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. 2022 Nov 28:12:966870.
doi: 10.3389/fcimb.2022.966870. eCollection 2022.

In silico analysis of SARS-CoV-2 genomes: Insights from SARS encoded non-coding RNAs

Neha Periwal  1 , Urvashi Bhardwaj  1 , Sankritya Sarma  2 , Pooja Arora  2 , Vikas Sood  1
Affiliations

In silico analysis of SARS-CoV-2 genomes: Insights from SARS encoded non-coding RNAs

Neha Periwal et al. Front Cell Infect Microbiol. .

Abstract

The recent pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 has resulted in enormous deaths around the world. Clues from genomic sequences of parent and their mutants can be obtained to understand the evolving pathogenesis of this virus. Apart from the viral proteins, virus-encoded microRNAs (miRNAs) have been shown to play a vital role in regulating viral pathogenesis. Thus we sought to investigate the miRNAs encoded by SARS-CoV-2, its mutants, and the host. Here, we present the results obtained using a dual approach i.e (i) identifying host-encoded miRNAs that might regulate viral pathogenesis and (ii) identifying viral-encoded miRNAs that might regulate host cell signaling pathways and aid in viral pathogenesis. Analysis utilizing the first approach resulted in the identification of ten host-encoded miRNAs that could target the SARS, SARS-CoV-2, and its mutants. Interestingly our analysis revealed that there is a significantly higher number of host miRNAs that could target the SARS-CoV-2 genome as compared to the SARS reference genome. Results from the second approach resulted in the identification of a set of virus-encoded miRNAs which might regulate host signaling pathways. Our analysis further identified a similar "GA" rich motif in the SARS-CoV-2 and its mutant genomes that was shown to play a vital role in lung pathogenesis during severe SARS infections. In summary, we have identified human and virus-encoded miRNAs that might regulate the pathogenesis of SARS coronaviruses and describe similar non-coding RNA sequences in SARS-CoV-2 that were shown to regulate SARS-induced lung pathology in mice.

Keywords: SARS; SARS-CoV-2; coronavirus; miRNAs; non-coding RNAs.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Shows the host-encoded miRNAs that could target SARS, SARS-CoV-2, and its variants. (A) Common miRNAs that could target 45% of genomes from the study. (B) Host miRNAs that could target 80% of the genomes from the study and (C) Top 10 miRNAs targeting all the forward and reverse genomes used in this study.
Figure 2
Figure 2
Showing the viral encoded miRNAs that had similarity with that of miRNAs encoded by the H sapiens. (A) Heatmap showing miRNAs encoded by 45% of the genomes under study. (B) Top 10 miRNAs that could target various genomes used in the study. (C) Common miRNAs among the forward and the reverse genomic sequences of SARS, SARS-CoV-2 and its variants. (D) Top 10 miRNAs targeting forward and the reverse genomes used in the study.
Figure 3
Figure 3
Showing the alignment of genomic regions of SARS-CoV-2 and its mutants with those regions of SARS that were shown to produce non-coding RNAs. (A) (i-xi)) represents the genomic regions where SARS encoded ncRNAs were identified (Morales et al., 2017). (B, C) Represent the sequences of SARS-CoV-2 variants that were used for the comparison.
See this image and copyright information in PMC

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