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T he 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). The Rc-o319 genome was 77.8% identical to that of SARS-CoV. Of the 6,590 mutated bases, 5,871 bases (89.1%) were point mutations, and 719 bases (10.9%) from 33 sites were indels. Of the 33 indel sites, 15 sites had deletion-with-insertions, 12 sites had sole deletions, and 6 sites had sole insertions. These mutations were concentrated in the open reading frame 1a (ORF1a) and S1 genes. The base lengths involved in the deletion-with-insertions ranged from 10 to 151 consecutive bases. The base lengths involved in the sole deletions ranged from 1 to 9 consecutive bases, and those involved in the sole insertions ranged from 1 to 29 consecutive bases. There were 14 medium-sized indels (13 with deletion-with-insertions and 1 with a sole insertion) involving 10 to 100 consecutive bases (Table 1). A line graph of the rolling average (650 bases) for the point mutation rate at each base position and the distribution of indels across the Rc-o319 genome is shown in Fig. 1. The actual sequences involved in the deletion-with-insertions are shown in the lower panels. This type of mutation is different from classical mutations, such as sole insertions, sole deletions, inversions, duplications, translocations, or variable number tandem repeats. No parts of the long indels could be identified in the genomes of 2003 SARS-CoV or 2013 Rc-o319, in both the normal and inverse directions. Furthermore, most of the identified long indels differed from those identified between the genomes of 2003 SARS-CoV and 2019 SARS-CoV-2. The results of the present study imply the presence of a novel type of mutation based on deletion-with-insertions that broadly exists among SARS-like coronaviruses. Although relatively long sole insertions or deletions, such as the D382 variant (5), have been reported Editor Tom Gallagher, Loyola University Chicago Copyright © 2022 American Society for Microbiology. All Rights Reserved. Address correspondence to Tetsuya Akaishi, [email protected]. The authors declare no conflict of interest.