Consensus Proposals for a Unified System of Nomenclature of Hepatitis C Virus Genotypes in the Future

International standardization and coordination of the nomenclature of variants of hepatitis C virus (HCV) is increasingly needed as more is discovered about the scale of HCV-related liver disease and important biological and antigenic differences that exist between variants.

A group of scientists expert in the field of HCV genetic variability, and those involved in development of HCV sequence databases, the Hepatitis Virus Database (Japan), euHCVdb (France), and Los Alamos (United States), met to re-examine the status of HCV genotype nomenclature, resolve conflicting genotype or subtype names among described variants of HCV, and draw up revised criteria for the assignment of new genotypes as they are discovered in the future.

A comprehensive listing of all currently classified variants of HCV incorporates a number of agreed genotype and subtype name reassignments to create consistency in nomenclature.

The paper also contains consensus proposals for the classification of new variants into genotypes and subtypes, which recognizes and incorporates new knowledge of HCV genetic diversity and epidemiology.

A proposal was made that HCV variants be classified into 6 genotypes (representing the 6 genetic groups defined by phylogenetic analysis).

Subtype name assignment will be either confirmed or provisional, depending on the availability of complete or partial nucleotide sequence data, or remain unassigned where fewer than 3 examples of a new subtype have been described.

The authors conclude, “These proposals provide the framework by which the HCV databases store and provide access to data on HCV, which will internationally coordinate the assignment of new genotypes and subtypes in the future.”

Table 1. Confirmed HCV Genotypes/Subtypes

Table 2. Listing of HCV Variants With Proposed Changes
in Genotype Nomenclature

Table 3. Provisionally Assigned HCV Subtypes

09/30/05

Reference
P Simmonds and others. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 42(4): 962-973.

Table 1. Confirmed HCV Genotypes/Subtypes

Genotype^*	Locus/Isolate(s)	Accession number(s)	Reference(s)

Genotype 1
1a	HPCPLYPRE, HPCCGAA	M62321, M67463	[67],[68]
1b	HPCJCG, HPCHUMR	D90208, M58335	[69],[70]
1c	HPCCGS, AY051292	D14853, AY051292	[71]
Genotype 2
2a	HPCPOLP, JFH-1	D00944, AB047639	[72],[73]
2b	HPCJ8G, JPUT971017	D10988, AB030907	[9],[74]
2c	BEBE1	D50409	[75]
2k	VAT96	AB031663	[58]
Genotype 3
3a	HPCEGS, HPCK3A	D17763, D28917	[76],[77]
3b	HPCFG	D49374	[78]
3k	HPCJK049E1	D63821	[59]
Genotype 4
4a	HCV4APOLY	Y11604	[79]
Genotype 5
5a	EUH1480, SA13	Y13184, AF064490	[80],[81]
Genotype 6
6a	HCV12083, 6a33	Y12083, AY858526	[82]
6b	Th580	D84262	[83]
6d	VN235	D84263	[83]
6g	HPCJK046E2	D63822	[59]
6h	VN004	D84265	[83]
6k	VN405	D84264	[83]

   NOTE. Tables 1, 2, and 3 were compiled by a working group of Donald Murphy, Erwin Sablon, and Phillipe Halfon.
  ^* Consensus proposed genotype/subtype names. For instances in which multiple sequences of a HCV genotype are available, two sequences have been listed, prioritized by (1) publication date, or (2) submission date when unpublished.
   Locus (or isolate name, if locus is the same as the accession number).
   Sequence obtained from acute phase plasma of a chimpanzee experimentally infected with (human-derived) isolate SA13.
Simmonds et al. Hepatology 42(4). October 2005.

