Skip to main content

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