Genotyping and pathotyping of diversified strains of infectious bronchitis viruses circulating in Egypt

Table 1 Phylogenetic grouping of infectious bronchitis virus in the study

Isolate No.	Isolate name	Age of birds (d)	Governorate	GeneBank accession number	Phylogenetic group
1	IBV-EG/12773F(3)-2012	20	Beni-Suef	KC608180	Classic1
2	IBV-EG/11539F-2011	23	Kafr-El-Shikh	JQ839289	Classic
3	IBV-EG/10643F(1-7)-2010	19	Sharqia	KC608171	Classic
4	IBV-EG/116F-1(1)-2011	30	Gharbia	KC608176	Classic
5	IBV-EG/11673F-2011	20	Alexandria	KC608173	Egy Var I
6	IBV-EG/11413F-2011	25	Sharqia	KC608177	Egy Var I
7	IBV-EG/10324F-2010	17	Giza	KC608172	Egy Var I
8	IBV-EG/1299B-2012	18	Fayoum	KC608182	Egy Var I
9	IBV-EG/1196F-2011	15	Behira	KC608174	Egy Var I
10	IBV/EG/IBV1-2011	25	Suez	JQ839288	Egy Var I
11	IBV-EG/1138F-4-2011	18	Dakahlia	KC608175	Egy Var II
12	IBV-EG/Qalyobia/121-2012	22	Qaliobeya	KC608181	Egy Var II
13	IBV-EG/1212B-2012	14	Al Behira	JQ839287	Egy Var II
14	IBV-EG/1293B-2012	21	Fayoum	KC608178	Egy Var II
15	IBV-EG/1262F(3)-2012	28	Ismalia	KC608179	Egy Var II
16	CH/EGYPT/13200F/2013	20	Giza	KT832805	Egy Var II
17	CH/EGYPT/13950F/2013	25	Alexandria	KT832806	Egy Var II
18	CH/EGYPT/14251F/2014	22	Suez	KT832807	Egy Var II
19	CH/EGYPT/141107F/2014	32	Giza	KT832808	Egy Var II
20	CH/EGYPT/15919F/2015	26	Dakahlia	KT832809	Egy Var II

¹Massachusetts - like strain.

Table 2 Nucleotide and deduced amino acid identities of infectious bronchitis virus Egyptian isolates with other selected references and vaccine strains from different serotypes

Strain namenucleotide identity (%) (upper right)amino acid identity (%) (lower left)	Egypt/Beni-Suef/01	IB-isolate-variant-2-S1	IBV-IS-1494-06-S1	IBV-isolate-IS-885-S1	QXIBV	IBV-H120	IBV-Ma5	IBV-M41	IBV-variant-1-S1-(1/96)	IBV-4-91	IBV-CR12188	IBV-D274	IBV-Eg/11539F-2011 (Classic)	IBV-Eg/IBV1-2011 (EGY-Var-1)	IBV-Eg/1212B-2012 (EGY-Var-2)
Egypt/Beni-Suef/01		72	73	70	86	65	65	64	81	68	80	82	68	98	89
IB-isolate-variant-2-S1	97		99	92	91	87	87	87	63	90	63	66	84	70	67
IBV-IS-1494-06-S1	99	98		94	91	87	87	87	63	90	63	66	84	71	68
IBV-isolate-IS-885-S1	90	88	90		90	86	86	86	63	89	62	65	83	69	69
QXIBV	86	85	86	84		85	85	85	63	92	63	65	82	67	66
IBV-H120	79	79	79	76	76		100	100	61	83	60	65	95	65	64
IBV-Ma5	79	79	79	76	76	100		100	61	83	60	65	95	65	64
IBV-M41	79	79	79	76	76	99	99		61	83	60	65	95	65	64
IBV-variant-1-S1 (1/96)	80	80	80	79	85	72	72	71		69	98	82	63	80	81
IBV-4-91	83	83	83	82	87	74	74	73	95		68	66	80	66	65
IBV-CR12188	82	81	82	80	86	72	72	71	96	95		83	62	79	80
IBV-D274	82	82	83	80	83	78	78	77	80	83	83		68	82	81
IBV-Eg/11539F-2011 (Classic)	77	77	77	74	74	98	98	97	71	73	71	76		81	78
IBV-Eg/IBV1-2011 (EGY-Var-1)	97	94	96	88	84	81	81	81	78	81	80	80	79		88
IBV-Eg/1212B-2012 (EGY-Var-2)	89	87	89	90	83	80	80	80	81	83	81	82	78	87

IBV: Infectious bronchitis virus.

Table 3 Necropsy findings of specific pathogen free chicks infected with infectious bronchitis viruses at one-day-old and the examined survivor and dead birds during the 14 d observation

Group	IBV isolates code	Necropsy
		Trachea				Kidney
		No Lesion	Slight mucin	Excessive mucin	Mucosal congestion	No Lesion	Swelling	Ureate	Congestion
1	IBV-EG/1212B-2012	0	2	5	3	0	6	2	2
2	IBV-EG/IBV1-2011	0	5	3	2	0	5	2	3
3	IBV-EG/11539F-2011	3	6	0	1	10	0	0	0
4	Negative control	10	0	0	0	10	0	0	0

Kidney and trachea score = no of chicks with lesion score of ≥ 1. IBV: Infectious bronchitis virus.

Table 4 Pathogenicity index based on clinical scoring and necropsy of kidney and trachea of specific pathogen free chicks infected at one-day-old with infectious bronchitis viruses with examining survivors and dead birds during 14 d observation

Group	IBV isolates code	Observation record			Clinical score1	Gross lesion score2		Pathogenicity index3	Pathotyp4
		Dead	Survived	Mortality (%)		Trachea	Kidney
1	IBV-EG/1212B-2012	5/10	5/10	50	3	10	10	25	High
2	IBV-EG/IBV1-2011	4/10	6/10	40	2	10	10	24	High
3	IBV-EG/11539F-2011	1/10	9/10	10	1	7	0	8	Low
4	Negative control	0/10	10/10	0	0	0	0	0	No

¹Clinical score[2,28]: Score 0: No clinical signs; score 1: Lacrimation, slight shaking of head, watery feces; score 2: Lacrimation, presence of nasal exudate, depression, watery feces; score 3: Strong lacrimation, presence of nasal exudates, severe watery feces;

²kidney and trachea score: No of chicks with lesion score of ≥ 1;

³pathogenicity index: No of chicks with lesion score ≥ 1 + 1 point for every 10% mortality;

⁴pathotypes: Low (pathogenicity index value 1-9), intermediate (pathogenicity index value 10-18), high (pathogenicity index value ≥ 19). IBV: Infectious bronchitis virus.

Table 5 Virus detection from various organs of chicks post-inoculated with different infectious bronchitis viruses using reverse transcription-polymerase chain reaction

Group	IBV isolates	Phylogenetic group	Virus detection (number of positive/total)
			Trachea	Kidney	Lung
1	IBV-EG/1212B-2012	Egy Var II	10/10	9/10	6/10
2	IBV-EG/IBV1-2011	Egy Var I	8/10	10/10	0/10
3	IBV-EG/11539F-2011	Classic (mass-like strain)	5/10	0/10	0/10
4	Negative control		0/10	0/10	0/10

IBV: Infectious bronchitis virus.