A comparative study of adaptive molecular evolution in different HIV clades

Marc ChoisyCEPM UMR CNRS-IRD 9926

Montpellier, France

HIV-2

HIV-1

HIV-2

HIV-1 M

HIV-1 N

HIV-1 O

Adaptive evolution ?

Purifying selection

Adaptive evolution

Darwinian evolution(mutation + selection)

Neutral evolution(mutation alone)

No selectionSelection

A A A T GGCA T

Lys TrpThr

dS

Lys TrpThr

A A T GGCA T G

dN

Asn TrpThr

A A T GGCA T C

Molecular evolutiondN/dS>1

dN/dS<1

dN/dS=1

envelop proteins

env

Lipid membrane

gp41gp120

Capsid

gagRNA

0 10000

pol

enzymes

1

HIV-2 A HIV-1 M A

HIV-1 M B

HIV-1 M C

dN/dS

0

HIV-2 A

HIV-1 M AHIV-1 M BHIV-1 M C

w = dN/dS

w = dN/dS = p0*w0+ p1*w1+ p2*w2+ p3*w3

w3w2w1w0

p1

p2p0

p3

w = dN/dS = p0*w0+ p1*w1+ p2*w2

LRT

w = dN/dS = p0*w0+ p1*w1+ p2*w2

w = dN/dS = p0*w0+ p1*w1+ p2*w2

0.0

0.2

0.4

0.6

0.8

1.0

Prior probabilities : p0, p1, and p2

0.0

0.2

0.4

0.6

0.8

1.0

Posterior probabilities : f0i, f1

i, and f2i

wi = dN/dSi = f0

i*w0+ f1i*w1+ f2

i*w2

5’ 3’

2

95%

1

HIV-1 M AHIV-1 M BHIV-1 M DHIV-1 M C

HIV-1 O

HIV-2 A

0.0

0.2

0.4

0.6

0.8

1.0

95%

2

1

wi = f0i*w0+ f1

i*w1+ f2i*w2

0.0

0.2

0.4

0.6

0.8

1.0

95%

1

HIV-1 M A1 MRAMGIQR-NCQ-SL-WRWG------IMILGMIIICSAA----GNLWVTVYYGVPVWKDAET--TLFCASDAKAYTTEVH 80 HIV-1 M B MTVKGTRK-NYR-HL-WTWG------TMILGILMICSAA----NNFWVTVYYGVPVWREATT--TLFCASDAKAYDEEVH 80 HIV-1 M C MRATGIQR-NCQ-QW-WIWG------ILGFWMLMICNVM----GNLWVTVYYGVPVWKEATT--TLFCASDAKAYDTEAH 80

HIV-1 M D MRVKGIKR-NYQ-PL-WKWG------IMLLGMLMMTYSAA---DNLWVTVYYGVPVWKEATT--TLFCASDAKSYKTEAH 80

HIV-1 O MKA----MEKR---NKKLW-----TLYLAMALITPCLSL----RQLYATVYAGVPVWEDATP--VLFCASDANLTSTEKH 80 SIVcpz MR-----KPIH-----IIW---GLALLIQFIE----KGT----NEDYVTVFYGVPVWRNATP--TLFCATNASMTSTEVH 80

HIV-1 M A1 NVWATHACVPTDPNPQEINLENVTEKFNMWKNNMVEQMHTDIISLWDQSLQPCVKLTPLCVTLNCSDVNVNAT------- 160 HIV-1 M B NVWATHACVPTDPNPQEVELINVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVSLNCTDAKNTTN------- 160 HIV-1 M C NVWATHACVPTDPNPQEMVLKNVTEDFNMWKNDMVDQMHQDIISLWDQSLKPCVKLTPLCVTLDCKNANATHN------- 160

HIV-1 M D NIWATHACVPTDPNPQEIELKNVTENFNMWKNNMVDQMHEDIISLWDQSLKPCVKLTPRCVTLNCTDASRNST------- 160

HIV-1 O NIWASQACVPTDPTPYEYPLHNVTDDFNIWKNYMVEQMQEDIISLWDQSLKPCVQMTFLCVQMECTNIAGTTN------- 160 SIVcpz NVWATTSCVPIDPDPIVVRL-NTSVWFNAYKNYMVESMTEDM?QLFQQSHKPCVKLTPMCIKMNCTGYNGTPT------- 160

