TABLE 1 .

Viral sequence characteristics in acute and chronic infection

Infection status	Subject no.	Genotype	Region(s) covered	No. of amplicons	Mean intralineage nucleotide diversity (%)a	No. of T/F genomesb
Acute	10002	1a	5′ half	31	0.104	13
	10012	1a	5′ half	129	0.035	3
	10017	1a	5′ half	192	0.037	4
	10020	1a	5′ half	64	0.046	10
	10021	1a	5′ UTR	6	0.000	1
			5′ half	96	0.027
			3′ half	27	0.031
			Poly(U/UC)	46	NAc
			X-tail	4	0.000
	10024	1a	5′ half	112	0.025	6
	10025	1a	5′ UTR	5	0.000	1
			5′ half	92	0.044
			3′ half	16	0.042
			Poly(U/UC)	22	NA
			X-tail	5	0.460
	10029	1a	5′ half	201	0.037	9
	10062	1a	5′ half	140	0.025	3
	105686	1a	5′ half	23	0.055	2
	106889	1a	5′ half	87	0.024	>30
	110069	1a	5′ UTR	8	0.000	4
			5′ half	118	0.021
			3′ half	22	0.035
			Poly(U/UC)	33	NA
			X-tail	12	0.000
	6213	1a	5′ half	41	0.000	3
	6222	1a	5′ half	17	0.082	4
	10051	1b	5′ UTR	10	0.250	1
			5′ half	124	0.020
			3′ half	28	0.042
			Poly(U/UC)	38	NA
			X-tail	11	0.235
	9055	3a	5′ UTR	8	0.031	1
			5′ half	157	0.034
			3′ half	9	0.020
			Poly(U/UC)	45	NA
			X-tail	4	0.000
	10003	3a	5′ half	133	0.031	>30
	105431	4a	5′ UTR	40	0.026	2
			5′ half	59	0.017
			3′ half	43	0.029
			Poly(U/UC)	69	NA
			X-tail	15	0.000
Chronic	ARJA6267	1a	5′ half	43	1.249	NA
			Poly(U/UC)	8	NA
	BLMI6862	1a	5′ half	22	1.013	NA
			Poly(U/UC)	14	NA
	JOTO6422	1a	5′ half	21	1.555	NA
			Poly(U/UC)	9	NA
	KNPH3730	1a	5′ half	13	0.929	NA
			Poly(U/UC)	23	NA
	LAST90001	1a	5′ half	19	0.730	NA
	ROMI6847	1a	5′ half	18	0.879	NA
			Poly(U/UC)	9	NA
	SLRO5563	1a	5′ half	29	1.087	NA
			Poly(U/UC)	13	NA
	WEPA5774	1a	5′ half	44	1.708	NA
			Poly(U/UC)	10	NA
	WHRO3882	1a	5′ half	22	0.504	NA
	WIMI4025	1a	5′ half	36	1.323	NA
			Poly(U/UC)	16	NA
	WIMI90003	1a	5′ half	28	1.013	NA

^aPercent divergence scores for all regions except the poly(U/UC) were determined by multiple pairwise alignment analysis using the DIVEIN software suite.

^bT/F estimates are based on combined quarter- and half-genome analysis.

^cNA, not applicable.