Table 1. Sublineage distribution and associated SIT designations for each of the lineages in the study.

Lineage	Sublineage	SIT
AFRI n = 195 (47.10%)	AFRI_1 n = 194	SIT181 n = 96
		SIT187 n = 46
		orphan n = 26
		SIT536 n = 6
		SIT188 n = 3
		SIT318 n = 2
		SIT326 n = 2
		SIT525 n = 2
		SIT530 n = 2
		SIT532 n = 2
		SIT3104 n = 2
		SIT3118* n = 2
		SIT324 n = 1
		SIT537 n = 1
		SIT3130 n = 1
	AFRI_3 n = 1	orphan n = 1
LAM n = 75 (18.12%)	LAM9 n = 43	SIT42 n = 36
		SIT2201 n = 2
		SIT3020* n = 2
		SIT766 n = 1
		SIT866 n = 1
		orphan n = 1
	LAM1 n = 14	SIT20 n = 11
		SIT534 n = 3
	LAM4 n = 9	SIT60 n = 7
		SIT828 n = 1
		orphan n = 1
	LAM5 n = 3	SIT93 n = 1
		orphan n = 2
	LAM2 n = 2	SIT604 n = 2
	LAM3 n = 2	SIT4 n = 1
		SIT3101* n = 1
	LAM10-CAM n = 2	SIT61 n = 2
T clade n = 53 (12.80%)	T1 n = 41	SIT53 n = 10
		SIT244 n = 7
		SIT334 n = 3
		SIT804 n = 3
		orphan n = 4
		SIT3100* n = 3
		SIT196 n = 2
		SIT522 n = 2
		SIT535 n = 2
		SIT230 n = 1
		SIT521 n = 1
		SIT611 n = 1
		SIT801 n = 1
		SIT888 n = 1
	T n = 8	SIT73 n = 5
		SIT3129* n = 2
		SIT2440 n = 1
	T5 n = 3	orphan n = 2
		SIT44 n = 1
	T2 n = 1	orphan n = 1
Haarlem n = 37 (8.94%)	H1 n = 22	SIT47 n = 18
		SIT62 n = 1
		SIT531 n = 1
		SIT2030* n = 1
		orphan n = 1
	H3 n = 15	SIT50 n = 12
		SIT533 n = 2
		SIT75 n = 1
EAI n = 25 (6.04%)	EAI5 n = 20	SIT527 n = 9
		SIT528 n = 4
		orphan n = 4
		SIT458 n = 2
		SIT236 n = 1
	EAI-SOM n = 4	SIT529 n = 3
		SIT538 n = 1
	EAI6-BGD n = 1	SIT129 n = 1
Unknown signatures n = 13 (3.14%)	Unk n = 13	orphan n = 6
		SIT2445 n = 2
		SIT3131* n = 2
		SIT523 n = 1
		SIT1200 n = 1
		SIT1204 n = 1
Beijing n = 7 (1.69%)	Beijing n = 7	SIT1 n = 7
× clade n = 4 (0.97%)	×3 n = 2	SIT92 n = 2
	×1 n = 2	SIT119 n = 2
Manu n = 4 (0.97%)	Manu2 n = 2	SIT54 n = 1
		orphan n = 1
	Manu1 n = 1	SIT3132* n = 1
	Manu-ancestor n = 1	SIT523 n = 1
CAS n = 2 (0.48%)	CAS1-DEL n = 2	SIT3111 n = 2

Newly-defined SITs are shown by an asterisk while the prototypes defining a sublineage in SITVIT2 database are shown in bold italics.