Duck gut viral metagenome analysis captures snapshot of viral diversity

Abstract

BackgroundDucks (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.MethodsTo 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.ResultIn 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.ConclusionThis study increases our understanding of the viral diversity and expands the knowledge about the spectrum of viruses harboured in the enteric tract of ducks.

Metagenomic Analysis of the Jinding Duck Fecal Virome

“…The four strains contained the five phage viruses as follows: myoviruses, siphoviruses, podoviruses, inoviruses, and microviruses. This was consistent with the previously reported phage composition of ducks, human, pig, and equine feces by metagenomic analysis [11,13,[24][25][26]. A high percentage (99.43, 69.17, 95, 97.68%) of phage reads was double-stranded DNA viruses and belonged to the order Caudovirales, while the B strain had a higher percentage of inovirus reads than the A, C, or D strains.…”

“…Duck circovirus reads were detected in the B strain. Anatid herpesvirus 1, known as DPV, Fowlpox virus, Canarypox virus, and pigeonpox virus reads related to duck were found and relatively scarce, and those viral reads were identified in Indian ducks feces [13]. The result suggested that the sensitivity of PCR was not high; we should adopt a variety of methods to identify pathogens in samples.…”

“…With the development and use of viral metagenomic analyses, many of these limitations and shortcomings can now be avoided. These methods have been used since their inception to identify the unbiased viral diversity from the digestive tract of humans [8], bats [9], turkey [10], pigs [11], pigeons [12], and ducks [13].…”

Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods

“…Detection of viromes of duck guts has been reported recently and 18 classified viral families were identified (Fawaz et al, 2016). Seven of these 18 families (Circoviridae, Dicistroviridae, Iflaviridae, Parvoviridae, Picornaviridae, Phycodnaviridae, and Virgaviridae) were also identified in the duck feces sample through this study.…”

A decade of RNA virus metagenomics is (not) enough

“…Most importantly for veterinarians, RNA virus metagenomics has revealed a number of candidate etiological agents for a variety of animal ailments including avian proventricular dilatation disease, mink shaking syndrome, snake inclusion body disease, python respiratory illness, dairy cow disease, and tilapia die-offs (Kistler et al, 2008;Gancz et al, 2009;Blomström et al, 2010;Stenglein et al, 2014Stenglein et al, , 2012Uccellini et al, 2014;Hoffmann et al, 2012;Bacharach et al, 2016). Animal feces has proven fruitful hunting for metagenomicists, with canine, feline, porcine, equine, goose, duck, and shrew fecal RNA viromes turning up a plethora of mostly novel picorna-like viruses, albeit with an unclear relationship to disease and perhaps some more closely linked to the invertebrates indicated above (Fawaz et al, 2016;Greninger and Jerome, 2016;Li et al, 2011;Moreno et al, 2017;Nagai et al, 2015;Ng et al, 2014b;Phan et al, 2011;Reuter et al, 2012;Sano et al, 2016;Sasaki et al, 2015;Zhang et al, 2014). The recovery of Ancient Northwest Territories cripavirus from 700-year old frozen caribou feces illustrated an incredible stability of encapsidated RNA (Ng et al, 2014a).…”