Metagenomic analysis of the shrew enteric virome reveals novel viruses related to human stool-associated viruses

Abstract

Shrews are small insectivorous mammals that are distributed worldwide. Similar to rodents, shrews live on the ground and are commonly found near human residences. In this study, we investigated the enteric virome of wild shrews in the genus Crocidura using a sequence-independent viral metagenomics approach. A large portion of the shrew enteric virome was composed of insect viruses, whilst novel viruses including cyclovirus, picornavirus and picorna-like virus were also identified. Several cycloviruses, including variants of human cycloviruses detected in cerebrospinal fluid and stools, were detected in wild shrews at a high prevalence rate. The identified picornavirus was distantly related to human parechovirus, inferring the presence of a new genus in this family. The identified picorna-like viruses were characterized as different species of calhevirus 1, which was discovered previously in human stools. Complete or nearly complete genome sequences of these novel viruses were determined in this study and then were subjected to further genetic characterization. Our study provides an initial view of the diversity and distinctiveness of the shrew enteric virome and highlights unique novel viruses related to human stool-associated viruses.

Highly diverse population of Picornaviridae and other members of the Picornavirales, in Cameroonian fruit bats

“…We obtained a near complete genome of 7081 nt (Table 3), although it seems that a few nucleotides at the 5’ and 3’ ends are missing. The genome contains a predicted single large ORF encoding a putative polyprotein of 2173 aa, although the initiation codon (AUG) was not located in the Kozak consensus sequence (AAGAUGG) like in the CroV-1 genome [29]. The ORF is bordered by a 508 nt long 5’ UTR and 54 nt long 3’ UTR and the potential polyprotein cleavage sites are as shown in Fig.…”

“…Therefore, we speculate that fruit eating bats are most likely the host of the kunsagivirus identified in this study. Similarly, crohivirus (CroV1, AB937989), first isolated from a Zambian shrew [29] is a yet unclassified picornavirus with a pasivirus-like genome organization. The bat crohivirus has the same genome organization and shares the same features with the one from a shrew, although little sequence similarity may suggest a third pasivirus species.…”

Methods for virus classification and the challenge of incorporating metagenomic sequence data

“…As examples, the PubMed search 'virus AND metagenomic' identified 579 papers, of which the first 10 to describe samples described sequences from tissues of Pacific starfish with unexplained wasting disease, bronchoalveolar lavage samples from transplant patients, Yellowstone lake water, shrew faeces, carrots, a diarrhoea sample from a Chinese child, Brazilian free-tailed bats, urban air filters in the USA, 700-year-old caribou faeces and human oropharyngeal samples (Adams et al, 2014;Cibulski et al, 2014;Hewson et al, 2014;Ng et al, 2014;Sasaki et al, 2014;Yolken et al, 2014;Young et al, 2014;Yu et al, 2014;Zhou et al, 2014). This sheer diversity of sources would seem to preclude systematic recording of sample information that may contribute to their classification.…”

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).…”