TABLE 2.
Sample description and GenBank accession numbers of the H1N1pdm sequences obtained in this study
| Strain (H1N1pdm) | Collection date (day/mo/yr) |
Epi form; intensitya | Genogroupb | GenBank accession no. |
Sequencing methodc |
|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PB2 | PB1 | PA | HA | NP | NA | M | NS | |||||
| A/Cat/France/0514/2009 | 26/11/2009 | Pneumonia | 3 | CY110768 | CY110769 | HE603922 | FR872140 | HE577050 | FR872139 | FR878009 | HE577051 | Sanger |
| A/swine/Cotes d’Armor/110466/2010 | 03/02/2010 | Recurrent; high | 3 | KC477397 | KC477395 | KC345642 | KC345640 | KC477391 | KC345641 | KC514527 | KC345639 | Sanger |
| A/swine/Sarthe/0255/2010 | 03/11/2010 | ND; high | 7 | HE603920 | HE603924 | CY110772 | CY110773 | HE577053 | HE600191 | HE603923 | HE577052 | NGS1 |
| A/swine/Sarthe/0262/2010 | 08/11/2010 | ND; standard | 7 | KC345635 | HE603925 | KC345637 | FR871195 | KC477393 | CY110914 | KC514526 | KC345636 | NGS1 |
| A/swine/Haute-Loire/0578/2011 | 18/10/2011 | Classical; standard | 7 | KC345645 | KC477394 | KC477392 | CY114522 | KC345643 | CY114523 | KC514528 | KC345644 | NGS1 |
| A/swine/France/18-120158/2012 | 25/04/2012 | None | 7 | KC345621 | KC477389 | KC345620 | KC345616 | KC345618 | KC345617 | KC514524 | KC345619 | NGS1 |
| A/swine/France/18-120333/2012 | 27/09/2012 | Recurrent; standard | 7 | KC345651 | KC477396 | KC345650 | KC345646 | KC345649 | KC345647 | KC514530 | KC345648 | NGS1 |
| A/swine/France/71-130116/2013 | 07/03/2013 | Classical; standard | 7 | KF229767 | KF229768 | KF229769 | KF229766 | KF229770 | KF229771 | KF229772 | KF229773 | NGS2 |
| A/swine/France/57-140136/2014 | 20/02/2014 | Classical; standard | SeL | MH785051 | MH785052 | MH785053 | MH785054 | MH785055 | MH785056 | MH785057 | MH785058 | NGS2 |
| A/swine/France/35-140382/2014 | 24/06/2014 | Recurrent; standard | SeL | MH785035 | MH785036 | MH785037 | MH785038 | MH785039 | MH785040 | MH785041 | MH785042 | NGS2 |
| A/swine/France/35-140384/2014 | 24/06/2014 | Recurrent; standard | SeL | MH785075 | Sanger | |||||||
| A/swine/France/64-150052/2015 | 29/01/2015 | Classical; high | SwD | MH785059 | MH785060 | MH785061 | MH785062 | MH785063 | MH785064 | MH785065 | MH785066 | NGS2 |
| A/swine/France/12-150058/2015 | 22/01/2015 | Recurrent; standard | SwD | KY241117 | KY241118 | Sanger | ||||||
| A/swine/France/64-150091/2015 | 12/02/2015 | Classical; standard | SeL | KY241119 | KY241120 | Sanger | ||||||
| A/swine/France/01-150203/2015d | 11/05/2015 | Classical; high | SwD | MH785027 | MH785028 | MH785029 | MH785030 | MH785031 | MH785032 | MH785033 | MH785034 | NGS2 |
| A/swine/France/65-160089/2016 | 01/02/2016 | Classical; standard | SwD | KY364085 | KY364086 | KY364087 | KY364088 | KY364089 | KY364090 | KY364091 | KY364092 | NGS2 |
| A/swine/France/40-160098/2016 | 29/01/2016 | Recurrent; standard | SwD | KY364101 | KY364102 | KY364103 | KY364104 | KY364105 | KY364106 | KY364107 | KY364108 | NGS2 |
| A/swine/France/40-160120/2016 | 16/02/2016 | Classical; standard | SwD | MH785043 | MH785044 | MH785045 | MH785046 | MH785047 | MH785048 | MH785049 | MH785050 | NGS2 |
| A/swine/France/12-160129/2016 | 07/03/2016 | Classical; standard | SeL | KY364141 | KY364142 | KY364143 | KY364144 | KY364145 | KY364146 | KY364147 | KY364148 | NGS2 |
| A/swine/France/72-160174/2016 | 22/04/2016 | Classical; standard | SeL | KY364165 | KY364166 | KY364167 | KY364168 | KY364169 | KY364170 | KY364171 | KY364172 | NGS2 |
| A/swine/France/35-160233/2016 | 22/06/2016 | Classical; high | SeL | MH785067 | MH785068 | MH785069 | MH785070 | MH785071 | MH785072 | MH785073 | MH785074 | NGS2 |
| A/swine/France/AR2675/2015 | 20/10/2015 | ND | SeL | EPI1080442e | EPI1080443e | Sanger | ||||||
| A/swine/France/AR271/2016 | 19/01/2016 | ND | SeL | EPI1080446e | EPI1080447e | Sanger | ||||||
| A/swine/France/AR9191/2016 | 14/11/2016 | ND | SeL | EPI1080448e | EPI1080449e | Sanger | ||||||
a
Influenza virus epidemiological form (classical or recurrent) and clinical sign intensity (standard or high) as reported by the veterinarians who collected the samples. ND, not determined.
b
Genogroup numbers correspond to those defined by Nelson and colleagues (33). Seasonal-like (SeL) and swine divergent (SwD) genogroups were defined in this study.
c
NGS1/NGS2 sequences were obtained by two different new-generation sequencing pipelines. See Materials and Methods for details.
d
Strain A/swine/France/01-150203/2015 was isolated from a pig coinfected with viruses from both H1N1pdm and H1avN1 lineages.
e
GSAID EpiFlu database accession number.