Table 2 Summary of chicken samples used in the study
From: Viral metagenomic analysis of chickens with runting-stunting syndrome in the Republic of Korea
ID | 05D72 | 07D11 | 13D62 | 13Q45 | Control |
|---|---|---|---|---|---|
year | 2005 | 2007 | 2013 | 2013 | – |
species | Broiler | Broiler | Broiler | Broiler | SPF |
age (weeks) | 6 | 2 | 3 | 4 | 4 |
final diagnosis | RSS, IB | RSS | RSS, IBH | RSS, Coccidiosis | – |
morbidity (%) | uk | uk | 48.6 | 52.5 | – |
sample | small intestine | small intestine | intestinal contents | intestinal contents | intestinal contents |
total reads | 14,893,900 | 17,152,624 | 19,711,846 | 18,325,438 | 18,906,096 |
No. of sequences | 18,777 | 57,429 | 42,806 | 20,526 | 60,556 |
mean length | 182 | 192 | 176 | 162 | 193 |
total viral reads | 226,870 | 162,917 | 1,766,642 | 48,979 | 339,024 |
bacteriophage | 7463 (3.3)a | 2618 (1.6) | 109,672 (6.2) | 10,337 (21.1) | 339,024 (100) |
Leviviridae | 7463 | 1937 | 17,237 | 3836 | 270,026 |
Siphoviridae | – | – | 82,207 | 3248 | 71 |
Myoviridae | – | – | 6035 | 36 | 3731 |
Podoviridae | – | – | 907 | 3118 | 5433 |
unassigned phage | – | 684 | 3286 | 99 | 3898 |
Astroviridae | 128 (0.1) | 3424 (2.1) | 1,328,548 (75.2) | 4208 (8.6) | – |
Picornaviridae | 214,648 (94.6) | 39,646 (24.3) | 207,500 (11.8) | 18,567 (37.9) | – |
Parvoviridae | – | 9563 (5.9) | 13,793 (0.8) | 2599 (5.3) | – |
Reoviridae | – | 107,666 (66.1) | 67,458 (3.8) | – | – |
Caliciviridae | – | – | 19,802 (1.1) | 7822 (16.0) | – |
Picobirnaviridae | – | – | 16,128 (0.9) | 5446 (11.1) | – |
Adenoviridae | – | – | 3741 (0.2) | – | – |
Coronaviridae | 409 (0.2) | – | – | – | – |
Anelloviridae | 4222 (1.9) | – | – | – | – |