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Table 4 Direct coupling terms for specific amino acid variants at covarying positions within the HIV-1 integrase

From: Molecular evolution of HIV-1 integrase during the 20 years prior to the first approval of integrase inhibitors

Position i

Amino acid α

Position j

Amino acid β

eij (α, β)

Time trend

Minor INSTI resistance mutation

INSTI-selected mutation

10

D

122

I

0.0683

  

*

10

E

122

I

−0.0753

  

*

11

D

119

S

−0.0940

*

  

11

D

154

I

−0.0527

*

 

*

11

D

154

M

0.0335

*

  

11

E

119

S

0.0909

*

  

11

E

154

I

0.0577

*

 

*

11

E

154

M

−0.0368

*

  

17

N

124

A

0.0690

 

*

 

17

S

124

A

−0.0598

 

*

 

23

A

201

I

−0.0490

  

*

23

A

201

V

0.0525

  

*

23

V

201

I

0.0432

  

*

23

V

201

V

−0.0443

  

*

31

I

154

I

−0.0438

  

*

31

V

154

I

0.0352

  

*

39

C

154

I

−0.0329

  

*

39

C

201

I

0.0776

  

*

39

C

201

V

−0.0725

  

*

39

S

154

I

0.0384

  

*

39

S

201

I

−0.0859

  

*

39

S

201

V

0.0828

  

*

72

I

265

A

0.0587

*

  

72

I

265

V

−0.0612

*

  

72

V

265

A

−0.0622

*

  

72

V

265

V

0.0676

*

  

101

I

111

K

−0.0743

  

*

101

I

111

T

0.0334

  

*

101

I

154

I

−0.0462

*

 

*

101

I

154

M

0.0645

*

 

*

101

L

154

I

0.0606

*

 

*

101

L

154

M

−0.0695

*

  

112

A

124

A

0.0205

 

*

 

112

I

124

A

0.0205

 

*

 

112

I

201

I

0.0482

  

*

112

I

201

V

−0.0538

  

*

112

T

124

A

−0.0447

 

*

 

112

T

201

I

−0.0483

  

*

112

T

201

V

0.0490

  

*

119

G

122

I

0.0576

  

*

119

P

122

I

0.1303

  

*

119

S

122

I

−0.1695

*

 

*

119

T

122

I

−0.0194

  

*

124

A

125

T

0.0266

 

*

 

124

A

125

V

−0.0288

 

*

 

124

A

211

K

−0.0568

 

*

 

124

A

211

R

0.0263

 

*

 

124

A

211

T

0.0294

 

*

 

124

S

125

A

0.0244

  

*

124

T

125

A

−0.0205

  

*

154

I

165

I

0.0893

*

 

*

154

I

165

V

−0.0976

*

 

*

154

I

256

D

0.0333

  

*

154

I

256

E

−0.0369

*

 

*

154

I

265

A

0.0520

*

 

*

154

I

265

V

−0.0484

*

 

*

154

M

165

I

−0.1011

*

  

154

M

165

V

0.1118

*

  

154

M

256

E

0.0525

*

  

154

M

265

A

−0.0496

*

  

154

M

265

V

0.0482

*

  

157

Q

160

K

−0.0632

 

*

 

157

Q

160

Q

0.0649

 

*

 

201

I

256

D

0.0623

  

*

201

I

256

E

−0.0611

*

 

*

201

I

265

A

0.0484

*

 

*

201

I

265

V

−0.0466

*

 

*

201

V

256

E

0.0604

*

  

201

V

265

A

−0.0535

*

  

201

V

265

V

0.0547

*

  
  1. Couplings with time-trending amino acid variants, minor INSTI resistance mutations, and INSTI-selected mutations are indicated by a star
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Virology Journal

ISSN: 1743-422X