Table 2 Viruses detected in the six juvenile Pacific black duck (MAD) faecal sample pool.

From: Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds

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

  1. 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.
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