BioAfrica - Oxford HBV Alignment and Subtyping Process

Oxford HBV Subtyping Process & Alignment

The subtyping process consists of three steps:

The initiat steps involves the identification of the genomic region at the NC_003977 HBV reference sequence. This process uses BLAST software.

The second step involves the alignment of the query sequences with complete K1 reference sequences for HHV8 subtypes A, B, C, D, F, G and H. More information on the alignment is found in a table 1.

The final step involves construction of a phylogenetic tree using HKY distance method with gamma distribution in PAUP* software. The HBV subtypes are identified using JAVA software.

Strain	Genotype	Accession number
AHBVADW2	A	gi\|22530871\|gb\|AY128092.1\|
AHVHEPB	A	gi\|1155012\|emb\|X51970.1\|HVHEPB
AG527295	A	gi\|95007770\|dbj\|AB241114.1\|
BHPBADW1	B	gi\|221497\|dbj\|D00329.1\|HPBADW1
BAB010298	B	gi\|6566405\|dbj\|AB010289
CHEHBVAYR	C	gi\|59585\|emb\|X04615.1\|HEHBVAYR
CHPBADRA	C	gi\|22415734\|gb\|AY123041.1\|
C22Y04HCC	C	gi\|3582357\|dbj\|AB014381.1\|
DHPBHBVAA	D	gi\|329667\|gb\|M32138.1\|HPBHBVAA
DHBVPRES12	D	gi\|736003\|emb\|X85254.1\|HBVPRES12
EHHVBBAS	E	gi\|452617\|emb\|X75657.1\|HHVBBAS
EHBVCh195	E	gi\|6691492\|dbj\|AB032431.1\|
FHBVADW4A	F	gi\|59422\|emb\|X69798.1\|HBVADW4A
FVNZ8251	F	gi\|11191875\|dbj\|AB036910.1\|
FC1858	F	gi\|12247041\|gb\|AF223965.1\|AF223965
GIG29227	G	gi\|6983934\|gb\|AF160501.1\|AF160501
GUSG769	G	gi\|18146661\|dbj\|AB064310.1\|
G23501	G	gi\|19849032\|gb\|AF405706.1\|
H1853Nic	H	gi\|22135696\|gb\|AY090454.1\|
H2928Nic	H	gi\|22135711\|gb\|AY090457.1\|
HLAS2523	H	gi\|22135726\|gb\|AY090460.1\|

Submit sequences

How to cite

HBV Tutorials

HBV Decision Trees

HBV Subtyping Process

HBV Example Sequences

Developed by: Tulio de Oliveira, Sharon Cassol, Emmanouil Magiorkinis, Dimitrios Paraskevis and Andrew Rambaut

Developed in cooperation with the Evolutionary Biology Group at University of Oxford, UK and the the HIV-1 Pathogenesis and Immunotherapeutics Program at University of Pretoria, South Africa.

Funded by the Marie Curie Fellowship, Wellcome Trust and Royal Society, UK.

Suggestions or problems on the program please contact: Dr Tulio de Oliveira.