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Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing
Using next generation sequencing technology, we identified a novel SARS-CoV-2 variant with a truncated ORF8 protein mutation near the end of the viral genome from nucleotides 27,878 to 27,958. This point mutation from C to T at nucleotide 27,956 changed the amino acid codon CAA (glutamine) to a stop...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8929288/ https://www.ncbi.nlm.nih.gov/pubmed/35301412 http://dx.doi.org/10.1038/s41598-022-08780-2 |
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author | DeRonde, Stephanie Deuling, Hannah Parker, Jayme Chen, Jack |
author_facet | DeRonde, Stephanie Deuling, Hannah Parker, Jayme Chen, Jack |
author_sort | DeRonde, Stephanie |
collection | PubMed |
description | Using next generation sequencing technology, we identified a novel SARS-CoV-2 variant with a truncated ORF8 protein mutation near the end of the viral genome from nucleotides 27,878 to 27,958. This point mutation from C to T at nucleotide 27,956 changed the amino acid codon CAA (glutamine) to a stop codon, TAA, created a novel stop codon in ORF8 gene, resulting in a much smaller ORF8 protein (26 aa) than the wild type ORF8 protein (121 aa). This variant belongs to Pango lineage B.1.1291, which also contains the D614G mutation in the Spike (S) gene. The B.1.1291 lineage is predominantly circulated in the United States of America (97.18%), although it was also found in other counties (Russia, Canada, Latvia, Chile, India, Japan, Colombia, Germany, Greece, Mexico, and UK). A total of 340 closely related variants to this novel variant were identified in GISAID database with collection dates ranged from 3/6/2020 to 10/21/2020. In addition, a search within NCBI Genbank database found that 108,405 of 873,230 (12.4%) SAR-CoV-2 complete genomes contain this truncated ORF8 protein mutation, indicating this mutation may arise spontaneously in other lineages as well. The wide distribution of this mutation indicates that this truncated ORF8 protein mutation may provide the virus a growth advantage and adaptive evolution. |
format | Online Article Text |
id | pubmed-8929288 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-89292882022-03-17 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing DeRonde, Stephanie Deuling, Hannah Parker, Jayme Chen, Jack Sci Rep Article Using next generation sequencing technology, we identified a novel SARS-CoV-2 variant with a truncated ORF8 protein mutation near the end of the viral genome from nucleotides 27,878 to 27,958. This point mutation from C to T at nucleotide 27,956 changed the amino acid codon CAA (glutamine) to a stop codon, TAA, created a novel stop codon in ORF8 gene, resulting in a much smaller ORF8 protein (26 aa) than the wild type ORF8 protein (121 aa). This variant belongs to Pango lineage B.1.1291, which also contains the D614G mutation in the Spike (S) gene. The B.1.1291 lineage is predominantly circulated in the United States of America (97.18%), although it was also found in other counties (Russia, Canada, Latvia, Chile, India, Japan, Colombia, Germany, Greece, Mexico, and UK). A total of 340 closely related variants to this novel variant were identified in GISAID database with collection dates ranged from 3/6/2020 to 10/21/2020. In addition, a search within NCBI Genbank database found that 108,405 of 873,230 (12.4%) SAR-CoV-2 complete genomes contain this truncated ORF8 protein mutation, indicating this mutation may arise spontaneously in other lineages as well. The wide distribution of this mutation indicates that this truncated ORF8 protein mutation may provide the virus a growth advantage and adaptive evolution. Nature Publishing Group UK 2022-03-17 /pmc/articles/PMC8929288/ /pubmed/35301412 http://dx.doi.org/10.1038/s41598-022-08780-2 Text en © The Author(s) 2022 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 DeRonde, Stephanie Deuling, Hannah Parker, Jayme Chen, Jack Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing |
title | Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing |
title_full | Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing |
title_fullStr | Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing |
title_full_unstemmed | Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing |
title_short | Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing |
title_sort | identification of a novel sars-cov-2 variant with a truncated protein in orf8 gene by next generation sequencing |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8929288/ https://www.ncbi.nlm.nih.gov/pubmed/35301412 http://dx.doi.org/10.1038/s41598-022-08780-2 |
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