HIV-1 M A1 -------------NYNVNDTINMKEEIRNCSFNMTTE-LRDRKQKVYSLFYRLDVVQMNN-------------------S 240 HIV-1 M B -----SNTNSSSSTNSSSLEQGKAGEIKNCSFNITTN-MRDKVQKQYALFYSLDIVPIDD-------------------K 240 HIV-1 M C ---------------GTIDNRTMGGEIKNCSFNITTE-LKDKKQRAHALFYSLDIVQLDG-------------------- 240

HIV-1 M D -------------DNNSTLPTVKPGEMKNCSFNITTV-VTDKRKQVHALFYRLDVVQIDN-------------EGKNEIN 240 HIV-1 O -----------------------ENLMKKCEFNVTTV-IKDKKEKKQALFYVSDLMELNE--------------TSSTNK 240 SIVcpz ----TPSTTTSTVTPKTTTPIVDGMKLQECNFNQSTG-FKDKKQKMKAIFYKGDLMKCQD-------------------N 240

HIV-1 M A1 NNSNQYRLINCNTSAI-TQACPKVSFEPIPIHYCAPAGYAILKCKDKEFNGT--GLCKNVST-VQCTHGIKPVVSTQLLL 320 HIV-1 M B GNDTSYRLISCNTSVI-TQACPKISFEPIPIHYCAPAGFAILKCNEKGFNGK--GPCKNVST-VQCTHGIRPVVSTQLLL 320 HIV-1 M C --GGSYRLISCNTSAI-TQACPKVSFDPIPIHYCAPAGYAILKCNNKTFNGT--GQCNNVST-VQCTHGIKPVISTQLLL 320

HIV-1 M D DTYGTYRLINCNTSAI-TQACPKVSFEPIPIHYCAPAGFAILKCNDKRFNGT--GPCKNVSS-VQCTHGIRPVVSTQLLL 320 HIV-1 O TNSKMYTLTNCNSTTI-TQACPKVSFEPIPIHYCAPAGYAIFKCNSTEFNGT--GTCRNITV-VTCTHGIRPTVSTQLIL 320 SIVcpz NETNCYYLWHCNTTTI-TQSCEKSTFEPIPIHYCAPAGYAILRCEDEDFTGV--GMCKNVSV-VHCTHGISPMVATWLLL 320

HIV-1 M A1 -NGSLAE-SKVMIRSENIT-NNAKNILVQLTSPVNISCIRPNNNT--RKSVRI---GPGQAFYATGE----IIGNIRQAY 400 HIV-1 M B -NGSLAE-EEVVIKSDNFT-NNAKTIIVQLNTSVEITCVRPNNNT--RRSIPI---GPGRAFYTT-E----IIGDIRQAY 400 HIV-1 M C -NGSLAE-EEIIIRSENLT-NNAKTIIVHLKDPVEIECTRPNNNT--RKSIRI---GPGQILYATGD----IIGDIRQAH 400

HIV-1 M D -NGSLAE-EEIVIRSENLT-NNAKIIIVHLNQSVEINCTRPYKKE--RQRTPI---GQGQALYTTRY----TTRIIGQAY 400 HIV-1 O -NGTLSK-GKIRMMAKDIL-EGGKNIIVTLNSTLNMTCERPQI-D--IQEMRI---GPMAWYSMGIG--GTAGNSSRAAY 400 SIVcpz -NGTYQT-NTSVVMNGRKN-ESVLVRFGKEFENLTITCIRPGNRT--VRNLQI---GPGMTFYNVEI----ATGDTRKAF 400

HIV-1 M A1 CNVNRSEWNEALREVVKQLR--TYF------NKTIIFDNSS-GGDLEITTHSFNCGGEFFYCNTSRLFNSTW-----NDT 480 HIV-1 M B CNITKANWTDTLQKVAIKLR--EQF------NKTIAFKPSS-GGDPEIVTHSFNCGGEFFYCNSTQLFNGTW-----NGT 480 HIV-1 M C CNINETKWNKTLQDVSEKLA--KYFP-----NKTINFAQPS-GGDLEIVTHSFNCRGEFFYCNTSKLFNSTD-------- 480

HIV-1 M D CNISGVKWNNTLRQVARKLG--NLLN-----QTKIIFKPSS-GGDPEITTHSFNCGGEFFYCNTSGLFNSAW------NI 480 HIV-1 O CKYNATDWGKILKQTAERYL-ELVNNT---GSINMTFNHSS-GGDLEVTHLHFNCHGEFFYCNTAKMFNYTF----SCNG 480 SIVcpz CTVNKTLWEQARNKTEHVLA--EHWKKVDNKTNAKTIWTF-QDGDPEVKVHWFNCQGEFFYCDITPWFNATY------TG 480

