Table 1. avian IAV strains characterized in our study.

Virus Name	Subtype	Cq	Virus isolation	Abbreviation	Genome sequencing status	GenBank Acc. no.	Number
A/mallard/CZE/15902-3K/09	N9	33.8	No	P/3K	partial: NP, NS	KC599271-73	1
A/mallard/CZE/15902-4K/09	H6	34.3	No	P/4K	partial: PB1, H6, MP, NS	KC599274-76	2
A/mallard/CZE/15902-9K/09	nd	35.5	No	P/9K	partial: PB2, PB1, PA, MP, NS	KC599277-80	3
A/mallard/CZE/15902-12K/09	H11N2	36.8	No	P/12K	partial: PB1, PA, H11, NP, N2, MP, NS	KC599281-87	4
A/mallard/CZE/15902-14K/09	H6N2	29.7	No	P/14K	partial: PB2, PB1, PA, H6, NP, MP, NS	KC599288-94	5
A/mallard/CZE/15902-17K/09	H6N2	21.3	Yes	P/17K	entire coding genome	HQ244427-34	6
A/mallard/CZE/15902-18K/09++	H11N9	25.8	Yes	P/18K_H11	entire coding genome	JF682618-25	7
	H6N9			P/18K_H6	entire coding genome	KC599295-302	8
A/mallard/CZE/15902-23K/09	H6N2	29.6	No	P/23K	each segment partial	KC599309-16	9
A/mallard/CZE/15902-25K/09	H11N9	31.0	No	P/25K	each segment partial	KC599317-24	10
A/mallard/CZE/15902-18T/09++	H6	32.4	No	P/18T	partial PB2, PB1, PA, H6, NP, MP, NS	KC599303-08	11
A/mallard/CZE/15962-1T/10	H6N9	27.4	No	H/1T	entire coding genome	JQ737234-41	12
A/mallard/CZE/15962-4T/10	H6N9	26.6	No	H/4T	each segment partial	KC599325-32	13

The number assigned for each strain corresponds to Figure 2.

CZE, Czech Republic.

T, tracheal swab.

K-cloacal swab.

P, H sampling localities (see the Figures S1 and S2 in File S1).

nd, not determined.

⁺⁺samples 18K and 18T did not originate from the same organism.

The Cq values correspond to the reference 20.