Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations

Abstract

Viruses package host RNAs in their virions which are associated with a range of functions in the viral life cycle. Previous transcriptomic profiling of host RNA packaging mostly focused on retroviruses. Which host RNAs are packaged in other viruses at the transcriptome level has not been thoroughly examined. Here we perform proof-of-concept studies using both small RNA and large RNA sequencing of six different SARS-CoV-2 viral isolates grown on VeroE6 cells to profile host RNAs present in cell free viral preparations and to explore SARS-CoV-2 genomic RNA modifications. We find selective enrichment of specific host transfer RNAs (tRNAs), tRNA fragments and signal recognition particle (SRP) RNA in SARS-CoV-2 viral preparations. Different viral preparations contain the same set of host RNAs, suggesting a common mechanism of packaging. We estimate that a single SARS-CoV-2 particle likely contains up to one SRP RNA and four tRNA molecules. We identify tRNA modification differences between the tRNAs present in viral preparations and those in the uninfected VeroE6 host cells. Furthermore, we find uncharacterized candidate modifications in the SARS-CoV-2 genomic RNA. Our results reveal an under-studied aspect of viral-host interactions that may be explored for viral therapeutics.

Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease

“…Hypotheses 3: The Nsp5-TRMT1 interaction could allow the virus to bind tRNAs that are packaged in viral particles as suggested previously (Pena et al, 2022). The finding that expression of the non-cleavable TRMT1-Q530N variant enhances viral replication and infectivity supports the hypothesis that TRMT1 could facilitate tRNA uptake into viral particles.…”

Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease

“…The inhibition of host translation may be beneficial to certain viruses that can locally maintain a tRNA pool optimized for viral translation (Hernandez-Alias et al , 2021; Pavon-Eternod et al , 2013; van Weringh et al , 2011; Yang et al , 2021). Another possibility is that Nsp5-TRMT1 interaction facilitates the packaging of specific tRNAs into viral particles as suggested previously (Pena et al ., 2022). The observation that expression of the non-cleavable TRMT1-Q530N variant enhances viral replication and infectivity supports the hypothesis that TRMT1 could facilitate tRNA uptake into viral particles.…”

“…In a recent study, Chikungunya RNA virus infection has been shown to increase the expression of a human tRNA modification enzyme and alter tRNA modification patterns to favor viral protein expression (Jungfleisch et al , 2022). Interestingly, SARS-CoV-2 viral particles exhibit an enrichment of specific host tRNAs with distinct modification profiles (Pena et al , 2022). Moreover, analysis of RNA extracted from human nose swabs have identified tRNA profiles and modification signatures associated with mild versus severe COVID-19 (Katanski et al , 2022).…”

Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease

“…In a recent study, Chikungunya RNA virus infection has been shown to increase the expression of a human tRNA modification enzyme and alter tRNA modification patterns to favor viral protein expression (Jungfleisch et al, 2022). Interestingly, SARS-CoV-2 viral particles exhibit an enrichment of specific host tRNAs with distinct modification profiles (Pena et al, 2022). Moreover, analysis of RNA extracted from human nose swabs have identified tRNA profiles and modification signatures associated with mild versus severe COVID-19 (Katanski et al, 2022).…”