HIV-1 M A1 TSMLN--DTKPN-------DTITLPCRIKQIINM-WQR-AGQAIYAPPIQ-GVIRCESNITGLILTRDGGGN-------S 560 HIV-1 M B WINGTWKSSYGNDT-----TNITLPCRIKQIINM-WQE-VGKAMYAPPIR-GQIKCTSNITGLLLTRDGGNS-----NTT 560 HIV-1 M C -RSS---STES--------ANITIPCRIKQIINM-WQG-VGRAMYAPPIK-GKITCKSNITGLLLTRDGGTT-------- 560 HIV-1 M D SGHS---TGLND-------TIITIPCRIKQIINM-WQE-VGKAMYAPPIE-GQINCSSNITGLLLTRDGGAN-------- 560 HIV-1 O TTCS----VSNVSQG-NN-GT--LPCKLRQVVRS-WIR-GQSGLYAPPIK-GNLTCMSNITGMILQMDNTWN-------S 560 SIVcpz NLI-------TN-------GALIAHCRIKQIVNH-WGI-VSKGIYLAPRR-GNVSCTSSITGIMLEGQIYNE-------- 560 HIV-1 M A1 SVSSETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVV------EREKRAV-G-LGAV-FIG-FLGAAGSTMG 640 HIV-1 M B DNSTETFRPGGGDMRDNWRSELYRYKVVQVEPLGIAPTRAKRRVV------QREKRAV-G-IGAM-FLG-FLGAAGSTMG 640 HIV-1 M C NDSTEAFRPAGGDMKDNWRSELYKYKVVEIKPLGVAPTKAKRRVV------EREKRAV-G-IGAV-FLR-FLGAAGSTMG 640 HIV-1 M D NTQNDTFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVV------EREKRAI-G-LGAM-FLG-FLGAAGSTMG 640 HIV-1 O SNNNVTFRPIGGDMKDIWRTELFNYKVVRVKPFSVAPTRIARPVISTRT--HREKRAV-G-LGML-FLG-VLSAAGSTMG 640 SIVcpz ---TVKVSP-AARVADQWRAELSRYQVVEI?PLSVAPTT?KRPEIKQH---SRQKRGI-G-IGLF-FLG-LLSAAGSTMG 640 HIV-1 M A1 AASITLTVQARQLLSGIVQQQ-SNLLRAIEAQQHLLKLTVWGIKQLQARVLALERYLRD-QQILGIWGCSGKLICTTNVP 720 HIV-1 M B AASVTLTVQARQLLSGIVQQQ-NNLLRAIEAQQHMLQLTVWGIKQLQARVLAVERYLRD-QQLLGLWGCSGKLICTTTVP 720 HIV-1 M C AASITLTVQARQLLSGIVQQQ-SNLLRAIETQQHMLQLTVWGIKQLQTRVLAIERYLKD-QQLLGIWGCSGKLICTTAVP 720 HIV-1 M D AASMTLTVQARQVLSGIVQQQ-NNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKD-QQLLGIWGCSGKHICTTTVP 720 HIV-1 O AAATTLAVQTHTLLKGIVQQQ-DNLLRAIQAQQQLLRLS?WGIRQLRARLLALETLLQN-QQLLSLWGCKGKLVCYTSVK 720 SIVcpz AASIALTAQTRNL?HGIVQQQ-ANLLQAIETQQHLLQLSVWGVKQLQARMLAVEKYLRD-QQLLSLWGCADKVTCHTTVP 720 HIV-1 M A1 WNSSWS-N---------KSQSEIW--ENMTWLQWDKEISNYTHIIYTLLEESQIQQEKNEQDLLALDKWANLWNWFDITN 800 HIV-1 M B WNTSWS-N---------KTLEKIW--DNMTWMQWETEINNYTNIIYTLLEESQNQQEKNEKDLLELDQWANLWNWFTISN 800 HIV-1 M C WNDSWSNN---------KTLGDIW--NSTTWMQWDREISNYTNTIYRLLEDSQNQQEQNEKDLLALDKWQNLWSWFDITN 800 HIV-1 M D WNSSWS-N---------RSVEYIW--GNMTWMQWEREIDNYTGLIYNLIEESQIQQEKNEKELLELDKWASLWNWFSITQ 800 HIV-1 O WNRTWI-G-----------NESIW--DTLTWQEWDRQISNISSTIYEEIQKAQVQQEQNEKKLLELDEWASIWNWLDITK 800 SIVcpz WNNSWV-NFTQTCAKNSSDIQCIW--ENMTWQEWDRLVQNSTGQIYNILQIAHEQQERNKKELYELDKWSSLWNWFDITQ 800 HIV-1 M A1 WLWYIKIFIM-IVGGLIGLRIVFTVLSIINRVRQGYSPLSFQTHTP-NPGG-LDRPRRIEEEGGEQDRDRSIRLVGGFLT 880 HIV-1 M B WLWYIKIFIM-IVGGLIGLRIVFTVFSIVNRVRQGYSPLSFQTHLP-TPRG-PDRPEGIEEEGGERGRGSSTRLVHGFLA 880 HIV-1 M C WLWYIKIFIM-IVGGLIGLRIIFAILSIVNRVRQGYSPLSFQTLTP-SPRG-PDRLGRIEEEGGEQDRDRSIRLVSGFLA 880 HIV-1 M D WLWYIKIFIM-IVGGLIGLRIVFAVLSIVNRVRQGYSPLSFQTLLP-APRG-PDRPEGIEEEGGEQDRGTSIRLVNGFSA 880 HIV-1 O WLWYIKIAII-IVGALVGVRVIMIVLNIVKNIRQGYQPLSLQIPNH-HQEE-AGTPGRTGGGGGEEGRPRWIPSPQGFLP 880 SIVcpz WLWYIKIFIM-IVGAIVGLRILLVLVSCLRKVRQGYHPLSFQIPTQ-NQQD-PEQPEEIREEGGRKDRIRWRALQHGFFA 880 HIV-1 M A1 LVWDDLRSLCLFSYHRLRDFTLIAARTVELLGHSSLKGLRLGWEGLKYLGNLLLYWGRELRISAINLLDTIAIIIAGWTD 960 HIV-1 M B LFWDDLRSLCLFSYHRLRDLLLIVTRIVELLGRG-------GWEALKYWWNLLQYWRQELQKSAVSLFNATAIAVAEGTD 960 HIV-1 M C LAWDDLRSLCLFSYHRLRDLILIATRVVELLGRSSLRGLQRGWEILKYLGSLVQYWGLELKKSAINLLNITAIAVAEGTD 960 HIV-1 M D LIWDDLRNLCLFSYHRLRELILIAARIVELLGRR-------GWEALKYLWNLLQYWSRELKNSAISLVDATAIAVAEGTD 960 HIV-1 O LLYTDLRTIILWTYHLLSNLASGIQKVISYLRLGLWILGQKIINVCRICAAVTQYWLQELQNSATSLLDTLAVAVANWTD 960 SIVcpz LLWVDLTSIIQWIYQICRTCLLNLWAVLQHL------CRITFRLCNHLENNLSTLW-TIIRTEIIKNIDRLAIWVGEKTD 960

