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Table 1 Patient characteristics, resistance mutations and evolution

From: Persistence of frequently transmitted drug-resistant HIV-1 variants can be explained by high viral replication capacity

ID

Gender

Last negative HIV test

Country of origin

Diagnosis

Risk group

Months after first analysis

Plasma HIV RNA

(copies/ml)

CD4 count

Sub-type

Resistance Profile PR

Resistance Profile RT

p-distance

p-value dN/dS

Transmitted variants harboring only NRTI-related mutations

P01

Male

 

NL

May 2007

MSM

0

>750000

461

B

 

M41L

  
      

10

    

M41L

0.001

1.000

      

16

    

M41L

0.002

0.290

P02

Male

 

NL

Jan 2008

MSM

0

21800

423

B

 

M41L

  
      

12

    

M41L

0.005

0.225

      

28

    

M41L

0.005

0.225

P03

Male

Jan 2004

BE

Jun 2005

MSM

0

41000

483

B

 

M41L

  
      

11

    

M41L

0.000

1.000

      

32

    

M41L

0.002

0.152

P04

Male

 

NL

Feb 2007

MSM

0

102000

322

B

 

L210LS

  
      

11

    

-

0.000

1.000

      

25

    

-

0.002

1.000

P05

Male

 

SL

Jun 2001

MSM

0

12267

950

B

 

T215D

  
      

12

    

T215D

0.011

0.060

      

99

    

T215D

0.007

0.428

P06

Male

Mar 2005

SL

Feb 2006

MSM

0

797000

953

B

 

T215S

  
      

14

    

T215S

0.000

1.000

      

21

    

T215S

0.000

1.000

P07

Male

 

NL

Sep 2008

MSM

0

36300

521

B

 

T215D

  
      

11

    

T215D

0.000

1.000

      

27

    

T215D

0.000

1.000

P08

Male

Sep 2004

NL

Dec 2004

MSM

0

583000

596

B

 

T215IT

  
      

13

    

-

0.000

1.000

P09

Male

Sep 2006

NL

Sep 2007

MSM

0

158000

678

B

 

T215AT

  
      

13

    

T215AT

0.001

0.294

      

20

    

T215A

0.000

1.000

P10

Male

Oct 2003

NL

Jan 2005

MSM

0

89800

289

B

 

K219N

  
      

11

    

K219N

0.000

1.000

      

44

    

K219N

0.000

1.000

P11

Male

 

BE

Mar 2006

HSX

0

318000

966

B

 

D67N T215C

  
      

13

    

D67N T215C

0.001

0.291

P12

Male

 

NL

Feb 2007

MSM

0

55900

609

B

 

D67G T215C K219E

  
      

11

    

D67G T215C K219E

0.007

0.156

      

24

    

D67G T215C K219E

0.000

1.000

P13

Male

Jul 2004

NL

Nov 2007

MSM

0

294000

531

B

 

D67G T215C K219E

  
      

12

    

D67G T215C K219E

0.000

1.000

      

14

    

D67G T215C K219E

0.000

1.000

P14

Male

Apr 2005

NL

Jun 2005

HSX

0

750000

577

B

 

D67G T215C K219E

  
      

14

    

D67G T215C K219E

0.000

1.000

P15

Male

 

NL

Aug 2005

MSM

0

81000

470

B

 

M41L T69S T210E T215ST

 

1.000

      

11

    

M41L T69S T210DE T215ST

0.000

1.000

      

39

    

M41L T69S T210E T215ST

0.000

1.000

      

77

    

M41L T69S T210E T215ST

0.000

1.000

P16

Male

Mar 2005

NL

Jun 2006

MSM

0

34600

1129

B

 

M41L T69S T210E T215ST

  
      

13

    

M41L T69AS T210E T215ST

0.000

1.000

      

33

    

M41L T69S T210E T215ST

0.001

1.000

      

49

    

M41L T69S T210E T215ST

0.001

1.000

Transmitted variants harboring only NNRTI-related mutations

P17

Male

Feb 2005

NL

Sep 2006

MSM

0

5990

790

B

 

K103N

  
      

12

    

K103N

0.000

1.000

      

30

    

K103N

0.000

1.000

P18

Male

Jun 2004

BE

Apr 2006

MSM

0

39900

648

B

 

K103N

  
      

12

    

K103N

0.000

1.000

      

28

    

K103N

0.000

1.000

P19

Male

 

NL

Sep 2005

MSM

0

21400

359

B

 

K103Q

  
      

12

    

K103Q

0.000

1.000

      

59

    

K103Q

0.001

0.304

P20

Male

1995

SL

Sep 2005

MSM

0

29300

421

B

 

Y181C

  
      

11

    

Y181C

0.000

1.000

      

49

    

Y181C

0.002

0.305

P21

Female

 

GR

Sep 2004

HSX

0

905

699

B

 

G190A

  
      

10

  

B

 

G190A

0.005

0.866

P22

Male

 

GR

Jun 2004

?

0

10500

918

B

 

G190A

  
      

13

  

B

 

G190A

0.005

0.387

Transmitted variants harboring only PI-related mutations

P23

Male

 

NL

Apr 2007

HSX

0

700000

664

B

M46L

   
      

14

   

M46L

 

0.000

1.000

      

22

   

M46L

 

0.000

1.000

P24

Male

Jan 2006

NL

Apr 2008

MSM

0

5170

742

B

M46L

   
      

10

   

M46L

 

0.001

0.310

      

29

   

M46L

 

0.004

0.471

P25

Male

Jul 2005

NL

Aug 2008

MSM

0

421000

409

B

M46L

   
      

14

   

M46L

 

0.000

1.000

      

23

   

M46L

 

0.000

1.000

P26

male

 

NL

Aug 2008

MSM

0

111000

657

B

M46L

   
      

14

   

M46L

 

0.000

1.000

      

26

   

M46L

 

0.001

0.299

P27

male

05-11-04

NL

Apr 2007

MSM

0

18100

699

B

M46L

   
      

13

   

M46L

 

0.000

1.000

      

38

   

M46L

 

0.001

0.306

P28

male

15-02-03

NL

Mar 2005

MSM

0

69000

480

B

L90M

   
      

13

   

L90M

 

0.000

1.000

Transmitted variants harboring mutations against two drug classes

P29

male

 

NL

Dec 2001

MSM

0

288

1468

B

 

D67G Y181CY T215C K219E

  
      

10

    

D67G T215C K219E

0.006

0.148

      

46

    

D67G T215C K219E

0.000

1.000

P30

male

 

NL

Jan 2005

HSX

0

26600

667

B

G73S L90M

K103N

  
      

12

   

L90M

K103N

0.001

0.306

      

18

   

L90M

K103N

0.001

0.306

P31

female

 

GR

Jul 2004

HSX

0

696

1288

B

I54V V82A L90M

M41L D67N L210W T215D

  
      

10

   

F53FL I54V V82A L90M

M41L D67N L210W T215D

0.001

0.293

  1. Abbreviations: PR protease, RT reverse transcriptase, NRTI nucleoside reverse transcriptase inhibitor, NNRTI non- nucleoside reverse transcriptase inhibitor, PI protease inhibitor, BE Belgium, GR Greece, NL the Netherlands, SL Slovenia, HSX heterosexual, MSM Men having sex with men? unknown route of transmission.