Additional Data

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Table S1. Correspondences of the nomenclature of the strains used in Chapter 3 and 4.

Chapter 3 Chapter 4

H1N1 01 S1

H1N1 02 S2

H1N1 03 Not used

H1N1 04 S3

H1N1 05 S4

H1N1 06 S5

Longitudinal strain 99.3 S6

H1N2 01 S8

H1N2 02 S9

H1N2 03 S7

H1N2 04 S10

H3N2 01 S11

H3N2 02 S12

H3N2 03 S13

H3N2 04 S14

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Table S2. Accession numbers of the ISD dataset of whole genome viruses.

Whole genome strains

Strain name Subtype Accession numbers

A/sw/Shizuoka/110/97 H3N2

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Table S3. Accession numbers of the added European strains for the determination of the closest relative strain for each gene segment.

Accession Strain name Subtype Gene

AJ306849 A/swine/Italy/1521/98 H1N2 PB2 AJ306845 A/swine/Cotes d'Armor/790/97 H1N2 PB2 AJ306848 A/swine/Cotes d'Armor/1488/1999 H1N1 PB2 AJ306854 A/swine/Cotes d'Armor/2433/98 H1N2 PB2 AJ306842 A/swine/Ille et Vilaine/1455/1999 H1N1 PB2 AJ306843 A/swine/Italy/2064/99 H1N2 PB2 AJ306851 A/Swine/Italy/1513-1/98 H1N1 PB2 AJ306850 A/swine/Cotes d'Armor/604/99 H1N2 PB2 AJ311457 A/swine/Finistere/2899/1982 H1N1 PB2

AJ311459 A/Swine/Italy/1523/98 H3N2 PB2

JF290388 A/swine/England/1382/2010 H1N2 PB2

M55471 A/swine/Germany/2/1981 H1N1 PB2

AJ306866 A/swine/Ille et Vilaine/1455/1999 H1N1 PB1 AJ306856 A/swine/Cotes d'Armor/1488/1999 H1N1 PB1 AJ306864 A/swine/Cotes d'Armor/2433/98 H1N2 PB1 AJ306863 A/swine/Cotes d'Armor/604/99 H1N2 PB1 AJ306865 A/swine/Cotes d'Armor/790/97 H1N2 PB1 AJ306862 A/swine/Italy/1521/98 H1N2 PB1 AJ306861 A/Swine/Italy/1513-1/98 H1N1 PB1 JF432093 A/swine/Italy/321986/2009 H1N2 PB1 GU236515 A/swine/Skane/1321/1983 H1N1 PB1

DQ836168 A/swine/Jena/5/1996 H3N2 PB1

DQ836169 A/swine/Karrenzien/2/87 H3N2 PB1 DQ836170 A/swine/Bakum/8602/99 H3N2 PB1 DQ836171 A/swine/Potsdam/35/82 H3N2 PB1

DQ836172 A/swine/Lohne/1/97 H3N2 PB1

DQ836173 A/swine/Leipzig/1/97 H3N2 PB1

DQ836174 A/swine/Potsdam/15/81 H1N1 PB1 DQ836175 A/swine/Schwerin/103/89 H1N1 PB1

DQ836176 A/swine/Bakum/5/95 H1N1 PB1

DQ836177 A/swine/Belzig/2/2001 H1N1 PB1 AJ311462 A/swine/Finistere/2899/1982 H1N1 PB1 AJ311208 A/swine/Cotes d'Armor/1488/1999 H1N1 PA AJ311207 A/swine/Cotes d'Armor/790/97 H1N2 PA AJ311205 A/swine/Cotes d'Armor/2433/98 H1N2 PA AJ312838 A/swine/Cotes d'Armor/604/99 H1N2 PA AJ311210 A/swine/Italy/2064/99 H1N2 PA AJ311209 A/swine/Italy/1081/00 H1N2 PA AJ311206 A/swine/Italy/1521/98 H1N2 PA AJ311463 A/swine/Finistere/2899/1982 H1N1 PA AJ311465 A/Swine/Italy/1513-1/98 H1N1 PA AJ307068 A/swine/Ille et Vilaine/1455/1999 H1N1 NP

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AJ311510 A/swine/Italy/1509-6/97 H1N1 NP AJ307066 A/swine/Cotes d'Armor/2433/98 H1N2 NP U04855 A/swine/Northern Ireland/1938 H1N1 NP

U04856 A/swine/Cambridge/1939 H1N1 NP

AJ311510 A/swine/Italy/1509-6/97 H1N1 NP AJ293942 A/Swine/Italy/1523/98 H3N2 NP JN624324 A/swine/Italy/22530/2002 H1N2 NP AJ307062 A/swine/Italy/2064/99 H1N2 NP

