The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology

Bas B. Oude Munnink; Nathalie Worp; David F. Nieuwenhuijse; Reina S. Sikkema; Bart Haagmans; Ron A.M. Fouchier; Marion Koopmans

doi:10.1038/s41591-021-01472-w

The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology

Bas B. Oude Munnink, Nathalie Worp, David F. Nieuwenhuijse, Reina S. Sikkema, Bart Haagmans, Ron A.M. Fouchier, Marion Koopmans^*

^*Corresponding author for this work

Virology

Research output: Contribution to journal › Review article › Academic › peer-review

164 Citations (Scopus)

Abstract

The current coronavirus disease 2019 (COVID-19) pandemic is the first to apply whole-genome sequencing near to real time, with over 2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequences generated and shared through the GISAID platform. This genomic resource informed public health decision-making throughout the pandemic; it also allowed detection of mutations that might affect virulence, pathogenesis, host range or immune escape as well as the effectiveness of SARS-CoV-2 diagnostics and therapeutics. However, genotype-to-phenotype predictions cannot be performed at the rapid pace of genomic sequencing. To prepare for the next phase of the pandemic, a systematic approach is needed to link global genomic surveillance and timely assessment of the phenotypic characteristics of novel variants, which will support the development and updating of diagnostics, vaccines, therapeutics and nonpharmaceutical interventions. This Review summarizes the current knowledge on key viral mutations and variants and looks to the next phase of surveillance of the evolving pandemic.

Original language	English
Pages (from-to)	1518-1524
Number of pages	7
Journal	Nature Medicine
Volume	27
Issue number	9
DOIs	https://doi.org/10.1038/s41591-021-01472-w
Publication status	Published - 9 Sept 2021

Bibliographical note

Funding Information:
This work has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement no. 874735 (VEO) and from ZonMW (grant agreement no. 10150062010005).

Publisher Copyright:
© 2021, Springer Nature America, Inc.

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Cite this

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abstract = "The current coronavirus disease 2019 (COVID-19) pandemic is the first to apply whole-genome sequencing near to real time, with over 2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequences generated and shared through the GISAID platform. This genomic resource informed public health decision-making throughout the pandemic; it also allowed detection of mutations that might affect virulence, pathogenesis, host range or immune escape as well as the effectiveness of SARS-CoV-2 diagnostics and therapeutics. However, genotype-to-phenotype predictions cannot be performed at the rapid pace of genomic sequencing. To prepare for the next phase of the pandemic, a systematic approach is needed to link global genomic surveillance and timely assessment of the phenotypic characteristics of novel variants, which will support the development and updating of diagnostics, vaccines, therapeutics and nonpharmaceutical interventions. This Review summarizes the current knowledge on key viral mutations and variants and looks to the next phase of surveillance of the evolving pandemic.",

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AU - Fouchier, Ron A.M.

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The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology

Abstract

Bibliographical note

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