Supplement table 1. Oligonucleotide primers using for whole genome sequencing of IAV-H1N3 and IAV-H1N9

Gene / Primer name / Primer sequence / Annealing Tm. / References
H1 / HA Hoff F* / TAT-TCG-TCT-CAG-GGA-GCA-AAA-GCA-GGG-G / 50 °C / 1
H1R / TGY-TCY-TTR-CCY-ACY-GCW-GTG / 1
H1F / YDT-CGA-TGC-TCC-RGT-YCA--Y / 50 °C / 1
HA Hoff R* / ATA-TCG-TCT-CGT-ATT-AGT-AGA-AAC-AAG-GGT-GTT-TT / 1
N3 / N3 F1 / TGA-ATC-CAA-ATC-AGA-AGA-TAA / 45 °C / This study
N3 R1 / TGA-TTC-CY-AGY-AWW-GCY-CCT / This study
N3 F2 / TTC-ACA-AGG-ACA-ATG-CAA-TA / 45 °C / This study
N3 R2 / ACA-ACA-CAR-GTC-CCR-TCA-AT / This study
N3 F3 / TGC-ATG-ACW-GGR-AAT-GAY-AA / 45 °C / This study
N3 R3 / AYR-TTR-CTT-GGR-GAR-TCA-C / This study
N3 F4 / AYT-RGA-AAC-AGG-GTA-TGT-RT / 45 °C / This study
N3 R4 / TCT-RTT-ACT-TGG-GCA-TAA-ACC / This study
N9 / N9 A1F / TCC-AAA-TCA-GAA-GAT-TCT-ATG-CAC / 50 °C / This study
N9 A1R / TTG-TTT-GGT-CCT-GAT-ATA-CAT-ATT-GA / This study
N9 A2F / CGC-CCA-CAG-TAT-ACA-ACA-GC / 50 °C / This study
N9 A2R / GTC-ATT-CGG-TCG-GGG-ATT / This study
N9 A3F / GCA-GGG-CTC-AAA-TAG-ACC-AG / 50 °C / This study
N9 A3R / ATC-AGG-CCA-GTT-CCA-TTG-TC / This study

* Hoffmann E, Stech J, Guan Y, Webster RG, Perez DR (2001) Universal primer set for the full length amplification of all influenza A viruses. Arch Virol 146:2275-2289

Supplement table 2. Nucleotide identities of IAV-H1N3 and IAV-H1N9 by using BLAST analysis

Virus / Gene / GenBank accession # / Length nucleotide / Related viruses / % nucleotide identity
11836C (H1N3) / PB2 / KJ526005 / 2,233 / A/mallard/Mongolia/2377/2011(H3N6) / 99%
PB1 / KJ526006 / 2,274 / A/wild goose/Dongting/C1037/2011(H12N8) / 99%
PA / KU752354 / 2,098 / A/duck/Hunan/S11200/2012(H4N6) / 99%
HA / KJ526007 / 1,587 / A/wild waterfowl/Dongting/C2383/2012(H1N2) / 99%
NP / KJ526008 / 1,497 / A/duck/Jiangxi/5576/2013(mixed) / 99%
NA / KJ526009 / 1,410 / A/duck/Hokkaido/157/2012(H11N3) / 99%
M / KJ526010 / 982 / A/mallard/Chany/425/2009(H4N6) / 99%
NS / KJ526011 / 838 / A/mallard/Korea/NHG187/2008(H7N7) / 99%
11869 (H1N9) / PB2 / KJ161954 / 2,277 / A/pintail/Mongolia/2-11/2007(H4N2) / 98%
PB1 / KJ161955 / 2,241 / A/wild duck/Korea/CSM42-34/2011(H7N9) / 99%
PA / KJ161956 / 2,190 / A/duck/Vietnam/LBM1/2011(H4N6) / 99%
HA / KJ161957 / 1,700 / A/duck/Guangxi/GXd-1/2011(H1N2) / 97%
NP / KJ161958 / 1,497 / A/duck/Guangxi/GXd-4/2011(H1N2) / 99%
NA / KJ161965 / 1,413 / A/eurasianwigeon/Hong Kong/MPK655/2009(H11N9) / 99%
M / KJ161959 / 967 / A/duck/Thailand/CU-7519C/2010(H3N8) / 99%
NS / KJ161960 / 859 / A/mallard/Mongolia/1581/2010(H3N8) / 99%

Supplement table 3.Genetic analysis ofIAV-H1N3 and IAV-H1N9 at amino acid residues for avian and human viruses

Gene / Position / Avian virus residue / Human virus residue / pH1N1 2009 / H7N9 2013 / Thai H1N3 / Thai H1N9
PB2 / 44 / A / S / A / A / A / A
199 / A / S / A / A / A / A
271 / T / A / A / T / T / T
475 / L / M / L / L / L / L
567 / D / N / D / D / D / D
588 / A / I / T / A / A / A
613 / V / T / V / V / V / V
627 / E / K / E / K / E / E
702 / K / R / K / K / K / K
PB1 / 327 / R / K / R / R / R / R
336 / V / I / I / V / V / V
PA / 28 / P / L / P / P / P / P
55 / D / N / D / D / D / D
57 / R / Q / R / R / R / R
100 / V / A / V / A / V / V
225 / S / C / S / S / S / S
268 / L / I / L / L / L / L
356 / K / R / R / R / K / K
404 / A / S / A / A / A / A
409 / S / N / N / N / S / S
552 / T / S / T / T / T / T
NP / 16 / G / D / G / G / G / G
33 / V / I / I / V / V / V
61 / I / L / I / I / I / I
100 / R / V / V / R / R / R
109 / I / V / I / I / I / I
214 / R / K / R / R / R / R
283 / L / P / L / L / L / L
293 / R / K / R / R / R / R
305 / R / K / K / R / R / R
313 / F / Y / V / F / F / F
357 / Q / K / K / Q / Q / Q
372 / E / D / E / E / E / E
422 / R / K / R / R / R / R
442 / T / A / T / T / T / T
455 / D / E / D / D / D / D
M1 / 115 / V / I / V / V / V / V
121 / T / A / T / T / T / T
137 / T / A / T / T / T / T
M2 / 11 / T / I / T / T / I / T
20 / S / N / S / S / S / S
57 / Y / H / Y / Y / Y / Y
86 / V / A / V / V / V / V
93 / N / S / N / N / N / N
NS1 / 81 / I / M / I / I / I / I
227 / E / R / Delete / Delete / E / E
NS2 / 107 / L / F / L / L / L / L

Supplement Figure 1.

N3

N9