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Table 8 Results of env and pol endpoint dilution sequencing, showing the maximum pairwise distance sequences from the same sample, including the consensus sequence (using GTR with rates = Γ and shape = 0.5)

From: Recombination in feline immunodeficiency virus from feral and companion domestic cats

Sample

Env subtype*

No. env endpoint sequences^

Maximum pairwise distance (%)

Pol subtype*

No. pol endpoint sequences^

Maximum pairwise distance (%)

168

PR

12#

0.510

A

nd

 

258

PR

11#

0.524

U-NZpol1

nd

 

259

PR

10#

0.873

U-NZpol1

nd

 

260

PR

11

0.249

U-NZpol1

nd

 

GBI46

C

nd

 

U-NZpol1

10

0.442

GBI72

A

nd

 

U-NZpol1

10

0.660

GBI84

A

nd

 

U-NZpol1

10

0.667

MF21

U-NZenv

nd

 

U-NZpol2

10

0.661

MF29

U-NZenv

nd

 

U-NZpol2

13

1.844

PN9

C

nd

 

PR

9

0.437

PN17

PR

nd

 

U-NZpol1

10

0.672

PN18

PR

10

0.000

U-NZpol1

10

0.426

PN21

PR

10#

1.464

U-NZpol1

nd

 

PN22

PR

10

1.257

U-NZpol1

nd

 

PN23

PR

10#

0.375

U-NZpol1

11

0.658

PN24

C

nd

 

U-NZpol1

11

1.124

TKP73

U-NZenv

9

0.369

U-NZpol1

12

0.442

TKP88

U-NZenv

11

2.352

U-NZpol1

11

0.447

TKP94

U-NZenv

6

0.691

U-NZpol1

11

5.240

     

6 and consensus

1.599

     

4

0.661

TKP95

U-NZenv and C

13

25.717**

U-NZpol1

10

2.088

 

U-NZenv

10

2.313

   
 

C

3 and consensus

0.129

   
  1. # samples for which endpoint dilution sequencing was documented in Hayward et al. (2007), but here the sequence number has been extended from five to ten sequences per sample.
  2. *PR = putative recombinant
  3. **sample with dual infection
  4. ^nd = not done
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Virology Journal

ISSN: 1743-422X