TABLE 1 .

Numbers of SNPs, small indels, and large deletions between the incident and relapse isolates or between the first-relapse and second-relapse isolates (case 15R and case 17R)

Case IDa	Molecular type	No. of NPs	No. of small indels	No. of large deletions
1	VNI	6	1	0
8	VNI	1	0	1
14	VNI	1	0	0
15	VNI	2	1	0
15R	VNI	2	0	0
22	VNI	1	1	0
76	VNI	0	0	0
82	VNI	1	0	0
87	VNI	4	0	0
7	VNB	2	0	0
81	VNB	5	2	0
5	VNII	1	0	0
9	VNII	2	0	0
45	VNII	4	0	0
77	VNII	6	0	0
77R	VNII	4	0	0
90	VNII	5	0	0
91	VGI	0	0	0
31	VGIV	4	1	0
67	VGIV	1	0	0

^aID, identifier.