Cargando…

Insertion and deletion mutations preserved in SARS-CoV-2 variants

The insertion/deletion (indel) mutation profiles of SARS-CoV-2 variants, including Omicron, remain unclear. We compared whole-genome sequences from various lineages and used preserved indels to infer the ancestral relationships between different lineages. Thirteen indel patterns from twelve sites we...

Descripción completa

Detalles Bibliográficos
Autores principales: Akaishi, Tetsuya, Fujiwara, Kei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10064622/
https://www.ncbi.nlm.nih.gov/pubmed/37000302
http://dx.doi.org/10.1007/s00203-023-03493-0
_version_ 1785017937492443136
author Akaishi, Tetsuya
Fujiwara, Kei
author_facet Akaishi, Tetsuya
Fujiwara, Kei
author_sort Akaishi, Tetsuya
collection PubMed
description The insertion/deletion (indel) mutation profiles of SARS-CoV-2 variants, including Omicron, remain unclear. We compared whole-genome sequences from various lineages and used preserved indels to infer the ancestral relationships between different lineages. Thirteen indel patterns from twelve sites were seen in ≥ 2 sequences; six of these sites were located in the N-terminal domain of the viral spike gene. Preserved indels in the coding regions were also identified in the non-structural protein 3 (Nsp3), Nsp6, and nucleocapsid genes. Seven of the thirteen indel patterns were specific to the Omicron variants, four of which were observed in BA.1, making it the most mutated variant. Other preserved indels observed in the Omicron variants were also seen in Alpha and/or Gamma, but not Delta, suggesting that Omicron is phylogenetically more proximal to Alpha. We demonstrated distinct profiles of preserved indels among SARS-CoV-2 variants and sublineages, suggesting the importance of indels in viral evolution.
format Online
Article
Text
id pubmed-10064622
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Springer Berlin Heidelberg
record_format MEDLINE/PubMed
spelling pubmed-100646222023-03-31 Insertion and deletion mutations preserved in SARS-CoV-2 variants Akaishi, Tetsuya Fujiwara, Kei Arch Microbiol Original Paper The insertion/deletion (indel) mutation profiles of SARS-CoV-2 variants, including Omicron, remain unclear. We compared whole-genome sequences from various lineages and used preserved indels to infer the ancestral relationships between different lineages. Thirteen indel patterns from twelve sites were seen in ≥ 2 sequences; six of these sites were located in the N-terminal domain of the viral spike gene. Preserved indels in the coding regions were also identified in the non-structural protein 3 (Nsp3), Nsp6, and nucleocapsid genes. Seven of the thirteen indel patterns were specific to the Omicron variants, four of which were observed in BA.1, making it the most mutated variant. Other preserved indels observed in the Omicron variants were also seen in Alpha and/or Gamma, but not Delta, suggesting that Omicron is phylogenetically more proximal to Alpha. We demonstrated distinct profiles of preserved indels among SARS-CoV-2 variants and sublineages, suggesting the importance of indels in viral evolution. Springer Berlin Heidelberg 2023-03-31 2023 /pmc/articles/PMC10064622/ /pubmed/37000302 http://dx.doi.org/10.1007/s00203-023-03493-0 Text en © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
spellingShingle Original Paper
Akaishi, Tetsuya
Fujiwara, Kei
Insertion and deletion mutations preserved in SARS-CoV-2 variants
title Insertion and deletion mutations preserved in SARS-CoV-2 variants
title_full Insertion and deletion mutations preserved in SARS-CoV-2 variants
title_fullStr Insertion and deletion mutations preserved in SARS-CoV-2 variants
title_full_unstemmed Insertion and deletion mutations preserved in SARS-CoV-2 variants
title_short Insertion and deletion mutations preserved in SARS-CoV-2 variants
title_sort insertion and deletion mutations preserved in sars-cov-2 variants
topic Original Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10064622/
https://www.ncbi.nlm.nih.gov/pubmed/37000302
http://dx.doi.org/10.1007/s00203-023-03493-0
work_keys_str_mv AT akaishitetsuya insertionanddeletionmutationspreservedinsarscov2variants
AT fujiwarakei insertionanddeletionmutationspreservedinsarscov2variants