Feline fecal virome reveals novel and prevalent enteric viruses

Abstract

Humans keep more than 80 million cats worldwide, ensuring frequent contacts with their viruses. Despite such interactions the enteric virome of cats remains poorly understood. We analyzed a fecal sample from a single healthy cat from Portugal using viral metagenomics and detected five eukaryotic viral genomes. These viruses included a novel picornavirus (proposed genus “Sakobuvirus”) and bocavirus (feline bocavirus 2), a variant of feline astrovirus 2 and sequence fragments of a highly divergent feline rotavirus and picobirnavirus. Feline sakobuvirus A represents the prototype species of a proposed new genus in the Picornaviridae family, distantly related to human salivirus and kobuvirus. Feline astroviruses (mamastrovirus 2) are the closest relatives of the classic human astroviruses (mamastrovirus 1), suggestive of past cross-species transmission. Presence of these viruses by PCR among Portuguese cats was detected in 13% (rotavirus), 7% (astrovirus), 6% (bocavirus), 4% (sakobuvirus), and 4% (picobirnavirus) of 55 feline fecal samples. Co-infections were frequent with 40% (4/10) of cats shedding more than one of these viruses. Our study provides an initial unbiased description of the feline fecal virome indicating a high level of asymptomatic infections. Availability of the genome sequences of these viruses will facilitate future tropism and disease association studies.

Widespread distribution and structural diversity of Type IV IRESs in members of Picornaviridae

“…BLAST searches identified 47–102 nt-long elements with 64–74% identity to the FHMPV 5’UTR in the 5’UTRs of porcine sapelovirus 1, bat picornavirus 2 (BPV-2), Feline sakobuvirus A (SakV-A1) and Ia io picornavirus 1 (IiPV-1). These 5’UTRs contain Type IV IRES structures (Hellen and de Breyne, 2007; Lau et al, 2011, 2012; Ng et al, 2014), and the sequence homology with them maps to domain IIIe and flanking regions. A shorter (11–14nt-long) segment of the FHMPV 5’UTR matched precisely to domain IIIe in the Type IV IRESs of avian encephalomyelitis virus (AEV), duck hepatitis A virus 1 (DHAV-1) and Pigeon picornavirus B (PiPV-B) (Hellen and de Breyne, 2007; Kofstad and Jonassen, 2011) and to segments of the 5’UTRs of California sea lion sapelovirus 1 (Csl SapV-1), Ferret parechovirus (FPV) and Pasivirus 1 (PaV-A1).…”

“…The sole Type III IRES occurs in Hepatitis A virus (genus Hepatovirus )(Brown et al, 1994); Type V IRESs were recently identified in members of the genera Kobuvirus, Salivirus , and Oscivirus (Yu et al, 2011; Sweeney et al, 2012). Type IV IRESs were discovered in Hepatitis C virus (HCV) and Classical swine fever virus (CSFV), members of the genera Hepacivirus and Pestivirus of Flaviviridae , but have subsequently also been identified in several picornavirus genera, including Aquamavirus, Avihepatovirus, Kobuvirus, Megrivirus, Sapelovirus, Senecavirus, Teschovirus , and Tremovirus (Pisarev et al, 2004; Chard et al, 2006a; Hellen and de Breyne, 2007; Kapoor et al, 2008; Reuter et al, 2009; Honkavuori et al, 2011), in the proposed genera Aalivirus (Wang et al, 2014), Anativirus (duck picornavirus TW90A; Hellen and de Breyne, 2007; Tseng and Tsai, 2007), Colbovirus (pigeon picornavirus A (PiPV-A) and PiPV-B; Kofstad and Jonassen, 2011), Kunsagivirus (Boros et al, 2013), Phacovirus (quail picornavirus 1 (QPV-1); Pankovics et al, 2012) and Sakobuvirus (Ng et al, 2014), and in other species, including Bat picornavirus 1 (BPV-1), BPV-2 (Lau et al, 2011) and feline picornavirus 1 (FePV-1)(Lau et al, 2012), that have been provisionally assigned to the genus Sapelovirus .…”

“…The picornavirus type IV IRESs identified to date all contain the PK-IIId-IIIe core, including an apical GGG motif in domain IIId and a GA[U/C]A tetraloop in domain IIIe, but apical elements of domain III may be truncated or even absent. Domain II contains an internal loop near its base that enables it to switch between bent and extended conformations, and a ‘loop E’ motif (Lukavsky et al, 2003; Hellen and de Breyne, 2007; Boerneke et al, 2014; Ng et al, 2014; Wang et al, 2014). Very few picornavirus type IV IRESs contain an equivalent of domain IV (Hellen and de Breyne, 2007).…”

Zoonotic transmission of rotavirus: surveillance and control

“…Among these, RVH strains have been identified in humans in parts of Asia and in pigs in Asia and the Americas; however, no genetic relationship among human and porcine strains were reported [136][137][138]. RVI is a putative novel rotavirus species, which has been detected in cats and dogs in Europe and in a feral sea lion in the USA [139][140][141]. Because cats and dogs are thought to be the sources of human infections with RVA, closer monitoring for the zoonotic potential of RVI will be needed.…”

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

“…The advent of highthroughput sequencing technology has enabled comprehensive approaches for the simultaneous detection of many viral genomes and the identification of unknown viral genomes without viral isolation (Firth & Lipkin, 2013). Using high-throughput sequencing, viral metagenomics approaches have elucidated whole enteric viromes, resulting in the discovery of unknown viruses in a variety of mammals, including non-human primates, bats, pigs, rodents, cats, sea lions, martens, badgers, foxes, ferrets and pigeons (Baker et al, 2013;Bodewes et al, 2013;Dacheux et al, 2014;Donaldson et al, 2010;Ge et al, 2012;Handley et al, 2012;Li et al, 2010bLi et al, , 2011bNg et al, 2014;Phan et al, 2011Phan et al, , 2013aShan et al, 2011;Smits et al, 2013a;van den Brand et al, 2012;Wu et al, 2012). Further molecular characterization has revealed high nucleotide sequence diversity and unique genome organization of novel viruses (Boros et al, , 2013Li et al, 2010a;Phan et al, 2013b;Sauvage et al, 2012).…”