Table 1. Viruses detected by metagenomic sequencing of nasal swabs collected from cattle exhibiting acute clinical signs of BRD (symptomatic) and clinically normal pen-mates (asymptomatic) each from six feedlots in Mexico and four feedlots in the USA.
| Virus | Mexico | USA | Reads derived from symptomatic animals (%) | ||||
|---|---|---|---|---|---|---|---|
| No. of sites positive | Number of cattle positive (%) | No. of sites positive | Number of cattle positive (%) | ||||
| Symptomatic | Asymptomatic | Symptomatic | Asymptomatic | ||||
| IDV | 4/6 | 8/27 (29.6) | 1/26 (3.8) | 1/4 | – | 2/20 (10.0) | 385 395 (99.9 %) |
| BRAV | 4/6 | 5/27 (18.5) | 7/26 (26.9) | 4/4 | 18/20 (90.0) | 19/20 (95.0) | 2 185 274 (66 %) |
| BRBV | 5/6 | 7/27 (25.9) | 3/26 (11.5) | 4/4 | 4/20 (20.0) | 8/20 (40.0) | 246 256 (62 %) |
| EVE | 3/6 | 2/27 (7.4) | 2/26 (7.7) | 1/4 | 3/20 (15.0) | – | 20 008 (35.4 %) |
| EVF | 2/6 | 1/27 (3.7) | 1/26 (3.8) | 1/4 | 1/20 (5.0) | – | 623 (16.6 %) |
| UBPV6 | 4/6 | 5/27 (18.5) | 3/26 (11.5) | 2/4 | 1/20 (5.0) | 3/20 (15.0) | 5731 (22.4) |
| UTPV1 | 1/6 | – | 1/26 (3.8) | 2/4 | 5/20 (25.0) | 1/20 (5.0) | 220 520 (99.6 %) |
| BRSV | – | – | – | 2/6 | 1/20 (5.0) | 4/20 (20.0) | 20 004 (70.5 %) |
| BVDV1 | – | – | – | 3/4 | 3/20 (15.0) | 1/20 (5.0) | 50 787 (93.7 %) |
| BVDV2 | 1/6 | 1/27 (3.7) | – | – | – | – | 939 (100 %) |
| BCV | 2/6 | 3/27 (11.1) | – | 4/4 | 11/20 (55.0) | 9/20 (45.0) | 2 555 541 (70.8 %) |
| BNV | 2/6 | 1/27 (3.7) | 3/26 (11.5) | – | – | – | 1098 (12.2 %) |
| BPV3 | 2/6 | 3/27 (11.1) | – | 1/4 | 4/20 (20.0) | 4/20 (20.0) | 629 888 (97.8 %) |
| BAdV3 | 1/6 | 3/27 (11.1) | 5/26 (19.2) | 1/4 | – | 1/20 (5.0) | 399 (0.26 %) |
| BAAV | 1/6 | 3/27 (11.1) | 5/26 (19.2) | – | – | – | 47 (0.13 %) |
| BPIV3 | – | – | 1/26 (3.8) | 1/4 | – | 1/20 (5.0) | – |
| BTV | 1/6 | 1/27 (3.7) | – | – | – | – | 304 (100 %) |
| BHV1 | 1/6 | 1/27 (3.7) | – | – | – | – | 47 (100 %) |
| MdSGHV | 2/6 | 4/27 (14.8) | – | – | – | – | 1386 (100 %) |
| ssCDV | 4/6 | 4/27 (14.8) | 4/26 (15.4) | 2/6 | 3/20 (15.0) | – | 268 (50.9 %) |
| PBV | 1/6 | – | 1/26 (3.8) | – | – | – | – |
Abbreviations: BRBV, bovine rhinitis B virus; EVE, enterovirus E; EVF, enterovirus F; UBPV6, ungulate bocaparvovirus 6; UTPV1, ungulate tetraparvovirus 1; BCV, bovine coronavirus; BNV, bovine nidovirus; BPV3, bovine parvovirus 3; BAAV, bovine adeno-associated virus; BTV, bovine torovirus; MdSGHV, Musca domestica salivary gland hypertrophy virus; ssCDV, single-stranded circular DNA viruses; PBV, picobirnavirus.