Table 2. Listing of HCV Variants With Proposed Changes in Genotype Nomenclature

Proposed Designation^*	Published Designation	Status	Isolate	Region Sequenced^§	Reference(s)

Genotype 2
2k	2j	C	RU169	NS5B (D86532), 3UTR (D86532)	[83]
2j	2l	P	BA047	NS5B (D86530), 3UTR (D86530)	[83]
2n	2e	P	NL50	C/E1 (L39309), NS5B (L44602)	[84]
2o	4f/2f	P	FR4	C/E1 (L38333), NS5B (L38373)	[84]
2p	2f	P	NL33	C/E1, (L39300), BS5B (L44601)	[84]
2q	2k	P	BA045	NS5B (D86529), 3UTR (D86529)	[83]
Genotype 3
3k	10a	C	HPCJK049E1	Complete genome (D63821)	[59]
Genotype 4
4r	4a	P	Z4	C/E1 (U10236/L16652)	[12],[64]
			FrSSD120	C/E1 (AJ401097), NS5B (AJ291282)	[93]
4n	4 alfa	P	1359	C/E1 (AF271874)	[65]
4o	4 beta	P	2153	C/E1 (AF271882), NS5B (AF271815)	[65]
Genotype 6
6c	7d	P	Th846	C/E1 (D37843), NS5B (D37857)	[35]
6d	7b	C	VN235	Complete genome (D84263)	[83]
6e	7a	P	VN540	C/E1 (D88474), NS5B (D87361)	[34]
6f	7e	P	BB7	NS5B (D28541)	[96]
6f	7c	P	Th271	C/E1 (D37844), NS5B (D37858)	[35]
6g	11a	C	HPCJK046E	Complete genome (D63822)	[59]
6h	9a	C	VN004	Complete genome (D84265)	[83]
6i	9b	P	Th555	C/E1 (D37849), NS5B (D37863)	[35]
6j	9c	P	Th553	C/E1 (D37848), NS5B (D37862)	[35]
6k	8b	C	VN405	Complete genome (D84264)	[34]
6l	8a	P	VN507	C/E1 (D88470), NS5B (D87357)	[34]

  ^* Proposed new name based on revised criteria for genotype designations.
   Classification status; C: Confirmed; P: Provisional.
   Example of isolates referred to in associated publications (last column).
  ^§ Regions sequenced (accession numbers in parentheses), prioritized for (1) complete genome; (2) Core/E1 and NS5B regions; (3) other regions where core/E1 and NS5B regions are not both available.
Simmonds et al. Hepatology 42(4). October 2005

Table 3. Provisionally Assigned HCV Subtypes

	Isolate	Accession Number(s)^*		Reference(s)
	Isolate	Core/E1	NS5B	Reference(s)

Genotype 1
1d	HC1-N15, HC1-N16	L39299, L39302	L38377, L38372	[84]
1e	CAM1078, QC248	L38349(C), AY894555	L38361, AY894553	[62],[84]
1f	FR2	L38350	L38371	[84]
1g	2152, 1382	AF271822, AF271820	AF271798, AF271797	[65]
1h	98CM1521, QC94	AY256790(C), AY434131	AY257087, AY434132	[32],[62]
1i	FR16, QC77	n.a., AY434119	L48495, AY434120	[62],[85]
1j	QC2, QC89	AY434158, AY434128	AY434106, AY434129	[62]
1k	QC68, QC82	AY434112, AY434122	AY434113, AY434123	[62]
1l	98CM1383, 98CM1427	AY256789(C), AY256792(C)	AY257083, AY257091	[32]
Genotype 2
2d	NE92, BN177	L39294, n.a.	L29634, AF037244	[66],[86]
2e	JK020, JK025	D49745, D49746	D49760, D49761	[59]
2f	JK081, JK139	D49754, D49757	D49769, D49777	[59]
2g	MED017	n.a.	X93323	[26]
2h	MED007	n.a.	X93327	[26]
2i	FR13, HN4	n.a., X76411/X76415	L48492, L48499	[87],[88]
2j	BA047, QC106	n.a., AY894528	D86530, AY894526	[62],[83]
2l	FR15