Table 1.

Reference sequences for the different HTLV-1 genotypes and subgroups

Genotype	Subgroup	Reference strains	Country of origin	Genbank number	Refs.
a	A/Transcontinental (a-TC)	BOI	France	L36905	[13]
		TSP1	Japan	M86840	[16]
	B/Japanese (a-Jpn)	ATK	Japan	J02029	[12]
		YS	Japan	U19949	[145]
	C/West African (a-WA)	HS-35	Caribbean	NC001436	[14]
		FrGu1a	French Guyana	AY324785	[98]
	D/North African (a-NA)	BOa	Algeria	U12804	[21]
		Pr52a	Morocco	U12806	[21]
	E/Black Peruvian (a-Per)	Bl1a	Peru	Y16481	[22]
		RKI4a	Peru	AF054627	[22]
	F	Ethio10a	Ethiopia	KC493410	[23]
	Senegalese (a-Sen)	BD78883a	Senegal	DQ235700	[26]
		CV21	Cabo Verde	KX430030	[136]
b		ELa	Africa	M67514	[146]
		SF26	Brazil	JX507077	[141]
c	Melanesia	Mel5	Solomon Islands	L02534	[50]
		NCP201	New Caledonia	KX905203	[52]
	Australia	Aus-DF	Australia	KF242505	[53]
		Aus-GM	Australia	JX891478	[53]
d		Pyg19a	CAR	L76310	[27]
e		Efe1a	DRC	Y17014	[54]
f		Lib2a	Gabon	Y17017	[54]
g		2656NDa	Cameroon	AY818431	[55]
		HTLVsmm	Liberia	KU214243	[147]

Two strains have been proposed as reference strains for each subgroup within genotypes a and c, and for genotype b. When available, complete sequences are presented. Otherwise, historic strains are presented. Due to the limited number of available strains for genotypes d–g, a single strain is presented. Of note, the complete sequence HTLVsmm does not belong to a characterized human genotype

GenBank number corresponds to either the complete sequence, or alternatively the LTR sequence. For each strain, the genotype (and subgroup) is presented, together with the country of origin. The letter in the subgroup section corresponds to the historic name of the group; the second element corresponds to the current denomination of the subgroup

^aPartial sequences (The GenBank number corresponds to the complete or partial LTR sequence)