M63765 A/swine/Italy/2/1979 H1N1 NP

M63766 A/swine/Italy/141/1981 H1N1 NP

M60762 A/swine/Italy/147/1981 H1N1 NP

AJ307065 A/swine/Cotes d'Armor/790/97 H1N2 NP FJ805965 A/swine/Belgium/1/1998 H1N1 NP AJ307069 A/swine/Cotes d'Armor/1488/1999 H1N1 NP AJ307074 A/swine/Cotes d'Armor/604/99 H1N2 NP U85987 A/swine/England/191973/92 H1N7 NP GU236518 A/swine/Skane/1321/1983 H1N1 NP AM746619 A/wild boar/Germany/WS169/2006 H3N2 NP AM920725 A/swine/Germany/Vi3161/95 H3N2 NP AM920730 A/swine/Germany/Vi5698/1995 H1N1 NP AM920735 A/swine/Germany/SEC27/97 H3N2 NP AM920739 A/swine/Germany/SEk1178/2000 H1N2 NP AM920744 A/swine/Germany/S043/2002 H3N2 NP Z26856 A/swine/Germany/8533/1991 H1N1 NP M63769 A/swine/Cambridge/1/1935 H1N1 NP M30749 A/swine/Netherlands/12/1985 H1N1 NP

M22579 A/swine/Germany/2/1981 H1N1 NP

AJ293938 A/swine/Italy/1553-2/98 H3N2 M AJ316052 A/swine/Italy/1521/98 H1N2 M AJ316056 A/swine/Italy/2034/99 H1N1 M AJ316058 A/swine/Italy/1566/98 H1N1 M GQ404622 A/swine/Italy/v.45/1979 H1N1 M EU478802 A/swine/England/17394/96 H1N2 M U85985 A/swine/England/191973/92 H1N7 M AM920726 A/swine/Germany/Vi3161/95 H3N2 M AM920731 A/swine/Germany/Vi5698/1995 H1N1 M AM920734 A/swine/Germany/SEC27/97 H3N2 M AM920740 A/swine/Germany/SEk1178/2000 H1N2 M AM920745 A/swine/Germany/S043/2002 H3N2 M

DQ186975 A/swine/Bakum/5/95 H1N1 M

DQ186984 A/swine/Bakum/8602/99 H3N2 M

EU478801 A/swine/Bakum/909/93 H3N2 M

EU478803 A/swine/Bakum/1362/98 H3N2 M AJ311509 A/swine/Belgium/220/92 H3N2 M DQ186976 A/swine/Belzig/2/2001 H1N1 M

EU478806 A/swine/Belzig/54/01 H3N2 M

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EU478805 A/swine/Berlin/1578/00 H3N2 M EU478846 A/swine/Bad Griesbach/IDT5604/06 H1N1 M FJ805964 A/swine/Belgium/1/1998 H1N1 M GQ161131 A/swine/Bakum/IDT1769/2003 H3N2 M

GQ404616 A/swine/Brno/1/1992 H1N1 M

AJ316047 A/swine/Cotes d'Armor/1482/1999 H1N1 M AJ316049 A/swine/Cotes d'Armor/790/97 H1N2 M AJ316051 A/swine/Cotes d'Armor/604/99 H1N2 M AJ316061 A/swine/Ille et Vilaine/1455/1999 H1N1 M DQ186974 A/swine/Schwerin/103/89 H1N1 M DQ186979 A/swine/Potsdam/35/82 H3N2 M DQ186980 A/swine/Karrenzien/2/87 H3N2 M

DQ186982 A/swine/Jena/5/1996 H3N2 M

DQ186983 A/swine/Lohne/1/97 H3N2 M

EU478796 A/swine/Potsdam/1/81 H1N1 M

EU478798 A/swine/Gent/1/84 H3N2 M

EU478799 A/swine/Gent/V230/1992 H1N1 M EU478804 A/swine/Gent/7625/1999 H1N2 M EU478809 A/swine/Ehren/IDT2570/03 H1N2 M EU478815 A/swine/Nordwalde/IDT2197/03 H1N2 M EU478817 A/swine/Vechta/2623/03 H1N1 M EU478820 A/swine/Damme/IDT2890/04 H3N2 M EU478821 A/swine/Geldern/IDT2888/2004 H1N1 M EU478825 A/swine/Gudensberg/IDT2931/04 H1N2 M EU478826 A/swine/Lohne/IDT3357/04 H3N2 M EU478828 A/swine/Seesen/IDT3055/04 H3N2 M EU478834 A/swine/Harkenblek/IDT4097/05 H3N2 M EU478835 A/swine/Hertzen/IDT4317/05 H3N2 M EU478837 A/swine/Laer/IDT3893/2005 H1N2 M EU478838 A/swine/Laer/IDT4126/05 H3N2 M EU478839 A/swine/Merzen/IDT4114/05 H3N2 M EU478841 A/swine/Osterhofen/IDT4004/05 H3N2 M EU478843 A/swine/Stadtlohn/IDT3853/05 H1N2 M EU478845 A/swine/Wohlerst/IDT4093/05 H1N1 M EU478847 A/swine/Herzlake/IDT5335/06 H3N2 M GQ404581 A/swine/Czech Republic/1957 H1N1 M

