Fecal virome composition of migratory wild duck species

Abstract

The fecal virome comprises a complex diversity of eukaryotic viruses, phages and viruses that infect the host. However, little is known about the intestinal community of viruses that is present in wild waterfowl, and the structure of this community in wild ducks has not yet been studied. The fecal virome compositions of six species of wild dabbling ducks and one species of wild diving duck were thus analyzed. Fecal samples were collected directly from the rectums of 60 ducks donated by hunters. DNA and RNA virus particles were purified and sequenced using the MiSeq Illumina platform. The reads obtained from the sequencing were analyzed and compared with sequences in the GenBank database. Viral-related sequences from the Herpesviridae, Alloherpesviridae, Adenoviridae, Retroviridae and Myoviridae viral families showed the highest overall abundances in the samples. The virome analysis identified viruses that had not been found in wild duck feces and revealed distinct virome profiles between different species and between samples of the same species. This study increases our understanding of viruses in wild ducks as possible viral reservoirs and provides a basis for further studying and monitoring the transmission of viruses from wild animals to humans and disease outbreaks in domestic animals.

Studying the gut virome in the metagenomic era: challenges and perspectives

“…Depending on the targeted fraction of the virome, DNA extraction protocols may differ substantially. For instance, the active virome is primarily studied through the extraction of DNA from VLPs obtained by filtration, various chemical precipitations [14, 15, 29, 47], and/or (ultra)centrifugation [106, 107]. In contrast to studying the active virome, the concurrent targeting of both the silent and active virome (so-called “virome potential”) requires total nucleic acid isolation (TNAI) from all the bacteria and viruses in the sample [56–58].…”

Fishing for the Virome of Tropical Tuna

“…This strongly differs from observations in other vertebrates such as birds and mammals, where phages were found to be predominant within the gut microflora [ 18 , 19 , 20 ]. However, Ramírez-Martínez et al (2018) [ 21 ] also demonstrated that eukaryotic viruses were dominant in the fecal virome of various wild migratory duck species. Further studies are necessary to examine whether this is a particular feature in fish.…”

Molecular identification and phylogenetic characterization of influenza A virus at a wildlife-livestock interface in Mexico

“…Previous studies have identified IAV in waterfowl from the Lerma marshes (Cuevas-Dominguez et al, 2009;Ramirez-Martinez et al, 2018). IAV subtypes H7N3, H6N2, and H4N2 have been isolated from anatids, sentinel ducks, and wild bird habitats of the State of Mexico (Barron-Rodriguez, Chavez-Maya, Cuevas-Dominguez et al, 2009;Ornelas-Eusebio et al, 2015).…”

“…The Lerma marshes constitute a critical surveillance area where wild ducks, backyard poultry, backyard pigs, and humans co-occur in time and space. Some molecular studies in wild ducks and their environment have been conducted in this Natural Protected Area (Cuevas-Dominguez et al, 2009;Ornelas-Eusebio, Obregon-Ascencio, Chavez-Maya, & Garcia-Espinosa, 2015;Ramirez-Martinez, Loza-Rubio, Mosqueda, Gonzalez-Garay, & Garcia-Espinosa, 2018). Nevertheless, the aims of these studies were no centered on the interrelation among diverse species, and a persistent gap in knowledge about IAV dynamics in the wildlife -livestock interface remains in the region.…”