2 wi = f0i*w0+ f1

i*w1+ f2i*w2

Test 1 :H0 : no match between +vely selected sitesH1 : match between +vely selected sites

Positively selected sites tend to occur at the same position in different clades, except for HIV-2

HIV data set HIV-1 M:A HIV-1 M:B HIV-1 M:C HIV-1 M:D HIV-1 O E 2.018 HIV-1 M:B O 13 P 0.001

E 1.990 2.015 HIV-1 M:C O 16 15 P 0.001 0.001

E 1.760 1.793 1.741 HIV-1 M:D O 10 14 15 P 0.001 0.001 0.001

E 1.016 0.996 0.889 0.848 HIV O O 7 7 8 6 P 0.001 0.001 0.001 0.001

E 0.633 0.722 0.571 0.511 0.729 HIV-2 A O 3 1 2 2 1 P 0.024 0.535 0.104 0.091 0.539

Test 2 :H0 : random repartition of +vely selected sites with respect to epitopesH1 : no match between +vely selected sites and epitopesH2 : match between +vely selected sites and epitopes

Positively selected sites do not tend to be related to epitopic sites

Epitopes NIN OIN EIN PIN NOUT OOUT EOUT POUT

Ab 370 18 22.17 0.946 208 17 12.53 0.072

CTL 394 19 23.82 0.976 184 16 11.12 0.053

Th 499 26 30.16 0.989 79 9 4.78 0.028

Ab and CTL 507 30 30.64 0.726 71 5 4.17 0.401

Ab and Th 537 33 32.40 0.496 41 2 1.90 0.612

CTL and Th 524 27 31.67 0.999 54 8 2.92 0.018

H1 vs H0 H2 vs H0

Test 3 :H0 : no match between +vely selected sites and glycosylation sitesH1 : match between +vely selected sites and glycosylation sites

