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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 Numbera Subtype/ pathotype PCR results (cq value)
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
  1. 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)
  2. 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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