Weekly counts of identified variants for the whole of England.
data("covid_variants")An object of class grouped_df (inherits from tbl_df, tbl, data.frame) with 479 rows and 5 columns.
Counts of COVID-19 variants from the COGUK COVID-19 sequencing project. Positive samples were selected based on viral load on initial PCR testing and sent onward for testing. Prioritisation and over-sampling of cases with S-gene target failure happened so this data is not unbiased.
From late March 2023 onward, due to the low number of sequenced samples, the UK SARS-CoV-2 sequencing surveillance data is not updated on the Wellcome Sanger Institute COVID-19 Genomic surveillance dashboard. Due to changes since the end of mass COVID-19 testing in the UK since April 2022 - the Wellcome Sanger Institute COVID-19 Genomic surveillance dashboard only includes a subset of UK SARS-CoV-2 sequencing surveillance data and should not be used to estimate frequency of SARS-CoV-2 variants circulating. Not all samples sequenced and deposited in public databases are presented here. This data is not de-duplicated on a patient level - and may include targeted sequencing that may introduce biases.
covid_variants dataframe with 479 rows and 5 columns
date (date) The date - unclear if this was of the sample or result
class (fct) The variant description as a name and pango lineage
who_class (fct) The WHO short name
count (dbl) The number of sequences of this variant identified on this date
denom (dbl) The total number of sequences of all variants identified on this date
dplyr::glimpse(covid_variants)
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