Emergence of novel SARS-CoV-2 variants in the Netherlands

Abstract Coronavirus disease 2019 (COVID-19) has emerged in December 2019 when the first case was reported in Wuhan, China and turned into a pandemic with 27 million (September 9th) cases. Currently, there are over 95,000 complete genome sequences of the severe acute respiratory syndrome coronavirus...

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Autores principales:	Aysun Urhan, Thomas Abeel
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9c1c0c7c65b2453bac5a35c169170efe
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spelling	oai:doaj.org-article:9c1c0c7c65b2453bac5a35c169170efe2021-12-02T17:04:36ZEmergence of novel SARS-CoV-2 variants in the Netherlands10.1038/s41598-021-85363-72045-2322https://doaj.org/article/9c1c0c7c65b2453bac5a35c169170efe2021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85363-7https://doaj.org/toc/2045-2322Abstract Coronavirus disease 2019 (COVID-19) has emerged in December 2019 when the first case was reported in Wuhan, China and turned into a pandemic with 27 million (September 9th) cases. Currently, there are over 95,000 complete genome sequences of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, in public databases, accompanying a growing number of studies. Nevertheless, there is still much to learn about the viral population variation when the virus is evolving as it continues to spread. We have analyzed SARS-CoV-2 genomes to identify the most variant sites, as well as the stable, conserved ones in samples collected in the Netherlands until June 2020. We identified the most frequent mutations in different geographies. We also performed a phylogenetic study focused on the Netherlands to detect novel variants emerging in the late stages of the pandemic and forming local clusters. We investigated the S and N proteins on SARS-CoV-2 genomes in the Netherlands and found the most variant and stable sites to guide development of diagnostics assays and vaccines. We observed that while the SARS-CoV-2 genome has accumulated mutations, diverging from reference sequence, the variation landscape is dominated by four mutations globally, suggesting the current reference does not represent the virus samples circulating currently. In addition, we detected novel variants of SARS-CoV-2 almost unique to the Netherlands that form localized clusters and region-specific sub-populations indicating community spread. We explored SARS-CoV-2 variants in the Netherlands until June 2020 within a global context; our results provide insight into the viral population diversity for localized efforts in tracking the transmission of COVID-19, as well as sequenced-based approaches in diagnostics and therapeutics. We emphasize that little diversity is observed globally in recent samples despite the increased number of mutations relative to the established reference sequence. We suggest sequence-based analyses should opt for a consensus representation to adequately cover the genomic variation observed to speed up diagnostics and vaccine design.Aysun UrhanThomas AbeelNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Aysun Urhan Thomas Abeel Emergence of novel SARS-CoV-2 variants in the Netherlands
description	Abstract Coronavirus disease 2019 (COVID-19) has emerged in December 2019 when the first case was reported in Wuhan, China and turned into a pandemic with 27 million (September 9th) cases. Currently, there are over 95,000 complete genome sequences of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, in public databases, accompanying a growing number of studies. Nevertheless, there is still much to learn about the viral population variation when the virus is evolving as it continues to spread. We have analyzed SARS-CoV-2 genomes to identify the most variant sites, as well as the stable, conserved ones in samples collected in the Netherlands until June 2020. We identified the most frequent mutations in different geographies. We also performed a phylogenetic study focused on the Netherlands to detect novel variants emerging in the late stages of the pandemic and forming local clusters. We investigated the S and N proteins on SARS-CoV-2 genomes in the Netherlands and found the most variant and stable sites to guide development of diagnostics assays and vaccines. We observed that while the SARS-CoV-2 genome has accumulated mutations, diverging from reference sequence, the variation landscape is dominated by four mutations globally, suggesting the current reference does not represent the virus samples circulating currently. In addition, we detected novel variants of SARS-CoV-2 almost unique to the Netherlands that form localized clusters and region-specific sub-populations indicating community spread. We explored SARS-CoV-2 variants in the Netherlands until June 2020 within a global context; our results provide insight into the viral population diversity for localized efforts in tracking the transmission of COVID-19, as well as sequenced-based approaches in diagnostics and therapeutics. We emphasize that little diversity is observed globally in recent samples despite the increased number of mutations relative to the established reference sequence. We suggest sequence-based analyses should opt for a consensus representation to adequately cover the genomic variation observed to speed up diagnostics and vaccine design.
format	article
author	Aysun Urhan Thomas Abeel
author_facet	Aysun Urhan Thomas Abeel
author_sort	Aysun Urhan
title	Emergence of novel SARS-CoV-2 variants in the Netherlands
title_short	Emergence of novel SARS-CoV-2 variants in the Netherlands
title_full	Emergence of novel SARS-CoV-2 variants in the Netherlands
title_fullStr	Emergence of novel SARS-CoV-2 variants in the Netherlands
title_full_unstemmed	Emergence of novel SARS-CoV-2 variants in the Netherlands
title_sort	emergence of novel sars-cov-2 variants in the netherlands
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/9c1c0c7c65b2453bac5a35c169170efe
work_keys_str_mv	AT aysunurhan emergenceofnovelsarscov2variantsinthenetherlands AT thomasabeel emergenceofnovelsarscov2variantsinthenetherlands
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Emergence of novel SARS-CoV-2 variants in the Netherlands

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