Journal
CELL REPORTS
Volume 20, Issue 1, Pages 251-263Publisher
CELL PRESS
DOI: 10.1016/j.celrep.2017.06.021
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Funding
- Swedish Research Council
- Swedish Foundation for Strategic Research
- FORMAS
- Knut and Alice Wallenberg Foundation
- Carl Trygger Foundation
- Harald Jeanssons Stiftelse
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Genome delivery to the proper cellular compartment for transcription and replication is a primary goal of viruses. However, methods for analyzing viral genome localization and differentiating genomes with high identity are lacking, making it difficult to investigate entry-related processes and co-examine heterogeneous RNA viral populations. Here, we present an RNA labeling approach for single-cell analysis of RNA viral replication and co-infection dynamics in situ, which uses the versatility of padlock probes. We applied this method to identify influenza A virus (IAV) infections in cells and lung tissue with single-nucleotide specificity and to classify entry and replication stages by gene segment localization. Extending the classification strategy to co-infections of IAVs with single-nucleotide variations, we found that the dependence on intracellular trafficking places a time restriction on secondary co-infections necessary for genome reassortment. Altogether, these data demonstrate how RNA viral genome labeling can help dissect entry and co-infections.
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