HIV-1

data set

Sites of

N-glyc

Conserved

N-glyc

Observed Expected P-value

HIV-1 M:A 28 5 11 1.64 0.001

HIV-1 M:B 27 2 5 1.62 0.019

HIV-1 M:C 30 2 7 1.69 0.002

HIV-1 M:D 22 5 4 1.17 0.023

HIV-1 O 39 6 13 2.46 0.001

Positively selected sites tend to occur on N-glycosylation sites

Test 4 :H0 : +vely selected sites have the same strengthH1 : +vely selected sites do not have the same strength

HIV data set HIV-1 M:A HIV-1 M:B HIV-1 M:C HIV-1 M:D HIV-1 O HIV-1 M:B Z = 3.8266

N = 69

P = 0.0001

HIV-1 M:C Z = 1.2150

N = 67

P = 0.2244

Z = -2.1945

N = 62

P = 0.0282

HIV-1 M:D Z = 0.6009

N = 46

P = 0.5479

Z = -1.1021

N = 54

P = 0.2704

Z = -0.4077

N = 51

P = 0.6835

HIV-1 O Z = 0.3652

N = 23

P = 0.7149

Z = -1.853

N = 22

P = 0.0639

Z = -1.0934

N = 26

P = 0.2742

Z = 0.0000

N = 18

P = 1.0000

HIV-2 A Z = -0.4001

N = 11

P = 0.6891

Z = -1.0193

N = 10

P = 0.3081

Z = 1.8347

N = 10

P = 0.0665

Z = 0.8293

N = 9

P = 0.4069

Z = 2.2819

N = 7

P = 0.0225

Not that much difference between clades

CONCLUSIONS

Positively selected sites tend to occur at the same position in different clades, except for HIV-2

Positively selected sites do not tend to be related to epitopic sites

Positively selected sites tend to occur on N-glycosylation sites

Similar intensity of selection across clades

CONCLUSIONS

Positively selected sites tend to occur at the same position in different clades, except for HIV-2

Positively selected sites do not tend to be related to epitopic sites

Positively selected sites tend to occur on N-glycosylation sites

Similar intensity of selection across clades

Moderates conclusions from Gaschen et al 2002

CONCLUSIONS

Positively selected sites tend to occur at the same position in different clades, except for HIV-2

Positively selected sites do not tend to be related to epitopic sites

Positively selected sites tend to occur on N-glycosylation sites

Similar intensity of selection across clades

Confirms the glycan shield model of Kwong et al. 2002

Glycan shield model (Kwong et al. 2002)

Glycan shield model (Kwong et al. 2002)

Glycan shield model (Kwong et al. 2002)

Glycan shield model (Kwong et al. 2002)

Glycan shield model (Kwong et al. 2002)

Glycan shield model (Kwong et al. 2002)

Glycan shield model (Kwong et al. 2002)

Glycan shield model (Kwong et al. 2002)

Glycan shield model (Kwong et al. 2002)

Glycan shield model (Kwong et al. 2002)

Glycan shield model (Kwong et al. 2002)

Glycan shield model (Kwong et al. 2002)

Glycan shield model (Kwong et al. 2002)

Contributors:C. H. Woelk, University of California San Diego, USA.

D. L. Robertson, University of Manchester, UK.

J. F. Guégan, CEPM, UMR CNRS-IRD 9926, Montpellier, France.

Data:Kuiken, C., et al. (2000). HIV Sequence Compendium. Los Alamos, NM, USA: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory.

Korber, B., et al. (2000). HIV Molecular Immunology. Los Alamos, NM, USA: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory.

Programs:Yang, Z. H. (1997). PAML: a program package for the phylogenetic analysis by maximum likelihood. Computer Applications in the Biosciences 13, 555-556.

Hansen, J. E., et al. (1998) NetOglyc: prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glycoconjugate Journal 15, 115-130.

ACKNOWLEDGEMENTS

PAUP*

A.6

A.7

A.2

A.11A.3

A.17

A1.14A.16

A.12

A1.8

A.10A.4

A.9A1.5

A1.15

A.1

A.13

50 changes

ML on model of codon substitution

dN/dS= w0p0 + w1p1 + w2p2