Hepatitis C virus genetic variability and evolution

Table 1 Representative next generation sequencing platforms and their characteristics

Platform	Run time (h)	Read length (bp)	Throughput per run (Mb)	Typical errors	Main biological applications	Company URL
Roche 454 FLX +	23	700, up to 1000	700	Insertions/deletions (indels) at homopolymer regions	Microbial genome sequencing, human genome sequencing, transcriptomics, metagenomics	http://www.my454.com/
Illumina HySeq 1000 MySeq 2000 V3	8 10	2 × 100 2 × 150	400000 < 600000	Indels, especially end of reads	Microbial genome sequencing, human genome sequencing, transcriptomics, metagenomics	http://www.illumina.com/systems.ilmn
SOLiD 4	12	50 × 35	71000	End of read substitution errors	Microbial genome sequencing, human genome sequencing, transcriptomics, metagenomics	http://www.appliedbiosystems.com/ absite/us/en/home.html
Ion torrent PGM 318 Chip	3	200	1000	Indels at homopolymer regions	Microbial genome sequencing, human genome sequencing, transcriptomics, metagenomics	http://www.iontorrent.com/
Pacific Biosciences				Random indel errors	Full-length transcriptomics, discovering large structural variants and haplotypes	http://www.pacificbiosciences.com/

Table 2 Main features of intergenotype, intersubtype and intrapatient recombination in hepatitis C virus published cases

Strain	Genotype	Country	Recombination breakpoint(s)	Ref.
Intergenotype
RF1_2k/1b	2k/1b	Russia, Ireland, Uzbekistan, Georgia, France, Cyprus, Estonia	NS2, positions 3175-3176	[124-129]
D3	2i/6p	Viet Nam	NS2/NS3 junction, between positions 3405 and 3464	[130]
SE-03-07-1689	RF3_2b/1b	Philippines	NS3, positions 3466-3467	[137]
HC10-0804	2b/1b	Japan	NS2/NS3 junction, positions 3443-3444	[135]
B5808, M2123, M4430, M4416, M4414, M4431, M2777, M8774	2b/1b	Japan	NS2, putative position 3301	[136]
R1	2/5	France	NS2/NS3 junction, between residues 3420 and 3440	[132]
D177	RF_2b/6w RF_3a/1b RF_2a/1a	Taiwan Taiwan, China Taiwan	NS2/NS3 junction, position 3429 Undetermined Undetermined	[131,133]
JF779679	2b/1a	United States	NS2/NS3 junction, positions 3405-3416	[134]
Intersubtype	Subtypes
PE22	RF2_1b/1a	Peru	NS5B, position 8321	[141]
H23	1b/1a	Uruguay	Core, at position 387	[111]
HC-J1	1a/1c	Japan	2 sites in E1-E2, at positions 1407 and 2050	[142]
Khajal	1a/1c	India	5 sites, from core to NS3, at positions 801 1261, 2181, 3041 and 3781	[143]
R49	4a/4d	Portugal	Undetermined	[140]
EU246930	6a/6o	Viet Nam	NS5B, between positions 8345-9073	[144]
EU246932	6e/6o	Viet Nam	NS5B, between positions 8358-8977	[144]
EU246937	6n/6o	Thailand	NS5B, between positions 8372-9033	[144]
EU246931	6e/6h	Viet Nam	NS5B, between positions 8356-9019	[144]
Intrapatient	Subtype
	1b	Spain	NS5B, at residue 286	[145]
	1a, 1b, 3a	Spain	1 or 2 sites within E1-E2 or NS5A	[146]
	4a	Ireland	E2 glycoprotein, HVR1 region	[147]

Modified from ref. [49].