High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein
Abstract The highly contagious Delta variant of SARS‐CoV‐2 has become a prevalent strain globally and poses a public health challenge around the world. While there has been extensive focus on understanding the amino acid mutations in the Delta variant’s Spike protein, the mutational landscape of the...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2022-02-01
|
| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.15252/msb.202110673 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850201781884157952 |
|---|---|
| author | Rohit Suratekar Pritha Ghosh Michiel J M Niesen Gregory Donadio Praveen Anand Venky Soundararajan A J Venkatakrishnan |
| author_facet | Rohit Suratekar Pritha Ghosh Michiel J M Niesen Gregory Donadio Praveen Anand Venky Soundararajan A J Venkatakrishnan |
| author_sort | Rohit Suratekar |
| collection | DOAJ |
| description | Abstract The highly contagious Delta variant of SARS‐CoV‐2 has become a prevalent strain globally and poses a public health challenge around the world. While there has been extensive focus on understanding the amino acid mutations in the Delta variant’s Spike protein, the mutational landscape of the rest of the SARS‐CoV‐2 proteome (25 proteins) remains poorly understood. To this end, we performed a systematic analysis of mutations in all the SARS‐CoV‐2 proteins from nearly 2 million SARS‐CoV‐2 genomes from 176 countries/territories. Six highly prevalent missense mutations in the viral life cycle‐associated Membrane (I82T), Nucleocapsid (R203M, D377Y), NS3 (S26L), and NS7a (V82A, T120I) proteins are almost exclusive to the Delta variant compared to other variants of concern (mean prevalence across genomes: Delta = 99.74%, Alpha = 0.06%, Beta = 0.09%, and Gamma = 0.22%). Furthermore, we find that the Delta variant harbors a more diverse repertoire of mutations across countries compared to the previously dominant Alpha variant. Overall, our study underscores the high diversity of the Delta variant between countries and identifies a list of amino acid mutations in the Delta variant’s proteome for probing the mechanistic basis of pathogenic features such as high viral loads, high transmissibility, and reduced susceptibility against neutralization by vaccines. |
| format | Article |
| id | doaj-art-2cc1e88e04c54521bcb418b729fd04e2 |
| institution | OA Journals |
| issn | 1744-4292 |
| language | English |
| publishDate | 2022-02-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-2cc1e88e04c54521bcb418b729fd04e22025-08-20T02:11:55ZengSpringer NatureMolecular Systems Biology1744-42922022-02-0118211010.15252/msb.202110673High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike proteinRohit Suratekar0Pritha Ghosh1Michiel J M Niesen2Gregory Donadio3Praveen Anand4Venky Soundararajan5A J Venkatakrishnan6nference Labsnference Labsnferencenferencenference Labsnference LabsnferenceAbstract The highly contagious Delta variant of SARS‐CoV‐2 has become a prevalent strain globally and poses a public health challenge around the world. While there has been extensive focus on understanding the amino acid mutations in the Delta variant’s Spike protein, the mutational landscape of the rest of the SARS‐CoV‐2 proteome (25 proteins) remains poorly understood. To this end, we performed a systematic analysis of mutations in all the SARS‐CoV‐2 proteins from nearly 2 million SARS‐CoV‐2 genomes from 176 countries/territories. Six highly prevalent missense mutations in the viral life cycle‐associated Membrane (I82T), Nucleocapsid (R203M, D377Y), NS3 (S26L), and NS7a (V82A, T120I) proteins are almost exclusive to the Delta variant compared to other variants of concern (mean prevalence across genomes: Delta = 99.74%, Alpha = 0.06%, Beta = 0.09%, and Gamma = 0.22%). Furthermore, we find that the Delta variant harbors a more diverse repertoire of mutations across countries compared to the previously dominant Alpha variant. Overall, our study underscores the high diversity of the Delta variant between countries and identifies a list of amino acid mutations in the Delta variant’s proteome for probing the mechanistic basis of pathogenic features such as high viral loads, high transmissibility, and reduced susceptibility against neutralization by vaccines.https://doi.org/10.15252/msb.202110673coronavirusDelta variantmutationsproteomeSARS‐CoV‐2 |
| spellingShingle | Rohit Suratekar Pritha Ghosh Michiel J M Niesen Gregory Donadio Praveen Anand Venky Soundararajan A J Venkatakrishnan High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein Molecular Systems Biology coronavirus Delta variant mutations proteome SARS‐CoV‐2 |
| title | High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein |
| title_full | High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein |
| title_fullStr | High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein |
| title_full_unstemmed | High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein |
| title_short | High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein |
| title_sort | high diversity in delta variant across countries revealed by genome wide analysis of sars cov 2 beyond the spike protein |
| topic | coronavirus Delta variant mutations proteome SARS‐CoV‐2 |
| url | https://doi.org/10.15252/msb.202110673 |
| work_keys_str_mv | AT rohitsuratekar highdiversityindeltavariantacrosscountriesrevealedbygenomewideanalysisofsarscov2beyondthespikeprotein AT prithaghosh highdiversityindeltavariantacrosscountriesrevealedbygenomewideanalysisofsarscov2beyondthespikeprotein AT michieljmniesen highdiversityindeltavariantacrosscountriesrevealedbygenomewideanalysisofsarscov2beyondthespikeprotein AT gregorydonadio highdiversityindeltavariantacrosscountriesrevealedbygenomewideanalysisofsarscov2beyondthespikeprotein AT praveenanand highdiversityindeltavariantacrosscountriesrevealedbygenomewideanalysisofsarscov2beyondthespikeprotein AT venkysoundararajan highdiversityindeltavariantacrosscountriesrevealedbygenomewideanalysisofsarscov2beyondthespikeprotein AT ajvenkatakrishnan highdiversityindeltavariantacrosscountriesrevealedbygenomewideanalysisofsarscov2beyondthespikeprotein |