COG-UK counts of genomic variants by lower tier local authority

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.

Usage

data("covid_variants_ltla")

Format

An object of class tbl_df (inherits from tbl, data.frame) with 55785 rows and 8 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

Weekly counts of identified variants by Lower tier local authority (2019 names) This dataset has implicit zeros. The full range of areas can be got from the geography data set with: geography %>% dplyr::filter(codeType == "LAD19")

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_ltla` dataframe with 55785 rows and 8 columns

date (date): The date - unclear if this was of the sample or result
code (chr): The ONS geographical region code
codeType (chr): The type of ONS geographical code
name (chr): The ONS geographical region name
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_ltla)
#> Rows: 55,785
#> Columns: 8
#> $ date      <date> 2020-09-05, 2020-09-05, 2020-09-05, 2020-09-05, 2020-09-05,…
#> $ name      <chr> "Arun", "Aylesbury Vale", "Babergh", "Babergh", "Barking and…
#> $ codeType  <chr> "LAD19", "LAD19", "LAD19", "LAD19", "LAD19", "LAD19", "LAD19…
#> $ code      <chr> "E07000224", "E07000004", "E07000200", "E07000200", "E090000…
#> $ class     <fct> Other, Other, Other, Alpha (B.1.1.7), Other, Alpha (B.1.1.7)…
#> $ who_class <fct> Other, Other, Other, Alpha, Other, Alpha, Other, Alpha, Othe…
#> $ count     <dbl> 5, 3, 1, 1, 16, 4, 32, 7, 9, 2, 4, 2, 2, 2, 3, 8, 10, 5, 31,…
#> $ denom     <dbl> 5, 3, 2, 2, 20, 20, 39, 39, 11, 11, 6, 6, 2, 5, 5, 8, 15, 15…