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Evolution of Viral Pathogens Follows a Linear Order

Although lessons have been learned from previous severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) outbreaks, the rapid evolution of the viruses means that future outbreaks of a much larger scale are possible, as shown by the current coronavirus disease 2019 (COVID...

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Autores principales: Tan, Zi Hian, Yong, Kian Yan, Shu, Jian-Jun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8809352/
https://www.ncbi.nlm.nih.gov/pubmed/35107326
http://dx.doi.org/10.1128/spectrum.01655-21
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author Tan, Zi Hian
Yong, Kian Yan
Shu, Jian-Jun
author_facet Tan, Zi Hian
Yong, Kian Yan
Shu, Jian-Jun
author_sort Tan, Zi Hian
collection PubMed
description Although lessons have been learned from previous severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) outbreaks, the rapid evolution of the viruses means that future outbreaks of a much larger scale are possible, as shown by the current coronavirus disease 2019 (COVID-19) outbreak. Therefore, it is necessary to better understand the evolution of coronaviruses as well as viruses in general. This study reports a comparative analysis of the amino acid usage within several key viral families and genera that are prone to triggering outbreaks, including coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2], SARS-CoV, MERS-CoV, human coronavirus-HKU1 [HCoV-HKU1], HCoV-OC43, HCoV-NL63, and HCoV-229E), influenza A (H1N1 and H3N2), flavivirus (dengue virus serotypes 1 to 4 and Zika) and ebolavirus (Zaire, Sudan, and Bundibugyo ebolavirus). Our analysis reveals that the distribution of amino acid usage in the viral genome is constrained to follow a linear order, and the distribution remains closely related to the viral species within the family or genus. This constraint can be adapted to predict viral mutations and future variants of concern. By studying previous SARS and MERS outbreaks, we have adapted this naturally occurring pattern to determine that although pangolin plays a role in the outbreak of COVID-19, it may not be the sole agent as an intermediate animal. In addition to this study, our findings contribute to the understanding of viral mutations for subsequent development of vaccines and toward developing a model to determine the source of the outbreak. IMPORTANCE This study reports a comparative analysis of amino acid usage within several key viral genera that are prone to triggering outbreaks. Interestingly, there is evidence that the amino acid usage within the viral genomes is not random but in a linear order.
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spelling pubmed-88093522022-02-09 Evolution of Viral Pathogens Follows a Linear Order Tan, Zi Hian Yong, Kian Yan Shu, Jian-Jun Microbiol Spectr Research Article Although lessons have been learned from previous severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) outbreaks, the rapid evolution of the viruses means that future outbreaks of a much larger scale are possible, as shown by the current coronavirus disease 2019 (COVID-19) outbreak. Therefore, it is necessary to better understand the evolution of coronaviruses as well as viruses in general. This study reports a comparative analysis of the amino acid usage within several key viral families and genera that are prone to triggering outbreaks, including coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2], SARS-CoV, MERS-CoV, human coronavirus-HKU1 [HCoV-HKU1], HCoV-OC43, HCoV-NL63, and HCoV-229E), influenza A (H1N1 and H3N2), flavivirus (dengue virus serotypes 1 to 4 and Zika) and ebolavirus (Zaire, Sudan, and Bundibugyo ebolavirus). Our analysis reveals that the distribution of amino acid usage in the viral genome is constrained to follow a linear order, and the distribution remains closely related to the viral species within the family or genus. This constraint can be adapted to predict viral mutations and future variants of concern. By studying previous SARS and MERS outbreaks, we have adapted this naturally occurring pattern to determine that although pangolin plays a role in the outbreak of COVID-19, it may not be the sole agent as an intermediate animal. In addition to this study, our findings contribute to the understanding of viral mutations for subsequent development of vaccines and toward developing a model to determine the source of the outbreak. IMPORTANCE This study reports a comparative analysis of amino acid usage within several key viral genera that are prone to triggering outbreaks. Interestingly, there is evidence that the amino acid usage within the viral genomes is not random but in a linear order. American Society for Microbiology 2022-02-02 /pmc/articles/PMC8809352/ /pubmed/35107326 http://dx.doi.org/10.1128/spectrum.01655-21 Text en Copyright © 2022 Tan et al. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Research Article
Tan, Zi Hian
Yong, Kian Yan
Shu, Jian-Jun
Evolution of Viral Pathogens Follows a Linear Order
title Evolution of Viral Pathogens Follows a Linear Order
title_full Evolution of Viral Pathogens Follows a Linear Order
title_fullStr Evolution of Viral Pathogens Follows a Linear Order
title_full_unstemmed Evolution of Viral Pathogens Follows a Linear Order
title_short Evolution of Viral Pathogens Follows a Linear Order
title_sort evolution of viral pathogens follows a linear order
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8809352/
https://www.ncbi.nlm.nih.gov/pubmed/35107326
http://dx.doi.org/10.1128/spectrum.01655-21
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