civet 3.0 | Cluster Investigation and Virus Epidemiology Tool

civet report 2021-08-11



Table 1 | Summary of queries

Export table:
Name Lineage Source Catchment Sample Date Country Adm1 S:N501Y
England/QEUH-A01621/2020 B.1.1.7 background_data catchment_1 2020-09-30 UK England Y
Wales/PHWC-486F7A/2020 B.1.1.70 background_data catchment_2 2020-10-14 UK Wales Y
Wales/PHWC-486675/2020 B.1.1.70 background_data catchment_2 2020-10-16 UK Wales Y
Wales/PHWC-4868E8/2020 B.1.1.70 background_data catchment_2 2020-10-16 UK Wales Y
Wales/PHWC-486350/2020 B.1.1.70 background_data catchment_2 2020-10-15 UK Wales Y
Wales/PHWC-486174/2020 B.1.1.70 background_data catchment_2 2020-10-13 UK Wales Y
Wales/PHWC-48701C/2020 B.1.1.70 background_data catchment_2 2020-10-13 UK Wales Y
Wales/PHWC-485E23/2020 B.1.1.70 background_data catchment_2 2020-10-19 UK Wales Y
Wales/PHWC-48603B/2020 B.1.1.70 background_data catchment_2 2020-10-20 UK Wales Y
Wales/PHWC-4853AC/2020 B.1.1.70 background_data catchment_2 2020-10-19 UK Wales Y
Wales/PHWC-48452F/2020 B.1.1.70 background_data catchment_2 2020-10-19 UK Wales Y
Wales/PHWC-4849BA/2020 B.1.1 background_data catchment_2 2020-10-20 UK Wales Y
Wales/PHWC-4847CF/2020 B.1.1.70 background_data catchment_2 2020-10-19 UK Wales Y
Wales/PHWC-484B3C/2020 B.1.1.70 background_data catchment_2 2020-10-19 UK Wales Y
Wales/PHWC-48464A/2020 B.1.1.70 background_data catchment_2 2020-10-12 UK Wales Y
Wales/PHWC-483B3D/2020 B.1.1.70 background_data catchment_2 2020-10-14 UK Wales Y
England/CAMC-A660B3/2020 B.1.1.7 background_data catchment_1 2020-10-11 UK England Y
Wales/PHWC-482390/2020 B.1.1 background_data catchment_2 2020-10-20 UK Wales Y
Wales/PHWC-48254F/2020 B.1.1.70 background_data catchment_2 2020-10-20 UK Wales Y
Wales/PHWC-48221B/2020 B.1.1 background_data catchment_2 2020-10-20 UK Wales Y
Wales/PHWC-48207B/2020 B.1.1.70 background_data catchment_2 2020-10-14 UK Wales Y
Wales/PHWC-4829AD/2020 B.1.1.70 background_data catchment_2 2020-10-19 UK Wales Y
Wales/PHWC-48264C/2020 B.1.1.70 background_data catchment_2 2020-10-20 UK Wales Y
Wales/PHWC-482C0E/2020 B.1.1 background_data catchment_2 2020-10-20 UK Wales Y
England/CAMC-A80CA0/2020 B.1.1.70 background_data catchment_2 2020-10-13 UK England Y
Wales/PHWC-48105E/2020 B.1.1.70 background_data catchment_2 2020-10-16 UK Wales Y
Wales/PHWC-481A05/2020 B.1.1.70 background_data catchment_2 2020-10-02 UK Wales Y
Wales/PHWC-481A8D/2020 B.1.1.70 background_data catchment_2 2020-10-19 UK Wales Y
Wales/PHWC-480DB2/2020 B.1.1.70 background_data catchment_2 2020-10-16 UK Wales Y
Wales/PHWC-4814DA/2020 B.1.1.70 background_data catchment_2 2020-10-16 UK Wales Y
Wales/PHWC-48107C/2020 B.1.1.70 background_data catchment_2 2020-10-16 UK Wales Y
