TABLE 3

Selection pressures and positively and negatively selected codons of all coding regions of A(H3N2) viruses circulating between 1968 and 2011

Coding regionNo. of codonsdN/dSaNo. of selected sites (% of codons)
OverallInternalExternalInternal/externalPositively selectedeNegatively selected (FUBAR)b
FUBARbMEMEcDEPSd
PB27590.0770.0630.0880.716102628 (83)
PB16660.0750.0580.0860.674010459 (69)
PB1-N406350.0740.0590.0840.702010431 (68)
PB1-F2fNDNDNDNDNDNDND2ND
PA6540.0850.0700.0950.737041435 (67)
PA-N1555000.0940.0840.1000.840031327 (65)
PA-N1824730.0970.0900.1020.882031306 (65)
PA-XfNDNDNDNDNDNDND0ND
HA05660.3410.3010.3700.814101317274 (48)
HA13290.4660.4060.5150.788101215149 (45)
HA22210.1230.0930.1420.655001120 (54)
NP4980.0980.1090.0911.198010315 (63)
NA4690.2920.3110.2771.1232611233 (50)
M12290.0580.0780.0431.814010132 (58)
M2730.3910.2640.4810.5490007 (10)
NS11570.3520.3500.3530.99201333 (21)
NEP400.0740.0550.0870.63200011 (28)
  • a Calculated by SLAC.

  • b Posterior probability of ≥0.9.

  • c P value of <0.05.

  • d Bayes factor of >20.

  • e Information on the specific positively selected residues and their functions can be found in Table S5 in the supplemental material.

  • f ND, coding regions of PB1-F2 and PA-X were excluded from the codon-based analyses (SLAC, FUBAR, and MEME).