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 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.

COVID-19: why not learn from the past?

“…New variants of SARS-Cov2 keep being described [55][56][57][58] and deposited in old, as well as new, dedicated sequence databases (reviewed in [59]). As a measure of the staggering numbers of sequences, GenBank, which is continuously updated from laboratories around the world, had about 300 SARS-CoV-2 nucleotide sequences by the end of March 2020, and 27 660 by October 8, 2020, an almost 100-fold increase in just 6 months.…”

The First Molecular Characterization of Serbian SARS-CoV-2 Isolates From a Unique Early Second Wave in Europe

“…1 https://www.gisaid.org/ Moreover, it has been suggested that the current SARS-CoV-2 reference genome should be re-evaluated, even replaced with a new one that represents the viral population more accurately (Urhan and Abeel, 2021).…”

Emergence of highly infectious SARS-CoV-2 variants in Bangladesh: the need for systematic genetic surveillance as a public health strategy

“…In this context, Bangladeshi health experts emphasized the need to detect the novel variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that entered the country. As of this writing, the variants found in Bangladesh are the B.1.1.7 (Alpha) variant from the United Kingdom (UK), the B.1.351 (Beta) variant from South Africa, the P.1 (Gamma) variant from Brazil, and the B.1.617 (Delta) variant from India which are all considered as variants of concern (VOC) by the World Health Organization and the Centers for Disease Control and Prevention (CDC) [ 5 ]. During April to May 2021, the Beta variant accounted for 90% of all variants prevailing in Dhaka [ 5 ].…”

“…As of this writing, the variants found in Bangladesh are the B.1.1.7 (Alpha) variant from the United Kingdom (UK), the B.1.351 (Beta) variant from South Africa, the P.1 (Gamma) variant from Brazil, and the B.1.617 (Delta) variant from India which are all considered as variants of concern (VOC) by the World Health Organization and the Centers for Disease Control and Prevention (CDC) [ 5 ]. During April to May 2021, the Beta variant accounted for 90% of all variants prevailing in Dhaka [ 5 ]. However, when the Delta variant arrived in Bangladesh in early May 2021, it had become the most prominent variant constituting 68% of the variants circulating in the Dhaka city by the end of May 2021 [ 5 ].…”

“…During April to May 2021, the Beta variant accounted for 90% of all variants prevailing in Dhaka [ 5 ]. However, when the Delta variant arrived in Bangladesh in early May 2021, it had become the most prominent variant constituting 68% of the variants circulating in the Dhaka city by the end of May 2021 [ 5 ].…”