Wales/PHWC-481883/2020 B.1.1.70 background_data catchment_2 2020-10-19 UK Wales Y
Wales/PHWC-480945/2020 B.1.1 background_data catchment_2 2020-10-18 UK Wales Y
Wales/PHWC-480329/2020 B.1.1 background_data catchment_2 2020-10-17 UK Wales Y
Wales/PHWC-48009B/2020 B.1.1 background_data catchment_2 2020-10-17 UK Wales Y
Wales/PHWC-48013E/2020 B.1.1 background_data catchment_2 2020-10-08 UK Wales Y
Wales/PHWC-480927/2020 B.1.1 background_data catchment_2 2020-10-19 UK Wales Y
Wales/PHWC-480453/2020 B.1.1 background_data catchment_2 2020-10-18 UK Wales Y
Wales/PHWC-4802C2/2020 B.1.1 background_data catchment_2 2020-10-17 UK Wales Y
Wales/PHWC-48015C/2020 B.1.1.70 background_data catchment_2 2020-10-17 UK Wales Y
Wales/PHWC-4808DF/2020 B.1.1 background_data catchment_2 2020-10-19 UK Wales Y
Wales/PHWC-480B12/2020 B.1.83 background_data catchment_3 2020-10-17 UK Wales Y
Wales/PHWC-480B9A/2020 B.1.1 background_data catchment_2 2020-10-16 UK Wales Y
Wales/PHWC-48058D/2020 B.1.1 background_data catchment_2 2020-10-19 UK Wales Y
Wales/PHWC-480699/2020 B.1.1 background_data catchment_2 2020-10-19 UK Wales Y
England/MILK-A7C3B1/2020 B.1.1.7 background_data catchment_1 2020-10-15 UK England Y
England/MILK-A7C3EE/2020 B.1.1.7 background_data catchment_1 2020-10-15 UK England Y
England/MILK-A7A7A8/2020 B.1.1.7 background_data catchment_1 2020-10-15 UK England Y
Wales/PHWC-47FE86/2020 B.1.1.70 background_data catchment_2 2020-10-13 UK Wales Y
Wales/PHWC-47FCC8/2020 B.1.1.70 background_data catchment_2 2020-10-12 UK Wales Y
Wales/PHWC-47F84C/2020 B.1.1 background_data catchment_2 2020-10-07 UK Wales Y
Wales/PHWC-47F9FE/2020 B.1.1.70 background_data catchment_2 2020-10-12 UK Wales Y
Wales/PHWC-47FA64/2020 B.1.1.70 background_data catchment_2 2020-10-11 UK Wales Y
Wales/PHWC-47FDC5/2020 B.1.1.70 background_data catchment_2 2020-10-14 UK Wales Y
Wales/PHWC-47FA19/2020 B.1.1.70 background_data catchment_2 2020-10-11 UK Wales Y
Wales/PHWC-47F985/2020 B.1.1.70 background_data catchment_2 2020-10-12 UK Wales Y
Wales/PHWC-47FB52/2020 B.1.1.70 background_data catchment_2 2020-10-15 UK Wales Y
Wales/PHWC-47F008/2020 B.1.1.70 background_data catchment_2 2020-10-08 UK Wales Y
Wales/PHWC-47F25D/2020 B.1.1.70 background_data catchment_2 2020-10-05 UK Wales Y
Wales/PHWC-47FFFC/2020 B.1.1.70 background_data catchment_2 2020-10-15 UK Wales Y
Wales/PHWC-47FB70/2020 B.1.1.70 background_data catchment_2 2020-10-16 UK Wales Y
Wales/PHWC-47F493/2020 B.1.1.70 background_data catchment_2 2020-10-11 UK Wales Y
Wales/PHWC-47F439/2020 B.1.1 background_data catchment_2 2020-10-14 UK Wales Y
England/CAMC-A659AA/2020 B.1.1.7 background_data catchment_1 2020-10-11 UK England Y
