A tortoise-infecting picornavirus expands the host range of the family Picornaviridae

The radiation of New Zealand's skinks and geckos is associated with distinct viromes

BACKGROUND

New Zealand is home to over 120 native endemic species of skinks and geckos that radiated over the last 20-40 million years, likely driven by the exploitation of diverse habitats formed during the Miocene. The recent radiation of animal hosts may facilitate cross-species virus transmission, likely reflecting their close genetic relationships and therefore relatively low barriers for viruses to emerge in new hosts. Conversely, as animal hosts adapt to new niches, even within specific geographic locations, so too could their viruses. Consequently, animals that have niche-specialised following radiations may be expected to harbour genetically distinct viruses. Through a metatranscriptomic analysis of eight of New Zealand's native skink and gecko species, as well as the only introduced lizard species, the rainbow skink (Lampropholis delicata), we aimed to reveal the diversity of viruses in these hosts and determine whether and how the radiation of skinks and geckos in New Zealand has impacted virus diversity and evolution.

RESULTS

We identified a total of 15 novel reptilian viruses spanning 11 different viral families, across seven of the nine species sampled. Notably, we detected no viral host-switching among the native animals analysed, even between those sampled from the same geographic location. This is compatible with the idea that host speciation has likely resulted in isolated, niche-constrained viral populations that have prevented cross-species transmission. Using a protein structural similarity-based approach, we further identified a highly divergent bunya-like virus that potentially formed a new family within the Bunyavirales.

CONCLUSIONS

This study has broadened our understanding of reptilian viruses within New Zealand and illustrates how niche adaptation may limit viral-host interactions.

Structure and function of type IV IRES in picornaviruses: a systematic review

The Picornaviridae is a family of icosahedral viruses with single-stranded, highly diverse positive-sense RNA genomes. Virions consist of a capsid, without envelope, surrounding a core of RNA genome. A typical genome of picornavirus harbors a well-conserved and highly structured RNA element known as the internal ribosome entry site (IRES), functionally essential for viral replication and protein translation. Based on differences in their structures and mechanisms of action, picornaviral IRESs have been categorized into five types: type I, II, III, IV, and V. Compared with the type IV IRES, the others not only are structurally complicated, but also involve multiple initiation factors for triggering protein translation. The type IV IRES, often referred to as hepatitis C virus (HCV)-like IRES due to its structural resemblance to the HCV IRES, exhibits a simpler and more compact structure than those of the other four. The increasing identification of picornaviruses with the type IV IRES suggests that this IRES type seems to reveal strong retention and adaptation in terms of viral evolution. Here, we systematically reviewed structural features and biological functions of the type IV IRES in picornaviruses. A comprehensive understanding of the roles of type IV IRESs will contribute to elucidating the replication mechanism and pathogenesis of picornaviruses.

Characterization of a novel picornavirus prevalent in experimental rabbits (Oryctolagus cuniculus)

Here, using viral metagenomic method a novel picornavirus (named UJS-2019picorna, GenBank accession number OP821762) was discovered in fecal and blood samples of experimental rabbits (Oryctolagus cuniculus). The complete genome size of UJS-2019picorna is 7832 bp excluding the poly(A)-tail, with GC content of 44.00% and a nucleotide composition of 28.0% A, 28.0% U, 21.5% G, and 22.5% C. The viral genome has a typical picornavirus organization pattern from the 5'-3' direction: VPg-5' UTR-(L)-P1, (VP4-VP2-VP3-VP1)-P2, (2 A-2B-2C)-P3, (3 A-3B-3C-3D)-3' UTR-poly(A). The P1 region of UJS-2019picorna is related to Erbovirus with amino acid identity of 37.31%, while the P2 and P3 regions are the closest to Bopivirus with amino acid identity of 35.66%-39.53%. According to the Picornaviridae Study Group guidelines, UJS-2019picorna should be presumed to be a new genus belonging to the Picornaviridae family. Epidemiologic study revealed that this novel picornavirus was prevalent in a cohort of experimental rabbits, with prevalence rate of 23.68% (9/38) in feces and 18.4% (7/38) in blood samples. Further work is required to elucidate whether this virus is pathogenic to rabbits and whether it has influence on studies using rabbits as experimental animal.

