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Codon usage analysis of zoonotic coronaviruses reveals lower adaptation to humans by SARS-CoV-2
Since 2002, the world has witnessed major outbreaks of acute respiratory illness by three zoonotic coronaviruses (CoVs), which differ from each other in pathogenicity. Reasons for the lower pathogenicity of SARS-CoV-2 than the other two zoonotic coronaviruses, SARS-CoV and MERS-CoV, are not well und...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier B.V.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7843097/ https://www.ncbi.nlm.nih.gov/pubmed/33516969 http://dx.doi.org/10.1016/j.meegid.2021.104736 |
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author | Huang, Wanyi Guo, Yaqiong Li, Na Feng, Yaoyu Xiao, Lihua |
author_facet | Huang, Wanyi Guo, Yaqiong Li, Na Feng, Yaoyu Xiao, Lihua |
author_sort | Huang, Wanyi |
collection | PubMed |
description | Since 2002, the world has witnessed major outbreaks of acute respiratory illness by three zoonotic coronaviruses (CoVs), which differ from each other in pathogenicity. Reasons for the lower pathogenicity of SARS-CoV-2 than the other two zoonotic coronaviruses, SARS-CoV and MERS-CoV, are not well understood. We herein compared the codon usage patterns of the three zoonotic CoVs causing severe acute respiratory syndromes and four human-specific CoVs (NL63, 229E, OC43, and HKU1) causing mild diseases. We found that the seven viruses have different codon usages, with SARS-CoV-2 having the lowest effective number of codons (ENC) among the zoonotic CoVs. Human codon adaptation index (CAI) analysis revealed that the CAI value of SARS-CoV-2 is the lowest among the zoonotic CoVs. The ENC and CAI values of SARS-CoV-2 were more similar to those of the less-pathogenic human-specific CoVs. To further investigate adaptive evolution within SARS-CoV-2, we examined codon usage patterns in 3573 genomes of SARS-CoV-2 collected over the initial 4 months of the pandemic. We showed that the ENC values and the CAI values of SARS-CoV-2 were decreasing over the period. The low ENC and CAI values could be responsible for the lower pathogenicity of SARS-CoV-2. While mutational pressure appears to shape codon adaptation in the overall genomes of SARS-CoV-2 and other zoonotic CoVs, the E gene of SARS-CoV-2, which has the highest codon usage bias, appears to be under strong natural selection. Data from the study contribute to our understanding of the pathogenicity and evolution of SARS-CoV-2 in humans. |
format | Online Article Text |
id | pubmed-7843097 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Elsevier B.V. |
record_format | MEDLINE/PubMed |
spelling | pubmed-78430972021-01-29 Codon usage analysis of zoonotic coronaviruses reveals lower adaptation to humans by SARS-CoV-2 Huang, Wanyi Guo, Yaqiong Li, Na Feng, Yaoyu Xiao, Lihua Infect Genet Evol Research Paper Since 2002, the world has witnessed major outbreaks of acute respiratory illness by three zoonotic coronaviruses (CoVs), which differ from each other in pathogenicity. Reasons for the lower pathogenicity of SARS-CoV-2 than the other two zoonotic coronaviruses, SARS-CoV and MERS-CoV, are not well understood. We herein compared the codon usage patterns of the three zoonotic CoVs causing severe acute respiratory syndromes and four human-specific CoVs (NL63, 229E, OC43, and HKU1) causing mild diseases. We found that the seven viruses have different codon usages, with SARS-CoV-2 having the lowest effective number of codons (ENC) among the zoonotic CoVs. Human codon adaptation index (CAI) analysis revealed that the CAI value of SARS-CoV-2 is the lowest among the zoonotic CoVs. The ENC and CAI values of SARS-CoV-2 were more similar to those of the less-pathogenic human-specific CoVs. To further investigate adaptive evolution within SARS-CoV-2, we examined codon usage patterns in 3573 genomes of SARS-CoV-2 collected over the initial 4 months of the pandemic. We showed that the ENC values and the CAI values of SARS-CoV-2 were decreasing over the period. The low ENC and CAI values could be responsible for the lower pathogenicity of SARS-CoV-2. While mutational pressure appears to shape codon adaptation in the overall genomes of SARS-CoV-2 and other zoonotic CoVs, the E gene of SARS-CoV-2, which has the highest codon usage bias, appears to be under strong natural selection. Data from the study contribute to our understanding of the pathogenicity and evolution of SARS-CoV-2 in humans. Elsevier B.V. 2021-04 2021-01-28 /pmc/articles/PMC7843097/ /pubmed/33516969 http://dx.doi.org/10.1016/j.meegid.2021.104736 Text en © 2021 Elsevier B.V. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. |
spellingShingle | Research Paper Huang, Wanyi Guo, Yaqiong Li, Na Feng, Yaoyu Xiao, Lihua Codon usage analysis of zoonotic coronaviruses reveals lower adaptation to humans by SARS-CoV-2 |
title | Codon usage analysis of zoonotic coronaviruses reveals lower adaptation to humans by SARS-CoV-2 |
title_full | Codon usage analysis of zoonotic coronaviruses reveals lower adaptation to humans by SARS-CoV-2 |
title_fullStr | Codon usage analysis of zoonotic coronaviruses reveals lower adaptation to humans by SARS-CoV-2 |
title_full_unstemmed | Codon usage analysis of zoonotic coronaviruses reveals lower adaptation to humans by SARS-CoV-2 |
title_short | Codon usage analysis of zoonotic coronaviruses reveals lower adaptation to humans by SARS-CoV-2 |
title_sort | codon usage analysis of zoonotic coronaviruses reveals lower adaptation to humans by sars-cov-2 |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7843097/ https://www.ncbi.nlm.nih.gov/pubmed/33516969 http://dx.doi.org/10.1016/j.meegid.2021.104736 |
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