Table 1.

Proposed reference sequences for HBV genotypes, subgenotypes and clades

The number of sequences in each clade is given for each subgenotype and clade identified. Note that the total sum of the subgenotype sequence clusters may not correspond to the total number of genotype sequences, as a number of sequences did not group within a specific clade. Reference sequences for the genotypes are highlighted in grey boxes. In Figs 3–10, genotype references are marked with blue dots and subgenotype reference sequences are marked with red dots. Subgenotypes B5, C7, C9 and D6 are not included, as these sequences either did not cluster as monophyletic clades or were not retained in our analysis. Hamming distance indicates the number of nucleotide differences between the clade consensus and the chosen reference. The pairwise distance is the number of nucleotide differences between the clade consensus and the chosen reference normalized by length of the genome.

HBV genotype	Subgenotype	No. of sequences	Reference GenBank ID	Hamming distance	Pairwise distance	References	Collection year*	Country of origin
A	A1 (1)	50	KP168423	26	0.008	[55]	2012	Kenya
	A1 (2)	87	FJ692557	21	0.007	[56]	2006	Haiti
	A2	80	EU594385	5	0.002	[57]	2004	Estonia
	A3	9	AM184126	29	0.009	[58]	2005	Gabon
	A4	2	KM606737	n/a	n/a	[59]	2015	Cuba
	A5	25	FJ692601	10	0.003	[60]	2006	Haiti
	A6	2	GQ331046	n/a	n/a	[37]	2006	Belgium
B	B1	47	D23679	23	0.007	[61]	1993	Japan
	B2 (1)	131	JQ801514	15	0.005	[62]	2009	Thailand
	B2 (2)	294	GU815637	10	0.003	[63]	2010	Taiwan, ROC
	B3	106	AP011085	23	0.007	[64]	2001	Indonesia
	B4	69	AB073835	35	0.011	[65]	2001	Japan
	B6	36	AB287314	29	0.009	[66]	2006	Alaska
C	C1†	240	DQ089781	29	0.009	[67]	2005	Hong Kong SAR
	C2 (1)	261	KC774182	21	0.007	[68]	2012	PR China
	C2 (2)	280	GQ377617	14	0.004	[69]	2007	PR China
	C2 (3)	157	AP011098	10	0.003	[70]	2009	Indonesia
	C4	21	KF873526	68	0.021	[71]	2011	Australia
	C5	15	AP011099	41	0.013	[70]	2009	Indonesia
	C6‡	2	EU670263	28	0.009	[29]	2008	Philippines
	C8	15	AP011107	42	0.013	[70]	2009	Indonesia
	C10	21	KJ173333	33	0.010	[72]	2012	PR China
	C11§	28	AB554015	86	0.027	[28]	2010	Indonesia
	UA (1)	31	KC774298	15	0.005	[68]	2012	PR China
	UA (2)	16	DQ089802	55	0.018	[67]	2005	Hong Kong SAR
D	D1 (1)	216	AB222711	11	0.003	[73]	2005	Uzbekistan
	D1 (2)	106	KC875277	17	0.005	[74]	2013	India
	D2	100	MF925358	21	0.007	[75]	2015	Bangladesh
	D3	78	FJ692507	18	0.006	[60]	2006	Haiti
	D4	15	FJ692533	17	0.008	[60]	2006	Haiti
	D5	15	GQ205389	19	0.006	[76]	2008	India
	D7	15	FJ904435	44	0.014	[77]	2006	Tunisia
E	n/a	145	GQ161817	19	0.006	[78]	2006	Guinea
F	F1	26	HM585194	13	0.004	[79]	2007	Chile
	F2	13	DQ899143	26	0.008	[80]	2006	Venezuela
	F3	19	MH051986	17	0.005	[81]	2011	Venezuela
	F4	18	KJ843175	17	0.005	[82]	2012	Argentina
G	n/a	3	AB056513	n/a	n/a	[83]	2001	USA
H	n/a	11	FJ356715	36	0.011	[84]	2008	Argentina
I	I1	5	AB562463	17	0.005	[85]	2007	Vietnam
	I2	4	FJ023669	17	0.005	[86]	2008	Laos
J¶	n/a	1	AB486012	n/a	n/a	[86]	2006	Japan/Borneo

n/a, not applicable; (Subgenotype) this genotype does not diverge into multiple subtypes; (Hamming/Pairwise distance), too few sequences identified belonging to the genotype/subgenotype to generate consensus sequences for selection of closest biological isolate.

*Collection date of sample or year submitted to GenBank (if collection date not given).

†C1 is a large clade that also contains sequences labelled as subgenotype C3, with no clear separation between the two sets of sequences.

‡This sequence has been used previously as a subgenotype C7 reference in a number of publications [21, 22]. No other putative C7 sequences are proposed in the literature.

§C11, a large number of sequences were unpublished in this clade (>30 first closest seqs).

¶Genotype J remains putative, with a single isolate identified in a Japanese patient. The isolate shows considerable divergence from other known HBV strains and is thought to be a recombinant of genotype C and a gibbon HBV isolate.