Superinfection exclusion creates spatially distinct influenza virus populations

Abstract

Interactions between viruses during coinfections can influence viral fitness and population diversity, as seen in the generation of reassortant pandemic influenza A virus (IAV) strains. However, opportunities for interactions between closely related viruses are limited by a process known as superinfection exclusion (SIE), which blocks coinfection shortly after primary infection. Using IAVs, we asked whether SIE, an effect which occurs at the level of individual cells, could limit interactions between populations of viruses as they spread across multiple cells within a host. To address this, we first measured the kinetics of SIE in individual cells by infecting them sequentially with 2 isogenic IAVs, each encoding a different fluorophore. By varying the interval between addition of the 2 IAVs, we showed that early in infection SIE does not prevent coinfection, but that after this initial lag phase the potential for coinfection decreases exponentially. We then asked how the kinetics of SIE onset controlled coinfections as IAVs spread asynchronously across monolayers of cells. We observed that viruses at individual coinfected foci continued to coinfect cells as they spread, because all new infections were of cells that had not yet established SIE. In contrast, viruses spreading towards each other from separately infected foci could only establish minimal regions of coinfection before reaching cells where coinfection was blocked. This created a pattern of separate foci of infection, which was recapitulated in the lungs of infected mice, and which is likely to be applicable to many other viruses that induce SIE. We conclude that the kinetics of SIE onset segregate spreading viral infections into discrete regions, within which interactions between virus populations can occur freely, and between which they are blocked.

Exclusion of latecomers yields a patchwork of viral subpopulations within hosts

“…The cell remains open to secondary infection for a period of hours but then adopts an exclusionary state in which newly arriving viruses are not able to initiate sustained replication [3,4]. Sims and colleagues [2] show that this temporal effect gives rise to strong spatial patterning (Fig 1). Their data support a model in which only viruses that are nearby in space-because they are progeny of the same infected cell, for example-can readily coinfect within the time window that precedes exclusion.…”

“…Similarly, in swine, viral variants generated through reassortment formed spatially distinct subpopulations, typically with only a few novel genotypes detected at each site. In light of the findings of Sims and colleagues [ 2 ], both the low diversity within each site and the observed lack of mixing between them can be explained by superinfection exclusion: Only the first viruses to become established at a site are efficiently propagated, with any subsequently arriving viruses unable to penetrate.…”

“…Thus, consequential reassortment is reliant on viruses mixing within infected hosts. The observed spatial heterogeneity of influenza A virus populations indicates that such mixing is constrained [ 2 , 5 , 6 ]. By reducing opportunity for the generation of genetic diversity, this constraint diminishes adaptive potential.…”

“…Although the work of Sims and colleagues [ 2 ] offers a major advance by linking spatial structure within hosts to superinfection exclusion, many questions persist. While their study and related ones focused on the lower respiratory tract, the upper respiratory tract is an important site for influenza A virus replication and onward transmission.…”

“…A study in PLOS Biology indicates that this exclusion at the level of individual cells gives rise to a heterogenous landscape of infection within a host.Superinfection exclusion is a phenomenon in which a virus replicating within a cell blocks secondary infection of that cell by viruses of the same species [1]. Recently, in PLOS Biology, Sims and colleagues uncovered the role of superinfection exclusion in producing spatially discrete viral subpopulations [2]. While exclusion has long been recognized, its implications for the spatial structure of viral populations during in vivo infections had not been explored.…”