Table 1 Known viral species assembled from the RNA sequencing libraries. Twelve known RNA virus species and short DNA viruses were assembled. Reference library indicates the library from which a viral genome was obtained and used to estimate the nucleotide identity to the closest reference. Viruses with large DNA genomes (i.e. Herpesviruses) were not included due to the low coverage of the contigs obtained with RNA sequencing
Known viral sequences identified in samples | Consensus sequence RNA library | Reference Coverage | Nucleotide identity to closest reference | Closest reference accession number | Reference length | Assembly length | Assembly accession number |
|---|---|---|---|---|---|---|---|
Bovine nidovirus (BoNV)-(a) | L6 | 100% | 91.54% | KM589359.1 | 20261 | 20259 | ON330458 |
Bovine nidovirus (BoNV)-(b) | L4 | 100% | 91.39% | KM589359.1 | 20261 | 20331 | ON330451 |
Bovine rhinitis A virus (BRAV)-3 (a) | L13 | 100% | 83.2% | KT948520.1 | 7267 | 7367 | OP020167 |
Bovine rhinitis A virus (BRAV)-3 (b) | L13 | 94% | 83.10% | KT948520.1 | 7267 | 6799 | OP020171 |
Bovine coronavirus (BCoV) | L3 | 100% | 98.71% | FJ425189.1 | 30997 | 30983 | OP020176 |
Enterovirus E1 (EV-E1)(a) | L12 | 99% | 85.45% | MN598021.1 | 7447 | 7383 | OP020148 |
Enterovirus E1 (EV-E1)(b) | L12 | 99% | 85.29% | MN598021.1 | 7447 | 7386 | OP020151 |
Influenza D virus (IDV) segment 1 | L13 | 100% | 99.13% | LC494105.1 | 2319 | 2319 | OP020132 |
Influenza D virus (IDV) segment 2 | L9 | 99% | 98.23% | LC270266.1 | 2330 | 2314 | OP020133 |
Influenza D virus (IDV) segment 3 | L14 | 100% | 98.45% | LC494107.1 | 2133 | 2183 | OP020134 |
Influenza D virus (IDV) segment 4 (a) | L13 | 100% | 99.25% | LC494108.1 | 1995 | 2033 | OP020135 |
Influenza D virus (IDV) segment 4 (b) | L4 | 99% | 96.4% | LC270268.1 | 2049 | 2028 | OP020136 |
Influenza D virus (IDV) segment 5 | L9 | 99% | 98.36% | LC270269.1 | 1775 | 1766 | OP020137 |
Influenza D virus (IDV) segment 6 | L9 | 99% | 98.67% | LC128434.1 | 1219 | 1203 | OP020138 |
Influenza D virus (IDV) segment 7 | L4 | 99% | 97.68% | LC270271.1 | 868 | 862 | OP020139 |
Bovine rhinitis B virus (BRBV)-5 | L15 | 100% | 79.52% | KU159360.1 | 7494 | 7506 | OP020156 |
Bovine rhinitis B virus (BRBV)-2 | L15 | 100% | 88.68% | KU159357.1 | 7271 | 7505 | OP020160 |
Bovine respiratory syncytial virus | L4 | 89% | 87.24% | NC_038272.1 | 15140 | 13416 | OP020146 |
Bovine viral diarrhea virus-1c | L6 | 100% | 90.50% | M96751.1 | 12308 | 12287 | OP020142 |
Bovine viral diarrhea virus-1a | L8 | 96% | 91.44% | LR760748.1 | 12297 | 11788 | OP020143 |
Bovine astrovirus (BAstro) | L15 | 70% | 90.28% | KP264970.1 | 6099 | 1584/1745 | OP020144-5 |
Bovine hokovirus 1 (BPARV4)a | L14 | 76% | 99.55% | KU172423.1 | 5254 | 3969 | OP020140 |
Ungulate bocaparvovirus 6(UBPV6)a | L6 | 25% | 97.80% | KU172421.1 | 5224 | 1318 | OP020141 |