Sequence Exchange Involving Dozens of Consecutive Bases with External Origin in SARS-Related Coronaviruses.

Abstract

The coronavirus disease 2019 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global public health concern in 2022 (1). A recent study demonstrated that more than 30 sites with insertions and/or deletions (indels) existed between the genomes of SARS-CoV in 2003 and SARS-CoV-2 in 2019 (2). The majority of indels involved 10 or more consecutive bases, and 15 of the 17 sites had deletion-with-insertions, resulting in a thorough exchange of 10 to 330 consecutive bases. This type of mutation is not widely understood, and its prevalence among SARS-related coronaviruses other than SARS-CoV-2 is uncertain. Moreover, the exact origin and timing of the development of long indels in SARS-related coronaviruses remain unknown. Therefore, in this study, we compared the genomes of SARS-CoV in 2003 and SARS-related coronavirus, Rc-o319, which was sampled in 2013 from bats (Rhinolophus cornutus) in a cave in northern Japan (3), to determine the presence of this type of mutation in the natural environment. The genome sequences of SARS-CoV and Rc-o319 were obtained from the GenBank database at the National Institutes of Health (https://www.ncbi.nlm.nih.gov/genbank/). The GenBank accession ID for the SARS-CoV genome was AY345986 (4), and the GenBank accession ID for the Rc-o319 genome was LC556375 (3).