Limited transmission of avian influenza viruses, avulaviruses, coronaviruses and Chlamydia sp. at the interface between wild birds and a free-range duck farm

Table 1 Distribution of samples and positive type of sample

Year	Month	Week	Swabs from wild birds	Feces from cattle egrets	Positive ones	Blood from wild birds	Positive ones	Duck flocks	Identification of flocks sampled	Positive ones	Environment of duck areas	Identification of corresponding flocks	Positive results
2019	April	17						1	A
	June	23						1 *	B
	June	24						2 *	C; D	2 AIV
	July	30	184		1 AIV (SYLATR) 1 Chlam (PASM)
	August	35	256		2 AIV (PASD, MUS) 2 Chlam(AEG, SYL)	121	3 AIV (LUSMEG, FICUCA, SYLATR)
	September	37						1 *	E
	September	39						1 *	F
	October	43	240	30	1 AIV (MOTALB) 3 Chlam(2 MOTALB, SYLATR)	142	4 AIV (2 SYLATR, TURPHI, MOTALB)				4	G; H; I; J	1 coronavirus (H)
	November	45						1	G	1 coronavirus
	November	48	184	30	2 AIV (PASD, ANT)	75					2	K; L
	December	52						1	K	1 AIV 1 Chlam 1 coronavirus
2020	January	5	225		2 AIV (SYLATR, FRI)	112	1 AIV (PASM) 1 NDV (TURMER)				2	M; N	2 AIV 2 Chlam
	February	8						1 + 1*	M; N	2 AIV 1 Chlam(M)
	February	9	141		2 Chlam(AEG, FRI)	88	1 AIV (PASM) 1 NDV (TURMER)				4	M; N; O; P	1 AIV (M) 1 Chlam(O)
	May	19						1 *	Q
	May	22	168			140	4 AIV (LUSMEG, 2 SYLATR, TURPHI)				2	Q; R
	July	28						1	S
	November	46	225		1 Chlam(AEG PHYCOL)	147	6 AIV (2 ERIRUB, 2 PRU, PASD, TURPHI)				4	T; U; V; W	2 AIV (T; U) 2 Chlam(T; U) 2 coronavirus (T; V)
	December	51	47	70		40	3 AIV (3 MOTALB) 2 NDV (ANTPRA, MOTALB)				4	T; U; V; W	3 AIV (T; V; W) 4 Chlam
2021	February	6		25
	February	9	51	52	1 AIV (BUB)	40	3 AIV (PRU, ACC, MOTALB)
	March	12	10			5

* next to some duck flocks indicate that only the results of regulatory AIV surveillance were available. The flocks are identified by letters and are shown in bold when they are sampled several times, either by swabs or environmental samples of their outdoor foraging area. For each pathogen detected, positive flocks or wild bird groups (or species if known) are indicated between brackets when necessary. Species and groups of wild birds are coded as detailed in Additional file 1. AIV stands for avian influenza virus, Avu for avulaviruses, CoV for coronaviruses and Chlam for Chlamydia sp.

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