Table 4. SNaPshot extension primers.

Lineage	Targeted SNP	Primer sequence (5’→ 3’)
Lineage 1	G/A	AAA AAA AAA AAA ATC AGA TCG ACA AGG GCG AC
Lineage 2	C/T	AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA ATC GGC GTA TGG GAA GTA CC
Lineage 3	A/G	AAA AAA AAA AAA AAA AAA AAA AAG CGC CAC GAA CCC TGT C
Lineage 4	T/G	AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA CAG CCT TAA GAG CCA GAT CC
Lineage 5	G/C	AAA AAA AAA AAA AAA AAA AAA AAA AAA AGT GAC CCG TTC AAC CTG CAT
Lineage 6	G/A	AAA AGC GAG AAC CTG CAA ATC CC