Weekly counts of identified variants for the whole of England.
Usage
data("covid_variants")Format
An object of class grouped_df (inherits from tbl_df, tbl, data.frame) with 479 rows and 5 columns.
Source
https://covid19.sanger.ac.uk/lineages/raw Contains Ordnance Survey data © Crown copyright and database right 2019 Contains UK Health Security Agency data © Crown copyright and database right 2020 Office for National Statistics licensed under the Open Government Licence v.3.0
Details
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
Examples
dplyr::glimpse(covid_variants)
#> Rows: 479
#> Columns: 5
#> Groups: class [10]
#> $ date <date> 2020-09-05, 2020-09-05, 2020-09-12, 2020-09-12, 2020-09-19,…
#> $ class <fct> Other, Alpha (B.1.1.7), Other, Alpha (B.1.1.7), Other, Alpha…
#> $ who_class <fct> Other, Alpha, Other, Alpha, Other, Alpha, Other, Alpha, Othe…
#> $ count <dbl> 1182, 371, 1439, 588, 837, 429, 1685, 1157, 1208, 823, 1501,…
#> $ denom <dbl> 1553, 1553, 2027, 2027, 1266, 1266, 2842, 2842, 2031, 2031, …