Table 3.

Detection of recombination events of different ORFs of Saudi IBV strains

Gene	Breakpoint positions		Recombinant sequence(s)	Major parent	Minor parent	Detection methods ^c
Gene	Begin	End	Recombinant sequence(s)	Major parent	Minor parent	Detection methods ^c
S	828	4198	Ck/SA/Kharj-2/2023 & Ck/SA/Kharj-3/2023^a	KU238176\| D888/2/4/08_IR	JX173489\| Eg/CLEVB-1/IBV/012	M, C, S, 3 S
M	102	472	Ck/KSA/Shaqra-1/2023	H120	Ck/KSA/Kharj 2/2023	G, B, M, C, S, 3 S
M	16	101	Ck/KSA/Shaqra-1/2023	Ck/KSA/Kharj-2/2023	MN987230\| IBV/ck/EGY-Monuf/NR725/16	M, C, 3 S
N	692	1222	Ck/SA/Kharj-2/2023	KY805846\|IBV/Ck/EG/CU/4/2014	Ck/SA/Kharj-3/2023	R, G, M, C
	271	917	Ck/SA/Kharj-3/2023	MF421319\| UY/09/CA/01	MN987230 IBV/ck/EGY-Monuf/NR725/16	R, G, S, 3 S
	1008	1222	Ck/SA/Kharj-3/2023	B164	ON41988AR/13/BA/A255	R, G, M, C
3ab	122	331	Ck/SA/Kharj-2/2023 & Ck/SA/Kharj-3/2023	FN430414\| ITA/90,254/2005	KY805846\| IBV/Ck/EG/CU/4/2014, 4/91, B164, KP118880\| ck/CH/LHB/130,927	M, C, S, 3 S
5ab	430	141	Ck/SA/Kharj-3/2023^b	ON419883\|AR/13/BA/A255	FN430414/ ITA/90,254/2005	M. C

^aJX173488|Eg/CLEVB-2/IBV/012, KY028743|gammaCoV/Ck/Poland/G229/2015, MG233398| IS-1494, KU238171| D1344/2/4/10 EG showed the same recombination

^b4/91 and KP118880|ck/CH/LHB/130,927 (China)showed the same recombination

R: RDP- Recombination Detection Program, G: GENECONV, B: Bootscan, M: Maxchi, C: Chimaera, S: SiSscan, and 3 S: 3Seq

^c E-value Scores: Including e-value scores for each recombination method identified by the RDP program was presented in Suppl. 3