Genome-Wide Analysis to Identify Palindromes, Mirror and Inverted Repeats in SARS-CoV-2, MERS-CoV and SARS-CoV-1

Nimisha Ghosh,Dariusz Plewczynski,Indrajit Saha

doi:10.1109/access.2022.3154053

Abstract

Research pertaining to SARS-CoV-2 is in full swing to understand the origin and evolution of this deadly virus that can lead to its rapid detection. To achieve this, atypical genomic sequences which may be unique to SARS-CoV-2 or Coronaviridae family in general may be investigated. Such sequences in virus genomes may be responsible for target prediction, replication, defence mechanisms and viral packaging. This fact has motivated us to explore the different types of repeats such as palindromes, mirror repeats and inverted repeats in SARS-CoV-2, MERS-CoV and SARS-CoV-1. For this purpose, the respective reference sequence of SARS-CoV-2, MERS-CoV and SARS-CoV-1 is divided into descriptors of sequences of length <inline-formula> <tex-math notation="LaTeX">${k}$ </tex-math></inline-formula> using <inline-formula> <tex-math notation="LaTeX">${k}$ </tex-math></inline-formula>-mer technique. Thereafter, these descriptors are represented as a collection of tokens which are subsequently used for the identification of palindrome, mirror repeat and inverted repeat in the respective reference sequence. The highest number of palindromes, mirror repeats and inverted repeats are identified for descriptor length 10. As a result, for palindromes such values are 38, 42 and 33 and for mirror repeats they are 52, 38 and 33 for SARS-CoV-2, MERS-CoV and SARS-CoV-1 respectively. For inverted repeats, with a descriptor length 10 and intervening length 5, the values are 59, 56 and 70 respectively. Moreover, the identified repeats are then searched for in 108246, 291 and 340 SARS-CoV-2, MERS-CoV and SARS-CoV-1 virus sequences respectively to find the population coverage of such repeats. It surpasses 99% in most cases and even 100% for some. Furthermore, GC contents which mostly lie between 20%-50% are evaluated for these repeats as well in order to understand their binding efficacy.

Highlights

The outbreak of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the virus causing COVID-19, has caused more than five million deaths in different parts of the world leading to researches around the globe to control this virus
The aforementioned studies have motivated us to explore the different types of repeats such as palindromes, mirror repeats and inverted repeats in SARS-CoV-2, MERS-CoV and SARS-CoV-1
For MERS-CoV, for a mirror repeat length of 14, one of the the sequences is CAGATGTTGTAGAC at the genomic location 12574 and it belongs to the coding gene NSP8 while for SARS-CoV-1, for a length of 16, the mirror repeat is CTACTGACCAGTCATC at the genomic location 7643 and belongs to the coding gene NSP3

Summary

Introduction

The outbreak of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the virus causing COVID-19, has caused more than five million deaths in different parts of the world leading to researches around the globe to control this virus. Author et al.: Preparation of Papers for IEEE TRANSACTIONS and JOURNALS deadly virus This may lead to the immune-related studies of viruses [4]. Atypical genomic sequences which may be unique to SARS-CoV-2 or Coronaviridae family in general may be investigated [5]–[8]. Studies [9]– [11] have suggested that such sequences in virus genomes may be responsible for target prediction, replication, defence mechanisms and viral packaging. In this regard, Goswami et al [6] have identified inverted repeats in hotspot mutations using Palindrome analyzer webserver. Inverted repeats have many important biological functionalities that play significant role in genome instability and may lead to mutation and disease

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