analysis of recombination in the hiv-1pol gene richard myers division of infection and immunity...
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Analysis of Recombination in the HIV-1pol Gene
Richard Myers
Division of Infection and ImmunityUniversity College London
HIV-1 Recombination• HIV-1 sequence classification: 3 groups (M, N and O) and 9 subtypes (A-H, J and K).
•Recombination by superinfection / co-infection.
•There are ~16 HIV-1 CRFs – most common CRF01 (AE) and CRF02 (AG).
•Intra-subtype recombination exists, but is harder to detect and studied less extensively.
Detecting Recombination in polSeq Data: 10,545 HIV pol Sequences
STARRec-PSSM
Rec-Triplet(all data/pure subtypes)
SubtypesInter-subtypes
Non-Recombinant Subtypes
History analysis for each recombinant by
Phylogenetic Treesetc
Intra-subtypes
LOHA
STAR•High throughput subtyping tool that uses Position Specific Scoring Matrices (PSSMs).
Myers, R. E., Clarke, C., Khan, A., Kellam, P., Tedder, R. (2006). Genotyping Hepatitis B Virus from whole and sub-genomic fragments using position specific scoring matrices in STAR-HBV. J. Gen Virol. (In Press).
Myers, R. E., Gale, C. V., Harrison, A., Takeuchi, Y. & Kellam, P. (2005). A statistical model for HIV-1 sequence classification using the subtype analyser (STAR). Bioinformatics 21, 3535-40.
Gale, C. V., Myers, R., Tedder, R. S., Williams, I. G. & Kellam, P. (2004). Development of a novel human immunodeficiency virus type 1 subtyping tool, Subtype Analyzer (STAR): analysis of subtype distribution in London. AIDS Res Hum Retroviruses 20, 457-64.
http://www.vgb.ucl.ac.uk/starn.shtml
0.02
AAGBCDFKGHJNO
0.02
AAGBCDFKGHJNO
Subtyping Concordance
80
70
60
504520151050
Subtype
Ass
ign
men
t (%
)
REGA
STAR
HIVdb
10545 sequences from the UK National Resistance Database
STAR and Rec-PSSM Results
0
50
100
150
200
250
300
350
400
HIV-1 Subtype Recombination
Co
un
t
Subtype Frequency n.=10545
Distribution of Recombinant Architectures
1
10
100
1000
10000
HIV-1 Subtype
Lo
g C
ou
nt
0
10
20
30
40
50
60
70
80
Per
cen
t
NT_db
Percentage
CRF 03
CRF 04
Detection of CRF’sPutative Confirmed
CRF_03 5 1CRF_04 10 9CRF_05 1 0CRF_06 38 29CRF_07 4 1CRF_08 1 0CRF_09 16 15CRF_10 10 7CRF_11 7 7CRF_12 4 3CRF_13 8 7CRF_14 4 3CRF_15 1 0CRF_16 18 9Total 127 91
Conclusions•Large number of HIV-1 non-B subtypes in the UK (32.6%).
•The UK epidemic contains HIV-1 subtype recombinants (11%).
•Evidence for recombination outside of established CRFs.•Only ~10% of recombinant sequences appear to be established CRF’s (excluding CRF01/02•General mixing of HIV-1 sequences and breakdown of subtype classification.
HIV-1 Subtype Evolution?
Rambaut et al 2005; Nature Reviews Genetics
Acknowledgements
Paul KellamYasu TakeuchiCatherine GaleRobert GiffordArshad Kahn
MRC / UCL Centre for Medical Molecular Virology
Detecting Recombination in pol
•Detecting Recombination in HIV-1 pol is a 3 step process.
•1. Separate “pure subtype” sequences from putative recombinant sequences (Subtype Analyser – STAR, Rec-PSSM).
•2. Analyse putative recombinant sequences using a high throughput screen for inter-subtype recombination (Rec-PSSM).
•3. Analyse pure subtype sequences for intra-subtype recombination (Triplet-Rec).
STAR and Rec-PSSM Results
0
50
100
150
200
250
300
350
400
HIV-1 Subtype Recombination
Co
un
t
Subtype Frequency n.=10545
Distribution of Recombinant Architectures
1
10
100
1000
10000
HIV-1 Subtype
Lo
g C
ou
nt
0
10
20
30
40
50
60
70
80
Per
cen
t
NT_db
Percentage
0.02
AAGBCDFKGHJNO
0.02
AAGBCDFKGHJNO