Table 2. AI virus identification, isolation, and subtyping using different methods^*.

Sample No.	rRT-PCR	VI		cRT-PCR	NGS
		CE1	CE2
1	Pos	−	+	H11?	H11N3
2	Pos	+	+	H4N6	H4N6
3	Pos	+	+	H6N2	H6N2
4	Pos	+	+	?N1	H2N1
5	Pos	+	+	?N2	H9N2
6	Pos	+	+	H6N2	H6N2
7	Pos	+	+	?N8	H3N8
8	Pos	+	+	?N3	H1N3
9	Pos	−	+	?N1	H1N1, H7N1
10	Pos	+	+	H9N2	H9N2
11	Pos	+	+	H3N8	H3N8
12	Pos	+	+	H1N1	H1N1
13	Neg	+	+	H3N8	H3N8
14	Neg	+	+	?N1	H1N1, H7N1
15	Neg	+	+	?N1	H1N1
16	Pos	+	+	H1N1	H1N1
17	Pos	+	+	H3N8	H3N8
18	Pos	+	+	H6N2	H6N2
19	Neg	−	+	H3N6	H3N6
20	Neg	+	+	H2?	H2N7
21	Pos	−	+	H11N9	H11N9
22	Pos	+	+	H11N3	H11N3
23	Pos	+	+	H1N1	H1N1, H7N1
24	Pos	−	+	H1N1	H1N1, H7N1
25	Neg	−	+	H1N1	H1N1
26	Neg	−	+	H1N1	H1N1
27	Neg	−	+	H1N1	H1N1
28	Neg	+	+	?N3	H1N3
29	Neg	+	+	?N1	H2N1
30	Neg	−	+	H6N8	H6N8
31	Neg	+	+	H4N6	H4N6
32	Neg	−	+	H3N8	H3N8
33	Neg	+	+	H4N6	H4N6
34	Neg	+	+	H11N9	H11N9
35	Pos	+	+	H1N1	H1N1
36	Pos	−	+	N/A	H1N1
37	Neg	+	+	H1N1	H1N1
38	Pos	+	+	H11N?	H11N9
39	Pos	+	+	H6N1	H6?
40	Neg	+	+	H3N2	H3N2, H3N8
41	Neg	+	+	?N3	H1N3
42	Neg	+	+	H6N2	H6N2
43	Pos	+	+	H10N5	H10N5
44	Neg	+	+	H3N8	H3N8
45	Pos	−	+	H5N2	H5N2
46	Neg	+	+	H3N8	H3N8
47	Neg	+	+	H4N1	H4N1
48	Neg	+	+	H4N1	H4N1
49	Pos	+	+	H1N1	H1N1
50	Neg	+	+	H3N8	H3N2, H3N8

AI, avian influenza; rRT-PCR, real-time reverse transcription-polymerase chain reaction; VI, virus isolation; CE, chicken embryo; cRT-PCR, conventional reverse transcription-polymerase chain reaction; NGS, next generation sequencing.

^*A rRT-PCR CT value below 40 indicates a positive reaction (Pos) and negative reaction (Neg); Question marks denote uncertainty of identification; Specimen No. 9 contained H1 (1,776 bp, 38,994 reads) and H7 (1,663 bp, 336 reads); No. 14 contained H1 (1,554 bp, 40,047 reads) and H7 (1,345 bp, 498 reads); No. 23 contained H1 (1,777 bp, 34,024 reads) and H7 (1,729 bp, 376 reads); and No. 24 contained H1 (1,784 bp, 24,110 reads) and H7 (1,728 bp, 234 reads).