Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas
Background: Recently, differences in mortality rates of COVID-19 in different geographic areas have become an important subject of research because these different mortality rates appear to be associated with mutations that appeared in SARS-CoV-2. The part of the viral body called the spike protein...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-10-01
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| Series: | Biomedical Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2319417021000901 |
| _version_ | 1811299966196383744 |
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| author | Ysrafil Ysrafil Rosdiana Mus Noviyanty Indjar Gama Dwi Rahmaisyah Riskah Nur'amalia |
| author_facet | Ysrafil Ysrafil Rosdiana Mus Noviyanty Indjar Gama Dwi Rahmaisyah Riskah Nur'amalia |
| author_sort | Ysrafil Ysrafil |
| collection | DOAJ |
| description | Background: Recently, differences in mortality rates of COVID-19 in different geographic areas have become an important subject of research because these different mortality rates appear to be associated with mutations that appeared in SARS-CoV-2. The part of the viral body called the spike protein plays a critical role in the viral attachment and entry of the virus into the host cell. Accordingly, we hypothesized that mutations in this area will affect viral infectivity. Methods: A total of 193 sequences of spike SARS-CoV-2 were randomly retrieved from five different geographic areas and collection dates (from December 2019 until July 2020). Multiple sequence alignment for mutation and phylogenetic analyses was conducted using Bioedit, UniProt, and MEGA X. Results: We found 169 total mutations with 37 different mutations across the included samples. The D614G is the first and most frequently established mutation in different regions including Europe, Asia, America, Africa and Australia with the number of mutations of 49, 33, 17, 16 and 4, respectively. Furthermore, we also found mutations in several important domains in this virus including NTD and CTR/RBD of S1 subunit and at S2 subunit area, namely the peptide fusion (FP), and both heptad repetition (HR1 and 2) domains that suggested this could influence virus binding and virus-host cell membrane fusion. Conclusion: In summary, we concluded that mutation had generated diversity of spike SARS-CoV-2 sequences worldwide and is still growing. This analysis may provide important evidence that should be considered in vaccine development in different geographic areas. |
| first_indexed | 2024-04-13T06:44:20Z |
| format | Article |
| id | doaj.art-f28bd3c059ac450caff5f601a5bad903 |
| institution | Directory Open Access Journal |
| issn | 2319-4170 |
| language | English |
| last_indexed | 2024-04-13T06:44:20Z |
| publishDate | 2021-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Biomedical Journal |
| spelling | doaj.art-f28bd3c059ac450caff5f601a5bad9032022-12-22T02:57:39ZengElsevierBiomedical Journal2319-41702021-10-01445570581Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areasYsrafil Ysrafil0Rosdiana Mus1Noviyanty Indjar Gama2Dwi Rahmaisyah3Riskah Nur'amalia4Department of Pharmacy, Health Polytechnic of Gorontalo, Ministry of Health, Gorontalo, Indonesia; Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; Corresponding author. Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Bulaksumur Yogyakarta 55281, Indonesia.Diploma Degree Technology of Medical Laboratory, Faculty of Health Technology, Universitas Megarezky, Makassar, IndonesiaDepartment of Clinical Pharmacy, Faculty of Pharmacy, University of Mulawarman, Samarinda, IndonesiaMaster Program in Biomedical Science, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, IndonesiaDepartment of Physiotherapy, Faculty of Nursing, Universitas Hasanuddin, Makassar, IndonesiaBackground: Recently, differences in mortality rates of COVID-19 in different geographic areas have become an important subject of research because these different mortality rates appear to be associated with mutations that appeared in SARS-CoV-2. The part of the viral body called the spike protein plays a critical role in the viral attachment and entry of the virus into the host cell. Accordingly, we hypothesized that mutations in this area will affect viral infectivity. Methods: A total of 193 sequences of spike SARS-CoV-2 were randomly retrieved from five different geographic areas and collection dates (from December 2019 until July 2020). Multiple sequence alignment for mutation and phylogenetic analyses was conducted using Bioedit, UniProt, and MEGA X. Results: We found 169 total mutations with 37 different mutations across the included samples. The D614G is the first and most frequently established mutation in different regions including Europe, Asia, America, Africa and Australia with the number of mutations of 49, 33, 17, 16 and 4, respectively. Furthermore, we also found mutations in several important domains in this virus including NTD and CTR/RBD of S1 subunit and at S2 subunit area, namely the peptide fusion (FP), and both heptad repetition (HR1 and 2) domains that suggested this could influence virus binding and virus-host cell membrane fusion. Conclusion: In summary, we concluded that mutation had generated diversity of spike SARS-CoV-2 sequences worldwide and is still growing. This analysis may provide important evidence that should be considered in vaccine development in different geographic areas.http://www.sciencedirect.com/science/article/pii/S2319417021000901Spike proteinSARS-CoV-2MutationPandemic |
| spellingShingle | Ysrafil Ysrafil Rosdiana Mus Noviyanty Indjar Gama Dwi Rahmaisyah Riskah Nur'amalia Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas Biomedical Journal Spike protein SARS-CoV-2 Mutation Pandemic |
| title | Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas |
| title_full | Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas |
| title_fullStr | Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas |
| title_full_unstemmed | Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas |
| title_short | Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas |
| title_sort | emerging mutation in sars cov 2 spike widening distribution over time in different geographic areas |
| topic | Spike protein SARS-CoV-2 Mutation Pandemic |
| url | http://www.sciencedirect.com/science/article/pii/S2319417021000901 |
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