SARS-CoV-2 destabilizes host RNA to enhance health

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In a study recently published in the journal Nature Communications, scientists mapped the interactions between coronavirus 2 RNA (SARS-CoV-2) of severe acute respiratory syndrome and host RNA. They observed that the virus highly methylated its genome using the methylation machinery of the host’s RNA, resulting in an improvement in viral fitness.

background

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19), is an enveloped, positive-meaning, single-stranded RNA virus with a genome size of about 30 kb. The viral genome codes for four structural proteins, including the envelope, membrane, nucleocapsid and spike proteins, which are required for the viral budding and host cell entry processes.

In addition, the genome encodes several accessory proteins that are crucial for maintaining the viral life cycle in the host cells. In particular, accessory protein-mediated viral RNA replication results in the creation of a full-length viral genome and multiple subgenomic RNAs (sgRNAs). The viral RNA and full-length sgRNAs interact with host cell proteins and RNAs to regulate virus replication in infected cells.

Since its appearance in China in December 2019, SARS-CoV-2 has acquired more than 12,000 mutations that have led to the appearance of several virus variants. Although spike mutations predominate in the SARS-CoV-2 genome, some deletion mutations have been identified in the ORF8 region in many countries, including Singapore, Australia, Bangladesh, Taiwan, and Spain. In Singapore in particular, a 382 nucleotide deletion (Δ382) was found in the viral genome, which causes a shortening of ORF7 and a deletion of ORF8. Compared to wild-type SARS-CoV-2, variants containing Δ382 induce relatively mild infections in infected patients.

The study

In the current study, the scientists examined RNA-RNA interactions between the wild-type SARS-CoV-2 and the Δ382 mutant in host cells. They also studied host-virus interactions to identify functional elements throughout the viral genome.

Specifically, they used various high-throughput RNA techniques to study secondary structures within the viral genome. In addition, they performed proximity ligation sequencing to identify interactions between host RNA and viral RNA in infected cells.

Structural arrangements of the viral genome

The study results showed that both the wild-type virus and the Δ382 mutant maintain a highly stable and consistent genomic structure with limited alternative folding within the host cells. Twelve functional structural elements have been identified within the viral genome. In addition, a total of 21 single-stranded regions were identified that could potentially be used for COVID-19 treatment with siRNA targeting approaches.

With respect to pair-wise interactions across the viral genome, study identified 237 and 187 intramolecular interactions in the wild-type virus and in the Δ382 mutant, respectively. The majority of these interactions were transient remote interactions (> 1 kb). Upon further analysis, it was observed that ribosome breakpoints have more pair-wise interactions, suggesting that RNA structures play a critical role in regulating translation of the viral genome.

When comparing the genomes of the wild-type virus and the Δ382 mutant, it was observed that these paired interactions are arranged differently in two viruses. In addition, structural differences in genomic RNA and sgRNA were observed between the wild-type virus and the Δ382 mutant.

The long-read sequencing analysis performed in the study found that sgRNAs have different structures from the full-length genomic RNA and that different sgRNAs can acquire different structural arrangements even though they share the same sequences. Among various sgRNAs, the ORF7b sgRNA showed the highest single-stranded status both in the wild-type virus and in the Δ382 mutant.

Host-virus interactions

A total of 374 and 334 host RNAs were identified which interacted with the genomes of the wild-type virus and the Δ382 mutant, respectively. The highest interactions were observed between the viral RNA and host mitochondrial and small nuclear RNAs. In the case of SARS-CoV-2 infection, preferential translation and stabilization of strong interactors were observed.

Among the identified small nuclear RNAs, SNORD27 showed the strongest interaction with viral RNA. This RNA is known to regulate the 2′-O-methylation of 18 S-ribosomal RNA. As observed in the study, the interaction between SNORD27 and viral RNA resulted in extensive 2′-O-methylation of the viral genome that was 19-fold higher than the modifications observed in host mRNAs.

Host RNAs that interacted with the viral RNA showed higher methylation, while no modification was observed in distant sites. This suggests that the virus is sequestering the methylation machinery from the host’s RNA towards its genome. Due to a generalized loss of 2′-O-methylation on the host RNA, a decrease in cellular RNA was observed in the event of a virus infection.

Study significance

The study underscores an important observation that SARS-CoV-2 captures RNA methylation enzymes from host cells to destabilize host RNA and reduce its abundance. These changes in the host cells then facilitate viral replication and improve viral fitness.