Defective viral genomes are key drivers of the virus–host interaction

Abstract

Viruses survive often harsh host environments, yet we know little about the strategies they utilize to adapt and subsist given their limited genomic resources. We are beginning to appreciate the surprising versatility of viral genomes and how replicationcompetent and -defective virus variants can provide means for adaptation, immune escape and virus perpetuation. This Review summarizes current knowledge of the types of defective viral genomes generated during the replication of RNA viruses and the functions that they carry out. We highlight the universality and diversity of defective viral genomes during infections and discuss their predicted role in maintaining a fit virus population, their impact on human and animal health, and their potential to be harnessed as antiviral tools. Review ARticleNATuRe MicRoBiology extinction interfere with replication of a wild-type viral genome 29,30 . Hypermutations and mutations leading to frame shifts also result in defective viruses 31 (Fig. 1a). One example is mutations introduced by the cellular protein APOBEC3G into pro-retroviruses 32 . APOBEC3G deaminates deoxycytidine nucleotides in the viral DNA, leading to hypermutations that interfere with the ability of the viral genome to integrate into the host genome and replicate. Interestingly, in opposition to an interfering activity for these mutated pro-viruses, it has been proposed that defective proviruses enhance fitness and that complementation among them drives viral persistence and pathogenesis 33,34 .Deletions. The genomic viral species most commonly referred to as DVGs are truncated viral genomes resulting from large internal deletions occurring during viral replication. Deletion DVGs tend to bear single large truncations that remove several or all essential genes required for self-propagation while retaining 5′ and 3′ ends as well as other RNA structural elements required for polymerase binding, replication and/or packaging [35][36][37] . Multiple variants also exist, including DVGs that can be described as 'mosaic' in that they appear to be the result of multiple recombination and rearrangement events, including deletions, insertions, duplications and even inversions of parts of the genome [38][39][40] (Fig. 1b). Copy-backs.Copy-back and snap-back DVGs are rearranged genomes in which a sequence is duplicated in reverse complement to create theoretical stem-like structures (panhandle structures for copy-back DVGs or hairpin structures for snap-back DVGs) 41-43 . Copy-back DVGs have been reported in many negative-sense (ns) RNA viruses and are generated from the 5′ end of the genome in a process that produces DVGs with complementary 3′ and 5′ termini 44,45 . If the complementary region of the DVG comprises almost the entire sequence, the DVG can be further characterized as a snap-back DVG 43 (Fig. 1c). Copy-back DVGs are predicted to be generated when the viral RNA-dependent RNA polymerase (RdRP) detaches from the template and reattaches to the nascent strand, copying back the end of the genome 42,46 .

Induced copy-back RNA synthesis as a novel therapeutic mechanism against RNA viruses

“…By comparing the EV-A71 and PV RdRps, we provide evidence that the backtracked state is indeed an intermediate for template switching. Unexpectedly, for EV-A71 RdRp we observed a high frequency of intramolecular template switching, which has been coined "copyback RNA synthesis" in the literature 15 . Our data for EV-A71 RdRp also indicate that the pyrazine-carboxamide class of antiviral ribonucleotides enhances such switching and may function by promoting the formation of defective viral genomes 15 .…”

“…Unexpectedly, for EV-A71 RdRp we observed a high frequency of intramolecular template switching, which has been coined "copyback RNA synthesis" in the literature 15 . Our data for EV-A71 RdRp also indicate that the pyrazine-carboxamide class of antiviral ribonucleotides enhances such switching and may function by promoting the formation of defective viral genomes 15 . Our study therefore makes a clear mechanistic connection between recombination and copy-back RNA synthesis, and provides compelling evidence that an enhancement of the probability of template switching results in an antiviral effect.…”

“…This observation confirms that the reduction in replication-dependent reporter expression was indeed caused by a backtracking-induced phenomenon. Of the few possibilities, defective replicons produced by copy-back RNA synthesis is a likely possibility 15 . It was not possible to Figs.…”

“…Our study therefore makes a clear mechanistic connection between recombination and copy-back RNA synthesis, and provides compelling evidence that an enhancement of the probability of template switching results in an antiviral effect. The experimental paradigm reported here should prove useful in dissecting the contributions of the RdRp and the template capable of promoting formation of defective viral genomes, a newly emerging strategy for interfering with virus multiplication and attenuating viral pathogenesis 15 .…”

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

“…In addition to this PAMP, RNA viruses are generally also thought to generate a significant amount of double stranded RNA which can be recognized by the PRR, MDA5 (Schneider et al, 2014). In both examples, these PAMPs can derive from both full length genomic products or defective viral genomes (DVGs) which are known to accumulate to high numbers during the replicative process (Vignuzzi and Lopez, 2019). Following PAMP recognition, PRR induces its oligomerization and the assembly of a variety of scaffold proteins and kinases (Schneider et al, 2014).…”