Table 1. Distribution of test results of samples from pig farms in study of swine enteric coronaviruses in northern Italy, 2007–2014*.
| Sample no. | Farm no. | Year | Region | EM | PEDV ELISA | Pan-CoV RT-PCR | TGEV/ PRCV S1 | Sequences |
||
|---|---|---|---|---|---|---|---|---|---|---|
| RdRp | S1 | M | ||||||||
| 222654 | 1 | 2007 | Emilia Romagna | – | + | + | NA | NA | NA | NA |
| 1448 | 2 | 2007 | Emilia Romagna | – | + | – | NA | NA | NA | NA |
| 19908 | 3 | 2007 | Emilia Romagna | – | + | + | – | Cluster I | Cluster I | Cluster I |
| 70323 | 4 | 2007 | Lombardia | + | + | + | NA | NA | † | NA |
| 114372 | 5 | 2007 | Lombardia | + | + | + | NA | NA | NA | NA |
| 200079 | 6 | 2007 | Lombardia | – | + | + | NA | NA | † | NA |
| 320855/5 | 7 | 2007 | Lombardia | + | + | + | – | Cluster I | Cluster I | Cluster I |
| 320855/6 | 7 | 2007 | Lombardia | + | + | + | NA | † | † | NA |
| 3936/1 | 8 | 2008 | Lombardia | – | + | + | – | Cluster I | Cluster I | Cluster I |
| 3936/2 | 8 | 2008 | Lombardia | – | + | + | NA | † | NA | NA |
| 29177 | 9 | 2008 | Veneto | + | + | + | – | Cluster I | Cluster I | Cluster I |
| 43853 | 10 | 2008 | Lombardia | + | + | – | NA | NA | NA | NA |
| 7239‡ | 11 | 2009 | Lombardia | – | + | + | – | Cluster I | Cluster I | Cluster I |
| 20001 | 12 | 2009 | Lombardia | – | + | + | – | Cluster I | Cluster I | Cluster I |
| 20416 | 13 | 2009 | Lombardia | – | + | + | NA | † | † | NA |
| 22603 | 14 | 2009 | Lombardia | – | + | + | – | Cluster I | Cluster I | Cluster I |
| 26199/2 | 15 | 2009 | Lombardia | – | + | – | NA | NA | NA | NA |
| 87565 | 16 | 2009 | Emilia Romagna | – | + | + | NA | NA | † | NA |
| 111357/7 | 17 | 2009 | Lombardia | NA | + | – | NA | NA | NA | NA |
| 137442 | 18 | 2009 | Lombardia | + | + | + | – | Cluster II | Cluster II | Cluster II |
| 205396 | 19 | 2009 | Lombardia | + | + | – | NA | NA | NA | NA |
| 208995 | 20 | 2009 | Lombardia | + | – | + | NA | † | NA | NA |
| 213306‡ | 21 | 2009 | Lombardia | + | + | + | – | Cluster II | Cluster II | Cluster II |
| 244945 | 22 | 2009 | Emilia Romagna | + | + | – | NA | NA | NA | NA |
| 245242 | 22 | 2009 | Emilia Romagna | + | + | + | NA | † | NA | NA |
| 274771 | 23 | 2009 | Veneto | + | – | – | NA | NA | NA | NA |
| 307121 | 24 | 2009 | Emilia Romagna | + | + | + | – | Cluster II | Cluster II | Cluster II |
| 315994 | 25 | 2009 | Lombardia | + | – | – | NA | NA | NA | NA |
| 320695 | 26 | 2009 | Lombardia | + | + | + | NA | NA | † | † |
| 320825 | 26 | 2009 | Lombardia | + | + | + | – | Cluster II | Cluster II | Cluster II |
| 324345 | 27 | 2009 | Lombardia | + | + | + | NA | † | † | † |
| 324374 | 27 | 2009 | Lombardia | + | + | + | NA | † | † | † |
| 324397 | 27 | 2009 | Lombardia | + | + | + | – | Cluster II | Cluster II | Cluster II |
| 324507/1 | 28 | 2010 | Lombardia | + | + | + | – | Cluster II | Cluster II | Cluster II |
| 324507/2 | 28 | 2010 | Lombardia | + | + | + | NA | NA | † | † |
| 324507/3 | 28 | 2010 | Lombardia | + | + | + | NA | NA | NA | † |
| 324507/4 | 28 | 2010 | Lombardia | + | + | + | NA | NA | † | † |
| 5448/2 | 29 | 2011 | Emilia Romagna | NA | + | – | NA | NA | NA | NA |
| 28607 | 30 | 2012 | Lombardia | – | + | + | NA | NA | † | † |
| 29742 | 30 | 2012 | Lombardia | + | + | + | – | Cluster II | Cluster II | Cluster II |
| 30917 | 31 | 2012 | Lombardia | + | + | – | NA | NA | NA | NA |
| 35621/1 | 32 | 2012 | Lombardia | + | + | – | NA | NA | NA | NA |
| 35621/2 | 32 | 2012 | Lombardia | – | + | + | NA | NA | NA | NA |
| 41906 | 33 | 2012 | Lombardia | – | + | + | NA | NA | NA | NA |
| 44833 | 34 | 2012 | Lombardia | NA | + | + | – | Cluster II | Cluster II | Cluster II |
| 67322 | 8 | 2012 | Lombardia | – | + | + | NA | NA | NA | † |
| 273992 | 35 | 2012 | Lombardia | – | + | + | – | Cluster II | Cluster II | Cluster II |
| 32961 | 36 | 2013 | Piemonte | – | + | – | NA | NA | NA | NA |
| 32963 | 36 | 2013 | Piemonte | + | + | – | NA | NA | NA | NA |
| 178509 | 37 | 2014 | Emilia Romagna | NA | NA | + | – | Cluster III | Cluster III | Cluster III |
| 200885 | 38 | 2014 | Emilia Romagna | + | + | + | – | Cluster III | Cluster III | Cluster III |
*Cluster I represents strains circulating from 2007 through mid-2009; cluster II represents strains circulating from mid-2009 through 2012; and cluster III represents strains circulating since 2014. EM, electron microscopy; M, membrane; pan-CoV RT-PCR, pan-coronavirus reverse transcription PCR; PEDV, porcine epidemic diarrhea virus; PRCV, porcine respiratory coronavirus; RdRp, RNA-dependent RNA polymerase; S1, spike; TGEV, transmissible gastroenteritis virus; +, positive; –, negative; NA, not tested or sequenced. †Sequence available but not included in this study. ‡Samples selected for whole genome sequencing.