Novel picornavirus (family Picornaviridae) from freshwater fishes (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) in Hungary

In this study, a novel picornavirus (perchPV/M9/2015/HUN, GenBank accession no. MW590713) was detected in eight (12.9%) out of 62 faecal samples collected from three (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) out of 13 freshwater fish species tested and genetically characterized using viral metagenomics and RT-PCR methods. The complete genome of perchPV/M9/2015/HUN is 7,741 nt long, excluding the poly(A) tail, and has the genome organization 5'UTR^IRES-?/P1(VP0-VP3-VP1)/P2(2A₁^NPG↓P-2A₂^H-box/NC-2B-2C)/P3(3A-3B^VPg-3C^Pro-3D^Pol)/3'UTR-poly(A). The P1, 2C, and 3CD proteins had 41.4%, 38.1%, and 47.3% amino acid sequence identity to the corresponding proteins of Wenling lepidotrigla picornavirus (MG600079), eel picornavirus (NC_022332), and Wenling pleuronectiformes picornavirus (MG600098), respectively, as the closest relatives in the genus Potamipivirus. PerchPV/M9/2015/HUN represents a potential novel fish-origin species in an unassigned genus in the family Picornaviridae.

Virus Discovery in Desert Tortoise Fecal Samples: Novel Circular Single-Stranded DNA Viruses

The Sonoran Desert tortoise Gopherus morafkai is adapted to the desert, and plays an important ecological role in this environment. There is limited information on the viral diversity associated with tortoises (family Testudinidae), and to date no DNA virus has been identified associated with these animals. This study aimed to assess the diversity of DNA viruses associated with the Sonoran Desert tortoise by sampling their fecal matter. A viral metagenomics approach was used to identify the DNA viruses in fecal samples from wild Sonoran Desert tortoises in Arizona, USA. In total, 156 novel single-stranded DNA viruses were identified from 40 fecal samples. Those belonged to two known viral families, the Genomoviridae (n = 27) and Microviridae (n = 119). In addition, 10 genomes were recovered that belong to the unclassified group of circular-replication associated protein encoding single-stranded (CRESS) DNA virus and five circular molecules encoding viral-like proteins.

Viral Discovery in the Invasive Australian Cane Toad (Rhinella marina) Using Metatranscriptomic and Genomic Approaches

Cane toads are poisonous amphibians that were introduced to Australia in 1935 for insect control. Since then, their population has increased dramatically, and they now threaten many native Australian species. One potential method to control the population is to release a cane toad virus with high mortality rates, yet few cane toad viruses have been characterized. This study samples cane toads from different Australian locations and uses an RNA sequencing and computational approach to find new viruses. We report novel complete picornavirus and retrovirus sequences that were genetically similar to viruses infecting frogs, reptiles, and fish. Using data generated in other studies, we show that these viral sequences are present in cane toads from distinct Australian locations. Three sequences related to circoviruses were also found in the toad genome. The identification of new viral sequences will aid future studies that investigate their prevalence and potential as agents for biocontrol.

Cane toads are a notorious invasive species, inhabiting over 1.2 million km² of Australia and threatening native biodiversity. The release of pathogenic cane toad viruses is one possible biocontrol strategy yet is currently hindered by the poorly described cane toad virome. Metatranscriptomic analysis of 16 cane toad livers revealed the presence of a novel and full-length picornavirus, Rhimavirus A (RhiV-A), a member of a reptile- and amphibian-specific cluster of the Picornaviridae basal to the Kobuvirus-like group. In the combined liver transcriptome, we also identified a complete genome sequence of a distinct epsilonretrovirus, Rhinella marina endogenous retrovirus (RMERV). The recently sequenced cane toad genome contains 8 complete RMERV proviruses as well as 21 additional truncated insertions. The oldest full-length RMERV provirus was estimated to have inserted 1.9 million years ago (MYA). To screen for these viral sequences in additional toads, we analyzed publicly available transcriptomes from six diverse Australian locations. RhiV-A transcripts were identified in toads sampled from three locations across 1,000 km of Australia, stretching to the current Western Australia (WA) invasion front, while RMERV transcripts were observed at all six sites. Finally, we scanned the cane toad genome for nonretroviral endogenous viral elements, finding three sequences related to small DNA viruses in the family Circoviridae. This shows ancestral circoviral infection with subsequent genomic integration. The identification of these current and past viral infections enriches our knowledge of the cane toad virome, an understanding of which will facilitate future work on infection and disease in this important invasive species.

