Table 2.

Detection of recombination events of the ORF1ab of Saudi IBV strains

Breakpoint positions		Protein	Recombinant sequence(s)	Major parent	Minor parent	Detection methods*
Begin	End
419	2254	nsp2/nsp3	Ck/SA/Kharj-2/2023	Ck/KSA/Kharj-3/2023	H120, 4/91, Ma5	R, G, B, M, C, S, 3 S
4244	5200	nsp3	Ck/SA/Kharj-2/2023 & Ck/SA/Kharj-3/2023	FN430415| NGA/A116E7/2006	4/91	R, G, M, C, S, 3 S
6115	6476	nsp3	Ck/SA/Kharj-2/2023/ & Ck/SA/Kharj-3/2023	H120, Ma5	MN987230| IBV/ck/EGY-Monuf/NR725/16	R, G, M, C
13,756	14,064	nsp12	Ck/SA/Kharj-2/2023 & Ck/SA/Kharj-3/2023	FN430415| NGA/A116E7/2006	H120, Ma5	R, G, M, C, S
5593	5964	nsp3	Ck/SA/Kharj-2/2023 & Ck/SA/Kharj-3/2023	H120, Ma5	4/91	R, G, C, 3 S
4286	8252	nsp3-nsp5	Ck/KSA/Kharj-1/2023	4/91	MF421319| UY/09/CA/01	R, G, M, C, S, 3 S
8794	9888	nsp5-nsp6	Ck/KSA/Shaqra-1/2023	Ma5, H120	Ck/KSA/Kharj-2/2023 &Ck/KSA/Kharj-3/2023	R, G, M, C, S, 3 S
19,876	791	nsp2-nsp16	Ck/KSA/Shaqra-1/2023	H120, Ma5	Ck/KSA/Kharj-2/2023 & Ck/KSA/Kharj-3/2023	R, G, M, C, S
4740	5080	nsp3	Ck/KSA/Kharj-1/2023	MF421319|UY/09/CA/01	KR231009|B1648	R, G, M, C, 3 S
2360	3112	nsp3	Ck/KSA/Shaqra-1/2023 & Ck/KSA/Kharj-1/2023/	ON419883|AR/13/BA/A255	Ck/KSA/Kharj-2/2023 & Ck/KSA/Kharj-3/2023	R, G, M, C, S., 3 S
3360	4239	nsp3	Ck/KSA/Shaqra-1/2023 & Ck/KSA/Kharj-1/2023/	FN430415| NGA/A116E7/2006	Ck/KSA/Kharj-2/2023 & Ck/KSA/Kharj-3/2023	R, G, M, C
7392	7778	nsp5	Ck/KSA/Shaqra-1/2023	MF421319|UY/09/CA/01	FN430415| NGA/A116E7/2006	R, G, M, C,3 S
6861	6950	nsp4	Ck/KSA/Shaqra-1/2023	4/91	H120, Ma5	R, G, M, C,3 S
11,297	11,830	nsp10	Ck/KSA/Shaqra-1/2023	Ma5, H120	KR231009|B164	R, G, M, C

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

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