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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Main Authors:	Jennifer E Jones, Valerie Le Sage, Gabriella H Padovani, Michael Calderon, Erik S Wright, Seema S Lakdawala
Format:	article
Language:	EN
Published:	eLife Sciences Publications Ltd 2021
Subjects:	influenza virus evolution RNA interactions Medicine R Science Q Biology (General) QH301-705.5
Online Access:	https://doaj.org/article/2a9d9ec2f57e45d38cb227237c20f550
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spelling	oai:doaj.org-article:2a9d9ec2f57e45d38cb227237c20f5502021-11-15T05:37:22ZParallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships10.7554/eLife.665252050-084Xe66525https://doaj.org/article/2a9d9ec2f57e45d38cb227237c20f5502021-08-01T00:00:00Zhttps://elifesciences.org/articles/66525https://doaj.org/toc/2050-084XThe 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.Jennifer E JonesValerie Le SageGabriella H PadovaniMichael CalderonErik S WrightSeema S LakdawalaeLife Sciences Publications Ltdarticleinfluenza virusevolutionRNA interactionsMedicineRScienceQBiology (General)QH301-705.5ENeLife, Vol 10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	influenza virus evolution RNA interactions Medicine R Science Q Biology (General) QH301-705.5
spellingShingle	influenza virus evolution RNA interactions Medicine R Science Q Biology (General) QH301-705.5 Jennifer E Jones Valerie Le Sage Gabriella H Padovani Michael Calderon Erik S Wright Seema S Lakdawala Parallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships
description	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.
format	article
author	Jennifer E Jones Valerie Le Sage Gabriella H Padovani Michael Calderon Erik S Wright Seema S Lakdawala
author_facet	Jennifer E Jones Valerie Le Sage Gabriella H Padovani Michael Calderon Erik S Wright Seema S Lakdawala
author_sort	Jennifer E Jones
title	Parallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships
title_short	Parallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships
title_full	Parallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships
title_fullStr	Parallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships
title_full_unstemmed	Parallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships
title_sort	parallel evolution between genomic segments of seasonal human influenza viruses reveals rna-rna relationships
publisher	eLife Sciences Publications Ltd
publishDate	2021
url	https://doaj.org/article/2a9d9ec2f57e45d38cb227237c20f550
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Parallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships

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