GQ404585 A/swine/Minsk/1965 H1N1 M

GQ404591 A/swine/Czech Republic/2/1972 H3N2 M GQ404594 A/swine/Czech Republic/1/1975 H3N2 M GQ404607 A/swine/Czech Republic/1978 H3N2 M GQ404620 A/swine/Schleswig-Holstein/1/1993 H1N1 M GU236512 A/swine/Lidkoeping/1193/2002 H1N1 M GU236520 A/swine/Skane/1321/1983 H1N1 M M63525 A/swine/Netherlands/12/1985 H1N1 M Z26861 A/swine/Germany/8533/1991 H1N1 M Z26862 A/swine/Netherlands/25/1980 H1N1 M

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EU091680 A/swine/Italy/66945/2006 H3N1 NS1 EU091704 A/swine/Italy/1484/2002 H3N2 NS1 AJ344040 A/swine/Cotes d'Armor/799/00 H1N2 NS1

AJ293940 A/swine/Italy/636/87 H3N2 NS1

AJ344041 A/swine/Cotes d'Armor/1121/2000 H1N1 NS1 EU091706 A/swine/Italy/10169/2001 H1N1 NS1 AJ344024 A/Swine/Italy/1523/98 H3N2 NS1 GU236521 A/swine/Skane/1321/1983 H1N1 NS1 AJ293939 A/swine/Italy/13962/95 H3N2 NS1 GU236513 A/swine/Lidkoeping/1193/2002 H1N1 NS1 Z26865 A/swine/Germany/8533/1991 H1N1 NS1 Z26866 A/swine/Netherlands/25/1980 H1N1 NS1 AJ344027 A/swine/Cotes d'Armor/1488/1999 H1N1 NS1 AJ344029 A/Swine/Italy/1513-1/98 H1N1 NS1 AJ344031 A/swine/Cotes d'Armor/2433/98 H1N2 NS1 AJ344033 A/swine/Ille et Vilaine/1455/1999 H1N1 NS1 AJ344035 A/swine/Italy/1654-1/99 H1N2 NS1 AJ344038 A/swine/Cotes d'Armor/1482/1999 H1N1 NS1 AJ519462 A/swine/Italy/3364/00 H1N1 NS1 AJ344026 A/swine/Cotes d'Armor/790/97 H1N2 NS1 AJ344032 A/swine/Italy/2064/99 H1N2 NS1 AJ344034 A/swine/Scotland/410440/94 H1N2 NS1 CY077923 A/swine/Italy/526/1985 H3N2 NS1 M80967 A/swine/Netherlands/12/1985 H1N1 NS1 AM746620 A/wild boar/Germany/WS169/2006 H3N2 NS1 AM920727 A/swine/Germany/Vi3161/95 H3N2 NS1 AM920732 A/swine/Germany/Vi5698/1995 H1N1 NS1 AM920736 A/swine/Germany/SEC27/97 H3N2 NS1 AM920741 A/swine/Germany/SEk1178/2000 H1N2 NS1 AM920746 A/swine/Germany/S043/2002 H3N2 NS1

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Figures S1. Phylogenetic trees obtained with the European strains to determine the clustering of the isolates from the Chapter 3. Order as follows: a) PB2, b) PB1, c) PA, d) NP, e) M, f) NS

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a.

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b.

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c.

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d.

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e.

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f.

Figure S2. Summary of the results obtained in the longitudinal study. The types of isolates (by concatenated segments, type of Matrix and type of nucleocapsid gene segments) are represented by the circles in a given time of the sampling. Prevalence of each type per week are also shown.

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Figure S3. Maximum likelihood tree including 280 sequences obtained with the high-throughput sequencing from the animal 8.3. the consensus sequence obtained from the animals 8.3 and 76.3. and the closest relative strains for each one (reference strain). The segment used for the tree contained 357 nucleotides.

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Table S4. Values of grouping obtained with the factorial analysis. Bold type indicates the values of the representative subtype for each factor

Strain used Factor 1 Factor 2 Factor 3

Chi square statistic for 75 degrees of

liberty 230,24

p-value <0,01

.