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Relative synonymous codon usage of ORF1ab in SARS-CoV-2 and SARS-CoV
BACKGROUND: COVID-19, as a novel coronavirus disease caused by new coronavirus SARS-CoV-2, spreads all over the world, and brings harm to human in many countries. Humans suffered a lot from both SARS-CoV-2 now and by SARS-CoV in the year 2003. It is important to understand the differences and the re...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Singapore
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8258482/ https://www.ncbi.nlm.nih.gov/pubmed/34228320 http://dx.doi.org/10.1007/s13258-021-01136-6 |
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author | Li, Gun Zhang, Liang Du, Ning |
author_facet | Li, Gun Zhang, Liang Du, Ning |
author_sort | Li, Gun |
collection | PubMed |
description | BACKGROUND: COVID-19, as a novel coronavirus disease caused by new coronavirus SARS-CoV-2, spreads all over the world, and brings harm to human in many countries. Humans suffered a lot from both SARS-CoV-2 now and by SARS-CoV in the year 2003. It is important to understand the differences and the relationships between these two types of viruses. OBJECTIVE: To compare relative synonymous codon usage of ORF1ab gene in SARS-CoV-2 and SARS-CoV, relative synonymous codon usage of their genomes are studied in this paper from the bioinformatics perspective. METHODS: The ORF1ab gene, which is an important non-structural polyprotein coding gene and now used for nucleic acid detection markers in many measurement method, in both SARS-CoV-2 (30 strains) and SARS-CoV (20 strains) are considered to be the research object in the present paper. The relative synonymous codon usage values of the ORF1ab gene are calculated to characterize the differences and the evolutionary characteristics among 50 strains. RESULTS: There is a significant difference between SARS-CoV and SARS-CoV-2 when the relative synonymous codon usage value of ORF1ab genes is concerned. The results suggest that codon usage pattern of SARS-CoV is more similar to human than that of the SARS-CoV-2, and that the inner difference in SARS-CoV-2 strains is larger than that of SARS-CoV, which denote the larger diversity exits in the SARS-CoV-2 virus. CONCLUSION: These results show that the relative synonymous codon usage values in the coronavirus could be used for further research on their evolutionary phenomenon. |
format | Online Article Text |
id | pubmed-8258482 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Springer Singapore |
record_format | MEDLINE/PubMed |
spelling | pubmed-82584822021-07-06 Relative synonymous codon usage of ORF1ab in SARS-CoV-2 and SARS-CoV Li, Gun Zhang, Liang Du, Ning Genes Genomics Research Article BACKGROUND: COVID-19, as a novel coronavirus disease caused by new coronavirus SARS-CoV-2, spreads all over the world, and brings harm to human in many countries. Humans suffered a lot from both SARS-CoV-2 now and by SARS-CoV in the year 2003. It is important to understand the differences and the relationships between these two types of viruses. OBJECTIVE: To compare relative synonymous codon usage of ORF1ab gene in SARS-CoV-2 and SARS-CoV, relative synonymous codon usage of their genomes are studied in this paper from the bioinformatics perspective. METHODS: The ORF1ab gene, which is an important non-structural polyprotein coding gene and now used for nucleic acid detection markers in many measurement method, in both SARS-CoV-2 (30 strains) and SARS-CoV (20 strains) are considered to be the research object in the present paper. The relative synonymous codon usage values of the ORF1ab gene are calculated to characterize the differences and the evolutionary characteristics among 50 strains. RESULTS: There is a significant difference between SARS-CoV and SARS-CoV-2 when the relative synonymous codon usage value of ORF1ab genes is concerned. The results suggest that codon usage pattern of SARS-CoV is more similar to human than that of the SARS-CoV-2, and that the inner difference in SARS-CoV-2 strains is larger than that of SARS-CoV, which denote the larger diversity exits in the SARS-CoV-2 virus. CONCLUSION: These results show that the relative synonymous codon usage values in the coronavirus could be used for further research on their evolutionary phenomenon. Springer Singapore 2021-07-06 2021 /pmc/articles/PMC8258482/ /pubmed/34228320 http://dx.doi.org/10.1007/s13258-021-01136-6 Text en © The Genetics Society of Korea 2021 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic. |
spellingShingle | Research Article Li, Gun Zhang, Liang Du, Ning Relative synonymous codon usage of ORF1ab in SARS-CoV-2 and SARS-CoV |
title | Relative synonymous codon usage of ORF1ab in SARS-CoV-2 and SARS-CoV |
title_full | Relative synonymous codon usage of ORF1ab in SARS-CoV-2 and SARS-CoV |
title_fullStr | Relative synonymous codon usage of ORF1ab in SARS-CoV-2 and SARS-CoV |
title_full_unstemmed | Relative synonymous codon usage of ORF1ab in SARS-CoV-2 and SARS-CoV |
title_short | Relative synonymous codon usage of ORF1ab in SARS-CoV-2 and SARS-CoV |
title_sort | relative synonymous codon usage of orf1ab in sars-cov-2 and sars-cov |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8258482/ https://www.ncbi.nlm.nih.gov/pubmed/34228320 http://dx.doi.org/10.1007/s13258-021-01136-6 |
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