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Table 2 Selection pressure and positively selected sites in the HA and NA genes from viruses from different datasets.

From: Different evolutionary trends of swine H1N2 influenza viruses in Italy compared to European viruses

Gene Number of sequences Length of alignment (aa) Mean dN/dS Positively selected sites Domain1 Antigenic site2
    (95% CI) P = 0.1   
     SLAC FEL   
H1 avian-like 61 539 0.208 (019–0.22) 116 116 HA1 - E  
     137 137 HA1 -RBD  
      152 HA1 -RBD  
     159 159 HA1 -RBD Ca
     172 172 HA1 -RBD Sa
      185 HA1 -RBD Ca
      213 HA1 -RBD Sb
      232 HA1 -RBD  
     239 239 HA1 -RBD  
      392 HA2 - F  
      399 HA2 - F  
H1 human-like 65 555 0.225 (0.21-0.24) 102 102 HA1 - E  
      146 HA1 -RBD  
      158 HA1 -RBD Ca
      213 HA1 -RBD Sb
     271 271 HA1 -RBD  
     550 550 HA2 - F  
N2 EU sw H1N2 84 469 0.185 (0.17-0.20)   358 PIR H'  
      381   
      455   
N2 recent Italian H1N2 42 461 0.181 (0.15-0.22) 0 0   
N2 human H3N2 240 459 0.265 (0.24-0.29)   43 PIR A'  
     151 151 NA head domain  
     221 221 Antibody binding  
     267    
      339 PIR F' Antigenic site
     370 370   Antigenic site
  1. 1 → HA domains: E- vestigial esterase, RBD – Receptor binding domain, F – membrane fusion subdomain in the HA2 subunit [38]. NA domains: PIR – phylogenetically important regions described by Fanning et al. [39], NA head domain and antibody binding positions were previously reported by Gulati et al. [40].
  2. 2 → Antigenic sites in HA: Ca, Sa, Sb described by Caton et al. [37] and for H1N1pdm by Xu et al. [41]. Antigenic sites in NA: described by Colman et al. [42] and Air et al. [43].
  3. Numbering is based on defining the first amino acid of the open reading frame as amino acid n. 1.