Collective interactions augment influenza A virus replication in a host-dependent manner

Abstract

22implicated the PA gene segment as a major driver of this phenotype and quantification of viral 33RNA synthesis indicated that both replication and transcription were affected. These findings 34 indicate that multiple distinct mechanisms underlie IAV reliance on multiple infection and 35 underscore the importance of virus-virus interactions in IAV infection, evolution and emergence. 36Importantly, multiple infection with identical viral genomes can also alter infection 58 outcomes. Such cooperation was documented for VSV and HIV, where rates of transcription and 59 replication were enhanced with increasing multiplicity of infection (MOI) 23,24 . Similarly, faster 60 kinetics of virus production were seen at high MOI for poliovirus and IAV 19,25 . In these instances, 61 it is thought that increased copy number of infecting viral genomes provides a kinetic benefit 62 important in the race to establish infection before innate antiviral responses take hold. Indeed, it 63 has been suggested that multiple infection may be particularly relevant for facilitating viral growth 64 under adverse conditions, such as antiviral drug treatment 3,26 . 65For IAV, an important adverse condition to consider is that of a novel host environment. 66IAVs occupy a broad host range, including multiple species of wild waterfowl, poultry, swine, 67 humans and other mammals 27,28 . Host barriers to infection typically confine a given lineage to 68 circulation in one species or a small number of related species 29,30 . Spillovers occur occasionally, 69 however, and can seed novel lineages. When a novel IAV lineage is established in humans, the 70 result is a pandemic of major public health consequence 31,32 . The likelihood of successful cross-71 species transfer of IAV is determined largely by the presence, absence, and compatibility of host 72 factors on which the virus relies to complete its life cycle, and on the viruses' ability to overcome 73 antiviral defenses in the novel host [33][34][35] . 74Our objective herein was to assess the degree to which IAV relies on the delivery of 75 multiple viral genomes to a cell to ensure production of progeny. In particular, we sought to 76 determine whether this phenotype varies with host species. We therefore examined the 77 multiplicity dependence of one human and a panel of avian-origin viruses in multiple host systems. 78Results from all virus/cell combinations tested confirm prior reports that cells multiply-infected with 79 IAV produce more viral progeny than singly-infected cells. Importantly, however, the extent to 80 which viral progeny production is concentrated within the multiply-infected fraction of a cell 81 population varies greatly with virus-host context. Two poultry-adapted H9N2 viruses (A/guinea 82 fowl/HK/WF10/99 (GFHK99) and A/quail/HK/A28945/88 (QaHK88)) exhibit an acute dependence 83 on multiple infection in mammalian systems that is greatly diminished in natural host systems. 84This strong dependence on multiple infection is not seen for the human strain, influenza 85 ...

Cellular co-infection can modulate the efficiency of influenza A virus production and shape the interferon response

“…A model that allows for the onset times of viral production to depend on cellular MOI may therefore better capture the relationship between viral output and cellular MOI at this early time point. Our overall results are consistent with previous reports of earlier and higher rates of replication under high experimental MOI conditions [ 19 , 20 ].…”

“…Specifically, they observed an inverse relationship between the susceptibility of a given cell line to VSV infection and the extent to which cellular co-infection enhanced viral output. Similarly, Phipps et al observed that cellular co-infection could enhance influenza virus replication when the virus strain used was poorly adapted to the cell line used [ 20 ]. Along with these studies, our results illustrate the importance of considering variation between cell types.…”

Cellular co-infection can modulate the efficiency of influenza A virus production and shape the interferon response

“…A model that allows for the onset times of viral production to depend on cellular MOI may therefore better capture the relationship between viral output and cellular MOI at this early time point. Our overall results are consistent with previous reports of earlier and higher rates of replication under high experimental MOI conditions (19,20). For A549 cells, we considered the same set of time-dependent virus production rate models.…”

Heterogeneity in viral infections increases the rate of deleterious mutation accumulation

“…Viral output from cells can be affected by host cell characteristics such as size, cell type, and cell cycle stage (Brooke et al, 2013; Schulte and Andino, 2014; Heldt et al, 2015; Golumbeanu et al, 2018; Leviyang and Griva, 2018; Russell et al, 2018; Xin et al, 2018; Phipps et al, 2019; Vera et al, 2019). To consider the effect of heterogeneity in virus output on deleterious mutation accumulation, we extend our base model described above by adapting an approach used by Lloyd-Smith et al (2005) to describe population-level viral transmission heterogeneity (superspreading dynamics).…”

“…Virus output from cells can also be affected by cellular multiplicity of infection, with higher cellular MOI having the potential to increase viral yield (Phipps et al, 2019; Martin et al, 2020). To consider the effect that this source of cellular heterogeneity in virus output may have on deleterious mutation accumulation, we extended the base model to allow cellular multiplicity of infection to impact cellular output.…”