Modeling the Intracellular Dynamics of Influenza Virus Replication To Understand the Control of Viral RNA Synthesis

Abstract

bInfluenza viruses transcribe and replicate their negative-sense RNA genome inside the nucleus of host cells via three viral RNA species. In the course of an infection, these RNAs show distinct dynamics, suggesting that differential regulation takes place. To investigate this regulation in a systematic way, we developed a mathematical model of influenza virus infection at the level of a single mammalian cell. It accounts for key steps of the viral life cycle, from virus entry to progeny virion release, while focusing in particular on the molecular mechanisms that control viral transcription and replication. We therefore explicitly consider the nuclear export of viral genome copies (vRNPs) and a recent hypothesis proposing that replicative intermediates (cRNA) are stabilized by the viral polymerase complex and the nucleoprotein (NP). Together, both mechanisms allow the model to capture a variety of published data sets at an unprecedented level of detail. Our findings provide theoretical support for an early regulation of replication by cRNA stabilization. However, they also suggest that the matrix protein 1 (M1) controls viral RNA levels in the late phase of infection as part of its role during the nuclear export of viral genome copies. Moreover, simulations show an accumulation of viral proteins and RNA toward the end of infection, indicating that transport processes or budding limits virion release. Thus, our mathematical model provides an ideal platform for a systematic and quantitative evaluation of influenza virus replication and its complex regulation.

Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ

“…For Qβ and other ssRNA viruses, there is clearly an evolutionary mandate for efficient and accurate virion assembly (34). After the gRNA is replicated and coat proteins are produced, the rate-limiting step in virion production is encapsidation of the RNA (35). It was first proposed that the assembly pathway was initiated when the first coat protein dimer bound the operator hairpin, serving as a nucleation event for other coat protein dimers to "walk" down a "Hamiltonian path" binding neighboring RNAs until the virion is complete (36).…”

Detection of Single Influenza Viral RNA in Cells Using a Polymeric Sequence Probe

“…with ribavirin, which may be due to the vRNA molecules degradation after 2 h P.I. (15) The average number of vRNA per cell increased slightly after 4 h P.I., indicating the decrease of the drug effect after 4 h P.I. (13) No vRNA was observed in mock (no infection) or drug only control cells (6 h incubation with ribavirin but without virus infection), which confirms that the PSP probe has an extremely low nonspecific binding rate.…”

Identifying Selection in the Within-Host Evolution of Influenza Using Viral Sequence Data

“…Considering selection, the lowest resolution at which we report selection, of 0.1 per 12 h, is, accounting for two rounds of replication in the lifetime of an infected cell [10], [15], equivalent to a fitness difference of 0.05 per generation. As such, this part of the assumption holds if N is substantially larger than 20 viruses.…”

“…Based upon observed changes in viral titre over time, inferences have been made of many important properties of infection, including the reproductive number for cellular infection, the timescale and numbers of viruses produced during the infection of a cell, and the impact upon the viral population of both innate and adaptive immune responses [10]–[14]. Considering data of intracellular RNA levels, the fine detail of viral replication within a cell has been described [15]. Evolutionary models of competition between viral strains have clarified the relationship between selection for growth and transmission effects, and the dynamics of immune escape [16]–[18].…”