#15,970
In early January I suggested that if the word `pandemic' was the word of the year in 2020, `variant' was a slam dunk to take the mantle in 2021. Since then the world has become increasingly obsessed with these new emerging, and slightly revised, incarnations of SARS-CoV-2.
Most variants (and there are now thousands) pose no additional pandemic threat beyond what the `wild type' virus did in 2020, but a handful have demonstrated enhanced transmissibility, some signs of increased severity, and a few may have the potential to evade immunity to antibodies against the old strains, or the vaccines.
Much of their perceived threat is based on anecdotal, or incomplete, information, but public health agencies like the CDC, WHO, PHE, and ECDC continue to track and assess these variants, classifying them as VOIs (Variants of Interest) or VOCs (Variants of Concern).
ECDC: Public Health Impact of SARS-CoV-2 VOCs: Scoping Review Protocol
WHO COVID SitRep: Special Focus On Variant B.1.617.x
UK PHE: `Indian' Variant B.1.617.2 Reclassified As a Variant of Concern (VOC)
CDC U.S. Variant Update: B.1.1.7 Dominates As B.1.617.x Sublineages Begin To Appear
Whether a year from now we'll look back at variants and see them as pandemic game changers, or over-hyped threats, remains to be seen. Of the dozen or so we are watching, most will probably fall by the wayside, but one or two may prove to be genuine contenders.
All of which brings us to the ECDC's announcement today, unveiling a European Interactive Map/Dashboard which currently tracks the 3 major variants in that part of the world; B.1.1.7, B.1.351, and P.1.
ECDC releases new dashboard on SARS-CoV-2 variants
News
19 May 2021
A new dashboard released by ECDC now provides an overview of the proportion of SARS-CoV-2 variants of concern and variants of interest among sequenced samples in European Union (EU) and European Economic Area (EEA) countries, as well as sequencing volumes. It complements the data published in ECDC’s weekly country overview report.
Data are sourced from The European Surveillance System (TESSy) (weekly reports submitted to ECDC by countries) and the Genomic Signature Analysis Platform (GISAID) EpiCoV database (extracted weekly). The maps within the dashboard will be updated every Thursday afternoon, and the data behind the dashboard are available to download.
How to read and interpret the data
Where data for a country are available from more than one source, the default source used is the one with the highest number of sequences in the last two weeks.
Data for the most recent reporting week have been excluded, as they may be incomplete.
Categories used for sequencing volume are based on the sample selection guidance provided in ECDC’s technical guidance for sequencing of SARS-CoV-2 and its guidance for representative and targeted genomic SARS-CoV-2 monitoring:
- ≥500 or ≥10% of cases: 500 or more, or at least 10% of all samples sequenced, by week; if samples are randomly selected, it is possible to follow trends and to estimate the distribution of variants.Higher numbers would increase the accuracy and allow the detection of variants accounting for a smaller proportion of circulating viruses.
- 60-499: Above 60 but below 500 sequenced samples by week. If samples are randomly selected, it is possible to detect a variant accounting for more than 2.5% of all circulating variants and to follow trends, but estimating variants distribution would be inaccurate.
- <60: Under 60 selected samples by week, a specific variant would have to account for at least 5% of all circulating viruses to be detected, if sampling is performed in a random and representative manner. This means that the system will have a poor ability to detect circulating variants of concern before they have an impact on the overall epidemiological situation.
How to use the dashboard:
- Select the week number to filter maps and the variant distribution graph.
- Select the country to filter both graphs.
- The whole dashboard can be filtered to show only data when sequencing volumes were above those recommended by ECDC (>=500 sequences or >=10% of cases sequenced in a specific week) by clicking on "configure sources manually" and using the "source" filter (top-right) to switch sources.
Limitations:
As not all generated sequences are reported, underestimates of the sequencing activities in some countries might occur. Please see the country overview report for additional limitations.
The proportion of variants is only reliable when sequencing capacity is adequate (≥500 or ≥10% of total samples). Even then, estimates must be treated with caution since they may be biased if the sequenced viruses are not representative of all cases in the country. For TESSy data, no proportion of variants has been estimated where there is no reliable denominator available.
Background information
Since the discovery of SARS-CoV-2, three variants of concern, first identified in the United Kingdom (B.1.1.7), South Africa (B.1.351), and Brazil (P.1), have been associated with higher transmissibility and severity of disease, with potential implications for acquired immunity or the effectiveness of current vaccines. In addition, SARS-CoV-2 lineages B.1.617.1, B.1.617.2, and B.1.617.3, first reported in India in December 2020, have been increasingly detected in other countries.
While not currently tracked by the ECDC dashboard, the B.1.617.x lineage are prime candidates to be added in the weeks ahead. Last week the CDC began showing these variants on their bi-weekly report.
