Investigating the Diversity and Host Range of Novel Parvoviruses from North American Ducks Using Epidemiology, Phylogenetics, Genome Structure, and Codon Usage Analysis

Abstract

Parvoviruses are small single-stranded DNA viruses that can infect both vertebrates and invertebrates. We report here the full characterization of novel viruses we identified in ducks, including two viral species within the subfamily Hamaparvovirinae (duck-associated chapparvovirus, DAC) and a novel species within the subfamily Densovirinae (duck-associated ambidensovirus, DAAD). Overall, 5.7% and 21.1% of the 123 screened ducks (American black ducks, mallards, northern pintail) were positive for DAC and DAAD, respectively, and both viruses were more frequently detected in autumn than in winter. Genome organization and predicted transcription profiles of DAC and DAAD were similar to viruses of the genera Chaphamaparvovirus and Protoambidensovirus, respectively. Their association to these genera was also demonstrated by subfamily-wide phylogenetic and distance analyses of non-structural protein NS1 sequences. While DACs were included in a highly supported clade of avian viruses, no definitive conclusions could be drawn about the host type of DAAD because it was phylogenetically close to viruses found in vertebrates and invertebrates and analyses of codon usage bias and nucleotide frequencies of viruses within the family Parvoviridae showed no clear host-based viral segregation. This study highlights the high parvoviral diversity in the avian reservoir with many avian-associated parvoviruses likely yet to be discovered.

Newlavirus, a Novel, Highly Prevalent, and Highly Diverse Protoparvovirus of Foxes (Vulpes spp.)

“…After discovering the first Newlavirus fragment with the VidION method [ 23 ], the near complete genomes of 5 strains were obtained through a combination of genome walking [ 24 ] and specific PCRs designed based on newly obtained sequences. The sequences encompass the entire coding portion but lack the inverted non-coding repeats that form the terminal hairpins, which are difficult to obtain from non-cultured viruses ( Figure 2 ).…”

“…Virus discovery was initially performed on 68 stool samples collected from Labrador foxes with the VidION method as previously described [ 23 ]. Before sample pre-treatment, an approximately 0.5 cm 3 piece of stool was placed in a 2-mL screw-capped tube with 1 mL UTM and three 4.5-mm copper-coated steel beads (Crosman, Walmart, Mississauga, ON, Canada) for vortex-mediated fragmentation.…”

Co‐circulation of five species of dog parvoviruses and canine adenovirus type 1 among gray wolves (Canis lupus) in northern Canada

“…This implies that NWT-W78 is a previously undetected variant. Finally, all sequences presented an additional ORF at the beginning of the genome partially overlapping the NS1 ORF that could encode an additional nonstructural protein, similarly to other chaphamaparvoviruses (Canuti et al, 2021;Ge et al, 2020;Pénzes et al, 2019). No clear recombination signal among NWT sequences was observed over the complete genomes.…”

Small but mighty: old and new parvoviruses of veterinary significance

“…Discoveries of chapparvoviruses in other bird species include parakeets [ 328 ], peafowls [ 329 ], and red-crowned cranes [ 127 ]. A study of Canadian ducks detected duck-associated chapparvovirus (DAC) in paired oropharyngeal and cloacal swabs of apparently healthy ducks and Galliform chaphamaparvovirus 3 in a gull [ 330 ].…”