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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)