Identification of a novel Picornavirales virus distantly related to posavirus in swine feces

Abstract

De novo assembly of metagenomic sequencing reads from feces from a clinically normal pig identified two approximately 9 kb contigs which each consisted of a single large open reading frame. While one contig encoded a predicted 2990 amino acid protein with 83 % identity to the recently described posavirus 1, the other contig encoded a predicted 2942 amino acid protein with only 25 % identity limited to the genomic region encoding the RNA-dependent RNA polymerase (RdRp) of posavirus 2. Besides RdRp, search of the conserved domain database identified domains associated with picornavirus capsid proteins but failed to identify picornaviral helicase and proteinase domains. In addition, a domain representing a family of Mycoplasma and Ureaplasma immunoglobulin-blocking virulence proteins was identified near the 5'-terminus. Phylogenetic analysis found a distant relationship between this novel virus, provisionally named posavirus 3, to the unclassified posaviruses and fisavirus which are proposed to represent different genera in a novel family of the Picornavirales.

A novel genus in the order Picornavirales detected in human stool

“…All members of the order Picornavirales contain a Hel-Pro-Pol (Helicase, Protease and RNA-dependent RNA polymerase; RdRp) replication block (Le Gall et al, 2008). Recently, some highly divergent members of the order Picornavirales have been discovered: fish stool-associated RNA virus (fisavirus) in the intestinal content of a healthy carp (Reuter et al, 2015) and porcine stool-associated RNA viruses (posaviruses) in the faeces of healthy pigs (Shan et al, 2011;Hause et al, 2015). These viruses cluster with a cDNA sequence found in Ascaris suum (Wang et al, 2011), which most probably is the RdRp sequence of a virus infecting this parasite (Shan et al, 2011).…”

Highly diverse posaviruses in swine faeces are aquatic in origin

“…Previous characterization of posaviruses failed to identify a proteinase domain conserved amongst Picornavirales (Shan et al, 2011;Hause et al, 2015a). Seven of the posavirus genomes determined here had domains with homology to Picornavirales 3C proteinases located downstream of the Hel domain.…”

“…For strains with sequence information for the initiation codon, the Hel domain was located between aa 438 and 1260, and encompassed approximately 100 aa. Strain 10611 was 93 % identical to a previously described posavirus 3 that also lacked an identifiable Hel domain (Hause et al, 2015a). Hel domain expectation (e) values ranged from 5.6 e À5 to 8.3 e À20.…”

“…Similarly to posavirus 1 and 2, a Pro domain could not be identified; however, in contrast, neither could a Hel domain. Phylogenetic analysis of the Pol and identification of two picornavirus capsid domains near the 3¢ terminus suggested inclusion of posavirus 3 in a new, unassigned family of Picornavirales (Hause et al, 2015a). Posavirus was also identified in faecal samples from pigs in China (Zhang et al, 2014).…”

“…As posavirus cDNA could not be detected in A. suum DNA by PCR, and the nucleotide composition of both posavirus and A. suum were more similar to arthropods than plants or animals, the authors hypothesized that posaviruses infect nematodes parasitizing pigs (Shan et al, 2011). More recently, a novel posavirus with a Pol with only approximately 25 % amino acid similarity to posavirus 1 and 2 was also identified in swine faeces (Hause et al, 2015a). Similarly to posavirus 1 and 2, a Pro domain could not be identified; however, in contrast, neither could a Hel domain.…”