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LASP HTLV-1 Subtyping Process and Alignment


The subtyping process consists of three steps:

The initiat steps involves the identification of the genomic region at the ATK1 HTLV-1 reference sequence. This process uses BLAST software.

The second step involves the alignment of the query sequences with complete LTR reference sequences for HTLV-1 subtypes a-f. This alignment also include reference for subgroups of the HTLV-1 cosmopolitan subtype a. More information on the alignment is found in a table 1.

The final step involves construction of a phylogenetic tree using Tamura Nei distance method with gamma distribution in PAUP* software. The HTLV-1 subtypes and sub-groups are identified using JAVA software.

Table 1: Reference sequences for HTLV-1 subtyping:

Strain Subtype Subgroup Accession number Reference Country of origen
Mel5 c
L02534 Gessai et al., 1993 Solomon Island
TE4

Z46900 Ibrahim et al., 1995 Indonesia
Efe1 e
Y17014 Salemi,M. et al., 1998 Republic of Congo
Lib2 f
Y17017 Salemi,M. et al., 1998 Gabon
MOMJ b
Z31659 Vandamme et al., 1994 Democratic Republic of Congo
ITIS b
Z32527 Vandamme et al., 1994 Democratic Republic of Congo
MWMG b
Z31662 Vandamme et al., 1994 Democratic Republic of Congo
GB233 b
D23692 Miura et al., 1994 Gabon
PH236 b
L76307 Mahieux et al., 1997 Gabon
T49 b
L76305 Mahieux et al., 1997 Cameroon
H24 b
L76308 Mahieux et al., 1997 Cameroon
GAB7 b
L76311 Mahieux et al., 1997 Gabon
H23 d
L76312 Mahieux et al., 1997 Cameroon
pyg19 d
L76310 Mahieux et al., 1997 Cameroon
HS35 a C D13784 Malik et al., 1988 Caribbean
GH78 a C D23693 Miura et al., 1994 Ghana
OD a D U12805 Gasmi et al., 1994 Mauritanea
BO a D U12804 Gasmi et al., 1994 Algeria
Pr52 a D U12806 Gasmi et al., 1994 Morocco
Bl1 a E Y16481 Van Dooren et al., 1998 Peru
RKI4 a E AF054627 Ellerbrok et al., 1998 Peru
ATM a B J02030 Seiki et al., 1983 Japan
MT4 a B Z31661 Vandamme et al., 1994 Japan
ATK1 a B J02029 Seiki et al., 1983 Japan
ATLYS a B U19949 Chou et al., 1995 USA
Ni1 a B Y16484 Van Dooren et al., 1998 Peru
H5 a B M37299 Tsujimoto et al., 1988 Japan
BCI2-1 a B U32557 Picard et al., 1995 British Columbia
AMA a A X88871 Liu et al., 1996 Brazil
TBH4 a A L76028 Engelbrecht et al., 1996 South Africa
AINU a A D23694 Miura et al., 1994 Japan
73RM a A M81248 Dasgupta et al., 1992 USA
CMC a A X88872 Liu et al., 1996 Taiwan
KUW1 a A L42253 Voevodin et al., 1995 Kuwait
Cam a A AF063819 Talarmin et al., 1999 French Guiana
TBH2 a A L76025 Engelbrecht et al., 1996 South Africa
CR1 a A K02722 Joseph et al., 1984 Caribbean
Boi a A L36905 Bazarbachi et al., 1995 France
Bl2 a A Y16482 Van Dooren et al., 1998 Peru
HTLV04 a A DQ005557 Alcantara et al., 2005 South Africa
Qu1 a A Y16475 Van Dooren et al., 1998 Peru
FNN100 a A DQ005547 Alcantara et al., 2005 Brazil


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 HTLV Subtyping Process
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Developed by: Luiz Carlos J Alcantara,  Sonia Van Dooren, Anne-Mieke Vandamme, Bernardo Galvao-Castro, Tulio de Oliveira.

Developed in cooperation with the Evolutionary Biology Group at University of Oxford, UK, the REGA Institute at the Katholieke Universiteit Leuven, Belgium and the Laboratorio Avancado de Saude Publica (LASP) CPqGM/FIOCRUZ, Brazil.

Funded by the Marie Curie Fellowship, Flanders Bilateral Cooperation Program, PN-DST/AIDS (Ministry of Health) and FAPESB, Brazil.

For HTLV-1 subtyping questions please contact Dr Luiz Alcantara,
Suggestions or problems on the program please contact:  Dr Tulio de Oliveira.