Lineage A

Lineage summaries

A lineage summary figure

Lineage name Most common countries Date range Number of taxa Known Travel Recall value
A China (31%), India (10%), Japan (8%) January 05 to August 04 409 China to India, Australia, Vietnam (4), Saudia_Arabia to Turkey (2), USA to New_Zealand (1) 0.96
A.1 USA (86%), Australia (7%), Canada (2%) February 25 to July 14 987   0.99
A.1.1 Iceland (88%), USA (12%) March 11 to March 20 8 USA to Iceland (3) 1.0
A.2 Spain (66%), UK (15%), Panama (5%) February 26 to June 20 412 Italy to Spain (1), Spain to Brazil, China (2) 0.98
A.2.1 Panama (97%), Spain (3%) February 20 to July 04 78   0.92
A.2.2 Australia (92%), UK (6%), USA (1%) March 17 to April 16 71   1.0
A.2.3 UK (100%) March 12 to May 29 190   0.98
A.3 USA (79%), UK (8%), Australia (6%) January 28 to June 10 232 USA to Taiwan (1), United_States to USA (1) 0.99
A.4 USA (100%) March 13 to April 07 17   1.0
A.5 Spain (50%), UK (32%), Uruguay (3%) March 01 to June 04 202   0.98
A.6 Thailand (94%), Singapore (3%), Japan (3%) January 25 to April 07 36   0.91
A.7 India (100%) May 06 to May 10 15   1.0
A.9 India (100%) April 03 to May 12 13   0.9

Lineage descriptions

Lineage Notes
A Root of the pandemic lies within lineage A. Many sequences originating from China and many global exports; including to South East Asia, Japan, South Korea, Australia, the USA and Europe, represented in this lineage
A.1 A North American lineage (BS=16)
A.1.1 Iceland lineage (BS=94)
A.1.3 Previously Australian lineage, structure has split up into the diverity of A.1, so all reassigned A.1
A.2 Majoritively Spanish lineage now with a variety of other locations represented, including South and Central American sequences, other European countries and Kazakhstan.
A.2.1 Lineage with sequences predominantly from Panama
A.2.2 Australian lineage nested within the diversity of A.2
A.2.3 Scottish lineage nested within the diversity of A.2
A.3 USA and Australian lineage
A.4 USA lineage nested in A diveristy
A.5 A lineage with a lot of representation from Spanish-speaking countries. A Spanish/ South-American lineage, but now with sequences from an outbreak in Scotland
A.6 Lineage from an introduction event into Thailand, now including a couple of exports
A.7 Indian lineage, including Saudi Arabian & Turkish sequences. A.7, A.8 and A.9 are all lineages with diversity from India, however are difficult to resolve confidently, potentially due to ambiguities or homoplasies in the sequences. All are nested within the diversity of A.
A.8 Merged with sister Indian lineage A.7. A.7, A.8 and A.9 are all lineages with diversity from India, however are difficult to resolve confidently, potentially due to ambiguities or homoplasies in the sequences. All are nested within the diversity of A.
A.9 Indian lineage. A.7, A.8 and A.9 are all lineages with diversity from India, however are difficult to resolve confidently, potentially due to ambiguities or homoplasies in the sequences. All are nested within the diversity of A.