Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection

Abstract

Defective viral genomes (DVGs) are generated ubiquitously in many RNA viruses, including SARS-CoV-2. Their interference activity to full-length viruses and IFN stimulation provide the potential for them to be used in novel antiviral therapies and vaccine development.

Defective viral genomes: advances in understanding their generation, function, and impact on infection outcomes

“…Notably, these nucleotide compositions differed from SARS-CoV-2 and MERS-CoV transcription regulatory sequence (TRS)-like sequences, respectively, together suggesting that coronaviruses use distinct sequence patterns for DVG generation ( 3 ). Consistent with this finding, recent transcriptomic analysis of SARS-CoV-2 in vitro infection and patient-derived samples further identified four TRS-independent genomic “hotspots-”mediating deletion DVG formation ( 20 ).…”

“…Given the inherent error-prone nature of viral RNA-dependent RNA polymerases (RdRps), it was historically accepted that DVG generation is a random process. However, the dissociation (break point) and re-initiation (rejoin point) positions of both deletion and cbDVGs are consistently observed to cluster in certain genomic regions across different virus families ( 8 , 20 – 26 ), strongly arguing against the completely random generation theory. Additionally, microhomologies and specific nucleotide compositions have been observed to flank DVG break and rejoin points ( 3 , 6 , 27 ), further suggesting a sequence dependency for DVG generation ( Fig.…”

“…RNA secondary structures play key roles in viral replication, translation, packaging, and evasion of cellular dsRNA sensors for many positive-sense RNA viruses ( 29 – 32 ). Studies have experimentally or computationally identified RNA secondary structures in the genomes of different positive-sense RNA viruses contributing to their DVG generation ( 20 , 33 ). For example, predicted secondary structures of the poliovirus genome correlated with recombination sites of its deletion DVGs, leading to the hypothesis of the looping-out model ( Fig.…”

Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome

“…The virus exploits splicing, leaky scanning and frame-shifting to encode multiple protein products (63). Recent work has also revealed additional, perhaps more fortuitous mechanisms to DelVGs are produced by a diverse range of RNA viruses and have been shown to impact pathogenesis during human infections with influenza virus, respiratory syncytial virus, and SARS-CoV-2 (9,24,71,72). This raises the possibility that DPRs may be a generalizable feature of RNA virus replication.…”

“…Instead of mutating a single nucleotide, these errors create large internal deletions in genome segments (6,7). Most RNA viruses produce some version of deleted genomes, including important human pathogens like influenza virus, measles virus, SARS-CoV-2, and respiratory syncytial virus (8,9). Influenza virus deletion-containing viral genomes (DelVGs, sometimes referred to as defective viral genomes, DVGs) are aberrant replication products containing a deletion of more than 10 nts while retaining the cis-acting sequences necessary for replication, transcription and packaging into virions (6,(10)(11)(12)(13).…”