Molecular epidemiology, genetic variability and evolution of HTLV-1 with special emphasis on African genotypes

Retrovirology

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]
	A/Transcontinental (a-TC)	TSP1	Japan	M86840	[16]
	B/Japanese (a-Jpn)	ATK	Japan	J02029	[12]
	B/Japanese (a-Jpn)	YS	Japan	U19949	[145]
	C/West African (a-WA)	HS-35	Caribbean	NC001436	[14]
	C/West African (a-WA)	FrGu1^a	French Guyana	AY324785	[98]
	D/North African (a-NA)	BO^a	Algeria	U12804	[21]
	D/North African (a-NA)	Pr52^a	Morocco	U12806	[21]
	E/Black Peruvian (a-Per)	Bl1^a	Peru	Y16481	[22]
	E/Black Peruvian (a-Per)	RKI4^a	Peru	AF054627	[22]
	F	Ethio10^a	Ethiopia	KC493410	[23]
	Senegalese (a-Sen)	BD78883^a	Senegal	DQ235700	[26]
	Senegalese (a-Sen)	CV21	Cabo Verde	KX430030	[136]
b		EL^a	Africa	M67514	[146]
b		SF26	Brazil	JX507077	[141]
c	Melanesia	Mel5	Solomon Islands	L02534	[50]
	Melanesia	NCP201	New Caledonia	KX905203	[52]
	Australia	Aus-DF	Australia	KF242505	[53]
	Australia	Aus-GM	Australia	JX891478	[53]
d		Pyg19^a	CAR	L76310	[27]
e		Efe1^a	DRC	Y17014	[54]
f		Lib2^a	Gabon	Y17017	[54]
g		2656ND^a	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)

ISSN: 1742-4690