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Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda
Here, we report SARS-CoV-2 genomic surveillance from March 2020 until January 2021 in Uganda, a landlocked East African country with a population of approximately 40 million people. We report 322 full SARS-CoV-2 genomes from 39,424 reported SARS-CoV-2 infections, thus representing 0.8% of the report...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8318884/ https://www.ncbi.nlm.nih.gov/pubmed/34163035 http://dx.doi.org/10.1038/s41564-021-00933-9 |
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author | Bugembe, Daniel Lule Phan, My V. T. Ssewanyana, Isaac Semanda, Patrick Nansumba, Hellen Dhaala, Beatrice Nabadda, Susan O’Toole, Áine Niamh Rambaut, Andrew Kaleebu, Pontiano Cotten, Matthew |
author_facet | Bugembe, Daniel Lule Phan, My V. T. Ssewanyana, Isaac Semanda, Patrick Nansumba, Hellen Dhaala, Beatrice Nabadda, Susan O’Toole, Áine Niamh Rambaut, Andrew Kaleebu, Pontiano Cotten, Matthew |
author_sort | Bugembe, Daniel Lule |
collection | PubMed |
description | Here, we report SARS-CoV-2 genomic surveillance from March 2020 until January 2021 in Uganda, a landlocked East African country with a population of approximately 40 million people. We report 322 full SARS-CoV-2 genomes from 39,424 reported SARS-CoV-2 infections, thus representing 0.8% of the reported cases. Phylogenetic analyses of these sequences revealed the emergence of lineage A.23.1 from lineage A.23. Lineage A.23.1 represented 88% of the genomes observed in December 2020, then 100% of the genomes observed in January 2021. The A.23.1 lineage was also reported in 26 other countries. Although the precise changes in A.23.1 differ from those reported in the first three SARS-CoV-2 variants of concern (VOCs), the A.23.1 spike-protein-coding region has changes similar to VOCs including a change at position 613, a change in the furin cleavage site that extends the basic amino acid motif and multiple changes in the immunogenic N-terminal domain. In addition, the A.23.1 lineage has changes in non-spike proteins including nsp6, ORF8 and ORF9 that are also altered in other VOCs. The clinical impact of the A.23.1 variant is not yet clear and it has not been designated as a VOC. However, our findings of emergence and spread of this variant indicate that careful monitoring of this variant, together with assessment of the consequences of the spike protein changes for COVID-19 vaccine performance, are advisable. |
format | Online Article Text |
id | pubmed-8318884 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-83188842021-08-13 Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda Bugembe, Daniel Lule Phan, My V. T. Ssewanyana, Isaac Semanda, Patrick Nansumba, Hellen Dhaala, Beatrice Nabadda, Susan O’Toole, Áine Niamh Rambaut, Andrew Kaleebu, Pontiano Cotten, Matthew Nat Microbiol Article Here, we report SARS-CoV-2 genomic surveillance from March 2020 until January 2021 in Uganda, a landlocked East African country with a population of approximately 40 million people. We report 322 full SARS-CoV-2 genomes from 39,424 reported SARS-CoV-2 infections, thus representing 0.8% of the reported cases. Phylogenetic analyses of these sequences revealed the emergence of lineage A.23.1 from lineage A.23. Lineage A.23.1 represented 88% of the genomes observed in December 2020, then 100% of the genomes observed in January 2021. The A.23.1 lineage was also reported in 26 other countries. Although the precise changes in A.23.1 differ from those reported in the first three SARS-CoV-2 variants of concern (VOCs), the A.23.1 spike-protein-coding region has changes similar to VOCs including a change at position 613, a change in the furin cleavage site that extends the basic amino acid motif and multiple changes in the immunogenic N-terminal domain. In addition, the A.23.1 lineage has changes in non-spike proteins including nsp6, ORF8 and ORF9 that are also altered in other VOCs. The clinical impact of the A.23.1 variant is not yet clear and it has not been designated as a VOC. However, our findings of emergence and spread of this variant indicate that careful monitoring of this variant, together with assessment of the consequences of the spike protein changes for COVID-19 vaccine performance, are advisable. Nature Publishing Group UK 2021-06-23 2021 /pmc/articles/PMC8318884/ /pubmed/34163035 http://dx.doi.org/10.1038/s41564-021-00933-9 Text en © The Author(s) 2021 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Bugembe, Daniel Lule Phan, My V. T. Ssewanyana, Isaac Semanda, Patrick Nansumba, Hellen Dhaala, Beatrice Nabadda, Susan O’Toole, Áine Niamh Rambaut, Andrew Kaleebu, Pontiano Cotten, Matthew Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda |
title | Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda |
title_full | Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda |
title_fullStr | Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda |
title_full_unstemmed | Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda |
title_short | Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda |
title_sort | emergence and spread of a sars-cov-2 lineage a variant (a.23.1) with altered spike protein in uganda |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8318884/ https://www.ncbi.nlm.nih.gov/pubmed/34163035 http://dx.doi.org/10.1038/s41564-021-00933-9 |
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