Letter to the Editor: Significant mutation enrichment in inverted repeat sites of new SARS-CoV-2 strains.

In a recently published paper, we have found that SARS-CoV-2 hot-spot mutations are significantly associated with inverted repeat loci and CG dinucleotides. However, fast-spreading strains with new mutations (so-called mink farm mutations, England mutations and Japan mutations) have been recently described. We used the new datasets to check the positioning of mutation sites in genomes of the new SARS-CoV-2 strains. Using an open-access Palindrome analyzer tool, we found mutations in these new strains to be significantly enriched in inverted repeat loci.

SARS-CoV-2, a member of Coronaviridae family, has caused recent COVID-19 pandemic. In our previously published research [1], we have found that SARS-CoV-2 hot-spot mutations are significantly associated with inverted repeat loci (IRs) and CG dinucleotides. In the meantime, three novel alarming datasets of SARS-CoV-2 hot-spot mutations have been found: so-called mink farm dataset of recurrent SARS-CoV-2 mutations (16 November 2020) [2]; nonsynonymous mutations and deletions inferred to occur on the branch leading to B.1.1.7 ‘England’ lineage (19 December 2021) [3]; and lineage-defining mutations of the different B.1.1.28 clades detected in Brazil and Japan (11 January 2021) [4]. We have analyzed these new datasets of SARS-CoV-2 mutations by the Palindrome analyzer [5] and found a remarkably high and statistically significant (P-value < 2.2e−16) enrichment of mutations within the IRs in all three new SARS-CoV-2 strains (Figure 1). If we consider only the longer IRs (7+ nucleotides), the observed enrichment is even two-times higher (for all analyzed mutational datasets and overlays of IRs with tested mutations, see Supplementary Data available online at https://academic.oup.com/bib).

Figure 1

Relative percentual enrichment of SARS-CoV-2 mutational datasets within IRs. The assumption is that there is no enrichment of IRs within SARS-CoV-2 hotspots (zero value in the plot). A one-sample t-test was used to statistically compare the number of real SARS-CoV-2 mutations within IRs with random mutations localization (done in 100 replicates). *** indicates P-value < 0.001. Detailed information can be found in [1].

It is therefore evident that inverted repeat loci play an important role in SARS-CoV-2 genetic drift and should be extra monitored by predictive analyses and modelling. Our dataset is also in line with previously published data [6] saying that SARS-CoV-2 mutations are strongly biased toward C > U and U > C transitions (32 out of 67 analyzed mutations; 47.8% of all SARS-CoV-2 mutations in the novel datasets belong to C > U + U > C transitions, while the expected value is slightly above 15% for C > U + U > C in the SARS-CoV-2 genome [6]).

We have analyzed three novel datasets of SARS-CoV-2 hot-spot mutations.

IRs are a rich source of SARS-CoV-2 genetic instability.

These novel results can be further utilized for predictive analyses of further possible SARS-CoV-2 mutations.

Click here for additional data file.