Cargando…
Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design
As the SARS-CoV-2 pandemic is rapidly progressing, the need for the development of an effective vaccine is critical. A promising approach for vaccine development is to generate, through codon pair deoptimization, an attenuated virus. This approach carries the advantage that it only requires limited...
Autores principales: | , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7519053/ https://www.ncbi.nlm.nih.gov/pubmed/32973171 http://dx.doi.org/10.1038/s41598-020-72533-2 |
_version_ | 1783587500872171520 |
---|---|
author | Kames, Jacob Holcomb, David D. Kimchi, Ofer DiCuccio, Michael Hamasaki-Katagiri, Nobuko Wang, Tony Komar, Anton A. Alexaki, Aikaterini Kimchi-Sarfaty, Chava |
author_facet | Kames, Jacob Holcomb, David D. Kimchi, Ofer DiCuccio, Michael Hamasaki-Katagiri, Nobuko Wang, Tony Komar, Anton A. Alexaki, Aikaterini Kimchi-Sarfaty, Chava |
author_sort | Kames, Jacob |
collection | PubMed |
description | As the SARS-CoV-2 pandemic is rapidly progressing, the need for the development of an effective vaccine is critical. A promising approach for vaccine development is to generate, through codon pair deoptimization, an attenuated virus. This approach carries the advantage that it only requires limited knowledge specific to the virus in question, other than its genome sequence. Therefore, it is well suited for emerging viruses, for which we may not have extensive data. We performed comprehensive in silico analyses of several features of SARS-CoV-2 genomic sequence (e.g., codon usage, codon pair usage, dinucleotide/junction dinucleotide usage, RNA structure around the frameshift region) in comparison with other members of the coronaviridae family of viruses, the overall human genome, and the transcriptome of specific human tissues such as lung, which are primarily targeted by the virus. Our analysis identified the spike (S) and nucleocapsid (N) proteins as promising targets for deoptimization and suggests a roadmap for SARS-CoV-2 vaccine development, which can be generalizable to other viruses. |
format | Online Article Text |
id | pubmed-7519053 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-75190532020-09-29 Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design Kames, Jacob Holcomb, David D. Kimchi, Ofer DiCuccio, Michael Hamasaki-Katagiri, Nobuko Wang, Tony Komar, Anton A. Alexaki, Aikaterini Kimchi-Sarfaty, Chava Sci Rep Article As the SARS-CoV-2 pandemic is rapidly progressing, the need for the development of an effective vaccine is critical. A promising approach for vaccine development is to generate, through codon pair deoptimization, an attenuated virus. This approach carries the advantage that it only requires limited knowledge specific to the virus in question, other than its genome sequence. Therefore, it is well suited for emerging viruses, for which we may not have extensive data. We performed comprehensive in silico analyses of several features of SARS-CoV-2 genomic sequence (e.g., codon usage, codon pair usage, dinucleotide/junction dinucleotide usage, RNA structure around the frameshift region) in comparison with other members of the coronaviridae family of viruses, the overall human genome, and the transcriptome of specific human tissues such as lung, which are primarily targeted by the virus. Our analysis identified the spike (S) and nucleocapsid (N) proteins as promising targets for deoptimization and suggests a roadmap for SARS-CoV-2 vaccine development, which can be generalizable to other viruses. Nature Publishing Group UK 2020-09-24 /pmc/articles/PMC7519053/ /pubmed/32973171 http://dx.doi.org/10.1038/s41598-020-72533-2 Text en © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2020 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Kames, Jacob Holcomb, David D. Kimchi, Ofer DiCuccio, Michael Hamasaki-Katagiri, Nobuko Wang, Tony Komar, Anton A. Alexaki, Aikaterini Kimchi-Sarfaty, Chava Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design |
title | Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design |
title_full | Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design |
title_fullStr | Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design |
title_full_unstemmed | Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design |
title_short | Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design |
title_sort | sequence analysis of sars-cov-2 genome reveals features important for vaccine design |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7519053/ https://www.ncbi.nlm.nih.gov/pubmed/32973171 http://dx.doi.org/10.1038/s41598-020-72533-2 |
work_keys_str_mv | AT kamesjacob sequenceanalysisofsarscov2genomerevealsfeaturesimportantforvaccinedesign AT holcombdavidd sequenceanalysisofsarscov2genomerevealsfeaturesimportantforvaccinedesign AT kimchiofer sequenceanalysisofsarscov2genomerevealsfeaturesimportantforvaccinedesign AT dicucciomichael sequenceanalysisofsarscov2genomerevealsfeaturesimportantforvaccinedesign AT hamasakikatagirinobuko sequenceanalysisofsarscov2genomerevealsfeaturesimportantforvaccinedesign AT wangtony sequenceanalysisofsarscov2genomerevealsfeaturesimportantforvaccinedesign AT komarantona sequenceanalysisofsarscov2genomerevealsfeaturesimportantforvaccinedesign AT alexakiaikaterini sequenceanalysisofsarscov2genomerevealsfeaturesimportantforvaccinedesign AT kimchisarfatychava sequenceanalysisofsarscov2genomerevealsfeaturesimportantforvaccinedesign |