Volume 22, Number 1—January 2016
Dispatch
Porcine Epidemic Diarrhea Virus and Discovery of a Recombinant Swine Enteric Coronavirus, Italy
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.
1These first authors contributed equally to this article.
2Deceased.