Summary report: COG­UK geographic coverage of SARS­CoV­2 sample sequencing

Report on the week commencing on 9 November 2020 (week 46)This report was generated on 16 December 2020 using data downloaded on 12 December 2020

COG­UK captures SARS­CoV­2 samples from COVID­19 infections across the UK, and this summary includes information on sequencing coverage acrossthe UK. Coverage is defined as the number of sequences available in COG­UK out of the number of people with a COVID­19 infection.

In the week commencing on 9 November 2020 (week 46), 137,540 sequences out of 1,413,723 infected people (9.7%) passed basic quality checks andwere available in Medical Research Council Cloud Infrastructure for Microbial Bioinformatics (MRC CLIMB­COVID, the central computational infrastructurefor COG­UK).

This is an operational report – please interpret the results with caution due to the following limitations:

• Geographic information is currently lacking for ~8% of sequences which may result in apparent low coverage in some areas

• For a minority of numerator sequences, there may be more than one sequence per individual (i.e. no deduplication); this can lead to mismatchesbecause the denominator includes the total number of infected people, not the number of samples

• Coverage proportion by Pillar is currently not available for all countries but will be included in the report as soon as available. Frequency of sequencesby Pillar is shown in the table below

Table 1: Coverage, overall and by Pillar in the week commencing on 9 November 2020 (week 46)

Overall coverage Pillar 1 frequency Pillar 2 frequency

Cumulative Week Cumulative Week Cumulative Week

UK 137,540 (9.7%) 9,981 (5.9%) 63,708 2,466 73,832 7,515

Wales 15,299 (22.4%) 801 (14.0%) 13,473 799 1,826 2

Scotland 13,291 (16.0%) 201 (2.6%) 8,067 118 5,224 83

England 106,618 (8.8%) 8,978 (5.9%) 40,501 1,549 66,117 7,429

Northern Ireland 2,332 (5.0%) 1 (0.0%) 1,667 0 665 1

Cumulative coverage is the total number of sequences out of all COVID­19 infections. Week coverage is the number

of sequences collected in the week of interest out of all infections reported in the same week. Pillar 1 includes

NHS diagnostic labs. Pillar 2 includes lighthouse labs network and other large­scale diagnostic testing capacity.

Figure 1: Map of cumulative coverage up to the week commencing on 9 November 2020 (week 46) (left) and week coverage in the same week (right)

COG−UK cumulativesequencing coverageup to the week commencingon 9 November 2020

0%

1−4%

5−9%

10−19%

20% or more

COG−UK weeksequencing coveragein the week commencingon 9 November 2020

0%

1−4%

5−9%

10−19%

20% or more