Table 2.
Viruses detected in the six juvenile Pacific black duck (MAD) faecal sample pool.
| Virus | Family | Characteristics | NCBI virus reference sequence used for mapping | Percentage of identity to the closest virus for individual NGS reads | Likely source |
|---|---|---|---|---|---|
| Avian paramyxovirus 6 | Paramyxoviridae, Avulavirus | Negative-stranded RNA linear genome; enveloped, spherical. Diameter of about 150 nm. | AB759118 | 95–98% | Host |
| Gammacoronavirus | Coronaviridae, Coronavirinae; Gammacoronavirus | Monopartite, linear ssRNA(+) genome; enveloped, spherical, about 120 nm in diameter | KM454473 | 81–100% | Host |
| Deltacoronavirus | Coronaviridae, Coronavirinae; Deltacoronavirus | Monopartite, linear ssRNA(+) genome; enveloped, spherical, about 120 nm in diameter | NC016994 | 82–89% | Host |
| Virus related to chicken/duck/goose megrivirus | Picornaviridae, Megrivirus; unclassified Megrivirus. | Monopartite, linear ssRNA(+) genome; non-enveloped, spherical, about 30 nm in diameter | KC663628 and NC023857 | 77–83% | Host |
| Rotavirus G | Reoviridae, Sedoreovirinae; Rotavirus | Segmented linear dsRNA genome; non-enveloped with a double capsid structure | NC021580 | 80–89% | Host |
| Virus related to goose adenovirus 4 and duck adenovirus 2 | Adenoviridae; Aviadenovirus | Non-segmented, linear dsDNA; non-enveloped capsid with a pseudo T = 25 icosahedral symmetry | NC024486 and NC017979 | 75–87% | Host |
| Virus related to duck dependovirus/AAV | Parvoviridae; Parvovirinae; Dependoparvovirus | Linear, ssDNA genome, Non-enveloped, round, T = 1 icosahedral symmetry, 18–26 nm in diameter with capsid | KX583629 | 88% | Host |
| Avian encephalomyelitis virus | Picornaviridae; Tremovirus | Monopartite, linear ssRNA(+) genome; non-enveloped, spherical, about 30 nm in diameter | AY517471 | 82–86% | Host |
| Avian calicivirus: related to chicken/goose calicivirus | Caliciviridae | Monopartite, linear ssRNA(+) genome, non-enveloped, capsid of about 27–40 nm in diameter, with T = 3 icosahedral symmetry | NC024078 | 70–84% | Host |
| Virus related to Hubei picorna-like virus 19 | Unclassified RNA viruses | positive sense ssRNA genome | KX883724 | 79–82% | Leech |
| Virus related to Hubei picorna-like virus 51 | Unclassified RNA viruses | positive sense ssRNA genome | KX883953 | 98% | Dragonfly |
| Bacteriophage related to Enterobacteria phage N4 | Caudovirales; Podoviridae | Linear, dsDNA genome; non-enveloped, head-tail structure | EF056009 | 79–87% | Bacteria |
This table displays the viruses detected and characterised in the MAD faecal sample pool. The virus family and its characteristics are shown. We identified these viruses using the reference sequences mentioned in column 4 to which the NGS reads were mapped. We found how much the reads of our viruses are identical to the closest virus from the NCBI dataset using MEGA 6 or 7 software. However, for individual reads generated by NGS, we used BLASTN to identify the closest virus from the NCBI dataset. Their likely source of origin in our sample was determined using the NGS reads generated and correlating them from literature.