IMPORTANCE Cane toads are poisonous amphibians that were introduced to Australia in 1935 for insect control. Since then, their population has increased dramatically, and they now threaten many native Australian species. One potential method to control the population is to release a cane toad virus with high mortality rates, yet few cane toad viruses have been characterized. This study samples cane toads from different Australian locations and uses an RNA sequencing and computational approach to find new viruses. We report novel complete picornavirus and retrovirus sequences that were genetically similar to viruses infecting frogs, reptiles, and fish. Using data generated in other studies, we show that these viral sequences are present in cane toads from distinct Australian locations. Three sequences related to circoviruses were also found in the toad genome. The identification of new viral sequences will aid future studies that investigate their prevalence and potential as agents for biocontrol.

Two new species of betatorqueviruses identified in a human melanoma that metastasized to the brain

The role of viral infections in the etiology of brain cancer remains uncertain. Prior studies mostly focused on transcriptome or viral DNA integrated in tumor cells. To investigate for the presence of viral particles, we performed metagenomics sequencing on viral capsid-protected nucleic acids from 12 primary and 8 metastatic human brain tumors. One brain tumor metastasized from a skin melanoma harbored two new human anellovirus species, Torque teno mini virus Emory1 (TTMV Emory1) and Emory2 (TTMV Emory2), while the remaining 19 samples did not reveal any exogenous viral sequences. Their genomes share 63-67% identity with other TTMVs, and phylogenetic clustering supports their classification within the Betatorquevirus genus. This is the first identification of betatorqueviruses in brain tumors. The viral DNA was in its expected non-integrated circular form, and it is unclear if the viruses contributed to tumor formation. Whether the viruses originated from blood, or the primary skin tumor could not be ascertained. Overall, our results demonstrate the usefulness of viral metagenomics to detect previously unknown exogenous virus in human brain tumors. They further suggest that active viral infections are rare events in brain tumors, but support a follow-up larger scale study to quantify their frequency in different brain tumor subtypes.

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

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".

Detection of Mycoplasma spp., herpesviruses, topiviruses, and ferlaviruses in samples from chelonians in Europe

We tested samples from 1,015 chelonians in Europe for Mycoplasma spp., herpesviruses, ranaviruses, picornaviruses, and ferlaviruses by PCR. Mycoplasma spp. were detected in 42.1% and herpesviruses were detected in 8.0% of tested chelonians. Differentiation of the herpesviruses revealed that 46.9% of the detected chelonian viruses were testudinid herpesvirus 1 (TeHV-1) and 54.3% were TeHV-3, including co-detections of TeHV-1 and -3 in 3 tortoises. TeHV-4 was detected in a leopard tortoise ( Stigmochelys pardalis), and a herpesvirus that could not be further characterized was found in a pond slider ( Trachemys scripta). Picornaviruses (topiviruses) were detected in 2.2% of the tested animals; ferlaviruses were found in 0.6%; no ranaviruses were detected in any of the animals tested. Mycoplasma spp. were detected significantly more often in Horsfield’s tortoises ( Testudo horsfieldii), leopard tortoises, and Indian star tortoises ( Geochelone elegans) than in other species. Horsfield’s tortoises were also significantly more often positive for TeHV-1. Mycoplasma and TeHV-1 were co-detected in 3.0%, and mycoplasma and TeHV-3 in 2.3%. The TeHV-4–positive tortoise was also positive for mycoplasma. Mycoplasma and picornaviruses were co-detected in 1.2% of the tortoises. A spur-thighed tortoise ( Testudo graeca) was positive for mycoplasma and a ferlavirus. In some cases, >2 pathogens were detected. A significant correlation between mycoplasma and herpesvirus detection was found. Of all tested animals, 47.6% were positive for at least one pathogen, demonstrating the importance of pathogen detection in captive chelonians.

Genetic characterization of a second novel picornavirus from an amphibian host, smooth newt (Lissotriton vulgaris)

In this study, a novel picornavirus was identified in faecal samples from smooth newts (Lissotriton vulgaris). The complete genome of picornavirus strain newt/II-5-Pilis/2014/HUN (KX463670) is 7755 nt long with type-IV IRES and has 39.6% aa sequence identity in the protein P1 to the corresponding protein of bat picornavirus (KJ641686, unassigned) and 42.7% and 53.5% aa sequence identity in the 2C and 3CD protein, respectively, to oscivirus (GU182410, genus Oscivirus). Interestingly, the L-protein of newt/II-5-Pilis/2014/HUN has conserved aa motifs that are similar to those found in phosphatase-1 catalytic (PP1C) subunit binding region (pfam10488) proteins. This second amphibian-origin picornavirus could represent a novel species and could be a founding member of a potential novel picornavirus genus.

