WHO's Methods for the detectionof SARS-CoV-2 variants – first update21 Dec 2021 11:08
20 December 2021
Looks like we have all their concerns covered.
https://www.ecdc.europa.eu/sites/default/files/documents/Methods-for-the-detection-and-characterisation-of-SARS-CoV-2-variants-first-update.pdf
Whole genome sequencing
WGS is essential to identify, monitor and assess virus variants that may be more transmissible and associated with
increased disease severity, or may have adverse effects on public health and social control measures. Using either a
tiled amplicon approach or shotgun sequencing, the entire genome of the virus will be sequenced and can be
compared with other circulating strains [2]. WGS can be used to efficiently detect VOCs as it represents an unbiased
approach, without the need for prior knowledge on the presence of certain mutations in the viral genome.
Wastewater SARS-CoV-2 surveillance can be performed using WGS. While it can be a useful tool for SARS-CoV-2
prevalence estimation, extracting information at the variant level is complicated and requires specialised
bioinformatics pipelines. Results should be interpreted with care, especially for variants detected at low
proportions (below 5%).
WGS is a relatively resource-intensive method that can take from hours to several days to generate results,
depending on the protocol. Data storage issues and bioinformatics support also need to be considered. Guidance
on the implementation of WGS can be found in ECDC’s technical guidance on sequencing of SARS-CoV-2, and
WHO’s documents ‘Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on
public health’ and ‘SARS-CoV-2 genomic sequencing for public health goals: Interim guidance’ [2-4]. Further
guidance on sampling and sequencing strategy to ensure representativeness and reliability of findings can be
also found in ECDC’s ‘Guidance for representative and targeted genomic SARS-CoV-2 monitoring’ [5].
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