Supplementary Table 1.Amino acid differences betweenA/ck/Egypt/9402-CLEVB213/2007 and A/ck/Egypt/08124S-NLQP/2008.

Virus
Amino Acid # / Egypt/07 / Egypt/08
PB2 / 338 / V / I
473 / M / V
559 / A / T
PB1 / 117 / T / A
182 / T / I
214 / K / R
584 / H / R
642 / S / N
PA / 94 / I / V
321 / N / S
367 / R / K
465 / I / T
669 / A / V
716 / K / N
HA1 / 74a / S / P
94 / N / D
97 / N / D
110 / R / H
123 / P / S
140 / G / R
141 / P / S
144 / Y / F
162 / K / R
165* / H / N
184 / E / A
226 / V / M
235 / S / P
HA2 / 43 / K / R
183 / T / I
207 / F / S
NP / 34 / N / S
109 / I / V
287 / G / S
350 / A / T
371 / T / M
425 / V / I
NAb / 46 / A / D
188 / I / T
241 / V / I
339 / S / F
NS1c / 74 / D / G
127 / I / T
129 / I / T
M2 / 31 / N / S
PB1-F2 / 8 / P / L
18 / T / I
42 / Y / C
NS2 / 23 / Y / S
48 / V / A

a Changes a N-linked glycosylation site

b Numbering includes the 20 amino acid stalk deletion at position 49-68

c Numbering includes the 80-84 amino acid deletion