England/CAMC-A64871/2020 B.1.1.7 background_data catchment_1 2020-10-11 UK England Y
Wales/ALDP-A67B48/2020 B.1.1.70 background_data catchment_2 2020-10-10 UK Wales Y
Wales/PHWC-47DFFE/2020 B.1.1.70 background_data catchment_2 2020-10-12 UK Wales Y
Wales/PHWC-47EAB0/2020 B.1.1.70 background_data catchment_2 2020-10-12 UK Wales Y
Wales/PHWC-47E476/2020 B.1.1.70 background_data catchment_2 2020-10-12 UK Wales Y
Wales/PHWC-47DEA6/2020 B.1.1.70 background_data catchment_2 2020-10-12 UK Wales Y
England/CAMC-A58BA4/2020 B.1.1.7 background_data catchment_1 2020-10-08 UK England Y
Wales/CAMC-A588CB/2020 B.1.1.70 background_data catchment_2 2020-10-09 UK Wales Y
England/CAMC-A41D4E/2020 B.1.177 background_data catchment_4 2020-10-06 UK England Y
Wales/PHWC-16F88E/2020 B.1.1.70 background_data catchment_2 2020-10-08 UK Wales Y
Wales/PHWC-47DA93/2020 B.1.1.70 background_data catchment_2 2020-10-08 UK Wales Y
Wales/PHWC-47CFB3/2020 B.1.1.70 background_data catchment_2 2020-09-27 UK Wales Y
Wales/PHWC-47D4C2/2020 B.1.1.70 background_data catchment_2 2020-10-07 UK Wales Y
Wales/PHWC-47CF4A/2020 B.1.1.70 background_data catchment_2 2020-10-09 UK Wales Y
Wales/PHWC-47D83F/2020 B.1.1.70 background_data catchment_2 2020-10-08 UK Wales Y
Wales/PHWC-47D93C/2020 B.1.1.70 background_data catchment_2 2020-10-09 UK Wales Y
Wales/PHWC-47D116/2020 B.1.1.70 background_data catchment_2 2020-10-07 UK Wales Y
Wales/PHWC-47D899/2020 B.1.1.70 background_data catchment_2 2020-10-08 UK Wales Y
Wales/PHWC-47D547/2020 B.1.1.70 background_data catchment_2 2020-10-07 UK Wales Y
Wales/PHWC-47CEE3/2020 B.1.1.70 background_data catchment_2 2020-10-07 UK Wales Y
Wales/PHWC-47D143/2020 B.1.1.70 background_data catchment_2 2020-10-08 UK Wales Y
Wales/PHWC-47D34D/2020 B.1.1.70 background_data catchment_2 2020-10-08 UK Wales Y
Wales/PHWC-47D608/2020 B.1.1.70 background_data catchment_2 2020-10-08 UK Wales Y
Wales/PHWC-16F8AC/2020 B.1.1.70 background_data catchment_2 2020-10-07 UK Wales Y
Wales/PHWC-47D8B7/2020 B.1.1.70 background_data catchment_2 2020-10-07 UK Wales Y
Wales/PHWC-47D978/2020 B.1.1.70 background_data catchment_2 2020-10-08 UK Wales Y
Wales/PHWC-16E9E6/2020 B.1.1 background_data catchment_2 2020-10-04 UK Wales Y
Wales/PHWC-16F01D/2020 B.1.1.70 background_data catchment_2 2020-09-24 UK Wales Y
Wales/PHWC-16F37E/2020 B.1.1 background_data catchment_2 2020-10-04 UK Wales Y
Wales/PHWC-16F790/2020 B.1.1.70 background_data catchment_2 2020-10-01 UK Wales Y
Wales/PHWC-16F314/2020 B.1.1 background_data catchment_2 2020-10-04 UK Wales Y
Wales/PHWC-16EAE3/2020 B.1.1.70 background_data catchment_2 2020-10-04 UK Wales Y
Wales/PHWC-16E904/2020 B.1.1.70 background_data catchment_2 2020-10-05 UK Wales Y
Wales/PHWC-16F2BD/2020 B.1.1 background_data catchment_2 2020-10-04 UK Wales Y
