Parallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships

The influenza A virus (IAV) genome consists of eight negative-sense viral RNA (vRNA) segments that are selectively assembled into progeny virus particles through RNA-RNA interactions. To explore putative intersegmental RNA-RNA relationships, we quantified similarity between phylogenetic trees compri...

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Bibliographic Details
Published in:eLife 2021-08, Vol.10
Main Authors: Jones, Jennifer E, Le Sage, Valerie, Padovani, Gabriella H, Calderon, Michael, Wright, Erik S, Lakdawala, Seema S
Format: Article
Language:English
Subjects:
A549 Cells
Amino acid sequence
Biological Evolution
Canada
Confocal microscopy
Epidemics
evolution
Evolutionary Biology
Fluorescence microscopy
Genome, Viral
Genomics
Health aspects
Humans
Influenza
Influenza A
Influenza A Virus, H1N1 Subtype - genetics
Influenza A Virus, H3N2 Subtype - genetics
influenza virus
Influenza, Human - virology
Intermediates
Medical research
Medicine, Experimental
Microbiology and Infectious Disease
Mutation
Nucleotide sequence
Pandemics
Phylogenetics
Phylogeny
Protection and preservation
Ribonucleic acid
RNA
RNA interactions
RNA viruses
RNA, Viral - genetics
Viruses
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Summary:The influenza A virus (IAV) genome consists of eight negative-sense viral RNA (vRNA) segments that are selectively assembled into progeny virus particles through RNA-RNA interactions. To explore putative intersegmental RNA-RNA relationships, we quantified similarity between phylogenetic trees comprising each vRNA segment from seasonal human IAV. Intersegmental tree similarity differed between subtype and lineage. While intersegmental relationships were largely conserved over time in H3N2 viruses, they diverged in H1N1 strains isolated before and after the 2009 pandemic. Surprisingly, intersegmental relationships were not driven solely by protein sequence, suggesting that IAV evolution could also be driven by RNA-RNA interactions. Finally, we used confocal microscopy to determine that colocalization of highly coevolved vRNA segments is enriched over other assembly intermediates at the nuclear periphery during productive viral infection. This study illustrates how putative RNA interactions underlying selective assembly of IAV can be interrogated with phylogenetics.
ISSN:2050-084X
2050-084X
DOI:10.7554/elife.66525