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Existence of human-virus chimeric proteins generated during infection

ABSTRACT: Influenza A virus (IAV) is a threat to mankind because it generates yearly epidemics and poorly predictable sporadic pandemics with catastrophic potential. Influenza has a small RNA genome (~14 Kb) composed of 8 mini-chromosomes (segments). Segments encode both structural proteins and proteins expressed only during infection. Segments are constituted by a 5’UTR followed by a coding region and a 3’UTR. Transcription of IAV RNA into mRNA depends on host RNA Polymerase II, as the viral polymerase cleaves 5’ capped cellular nascent transcripts to be used as primers to initiate mRNA synthesis. We hypothesized that host nascent transcripts bearing AUG could generate upstream ORFs in the viral segments, a phenomenon that would depend on the translatability of the viral 5’UTRs. Using orthogonal datasets we report the existence of this mechanism, which generate host-virus chimeric proteins. We show that most segments encode proteins in this manner, expanding the proteome diversity of IAV in infected cells. Host-virus chimeric proteins are conserved across IAV strains, pointing to an evolutionary conservation of function achieved by sampling of the evolutionary space before gene fixation. Thus, we discover a mechanism that generate human-virus chimeric proteins during infection.

ORGANISM(S): Mus musculus

PROVIDER: GSE128519 | GEO | 2020/06/25

REPOSITORIES: GEO

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Project description:Infection with a single influenza A virus (IAV) is only rarely sufficient to initiate productive infection. Here, we exploit both single cell approaches and whole-animal systems to show that the extent of IAV reliance on multiple infection varies with virus strain and host species. Influenza A/guinea fowl/HK/WF10/99 (H9N2) [GFHK99] virus exhibits strong dependence on collective interactions in mammalian systems. This reliance focuses viral progeny production within coinfected cells and therefore results in frequent genetic exchange through reassortment. In contrast, GFHK99 virus has greatly reduced dependence on multiple infection in avian systems, indicating a role for host factors in viral collective interactions. Genetic mapping implicated the viral polymerase as a major driver of multiple infection dependence. Mechanistically, quantification of incomplete viral genomes showed that their complementation only partly accounts for the observed reliance on coinfection. Indeed, even when all polymerase components are detected in single cell mRNA sequencing, robust polymerase activity of GFHK99 virus in mammalian cells is reliant on multiple infection. In sum, IAV collective interactions not only augment reassortment, but can also overcome species-specific barriers to infection. These findings underscore the importance of virus-virus interactions in IAV infection, evolution and emergence. We used a single-cell sequencing platform (10x Genomics) to elucidate the differential infection rate of an avian influenza A virus on an avian cell line (DF1) and a mammalian (MDCK) cell line. Our work on IAV reassortment has raised new questions about the fundamental strategies that drive influenza virus evolution. Our data indicate that a large majority of influenza virus genomesare incomplete within cells, comprising less than the eight complete segments normally found in a replication competent infectious viral particle. This led us to ask: what underlying mechanisms give rise to incomplete genomes? What constitute an infectious unit? What are the implications for viral diversification, evolution and spread. By addressing these questions, we will advance he field by deepening our understanding how viral infections are initiated and propagated.

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Existence of human-virus chimeric proteins generated during infection

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