Comparative genomic signature representations of the emerging COVID-19 coronavirus and other coronaviruses: High identity and possible recombination between Bat and Pangolin coronaviruses.
Bat
COVID19
Genome signature
Pangolin
SARS-CoV-2
Yak
Journal
Genomics
ISSN: 1089-8646
Titre abrégé: Genomics
Pays: United States
ID NLM: 8800135
Informations de publication
Date de publication:
11 2020
11 2020
Historique:
received:
22
05
2020
revised:
22
06
2020
accepted:
02
07
2020
pubmed:
10
7
2020
medline:
1
1
2021
entrez:
10
7
2020
Statut:
ppublish
Résumé
Coronaviruses are responsible on respiratory diseases in animal and human. The combination of numerical encoding techniques and digital signal processing methods are becoming increasingly important in handling large genomic data. In this paper, we propose to analyze the SARS-CoV-2 genomic signature using the combination of different nucleotide representations and signal processing tools in the aim to identify its genetic origin. The sequence of SARS-CoV-2 was compared with 21 relevant sequences including Bat, Yak and Pangolin coronavirus sequences. In addition, we developed a new algorithm to locate the nucleotide modifications. The results show that the Bat and Pangolin coronaviruses were the most related to SARS-CoV-2 with 96% and 86% of identity all along the genome. Within the S gene sequence, the Pangolin sequence presents local highest nucleotide identity. Those findings suggest genesis of SARS-Cov-2 through evolution from Bat and Pangolin strains. This study offers new ways to automatically characterize viruses.
Identifiants
pubmed: 32645523
pii: S0888-7543(20)30636-4
doi: 10.1016/j.ygeno.2020.07.003
pmc: PMC7336935
pii:
doi:
Types de publication
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4189-4202Informations de copyright
Copyright © 2020 Elsevier Inc. All rights reserved.
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