Real-time reverse transcription PCR-based sequencing-independent pathotyping of Eurasian avian influenza A viruses of subtype H7

Graaf, Annika; Beer, Martin; Harder, Timm

doi:10.1186/s12985-017-0808-3

Virology Journal

Table 4 Diagnostic performance characteristics of the H7 pathotyping RT-qPCRs using HP and LP influenza A subtype H7 virus isolates and field samples collected from different countries and poultry holdings or wild bird species, 1999–2016

From: Real-time reverse transcription PCR-based sequencing-independent pathotyping of Eurasian avian influenza A viruses of subtype H7

No.	Sample ID	Type of sample	Accession Number^a	Subtype/ pathotype	PCR results (cq value)
No.	Sample ID	Type of sample	Accession Number^a	Subtype/ pathotype	M1.2	LP H7	HP H7 Italy	HP H7 Ems
1	A/duck/Potsdam/15/1980	I	AJ704797	H7N7 LP	17,03	NEG	NEG	NEG
2	A/duck/Potsdam/13/1980	I	SA	H7N7 LP	17,55	NEG	NEG	NEG
3	A/swan/Potsdam/64/1981	I	AM922155	H7N7 LP	20,07	NEG	NEG	NEG
4	A/turkey/Germany/R11/2001	I	AJ704812	H7N7 LP	18,89	12,74	NEG	NEG
5	A/mallard/NVP/1776–80/2003	I	NAV	H7N3 LP	25,3	16,41	NEG	NEG
6	A/mallard/NVP/41/2004	I	SA	H7N1 LP	15,44	12,49	NEG	NEG
7	A/mallard/Föhr/Wv190/2005	I	NAV	H7N7 LP	27,35	24,10	NEG	NEG
8	A/teal/Föhr/Wv180/2005	I	NAV	H7N2 LP	14,28	10,76	NEG	NEG
9	A/teal/Föhr/Wv177/2005	I	AM933237	H7N7 LP	24,41	21,76	NEG	NEG
10	A/mallard/Germany/R721/2006	I	SA	H7N7 LP	31,38	27,31	NEG	NEG
11	A/graylag goose/Germany/R752/2006	I	AM933236	H7N7 LP	26,15	17,27	NEG	NEG
12	A/mallard/Germany/R756/2006	I	SA	H7N4 LP	24,81	24,13	NEG	NEG
13	A/mute swan/Germany/R57/2006	I	EPI492518	H7N7 LP	27,73	24,20	NEG	NEG
14	A/mute swan/Germany/R901/2006	I	EPI359695	H7N1 LP	23,14	20,08	NEG	NEG
15	A/swan/Germany/736/2006	I	EPI492517	H7N4 LP	15,39	14,07	NEG	NEG
16	A/common pochard/Germany/R916/2006	I	SA	H7N7 LP	19,03	20,32	NEG	NEG
17	A/duck/Germany/R3129/2007	I	SA	H7N7 LP	15,34	11,59	NEG	NEG
18	A/sentinel-duck/Germany/SK207R/2007	I	NAV	H7N3 LP	27,64	22,09	NEG	NEG
19	A/mallard/Sko212-219 K/2007	I	SA	H7N3 LP	25,97	21,04	NEG	NEG
20	A/guineafowl/Germany/R2495/2007	I	AM930528	H7N3 LP	29,58	27,14	NEG	NEG
21	A/mallard/Germany/R192/2009	I	SA	H7N7 LP	14,65	13,28	NEG	NEG
22	A/turkey/Germany/R655/2009	F	EPI302173	H7N7 LP	13,34	11,76	NEG	NEG
23	A/nandu/Germany/AR142/2013	F	SA	H7N7 LP	28,35	28,90	NEG	NEG
24	A/turkey/Germany/AR502/2013	F	SA	H7N7 LP	18,67	19,12	NEG	NEG
25	A/turkey/Germany/AR618/2013	F	NAV	H7Nx LP	16,11	16,20	NEG	NEG
26	A/chicken/Germany/AR909/2013	F	SA	H7Nx LP	35,59	NEG	NEG	NEG
27	A/turkey/Germany/AR979/2013	F	NAV	H7Nx LP	25,59	21,79	NEG	NEG
28	A/environment/Germany/AR1251/2013	F	NAV	H7N LP	21,31	14,93	NEG	NEG
29	A/chicken/Germany/AR929/2015	F, EL	SA	H7N7 LP	30,39	30,02	NEG	NEG
30	A/chicken/Germany/AR930/2015	F, EL	SA	H7N7 LP	30,39	35,77	NEG	NEG
31	A/chicken/Germany/AR934/2015	F, EL	SA	H7N7 LP	30,07	32,88	NEG	NEG
32	A/chicken/Germany/AR943/2015	F, EL	SA	H7N7 LP	30,07	32,70	NEG	NEG
33	A/chicken/Germany/AR944/2015	F, EL	SA	H7N7 LP	30,07	31,03	NEG	NEG
34	A/chicken/Germany/AR945/2015	F, EL	SA	H7N7 LP	29,9	33,18	NEG	NEG
35	A/chicken/Germany/AR946/2015	F, EL	SA	H7N7 LP	29,9	33,32	NEG	NEG
36	A/duck/Germany/AR234/1/2016	F	SA	H7N7 LP	33,42	35,43	NEG	NEG
