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. 2020 Jul 1;85:104433. doi: 10.1016/j.meegid.2020.104433

Table 1.

IBV positive samples

NR Gov Type sample Date Flock size 1 Grouping by specific gene /segments
3ab 3a 3b HVR1-2 HVR3 3 S1 2 S1
NR 715/16 Monufia Broiler Trachea 3\2016 20000 C B/C C nd GI-23.2 EGY-var2
NR 718/16 Giza Broiler Trachea 5\2016 25000 C B/C C nd GI-23.2 EGY-var2
NR 719/16 Giza Broiler Trachea 5\2016 15000 C B/C C nd GI-23.2 EGY-var2
NR 725/16* Monufia Broiler Trachea 4\2016 300 B B/C B GI-23.3 GI-23.3 outgroup GI-23.3
NR 730/16 Behiera Layer Trachea 7\2016 1000 C B/C C nd GI-23.2 EGY-var2



SCU-1/2013 Monufia Broiler AAF 2\2013 20000 B B/C B nd Vac
SCU-2/2013 Cairo Broiler AAF 10\2012 10000 B B/C B nd GI-23.2 EGY-var2
SCU-3/2013 Giza Broiler AAF 5\2012 10000 B B/C B nd GI-23.2 EGY-var2
SCU-4/2013 Cairo Broiler AAF 7\2012 14000 A A A nd GI-23.2 EGY-var2
SCU-6/2013 Behera Broiler AAF 11\2012 60000 A A A nd GI-23.2 EGY-var2
SCU-7/2013 Behera Broiler AAF 11\2012 70000 A A A nd GI-23.2 EGY-var2
SCU-11/2013 Cairo Broiler AAF 7\2012 10000 A A A nd GI-23.2 EGY-var2
SCU-12/2013 Gharbia Broiler AAF 5\2012 12000 B B/C B nd GI-23.2 EGY-var2
SCU-13/2013 Gharbia Broiler AAF 5\2012 50000 B B/C B nd GI-23.2 EGY-var2
SCU-14/2013 Giza Broiler AAF 11\2012 20000 A A A nd GI-23.2 EGY-var2
USC-2/2013 Gharbia Broiler AAF 5\2012 15000 B B/C B nd GI-23.2 EGY-var2
USC-3/2013 Giza Broiler AAF 2\2012 20000 Vac Vac B nd GI-23.2 EGY-var2
USC-4/2013 Monufia Broiler AAF 11\2012 15000 A A A nd GI-23.2 EGY-var2
USC-5/2013* Monufia Broiler AAF 11\2012 80000 A A A GI-23.1 GI-23.1 EGY-var2 GI-23.2.2
USC-6/2013 Monufia Broiler AAF 11\2012 80000 Vac Vac B nd Vac



AR 545/18 Qualiobia Broiler Trachea 05/2018 5000 C B/C C outgroup GI-23.3 nd
AR 563/18 Giza Broiler Trachea 04/2018 9000 C noSeq C outgroup noSeq nd
AR 593/18 Fayoum Broiler Trachea 05/2018 7000 C B/C C outgroup GI-23.3 nd
AR 90/19 Beni-Suef Broiler Trachea 03/2019 5000 C B/C C outgroup noSeq nd
AR 93/19 Beni-Suef Broiler Trachea 04/2019 3500 C B/C C outgroup noSeq nd
AR 97/19 Beni-Suef Broiler Trachea 05/2019 8000 C B/C C noSeq noSeq nd



Pol/G052/2016 B B/C B GI-23.1 GI-23.1 EGY-var1 GI-23.1
ck/ISR/1494/2006 (B/C)) B/C A GI-23.1 GI-23.1 EGY-var1 GI-23.1

*Full genome sequence obtained in this study; nd: not done; noSeq: no sequence obtained with described method; AAF AmnionAllantoic fluid

1: number of animals per flock; 2: classification according gene S1 (Fig 1a); 3: classification according HVR3 within gene S1 (Fig 3e).