civet 3.0 | Cluster Investigation and Virus Epidemiology Tool

civet report 2021-10-12



Table 1 | Summary of queries

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Name Lineage Country Sample Date Catchment Source
Trinidad_and_Tobago/39213/2020 B.1.111 Trinidad_and_Tobago 2020-10-27 catchment_1 input_fasta
Trinidad_and_Tobago/37679/2020 B.1.111 Trinidad_and_Tobago 2020-08-22 catchment_1 input_fasta
Trinidad_and_Tobago/31166/2020 B.1.1.33 Trinidad_and_Tobago 2020-09-11 catchment_2 input_fasta
Trinidad_and_Tobago/30969/2020 B.1.1.33 Trinidad_and_Tobago 2020-09-11 catchment_2 input_fasta
Trinidad_and_Tobago/25889/2020 B.1.1 Trinidad_and_Tobago 2020-08-22 catchment_3 input_fasta
Trinidad_and_Tobago/25881/2020 B.1.1 Trinidad_and_Tobago 2020-08-22 catchment_3 input_fasta
Trinidad_and_Tobago/0825/2020 B.1.111 Trinidad_and_Tobago 2020-12-01 catchment_1 input_fasta
Trinidad_and_Tobago/0925/2020 B.1.111 Trinidad_and_Tobago 2020-12-01 catchment_1 input_fasta
Trinidad_and_Tobago/0895/2020 B.1.111 Trinidad_and_Tobago 2020-12-01 catchment_1 input_fasta
Trinidad_and_Tobago/0897/2020 B.1.111 Trinidad_and_Tobago 2020-12-01 catchment_1 input_fasta
Trinidad_and_Tobago/0845/2020 B.1.111 Trinidad_and_Tobago 2020-12-01 catchment_1 input_fasta
Trinidad_and_Tobago/0840/2020 B.1.111 Trinidad_and_Tobago 2020-12-01 catchment_1 input_fasta
Trinidad_and_Tobago/0876/2020 B.1.111 Trinidad_and_Tobago 2020-12-01 catchment_1 input_fasta
Trinidad_and_Tobago/1116/2020 B.1.111 Trinidad_and_Tobago 2020-12-01 catchment_1 input_fasta
Trinidad_and_Tobago/TT6949/2020 B.1.111 Trinidad_and_Tobago 2020-09-09 catchment_1 input_fasta
Trinidad_and_Tobago/TT1327/2020 B.1.111 Trinidad_and_Tobago 2020-08-28 catchment_1 input_fasta
Trinidad_and_Tobago/TT2238/2020 B.1.111 Trinidad_and_Tobago 2020-08-26 catchment_1 input_fasta
Trinidad_and_Tobago/TT7867/2020 B.1.111 Trinidad_and_Tobago 2020-08-14 catchment_1 input_fasta
Trinidad_and_Tobago/TT4707/2020 B.1.111 Trinidad_and_Tobago 2020-09-02 catchment_1 input_fasta
Trinidad_and_Tobago/TT9467/2020 B.1.111 Trinidad_and_Tobago 2020-08-19 catchment_1 input_fasta
Trinidad_and_Tobago/TT3347/2020 B.1.111 Trinidad_and_Tobago 2020-08-29 catchment_1 input_fasta
Trinidad_and_Tobago/TT7923/2020 B.1.111 Trinidad_and_Tobago 2020-09-14 catchment_1 input_fasta
Trinidad_and_Tobago/TT46686/2020 B.1.111 Trinidad_and_Tobago 2020-12-11 catchment_1 input_fasta
Trinidad_and_Tobago/TT47007/2020 B.1.111 Trinidad_and_Tobago 2020-12-17 catchment_1 input_fasta
Trinidad_and_Tobago/TT44048/2020 B.1.111 Trinidad_and_Tobago 2020-11-18 catchment_1 input_fasta
Trinidad_and_Tobago/TT44092/2020 B.1.111 Trinidad_and_Tobago 2020-11-26 catchment_1 input_fasta
Trinidad_and_Tobago/TT2158/2020 B.1.111 Trinidad_and_Tobago 2020-08-26 catchment_1 input_fasta
Trinidad_and_Tobago/TT6851/2020 B.1.111 Trinidad_and_Tobago 2020-09-09 catchment_1 input_fasta

Table 2 | Queries provided in fasta file

Name Seq N Content Seq Length
Trinidad_and_Tobago/39213/2020 0.08 29782
Trinidad_and_Tobago/37679/2020 0.05 29782
Trinidad_and_Tobago/31166/2020 0.11 29782
Trinidad_and_Tobago/30969/2020 0.19 29782
Trinidad_and_Tobago/25889/2020 0.09 29782
Trinidad_and_Tobago/25881/2020 0.17 29782
Trinidad_and_Tobago/0825/2020 0.05 29782
Trinidad_and_Tobago/0925/2020 0.05 29782
Trinidad_and_Tobago/0895/2020 0.05 29782
Trinidad_and_Tobago/0897/2020 0.01 29782
Trinidad_and_Tobago/0845/2020 0.01 29782
Trinidad_and_Tobago/0840/2020 0.01 29782
Trinidad_and_Tobago/0876/2020 0.04 29782
Trinidad_and_Tobago/1116/2020 0.04 29782
Trinidad_and_Tobago/TT6949/2020 0.02 29782
Trinidad_and_Tobago/TT1327/2020 0.03 29782
Trinidad_and_Tobago/TT2238/2020 0.02 29782
Trinidad_and_Tobago/TT7867/2020 0.01 29782
Trinidad_and_Tobago/TT4707/2020 0.01 29782
Trinidad_and_Tobago/TT9467/2020 0.01 29782
Trinidad_and_Tobago/TT3347/2020 0.01 29782
Trinidad_and_Tobago/TT7923/2020 0.01 29782
Trinidad_and_Tobago/TT46686/2020 0.13 29611
Trinidad_and_Tobago/TT47007/2020 0.15 29611
Trinidad_and_Tobago/TT44048/2020 0.07 29782
Trinidad_and_Tobago/TT44092/2020 0.08 29302
Trinidad_and_Tobago/TT2158/2020 0.04 29782
Trinidad_and_Tobago/TT6851/2020 0.04 29611
Name Seq N Content Seq Length

Catchment 1

Table 3 | Summary of Catchment 1

Information
Total 47
Query Count 24
Earliest Date 2020-02-20
Latest Date 2020-08-07
Country Colombia 34%
USA 25%
UK 25%
Australia 4%
Turkey 2%
Saudi_Arabia 2%
Vietnam 2%
Belgium 2%
Canada 2%
Other 2%
Lineage B.1 53%
B.1.111 40%
B.1.36 6%
Other 1%

Expansion

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Figure 1 | Catchment 1 phylogeny



2021-10-12T16:04:26.045253 image/svg+xml Matplotlib v3.4.2, https://matplotlib.org/