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Large Scale Sequence Analysis of Avian Influenza Isolates

Table 2. Distribution of PDZ ligand domains (PL) in 1,196 influenza NS proteins.

Distribution of PDZ ligand domains (PL) in 1,196 influenza NS proteins. PDZ-domain ligand sequences found in this population are listed in the PL column; the top blank entry refers to sequences in which the C-terminus is truncated to varying extents. The distribution of each PL sequence in Avian, Human, Swine, and Equine AIV isolates is shown. The residue at the -3 position from COOH clearly distinguishes these populations; avian and equine always having E/G at -3 and human never having E/G at -3. In contrast, human signatures have R/K at -3 92% of the time; the remaining 8% have avian signatures and are known to be of avian origin. Swine isolates can accommodate both PL motifs. The single isolate with the PL motif KSEV is from the 1918 NS1 sequence.

PL Avian Human Swine Equine -3
  5 2 4   E/G
EPEV 23 21 1 14
EPKV       1
ESEI 48   4  
ESEV 483 12 7 10
ESKV 55      
GPEV 2 1 19 2
GPKV     6  
GSEA 1      
GSEI     1  
GSEV 4   4  
GSKV 1 2    
           
KSEV   1     R/K
RPKV   1    
RSEA     1  
RSEV   22 4  
RSKI   9    
RSKV   403 21  
TSEV     1  
Totals 622 474 73 27