Table 3.

Sensitivity of SISPA – next generation sequencing for avian influenza viruses.

Virus	Virus titer (EID50/ml)	Ct Value	Gene segment	Read mappeda	Genome coverage	Mean depth of coveragec	Contig (s) by de novo assemblyd	Detection by metagenomicse
					(%)b
AIV H5N1	104.9	26.4	PB2	898	90.8	36.8
A/duck/Vn/NCVD-672/2011			PB1	755	66.3	83.6
			PA	60	78	3.7
			HA	202	89.3	16.6
			NP	104	99.1	10.7
			NA	101	84.8	12.8
			M	96	96.9	10.3
			NS	118	79.1	19.4
			Genome		85.5		Y	Y
	103.9	30.1	PB2	39	42.1	2.1
			PB1	7	0	0
			PA	185	81.2	24.2
			HA	6	0	0
			NP	88	56.2	1.9
			NA	17	44.1	1.8
			M	0	0	0
			NS	18	39	1.4
			Genome		32.8		N	Y
	102.9	33.5	Genome		10.4		N	N
AIV H9N2	104.5	28.7	PB2	1894	100	179.5
A/chicken/Jordan/13/2003			PB1	737	97.7	74.6
			PA	269	100	29.4
			HA	1631	94.9	225.5
			NP	188	97.6	28.4
			NA	2154	92.9	358.7
			M	908	100	212.2
			NS	12	91.4	2.9
			Genome		96.8		Y	Y
	103.5	30.8	PB2	532	82.6	47.4
			PB1	5940	97.2	244.9
			PA	254	66.7	18.1
			HA	28	36.3	2.7
			NP	35	55.2	3.8
			NA	355	81.1	44.6
			M	228	57.8	40.6
			NS	2	0	0
			Genome		59.6		N	Y
	102.5	34.3	Genome		12.9		N	Y

^aThe numbers of assembled sequencing reads to a reference genome.

^bThe breadth of coverage of a target genome (%).

^cThe average number of times that each base in the reference is covered by aligned reads.

^dThe formation of contigs in de novo genome assembly.

^eDetection of AIV viral genomes using Kraken metagenomics approach.