Metagenomic Next-Generation Sequencing Reveal Presence of a Novel Ungulate Bocaparvovirus in Alpacas

Abstract

Viruses belonging to the genus Bocaparvovirus (BoV) are a genetically diverse group of DNA viruses known to cause respiratory, enteric, and neurological diseases in animals, including humans. An intestinal sample from an alpaca (Vicugna pacos) herd with reoccurring diarrhea and respiratory disease was submitted for next-generation sequencing, revealing the presence of a BoV strain. The alpaca BoV strain (AlBoV) had a 58.58% whole genome nucleotide percent identity to a camel BoV from Dubai, belonging to a tentative ungulate BoV 8 species (UBoV8). Recombination events were lacking with other UBoV strains. The AlBoV genome was comprised of the NS1, NP1, and VP1 proteins. The NS1 protein had the highest amino acid percent identity range (57.89–67.85%) to the members of UBoV8, which was below the 85% cut-off set by the International Committee on Taxonomy of Viruses. The low NS1 amino acid identity suggests that AlBoV is a tentative new species. The whole genome, NS1, NP1, and VP1 phylogenetic trees illustrated distinct branching of AlBoV, sharing a common ancestor with UBoV8. Walker loop and Phospholipase A2 (PLA2) motifs that are vital for virus infectivity were identified in NS1 and VP1 proteins, respectively. Our study reports a novel BoV strain in an alpaca intestinal sample and highlights the need for additional BoV research.

Virome Profiling of an Eastern Roe Deer Reveals Spillover of Viruses from Domestic Animals to Wildlife

“…BoVs, belonging to the family Parvoviridae , are a group of single-stranded DNA viruses. They have a wide range of hosts, including humans, cats, dogs, pigs, sheep, and cow, and can cause respiratory and gastrointestinal tract diseases in juvenile animals and humans [ 18 ]. By de novo assembly and gap-filling PCR, we obtained a nearly full-length (4923 nt) CpBoV/XK/CHN/2021 genome.…”

Novel Virus Identification through Metagenomics: A Systematic Review

“…Potential pathogenic viruses for species at zoonotic risk to humans were also identified. For example, new Bocaparvoviruses were identified in different animal species, such as alpacas [200], wild squirrel [124] and tufted deer [121]. Novel Bocaparvoviruses were identified in different geographical areas and in different animal species, including bats [201], camels [202], gorillas [203], marmots [204], pigs [205] and rodents [206], and are associated with various veterinary diseases of the respiratory and gastrointestinal tract and acute respiratory diseases in humans.…”

High‐Throughput Metagenomics for Identification of Pathogens in the Clinical Settings

“…Many cases have demonstrated the superiority of mNGS in the identification of i) complex and atypical infections, such as Chlamydia psittaci , [ 176,177 ] Legionella spp ., [ 178 ] anaerobes that are difficult to culture, [ 179 ] and mycobacteria; [ 165,180 ] ii) zoonotic pathogens, such as Streptococcus suis , [ 181 ] Orientia tsutsugamushi , [ 182 ] Leptospira santarosai , [ 19 ] and Toxoplasma gondii ; [ 119 ] iii) emerging RNA and DNA viruses, such as Bocaparvovirus , [ 183 ] Ebola virus, [ 184 ] Zika and chikungunya viruses, [ 185 ] bornavirus, [ 186 ] and SARS‐CoV‐2. [ 187 ]…”