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Table 1 Amino acid substitutions or simple point mutations without accumulation of amino acid substitutions by using analysis of whole-genome sequencing of sixth-generation of viruses in each virus strain from both supernatants and cells

From: Identifying novel amino acid substitutions of hemagglutinin involved in virulence enhancement in H7N9 virus strains

H7N9 type Gene No. of mutation Base mutation AA mutation Change during passaging Mutation coverage
Anhui/1 HA 1 C96T NS C in P0,occurred in P1-6, T>C in P3 In MDCK1 and MDCK2, both MIX
   2 G421A NS G>A only in p1-5 A, recovered in P6 Only in MDCK2, MIX
   3 G427A A143T/135* G in P0,A occurred in P1,A>G in P3,G>A in all P4-6 virus Complete mutation in MDCK1, MIX in MDCK2
   4 C1554T NS C in P0, T occurred in P1-2,T>C in P3-6 In both MDCK1 and MDCK2; MIX
   1 G503A N168S/171# G in P0-1, A occurred in P2-3, A maintained in P4-6 In both MDCK1 and MDCK2;MIX
  NA 2 G996A G331S/335# G in P0-1, A occurred in P2-3 and maintained in P4-6 In both MDCK1 and MDCK2;MIX
   3 G1236A G412K/415# G in P0-1, A occurred in P2-3 and maintained in P4-6 In both MDCK1 and MDCK2;MIX
   1 G1027A A343T G in P0-3, A occurred in P4, A maintained in P5-6 In both MDCK1 and MDCK2; MIX
  PA 2 G1039A A347T G in P0-3, A occurred in P4, A maintained in P5-6 In both MDCK1 and MDCK2; MIX
   3 A1046G E349G G in P0-3, A occurred in P4, A maintained in P5-6 In both MDCK1 and MDCK2; MIX
   4 C135T NS C in P0, T occurred in P1, T maintained in P4-6 In both MDCK1 and MDCK2; MIX
   5 C720T NS C in P0, T occurred in P1, T maintained in P4-6 In both MDCK1 and MDCK2; MIX
   6 C1557T NS C in P0, T occurred in P1, T maintained in P4-6 In both MDCK1 and MDCK2; MIX
  PB1 1 G226A D76N G in P0-3, A occurred in P4, A maintained in P5-6 In only MDCK1, Mix
   2 T1356A V451E T in P0-3, A occurred in P4, A maintained in P5-6 In only MDCK1 Mix
  PB2 1 A260G D87G A in P0-3, G occurred in P4, G maintained in P5-6 In only MDCK1 Mix
   2 C990A NS C in P0, A occurred in P1-3, C maintained in P4-6 In both MDCK1 and MDCK2; MIX
  NP 1 G1117A A373T G in P0-4, A occurred in P5, A maintained in P6 In both MDCK1 and MDCK2; MIX
   2 G1071A NS G in P0, A occurred in P1, A maintained in P2-6 In both MDCK1 and MDCK2; MIX
  M 1 C900A NS C in P0-5, A occurred in P6 In only MDCK2 Mix
Shanghai/2 HA 1 C143T T48I/40* C in P0-2,T occurred in P3, T maintained in P4-6 Mix
   2 C236T T79I/71* C in P0-2,T occurred in P3, T maintained in P4-6 Mix
   3 G343A A117T/107* G in P0-2,A occurred in P3, A maintained in P4-6 Mix
   4 C494T T165I/157* C in P0-2,T occurred in P3, T maintained in P4-6 Mix
   5 G680A G227E/218* G in P0-2,A occurred in P3, A maintained in P4-6 Mix
   6 G694A V237I/223* G in P0, A occurred in P1,A maintained in P2-4, recovered in P5-6 Mix
   7 G1091A A369K/225* G in P0-2,A occurred in P3, A maintained in P4-6 Mix
   8 T618C NS T in P0-3:, T>C in P4:, P5:C>T,P6:T>C Mix
   9 G1011A NS P0-3:A>G, P4:G>=A,P5-6 converted to P0(G) Mix
  NA 1 C207T N73I/72 C in P0, T occurred in P1,T maintained in P2-4, recovered in P5-6 Mix
  PA 1 A256G M86V A in P0, G occurred in P1,G maintained in P2-3, recovered in P5-6 Mix
   2 A484G Y161A A in P0,G occurred in P1,G maintained in P2-5,G in P6 Complete mutation in P6
  PB1 1 C1544T S515F C in P0-2,T occurred in P3,G maintained in P4-6 Mix
   2 C1786T P596S C in P0-2,T occurred in P3,G maintained in P4-6 Mix
   3 C1143T NS P0-3:C, P4:C>T,P5-6:T>C  
   4 C1488T NS P0-3:C, P4:C>T,P5-6:T>C  
   5 G2061A NS P0-2:G, P3:G>A,P4:A>G,P5-6:G>A  
  PB2 1 T554G I185S T in P0-P3,G occurred in P4,G maintained in P5-6,G in P6 Complete mutation in P6
   2 C393T NS P0-3:C>T,P4-6 return to P0(C)  
   3 C717T NS P0-3:C>T,P4-6 return to P0(C)  
   4 G573A NS P0-4:G>A,P5-6 return to P0(G)  
  NP 1 G850A A284T G in P0, A occurred in P1,A maintained in P2-4, A in P5-6 Complete mutation in P5-6
   2 G1056A M352I G in P0, A occurred in P1,A maintained in P2-4, A in P5-6 Complete mutation in P5-6
   3 G987A NS P0-6:G>A, G=A in P3,P6 weaken Mix
   4 C1020A NS P0-4:C>A, P5-6 converted into P0(C) Mix
  NS 1 G301A D101N G in P0-P2, A occurred in P3-4, recovered in P5-6 Mix
   2 G622A E208K G in P0-P2, A occurred in P3-4, recovered in P5-6 Mix
   3 G651A NS P0-3:G,P4-6:G>A Mix
  1. *H7/H3 numbering; #N9/N2 numbering; NS: Only base mutations, but not amino acid mutations