Mini viral RNAs act as innate immune agonists during influenza virus infection

Abstract

and propose an intramolecular copy-choice mechanism for mvRNA generation. 43 By deep-sequencing RNA samples from lungs of ferrets infected with influenza 44viruses we show that mvRNAs are generated during infection of animal models. 45 We propose that mvRNAs act as main agonists of RIG-I during influenza virus 46infection and the ability of influenza virus strains to generate mvRNAs should be 47 considered when assessing their virulence potential. 48The negative sense viral RNA (vRNA) genome segments of influenza A viruses, 49 as well as the complementary RNA (cRNA) replicative intermediates, contain 5ʹ 50 triphosphates and partially complementary 5ʹ and 3ʹ termini that serve as the viral 51 promoter for replication and transcription of the viral RNA genome 6 . RIG-I has been 52 shown to bind and be activated by the dsRNA structure formed by the termini of 53 influenza virus RNAs 7,8 . However, it remains unclear how RIG-I gains access to this 54 dsRNA structure. Both vRNA and cRNA are assembled into ribonucleoprotein 55 complexes (vRNP and cRNP, respectively) in which the viral RNA polymerase, a 56 heterotrimeric complex of the viral proteins PB1, PB2 and PA, associates with the 57 partially complementary termini, while the rest of the RNA is bound by oligomeric 58 nucleoprotein (NP) 6 (Fig. 1a). The tight binding of the 5ʹ and 3ʹ termini of vRNA and 59for use under a CC0 license.This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/385716 doi: bioRxiv preprint first posted online Aug. 6, 2018; 3 cRNA by the RNA polymerase 9 is likely to preclude an interaction with RIG-I. 60Moreover, it has been demonstrated that IFN expression is triggered only in a fraction 61 of influenza virus infected cells 10,11 , suggesting that influenza viruses efficiently hide 62 their genome segments during infection by replicating them in the context of RNPs 11 . 63This led to the proposal that an aberrant RNA replication product might be binding to 64 RIG-I and triggering IFN expression 12 . Indeed, the influenza virus polymerase is known 65 to generate defective interfering (DI) RNAs, which are ≥178 nt long subgenomic RNAs 66 generated during high multiplicity infections 13 , and small viral RNAs (svRNAs), which 67 are 22-27 nt long and correspond to the 5ʹ end of vRNA segments. However, svRNAs 68 have been shown not to be involved in the induction of antiviral cellular defences 14 and 69 DI RNAs assemble into RNP structures (Fig. 1a) NP and a luciferase reporter to measure the activation of the IFN-b promoter (Fig. 1b). 82We found that the expression of mvRNAs induced significantly higher IFN expression 83 than full-length vRNA or DI RNA, comparable to the levels induced by transfection of 84 2 µg of poly(I:C), a known activator of IFN expression 18 . Similar results were ob...

Innate Immune Evasion by Human Respiratory RNA Viruses

“…Besides these different responses, most of which are IFN-mediated, small non-coding (micro, circular, ...) RNAs, RNAi, and IFN-independent antiviral responses can be regarded as part of the innate immune response package as well [29][30][31]. An emerging hot topic is also the interplay of innate immune response with cellular metabolism, so-called immunometabolism, which likely is quite relevant for respiratory viral infections [4,32,33].…”

An inability to maintain the ribonucleoprotein genomic structure is responsible for host detection of negative-sense RNA viruses

“…To this end, we found that infection with the untargeted NP control virus resulted in the accumulation of full length vRNA and the previously characterized small viral RNA (svRNA) ( Figure 3A) (Perez et al, 2010;Perez et al, 2012;Umbach et al, 2010). In contrast, while a complete loss of full length vRNA was observed in the NPtargeted virus, these same conditions showed the accumulation of a range of smaller viral RNA species comparable in size to the recently described mini viral RNA (mvRNA) -an NP-independent DVG ( Figure 3A) (Te Velthuis et al, 2018). In agreement with mvRNA being a potent inducer of the antiviral response, we also observed a correlation between its appearance and the induction of IFN ( Figure 3B).…”

“…As new genomes are generated, there is an immediate demand for available NP pools. As this dynamic progresses, NP inevitably becomes limiting thereby forming only a partial RNP complex, which promotes the formation of DVGs, perhaps in part by providing the viral RdRp with more flexibility to slide or disengage from the template strand during replication (Te Velthuis et al, 2018). DVGs generated by this process further exacerbate the problem as they too can be substrates for NP and the polymerase, thereby overwhelming the resources of the virus.…”

Passive immune therapy and other immunomodulatory agents for the treatment of severe influenza: Systematic review and meta‐analysis

“…But in a delicate balance, this immune response to an infection can also be harmful to the host. For example, an excessively pro‐inflammatory cytokine and chemokine environment has been cited as the key explanation for the severity of human infections with highly pathogenic avian influenza, and the 1918 H1N1 “Spanish flu” pandemic . This “cytokine storm” can rapidly result in multi‐organ dysfunction and acute respiratory distress syndrome (ARDS).…”

“…For example, an excessively pro-inflammatory cytokine and chemokine environment has been cited as the key explanation for the severity of human infections with highly pathogenic avian influenza, and the 1918 H1N1 "Spanish flu" pandemic. 10 This "cytokine storm" can rapidly result in multi-organ dysfunction and acute respiratory distress syndrome (ARDS). Similarly, in seasonal influenza damage to the airways and alveolae is mediated both by viral replication and by the innate immune response.…”