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Table 1 Summary of next-generation sequencing data and percent coverage of Newcastle disease virus genomes obtained from formalin-fixed paraffin-embedded tissue samples of wild pigeons collected in the U.S. between 2010 and 2016

From: Whole-genome sequencing of genotype VI Newcastle disease viruses from formalin-fixed paraffin-embedded tissues from wild pigeons reveals continuous evolution and previously unrecognized genetic diversity in the U.S.

SEPRL ID

Tissue

Species

Statea

Year

NDV readse

% cover.f

IHCg

1177-1 b

Kidney

ECDO c

MT

2010

26,069

99.8

+

1177-2

Liver

56,910

99.8

+

1177-3

Spleen

8030

99.77

+

1178-2

Liver

ECDO

NM

2013

  

+

1178-3

Spleen

  

+

1179-1

Kidney

ECDO

TX

2014

1108

99.01

+

1179-2

Liver

  

N

1179-3

Spleen

  

N

1180-1

Kidney

ECDO

TX

2014

14,317

99.81

+

1180-2

Liver

1761

99.64

+

1180-3

Spleen

7160

99.76

+

1181-1

Kidney

ECDO

UT

2015

111,778

99.87

+

1181-2

Liver

8780

99.76

+

1181-3

Spleen

32,218

99.86

+

1182-1

Kidney

ECDO

TX

2016

6387

99.84

+

1182-2

Liver

  

N

1182-3

Spleen

32,488

99.84

+

1183-1

Kidney

ECDO

TX

2015

  

+

1183-3

Liver

  

N

1184-1

Kidney

ECDO

TX

2015

2095

99.49

+

1184-2

Liver

  

N

1184-3

Spleen

  

N

1185-1

Kidney

ECDO

TX

2015

2292

99.58

+

1185-2

Liver

  

N

1185-3

Spleen

  

N

1187-1

Kidney

ROPId

PA

2011

  

N

1187-2

Liver

  

N

1187-3

Spleen

  

N

1188-1

Kidney

ROPI

MA

2014

10,533

99.84

+

1188-2

Liver

  

N

1188-3

Spleen

1373

98.72

+

1189-1

Kidney

ROPI

PA

2012

732

97.34

+

1189-2

Liver

  

N

1189-3

Spleen

  

N

1191-1

Kidney

ECDO

KS

2016

37,195

99.84

+

1191-2

Liver

  

+

1191-3

Spleen

20,824

99.77

+

1192-1

Kidney

ECDO

KS

2016

2495

99.57

+

1192-2

Liver

  

N

1192-3

Spleen

  

+

1193-1

Kidney

ECDO

KS

2016

8247

99.84

+

1193-2

Liver

  

N

1194-1

Kidney

ECDO

KS

2016

32,269

99.83

+

1194-2

Liver

  

N

1194-3

Spleen

  

N

1195-1

Kidney

ECDO

KS

2016

5481

99.82

+

1195-2

Liver

  

N

1195-3

Spleen

  

+

  1. aAbbreviations of states: MT Montana, PA Pennsylvania, TX Texas, NM New Mexico, UT Utah, MA Massachusetts, KS Kansas
  2. bPositive samples are in bold font
  3. cECDO (Eurasian collared-dove)
  4. dROPI (rock pigeon)
  5. eNumbers of paired reads used to re-call the final NDV consensus for each sequence
  6. fPercent coverage - the fraction of the expected full genome length covered by the consensus scaffold
  7. gIHC (immunohistochemistry); N (negative); + (positive)