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HIV-1 Subtying Tool Methods:


The subtyping process consists of four 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 group M pure reference sequences for subtypes A-D, F-H, J and K A to K..
  • The next step, involves construction of a second tree using the sequence under query, HIV-1 pure subtypes, and CRFs sequences.
  • In the third 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.





  Figure showing the steps used in the HIV-1 subtyping tool.
Reference Alignment:
Subtype or CRFs
 Sequence Name
A1
 A1_UG85U455  
A1_UG9292UG037
A2
 A2_CD9797CDKTB48
A2_CY9494CY01741
B
 B_NL0067100T36
B_US90WEAU160
C
 C_BR9292BR025
C_BW9696BW0502
D
 D_CM0101CM4412HAL
D_TZ01A280      
F1
 F1_BE93VI850
F1_FR96MP411
F2
 F2_CM195MP255
F2_CM95MP257
G
 G_FI93HH8793121
G_NG9292NG083 
H
 H_BE93VI991 
H_CF9090CF056
J
 J_SE93SE7887
J_SE94SE7022
K
 K_CD97EQTB11C
K_CM96MP535 
CRF01_AE
 01_AECF19090CF11697
01_AETH90CM240    
CRF02_AG
 02_AGCM9797CMP807
02_AGFR91DJ264  
CRF03_AB
 03_ABRU97KAL153
03_ABRU98RU98001
CRF04_CPX
 04_CPXG1R9197PVCH
04_CPXGR9797PVMY
CRF05_DF
 05_DFBEVI1310
05_DFBE93VI961
CRF06_CPX
 06_CPXAU96BFP90
06_CPXML9595ML84
CRF07_BC
 07_BCC1N9797CN001
07_BCCN9898CN009
CRF08_BC
 08_BCCN19797CNGX7F
08_BCCN9898CN006 
CRF10_CD
 10_CDTZ19696TZBF071
10_CDTZ9696TZBF110
CRF11_CPX
 11_CPXF1R99MP1298
11_CPXGRGR17    
CRF12_BF
 12_BFAR97A32989
12_BFU1Y99URTR23
CRF13_CPX
 13_CPXC1M961849
13_CPXCM964164
CRF14_BG
 14_BGE1S00X477
14_BGES99X397


Program software used in the tool:

PAUP* - Phylogenetic inference (step 1 and 2)
 Clustalw - Alignment (all steps)
TreePuzzle - Likelihood mapping (step 4)
 Readseq - Sequence formating (all steps)

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 HIV Subtyping Process
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Developed by: Tulio de Oliveira, Koen Deforche, Sharon Cassol, Andrew Rambaut and Anne-Mieke Vandamme.

Developed in cooperation with the Evolutionary Biology Group at University of Oxford, UK., the HIV-1 Pathogenesis and Immunotherapeutics Program at University of Pretoria, South Africa, and the REGA Institute at the Katholieke Universiteit Leuven, Belgium.
Funded by the Marie Curie Fellowship, Flanders Bilateral Cooperation Program and the Wellcome Trust (grant # 061238 ).

For questions, suggestions or problems please contact:  Dr. Tulio de Oliveira.