Duck gut viral metagenome analysis captures snapshot of viral diversity.
BACKGROUND
Ducks (Anas platyrhynchos) an economically important waterfowl for meat, eggs and feathers; is also a natural reservoir for influenza A viruses. The emergence of novel viruses is attributed to the status of co-existence of multiple types and subtypes of viruses in the reservoir hosts. For effective prediction of future viral epidemic or pandemic an in-depth understanding of the virome status in the key reservoir species is highly essential.


METHODS
To obtain an unbiased measure of viral diversity in the enteric tract of ducks by viral metagenomic approach, we deep sequenced the viral nucleic acid extracted from cloacal swabs collected from the flock of 23 ducks which shared the water bodies with wild migratory birds.


RESULTS
In total 7,455,180 reads with average length of 146 bases were generated of which 7,354,300 reads were de novo assembled into 24,945 contigs with an average length of 220 bases and the remaining 100,880 reads were singletons. The duck virome were identified by sequence similarity comparisons of contigs and singletons (BLASTx E score, <10(-3)) against viral reference database. Numerous duck virome sequences were homologous to the animal virus of the Papillomaviridae family; and phages of the Caudovirales, Inoviridae, Tectiviridae, Microviridae families and unclassified phages. Further, several duck virome sequences had homologous with the insect viruses of the Poxviridae, Alphatetraviridae, Baculoviridae, Densovirinae, Iflaviridae and Dicistroviridae families; and plant viruses of the Secoviridae, Virgaviridae, Tombusviridae and Partitiviridae families, which reflects the diet and habitation of ducks.


CONCLUSIONS
This study increases our understanding of the viral diversity and expands the knowledge about the spectrum of viruses harboured in the enteric tract of ducks.
OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India.
Mohammed
M
Fawaz
OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India.
Periyasamy
P
Vijayakumar
OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India.
Anamika
A
Mishra
OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India.
Pradeep N
PN
Gandhale
OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India.
Rupam
R
Dutta
OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India.
Nitin M
NM
Kamble
OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India.
Shashi B
SB
Sudhakar
College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Aizawl, Mizoram India.
Parimal
P
Roychoudhary
Laboratory of Immunology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh India.
Himanshu
H
Kumar
OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India.
Diwakar D
DD
Kulkarni
OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India.
Ashwin Ashok
AA
Raut
Duck; Gut; Next generation sequencing; Papillomaviridae; Viral metagenomics; Virome