Analysis Reveals Complex Architecture of SARS-CoV-2

By Reuters Staff

April 20, 2020

NEW YORK (Reuters Health) - High-resolution mapping of the SARS-CoV-2 transcriptome reveals a complex architecture, researchers from Korea report.

SARS-CoV-2, a betacoronavirus responsible for the COVID-19 pandemic, is an enveloped virus with a positive-sense, single-stranded RNA genome of about 30 kilobases. Defining the organization of the SARS-CoV-2 genome is critical for the development of diagnostic and therapeutic tools and the understanding of this new virus.

Dr. Hyeshik Chang from Institute for Basic Science and Seoul National University and colleagues used two complementary sequencing approaches to map the subgenomic RNAs (sgRNAs), open reading frames (ORFs), and transcription-regulatory sequences (TRSs) of SARS-CoV-2.

They used sequencing-by-synthesis (SBS), which has high accuracy and coverage but short read length, and direct RNA sequencing (DRS), which lacks sequencing accuracy but enables long-read sequencing that allows for the analysis of long nested coronavirus transcripts.

The transcriptome proved to be complex owing to numerous discontinuous transcription events, according to the online report in Cell.

Besides recognized genomic and subgenomic RNAs, SARS-CoV-2 produced transcripts that encoded unknown ORFs with fusion, deletion, and/or frameshift mutations.

DRS identified at least 41 RNA modification sites on viral transcripts, with AAGAA representing the most frequent motif.

"Like other RNA viruses, coronaviruses undergo frequent recombination, which may allow rapid evolution to change their host/tissue specificity and drug sensitivity," the authors explain. "The frequent fusion detected in this study may provide a basis for variant generation, and need to be investigated in detail."

"The new ORFs may serve as accessory proteins that modulate viral replication and host immune response," they note. "The RNA modifications may also contribute to viral survival and immune evasion in infected tissues as the innate immune system is known to be less sensitive to RNAs with nucleoside modification. It is yet to be examined if the ORFs and RNA modifications are unique to SARS-CoV-2 or conserved in other coronaviruses."

"Our data provide a rich resource and open new directions to investigate the mechanisms underlying the pathogenicity of SARS-CoV-2," the researchers conclude.

Dr. Chang and co-author Dr. V. Narry Kim did not respond to a request for comments.

SOURCE: Cell, online April 9, 2020.