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...
| Main Authors: | , , |
|---|---|
| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2022
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/160772 |
| _version_ | 1811681029911478272 |
|---|---|
| author | Tan, Zi Hian Yong, Kian Yan Shu, Jian Jun |
| author2 | School of Mechanical and Aerospace Engineering |
| author_facet | School of Mechanical and Aerospace Engineering Tan, Zi Hian Yong, Kian Yan Shu, Jian Jun |
| author_sort | Tan, Zi Hian |
| collection | NTU |
| 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. |
| first_indexed | 2024-10-01T03:34:27Z |
| format | Journal Article |
| id | ntu-10356/160772 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T03:34:27Z |
| publishDate | 2022 |
| record_format | dspace |
| spelling | ntu-10356/1607722022-08-02T07:41:02Z Evolution of viral pathogens follows a linear order Tan, Zi Hian Yong, Kian Yan Shu, Jian Jun School of Mechanical and Aerospace Engineering Engineering::Mechanical engineering Outbreak Viral Pathogen 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. Ministry of Education (MOE) Published version This work was supported by Singapore Ministry of Education Academic Research Fund Tier 1 (04MNP002133C160). 2022-08-02T07:41:02Z 2022-08-02T07:41:02Z 2022 Journal Article Tan, Z. H., Yong, K. Y. & Shu, J. J. (2022). Evolution of viral pathogens follows a linear order. Microbiology Spectrum, 10(1), e01655-21-. https://dx.doi.org/10.1128/spectrum.01655-21 2165-0497 https://hdl.handle.net/10356/160772 10.1128/spectrum.01655-21 35107326 2-s2.0-85124310422 1 10 e01655-21 en 04MNP002133C160 Microbiology Spectrum © 2022 Tan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. application/pdf |
| spellingShingle | Engineering::Mechanical engineering Outbreak Viral Pathogen 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 | Engineering::Mechanical engineering Outbreak Viral Pathogen |
| url | https://hdl.handle.net/10356/160772 |
| work_keys_str_mv | AT tanzihian evolutionofviralpathogensfollowsalinearorder AT yongkianyan evolutionofviralpathogensfollowsalinearorder AT shujianjun evolutionofviralpathogensfollowsalinearorder |