Development of a consensus reverse transcription PCR assay for the specific detection of tortoise picornaviruses

Picornaviruses (PVs) of different terrestrial tortoise species, previously designated as Virus “X,” have been frequently detected from various tissues by virus isolation in Terrapene heart cell culture as the preferred laboratory method for diagnosis. Here, we describe the development of 2 diagnostic reverse transcription (RT)-PCR–based assays for the identification and characterization of tortoise PVs belonging to the tentative genus Topivirus. To test the novel diagnostic systems, PVs were isolated from swab and tissue samples collected in Germany, Italy, and Hungary between 2000 and 2013. All 25 tested isolates gave positive results with both novel consensus primer sets. Sequencing of the amplified products confirmed that all studied viruses were members of the new proposed genus Topivirus. Phylogenetic analyses clearly distinguished 2 lineages within the genus. Based on sequence analysis, no association was observed between the geographic distribution and genetic relatedness. Furthermore, no strict host specificity was indicated. The PCR-based diagnosis may provide a time-saving and sensitive method to detect tortoise PVs, and evaluation of PV presence in these animals may help control virus spread.

Novel picornavirus in domestic rabbits (Oryctolagus cuniculus var. domestica)

Picornaviruses (family Picornaviridae) are small, non-enveloped viruses with positive sense, single-stranded RNA genomes. The numbers of the novel picornavirus species and genera are continuously increasing. Picornaviruses infect numerous vertebrate species from fish to mammals, but have not been identified in a member of the Lagomorpha order (pikas, hares and rabbits). In this study, a novel picornavirus was identified in 16 (28.6%) out of 56 faecal samples collected from clinically healthy rabbits (Oryctolagus cuniculus var. domestica) in two (one commercial and one family farms) of four rabbit farms in Hungary. The 8364 nucleotide (2486 amino acid) long complete genome sequence of strain Rabbit01/2013/HUN (KT325852) has typical picornavirus genome organization with type-V IRES at the 5'UTR, encodes a leader (L) and a single 2A(H-box/NC) proteins, contains a hepatitis-A-virus-like cis-acting replication element (CRE) in the 2A, but it does not contain the sequence forming a "barbell-like" secondary structure in the 3'UTR. Rabbit01/2013/HUN has 52.9%, 52% and 57.2% amino acid identity to corresponding proteins of species Aichivirus A (genus Kobuvirus): to murine Kobuvirus (JF755427) in P1, to canine Kobuvirus (JN387133) in P2 and to feline Kobuvirus (KF831027) in P3, respectively. The sequence and phylogenetic analysis indicated that Rabbit01/2013/HUN represents a novel picornavirus species possibly in genus Kobuvirus. This is the first report of detection of picornavirus in rabbit. Further study is needed to clarify whether this novel picornavirus plays a part in any diseases in domestic or wild rabbits.

Rabovirus: a proposed new picornavirus genus that is phylogenetically basal to enteroviruses and sapeloviruses

We have sequenced the genome of a novel picornavirus, rabovirus A (rat-borne virus, RaBoV-A, NC_026314), which was present in the feces of a Norway rat (Rattus norvegicus) from Berlin, Germany. This virus is related to members of the genera Enterovirus and Sapelovirus. RaboV-A contains a type II IRES that is unlike the type I IRES elements of enteroviruses and the type IV elements of sapeloviruses. Its genome is marked by an L protein and a chymotrypsin-like 2A protease. Our analysis of genome organization, pairwise identities, motif, phylogenic and UTR (GIMPU) indicates that RaBoV-A potentially represents a new picornavirus genus, for which we propose the name "Rabovirus". Spread by their rodent hosts and detected in New York and Berlin rats, these viruses may have a wide geographic distribution.

A highly divergent picornavirus in an amphibian, the smooth newt (Lissotriton vulgaris)

Genetically highly divergent picornavirus (Newt/2013/HUN, KP770140) was detected using viral metagenomics in faecal samples of free-living smooth newts (Lissotriton vulgaris). Newt picornavirus was identified by reverse transcription-polymerase chain reaction (RT-PCR) in six (25 %) of the 24 samples originating from individuals caught in two out of the six investigated natural ponds in Hungary. The first picornavirus in amphibians expands the host range of members of the Picornaviridae, and opens a new research field in picornavirus evolution in lower vertebrates. Newt picornavirus represents a novel species in a novel genus within the family Picornaviridae, provisionally named genus Ampivirus (amphibian picornavirus).