Summary: COGUK geographic coverage of SarsCov2 sample sequencing

2 November 2020 (week 45)

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 weekcommencing on 2 November 2020 (week 45), 117,381 sequences out of 1,245,015 infected people (9.4%) passed basic quality checks and were availablein Medical Research Council Cloud Infrastructure for Microbial Bioinformatics (MRC CLIMBCOVID, the central computational infrastructure for 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 2 November 2020 (week 45)

Overall coverage Pillar 1 frequency Pillar 2 frequency

Cumulative Week Cumulative Week Cumulative Week

UK 117,381 (9.4%) 7,542 (4.5%) 58,398 2,184 58,983 5,358

Wales 13,865 (22.1%) 984 (14.3%) 12,023 902 1,842 82

Scotland 12,495 (16.6%) 412 (4.9%) 7,545 225 4,950 187

England 89,018 (8.4%) 6,145 (4.2%) 37,491 1,056 51,527 5,089

Northern Ireland 2,003 (4.6%) 1 (0.0%) 1,339 1 664 0

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 2 November 2020 (week 45) (left) and week coverage in the same week (right)

COG−UK cumulativesequencing coverageup to the week commencingon 2 November 2020

0%

1−4%

5−9%

10−19%

20% or more

COG−UK weeksequencing coveragein the week commencingon 2 November 2020

0%

1−4%

5−9%

10−19%

20% or more