Table 2.
Viruses identified by metagenomics
| Virus | Family | Genome size (bp) | Largest contig size (bp) from any individual sample | Largest contig % AA identity (protein) | Total number of reads from all samples |
|---|---|---|---|---|---|
| FAdV‐A | Adenoviridae | 43,804 | 235 | 100 (short fibre) | 2 |
| BAV | Astroviridae | 6,233 | 6,126 | 96.2 (nsp1a) | 23,350 |
| PeSV | Betaflexiviridae | 8,041 | 344 | 95.6 (replicase) | 8 |
| BCV | Coronaviridae | 308,845 | 4,952 | 98.4 (polyprotein) | 77,240 |
| BVDV1 | Flaviviridae | 12,258 | 1,125 | 94.9 (polyprotein) | 1,452 |
| BVDV2 | Flaviviridae | 12,476 | 1,113 | 99.5 (polyprotein) | 158 |
| IDV | Orthomyxoviridae | 12,546 | 251 | 98.8 (PB2) | 2 |
| BRSV | Paramyxoviridae | 15,140 | 2,244 | 100 (nucleocapsid) | 13,167 |
| BPIV3 | Paramyxoviridae | 15,537 | 2,151 | 95.7 (phosphoprotein) | 312 |
| BPV2 | Parvoviridae | 5,610 | 1,670 | 94.2 (capsid) | 262 |
| BPV3 | Parvoviridae | 5,100 | 612 | 99.4 (non‐structural) | 20 |
| UTPV1 | Parvoviridae | 5,108 | 5,010 | 99.9 (minor capsid) | 71,761 |
| AAAV | Parvoviridae | 4,684 | 203 | 96 (rep) | 4 |
| EVE | Picornaviridae | 7,414 | 251 | 98.8 (polyprotein) | 4 |
| BRBV | Picornaviridae | 7,556 | 234 | 93.7 (polyprotein) | 9 |
| BPyV | Polyomaviridae | 4,697 | 285 | 99.6 (agnoprotein) | 8 |
Abbreviations: AA, amino acid; AAAV, avian adeno‐associated virus; BAV, bovine astrovirus; BCV, bovine coronavirus; bp, base pairs; BPIV3, bovine parainfluenza virus 3; BPV 2 and 3, bovine parvovirus 2 and 3; BPyV, bovine polyomavirus; BRBV, bovine rhinitis virus B; BRSV, bovine respiratory syncytial virus; BVDV 1 and 2, bovine viral diarrhoea virus 1 and 2; EVE, Enterovirus E; FAdV‐A, fowl aviadenovirus; IDV, influenza D virus; PeSV, pea streak virus; UTPV1, ungulate tetraparvovirus 1.
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