37	A/duck/Germany/AR2112/2016	F	NAV	H7N7 LP	36,17	NEG	NEG	NEG
38	A/duck/Germany/AR2868/2016	F	NAV	H7N7 LP	35,3	NEG	NEG	NEG
39	A/FPV/Rostock/45/1934	I	CY077420	H7N1 HP	17,25	NEG	NEG	13,94
40	A/chicken/Germany/“Taucha“/1979	I	SA	H7N7 HP	14,25	NEG	NEG	10,63
41	A/chicken/Germany/R28/2003	I	AJ704813	H7N7 HP	14,77	NEG	NEG	NEG
42	A/FPV/dutch/1927	I	NAV	H7N1 HP	16,52	NEG	NEG	32,14
43	A/chicken/Germany/AR1385/2015	F, EL	SA	H7N7 HP	18,76	NEG	NEG	19,01
44	A/chicken/Germany/AR1413/2015	F, EL	SA	H7N7 HP	29,9	NEG	NEG	35,48
45	A/chicken/Germany/AR1488/1/2015	F, EL	SA	H7N7 HP	29,31	NEG	NEG	22,72
46	A/environment/Germany/AR1536/2015	F, EL	SA	H7N7 HP	29,38	NEG	NEG	21,18
47	A/environment/Germany/AR1537/2015	F, EL	SA	H7N7 HP	29,38	NEG	NEG	25,7
48	A/environment/Germany/AR1539/2015	F, EL	SA	H7N7 HP	29,38	NEG	NEG	22,19
49	A/environment/Germany/AR1540/2015	F, EL	SA	H7N7 HP	29,38	NEG	NEG	24,69
50	A/environment/Germany/AR1541/2015	F, EL	SA	H7N7 HP	29,38	NEG	NEG	26,35
51	A/environment/Germany/AR1546/2015	F, EL	SA	H7N7 HP	30,12	NEG	NEG	25,19
52	A/turkey/Italy/472/1999	I	AJ704811	H7N1 LP	15,24	9,80	NEG	NEG
53	A/chicken/Italy/473/1999	I	EPI624438	H7N2 LP	13,73	10,71	NEG	NEG
54	A/turkey/Italy/2043/2003	I	CY022613, CY022615	H7N3 LP	24,34	21,45	NEG	NEG
55	A/duck/Italy/636/2003	I	NAV	H7N3 LP	22,05	20,49	NEG	NEG
56	A/chicken/Brescia/19/2002	I	AM922154	H7N1 HP	16,59	NEG	NEG	NEG
57	A/hen/Italy/444/1999	I	AJ704810	H7N1 HP	16,22	NEG	18,02	NEG
58	A/broiler/Italy/445/1999	I	AJ580353	H7N1 HP	17,02	NEG	16,35	NEG
59	A/turkey/Ireland/PV8/1995	I	AJ704799	H7N7 LP	16,19	13,07	NEG	NEG
60	A/houbara/Dubai/AR433/2014	I	SA	H7N1 LP	16,81	13,51	NEG	NEG
61	A/houbara/Dubai/AR434/2014	I	SA	H7N1 LP	14,67	11,27	NEG	NEG
62	A/houbara/Dubai/AR435/2014	I	SA	H7N1 LP	15,47	12,66	NEG	NEG
63	A/houbara/Dubai/AR436/2014	I	SA	H7N1 LP	12,23	9,23	NEG	NEG
64	A/houbara/Dubai/AR437/2014	I	SA	H7N1 LP	16,1	13,35	NEG	NEG
65	A/houbara/Dubai/AR438/2014	I	SA	H7N1 LP	13,71	10,08	NEG	NEG
66	A/peregrine falcon/Dubai/AR439/2014	I	SA	H7N1 LP	13,79	26,82	NEG	NEG
67	A/francolin/Dubai/AR440/2014	I	SA	H7N2 LP	15,85	17,84	NEG	NEG
68	A/wild bird/Dubai/AR3452/2014	F	SA	H7N1 LP	16,18	14,57	NEG	NEG
69	A/alexandria tyrode/T145/1948	I	SA	H7N1 HP	14,48	NEG	NEG	10
70	A/duck/Alberta/48/1976	I	SA	H7N3 LP	15,8	14,08	NEG	NEG
71	A/turkey/Ontario/18–1/2000	I	AF497552	H7N1 LP	28,61	NEG	NEG	NEG
72	A/mallard/Alberta/8734/2007	I	AM933238	H7N3 LP	18,63	NEG	NEG	NEG
73	A/chicken/BritishColumbia/CN-06/2004	I	KP055066	H7N3 HP	16,42	NEG	NEG	NEG
74	A/chicken/BritishColumbia/CN-07/2004	I	KP055076	H7N3 HP	24,71	NEG	NEG	NEG
75	A/Anhui/1/2013	I	AHZ60096	H7N9 LP	11,79	9,94	NEG	NEG

^aSequences were obtained from the EpiFlu database of the Global Initiative on Sharing Avian Influenza Data (GISAID) and from GenBank at the National Center for Biotechnology Information (NCBI)
LP low pathogenicity, HP high pathogenicity, SA sequence shown in either Additional file 1: Figure S1 or Additional file 2: Figure S2, otherwise accession numbers are indicated, NAV sequence not available, neg no positive signal detected, I Isolate, F Field sample, F, EL field sample from recent outbreak in Germany

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