology, glycoprotein density, and conducted subtomogram averaging of influenza glycoproteins. Application of this processing pipeline can aid in the structural characterization of not only influenza viruses, but other pleomorphic viruses and infected cells.

Automated summary

Influenza viruses are highly pleomorphic, making their structural characterization challenging. This report demonstrates the use of convolutional neural networks and cryo-electron tomography to successfully characterize the morphology and glycoprotein density of the H1N1 influenza strain. This approach improves the efficiency of influenza virus analysis and has potential applications in studying other pleomorphic viruses and infected cells.