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Oxford HCV Subtyping Process


The subtyping process consists of three steps:
  • The initial step involves construction of a phylogenetic tree using HKY distance method in PAUP* software.The alignment contains the sequence under query and HCV pure subtypes.
  • In the second step, the sequence under query sequence is divided into small segments and is analysed for recombination using bootscanning using a sliding window of 400 bps moving in steps of 50 bps.
  • Finally, in the fourth step, the alignment is examined to determine whether it contains sufficient phylogenetic signals for subtype determination using Treepuzzle software.


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HCV Subtype Reference Alignment:
Genotype 1



Genotype 1 subtype a


1a.COLONEL
1a.HCV_1
1a.HCV_H


Genotype 1 subtype b

1b.HCV_A
1b.HCV_JS
1b.HCV_J
1b.MD1_1


Genotype 1 subtype c


1c.AY051292
1c.HC_G9

Genotype 2



Genotype 2 subtype a

2a.G2AK3
2a.HC_J6CH
2a.NDM228
2a.Td_6


Genotype 2 subtype b


2b.HC_J8
2b.JPUT971017
2b.MD2B_1


Genotype 2 subtype c

2c.BEBE1

Genotype 2 subtype k

2k.VAT96
Genotype 3



Genotype 3 subtype a

3a.CB
3a.HCVCENS1
3a.K3A
3a.NZL1


Genotype 3 subtype b

3b.JP1996056672


Genotype 3 subtype k


3k.JK049
Genotype 4



Genotype 4 subtype a

4a.ED43

Genotype 5



Genotype 5 subtype a


5a.EUH1480
5a.SA13

Genotype 6


Genotype 6 subtype a


6a.EUHK2


Genotype 6 subtype b


6b.TH580

Genotype 6 subtype d


6d.VN235

Genotype 6 subtype g


6g.JK046

Genotype 6 subtype h


6h.VN004


Genotype 6 subtype k


6k.VN405



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Developed by: Tulio de Oliveira, Marco Salemi, Oliver Pybus, Sabrina Almeida,  Andrew Rambaut.

Developed by the Evolutionary Biology Group at University of Oxford, UK. Department of Pathology, Immunology & Laboratory Medicine, University of Florida, Gainesville, USA. Biotechnology department, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil.

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

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