TABLE 1.

Nucleotide and amino acid changes in the consensus sequence of p100pop compared to the reference sequence^a

HCV coding region	Nucleotide position reference Jc1-PSa	Nucleotide position Jc1-PS (−36 nt FLAG and 60 nt PS)b	Allele reference Jc1-PS	Allele P100pop	aa changea	aa change (−12 aa FLAG and 20 aa PS)b
5’UTR	28	28	G	A	c	c
5’UTR	301	301	T	C	c	c
Core	383	383	A	T	T15S	T15S
Core	572	572	A	G	K78Ed	K78E
Core	727	727	C	T	G129Gc	G129Gc
Core	859	859	C	T	S173Sc	S173Sc
E2	1535	1499	A	G	T399A	T387A
E2	1625	1589	A	G	N429D	N417D
P7	2675	2639	A	G	N779D	N767D
Peptide sequence	2859		T	C	V840Ad
NS2	2926	2830	C	T	I862Ic	I830Ic
NS2	2957	2861	A	G	T873Ad	T841A
NS2	3097	3001	T	C	G919Gc	G887Gc
NS2	3110	3014	A	C	I924L	I892L
NS2	3136	3040	T	G	L932Lc	L900Lc
NS3	4554	4558	G	A	R1405Q	R1373Q
NS3	5038	4942	C	T	L1566Lc	L1534Lc
NS3	5379	5283	A	T	Y1680F	Y1648F
NS4A	5464	5368	A	G	A1708Ac	A1676Ac
NS5A	7256	7160	T	C	C2306R	C2274R
NS5A	7549	7453	A	G	E2403Ec	E2371Ec
NS5A	7754	7658	G	A	V2472Md	V2440M
NS5B	8359	8263	A	G	Q2673Qc	Q2641Qc
NS5B	8406	8310	T	C	M2689Mc	M2657T
NS5B	8938	8842	C	T	L2866Lc	L2834Lc
NS5B	9058	8962	T	A	I2909Ic	I2874Ic
NS5B	9110	9014	T	G	S2924Ad	S2892A
NS5B	9373	9373	T	C	T3011Tc	T2979Tc

^a Nucleotide (nt) and amino acid (aa) positions are given in accordance to the coordinates of the infectious clone Jc1-PS (accession number OQ726017).

^b Nt and aa positions are given in accordance to the coordinates of the infectious clone Jc1-SP with the artificial sequences in the calculation excluded.

^c Unpublished noncoding mutations identified by NGS.

^d Compared to the Sanger Sequencing data (8) novel mutations identified by NGS brown (11).