Table 3. Co-occurring mutations, epitope escape mutants, and the associated frequency of occurrence and relative fitness of the NS3 region of subject THDS1086MX.

Time	Viral load (IU/ml)	Frequency	Relative fitness	1406KLVAMGLNAV1415mutations	Co-occurring mutations†
16DPI	235662	61.70%	1.000
		18.10%	1.000
		6.00%	1.000
		4.80%	0.364	V1408A
		4.60%	1.000
		1.70%	1.000
		1.60%	0.364	V1408A
		1.40%	1.000
72DPI	176550	48.50%	0.453		H1115T
		24.70%	0.453		H1115T
		6.20%	0.453		H1115T
		6.20%	0.453		H1115T
		3.70%	0.084		H1115T	C1318Y
		3.60%	0.453		H1115T
		3.30%	0.453		H1115T
		2.10%	0.084		H1115T
		1.80%	0.069		H1115T	C1318Y	V1458A
109DPI	108737	35.80%	0.223	I1412V	H1115S	R1118H
		19.10%	0.384	I1412L	H1115S
		8.60%	0.910	I1412L	V1112A	H1115S
		7.70%	0.360	I1412L	V1112I	H1115S
		6.30%	0.061	I1412L	H1115G
		5.70%	0.247	I1412L	H1115T
		3.70%	0.657	I1412L	V1112T	H1115S
		2.60%	0.145	I1412L	V1112A	H1115T
		2.30%	0.062	I1412L	V1112I	H1115G
		2.20%	0.229	I1412L	V1112I	H1115T
		2.20%	0.573	I1412L	V1112A	H1115T
		2.10%	0.624	I1412V	H1115S
		1.80%	0.309	I1412L	H1115A
198DPI	681389	73.60%	0.360	I1412L	V1112I	H1115S
		12.60%	2.149	I1412L *	V1112I	H1115S	A1593V
		4.70%	1.683	A1409T	V1112P	H1115S
		2.90%	0.360	I1412L	V1112I	H1115S
		1.80%	0.360	I1412L	V1112I	H1115S
		1.70%	1.683	A1409T	V1112P	H1115S
		1.60%	0.066	I1412L	V1112I	H1115S	M1268I
		1.20%	0.360	I1412L	V1112I	H1115S

^*Bold - indicate escape variants with fitness estimate ≥1.

^†Only non-synonymous mutations are shown.