Wales/PHWC-16F1DE/2020 B.1.1.70 background_data catchment_2 2020-10-04 UK Wales Y
England/MILK-A06B0F/2020 B.1.1.7 background_data catchment_1 2020-10-01 UK England Y
England/MILK-A06237/2020 B.1.1.7 background_data catchment_1 2020-09-30 UK England Y
Wales/PHWC-16DE7F/2020 B.1.1.70 background_data catchment_2 2020-10-02 UK Wales Y
Wales/PHWC-16E087/2020 B.1.1.70 background_data catchment_2 2020-10-02 UK Wales Y
Wales/PHWC-16DEBB/2020 B.1.1.70 background_data catchment_2 2020-10-02 UK Wales Y
Wales/PHWC-16E37F/2020 B.1.1.70 background_data catchment_2 2020-10-02 UK Wales Y
Wales/PHWC-16E324/2020 B.1.1.70 background_data catchment_2 2020-09-29 UK Wales Y
Wales/PHWC-16E4E5/2020 B.1.1.70 background_data catchment_2 2020-10-02 UK Wales Y
Wales/PHWC-16C924/2020 B.1.1 background_data catchment_2 2020-09-23 UK Wales Y
Wales/PHWC-16D686/2020 B.1.1.70 background_data catchment_2 2020-09-25 UK Wales Y
Wales/PHWC-16D9F6/2020 B.1.83 background_data catchment_3 2020-09-25 UK Wales Y
Wales/PHWC-16D853/2020 B.1.1.70 background_data catchment_2 2020-09-25 UK Wales Y
Wales/PHWC-16D914/2020 B.1.1.70 background_data catchment_2 2020-09-25 UK Wales Y
Wales/PHWC-16DA8A/2020 B.1.1 background_data catchment_2 2020-09-18 UK Wales Y
Wales/PHWC-16DA11/2020 B.1.1.70 background_data catchment_2 2020-09-27 UK Wales Y
Wales/PHWC-16D7A1/2020 B.1.1.70 background_data catchment_2 2020-09-25 UK Wales Y
Wales/MILK-9E1172/2020 B.1.1.70 background_data catchment_2 2020-09-20 UK Wales Y
England/MILK-9E2FE0/2020 B.1.1.7 background_data catchment_1 2020-09-21 UK England Y
Wales/MILK-9E04C5/2020 B.1.1.70 background_data catchment_2 2020-09-20 UK Wales Y
England/MILK-9E05B3/2020 B.1.1.7 background_data catchment_1 2020-09-20 UK England Y
Wales/PHWC-16B59A/2020 B.1.1.70 background_data catchment_2 2020-09-19 UK Wales Y
Wales/PHWC-16A59B/2020 B.1.1.70 background_data catchment_2 2020-09-07 UK Wales Y
Wales/PHWC-16A23A/2020 B.1.1.70 background_data catchment_2 2020-09-04 UK Wales Y

Catchment 1

Table 2 | Summary of Catchment 1

Information
Total 70
Query Count 12
Country UK 95%
South_Africa 1%
Spain 1%
Brazil 1%
Other 2%
Lineage B.1.1 94%
B.1.1.35 2%
B.1.1.68 1%
B.1.1.7 1%
Other 2%

Expansion

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Figure 1 | Catchment 1 phylogeny



2021-08-11T11:50:17.439755 image/svg+xml Matplotlib v3.4.2, https://matplotlib.org/

Figure 2 | snipit plot for queries in Catchment 1



Figure 3 | Timeline plot for queries in Catchment 1


Catchment 2

Table 3 | Summary of Catchment 2

Information
Total 18
Query Count 107
Country UK 50%
Serbia 22%
Denmark 11%
Switzerland 5%
North_Macedonia 5%
Austria 5%
Other 2%
Lineage B.1.1.70 61%
B.1.1 38%
Other 1%

Expansion

Colour by