High-throughput sequencing as a potential tool in the quality control of infectious bronchitis vaccines

Fig. 1.

Fig. 2.

Fig. 3.

Fig. 4.

The results of the analysis of the genetic composition of three commercial poultry infectious bronchitis vaccines carried out using the Kraken2 and Burrows–Wheeler Aligner (BWA) tools

Vaccine	Batch	Number of reads	BWA		Kraken2
			% of reads mapped to the IBV genome	% of reads mapped to the Gallus gallus genome	% of reads mapped to the avian coronavirus genome	% of reads mapped to eukaryotic genome	% of reads mapped to bacterial genome
V-01	01	3,911,175	86	14	73	13	15
	02	3,260,251	84	16	70	15	14
	03	3,971,161	89	10	75	10	15
V-02	01	4,172,990	85	14	83	8	9
	02	4,487,555	84	15	81	8	11
	03	5,090,925	85	14	83	7	10
V-03	01	4,712,611	68	31	58	23	19
	02	4,193,830	75	23	63	16	21
	03	1,181,940	51	48	43	39	18

The vcf-annotator tool results of viral variant type analyses of commercial poultry infectious bronchitis vaccines sequenced with high throughput

Vaccine Batch		Total variants				Unique variants
		Total number of variants	Type of changes			Number of unique variants	Type of changes
			Synonymous	Non-synonymous	Unknown		Synonymous	Non-synonymous	Unknown
V-01	01	35	8	22	5	7	2	2	3
	02	38	7	22	9	10	1	2	7
	03	35	7	21	7	7	1	1	5
V-02	01	7	1	4	2	0	0	0	0
	02	8	1	4	3	1	0	0	1
	03	11	1	4	6	4	0	0	4
V-03	01	3	1	0	2	0	0	0	0
	02	8	0	1	7	5	0	0	5
	03	5	0	2	3	2	0	1	1