Genomic characterization of a novel calicivirus, FHMCV-2012, from baitfish in the USA

Abstract

During regulatory sampling of fathead minnows (Pimephales promelas), a novel calicivirus was isolated from homogenates of kidney and spleen inoculated into bluegill fry (BF-2) cells. Infected cell cultures exhibiting cytopathic effects were screened by PCR-based methods for selected fish viral pathogens. Illumina HiSeq next generation sequencing of the total RNA revealed a novel calicivirus genome that showed limited protein sequence similarity to known homologs in a BLASTp search. The complete genome of this fathead minnow calicivirus (FHMCV) is 6564 nt long, encoding a polyprotein of 2114 aa in length. The complete polyprotein shared only 21% identity with Atlantic salmon calicivirus,followed by 11% to 14% identity with mammalian caliciviruses. A molecular detection assay (RT-PCR) was designed from this sequence for screening of field samples for FHMCV in the future. This virus likely represents a prototype species of a novel genus in the family Caliciviridae, tentatively named "Minovirus".

ICTV Virus Taxonomy Profile: Caliciviridae

“…Viruses of seven genera ( Lagovirus , Norovirus , Nebovirus , Recovirus [ 4 ], Sapovirus , Valovirus [ 5 ] and Vesivirus ) infect a wide range of mammals, members of two genera infect birds ( Bavovirus [ 6 ] and Nacovirus [ 7 ]) and members of two genera infect fish ( Minovirus [ 8 ] and Salovirus [ 9 ]), while caliciviruses have also been detected in the greater green snake and frogs [ 10 ], highlighting the wide host range of viruses in the family. Caliciviruses are similar to picornaviruses in the presence of VPg and in sequence similarity of their RNA-directed RNA polymerase and protease proteins.…”

A molecular assessment of infectious agents carried by Atlantic salmon at sea and in three eastern Canadian rivers, including aquaculture escapees and North American and European origin wild stocks

“…ASCV is often detected as a coinfection with other agents (e.g., with PRV), but studies to date have had variable and often inconclusive findings for its independent pathological effects (Mikalsen et al 2014;Wiik-Nielsen et al 2016). Interestingly, a related fish calcicivirus in baitfish was associated with clinical disease only when coinfected with a second virus (Mor et al 2017). Given its widespread prevalence, future studies should evaluate sequence variation among ASCV isolates across geographic regions and examine the potential role ASCV plays in disease progression in coinfections.…”

Emerging viruses in British Columbia salmon discovered via a viral immune response biomarker panel and metatranscriptomic sequencing

“…However, ASCV was also commonly 150 found in healthy fish and a more recent study found no correlation between ASCV and HSMI (36,37). However, there is evidence that co-infection of caliciviruses with other viruses could be linked to clinical manifestations of disease in baitfish (38). In this study, in farmed Atlantic salmon from BC, we discovered viral genomes extremely closely related to the ASCV genome first discovered and sequenced in Norway (36).…”

“…As expected, ASCV groups within a distinct clade from the mammalian caliciviruses ( Figure 3A), and is more 170 closely related to metatranscriptomic discovered fish caliciviruses (1) and fathead minnow calicivirus (38), a novel calicivirus isolated from farmed baitfish in Wisconsin, USA. It is becoming clear that caliciviruses are widespread in fish, and although we know very little of their direct role in lesion development, fish caliciviruses have been associated with diseased fish in an aquaculture setting (38). These newly described fish caliciviruses (1,38) are phylogenetically distinct from those first described in mammals, suggesting 175 that spillover from fish to mammals is not a common occurrence, as has been previously suggested (49, 50).…”

“…Interestingly, some caliciviruses 165 infect marine mammals (48), and remarkably, at least one fish species has been reported as reservoir for vesicular exanthema of swine virus (VESV), which can infect and cause disease in mammals (49, 50). More recently there has been a huge surge in calicivirus discovery in fish and amphibia (1,36,38).…”