Diverse papillomaviruses identified in Weddell seals

RNA virus diversity highlights the potential biosecurity threat posed by Antarctic krill

Antarctic krill Euphausia superba, one of the most abundant species on the planet, is a keystone species of the Southern Ocean ecosystem. In the present study, we analyzed the RNA virome of Antarctic krill via metatranscription methods. The results showed that only 0.39% (49/12, 558) of the resultant unigenes could be assigned to known viral taxa, which were most similar to 17 known viruses, including nine invertebrate viruses, two vertebrate viruses, three protozoan viruses and three mycoviruses. However, most of the detected viruses possessed low amino acid similarity with counterparts in the viral databases. Penaeus vannamei picornavirus (PvPV; Family Picornaviridae) and covert mortality nodavirus (CMNV; Family Nodaviridae) were the two most abundant viruses in the Antarctic krill RNA virome. Notably, PvPV and CMNV are known pathogens to multiple aquatic animals according to epidemiological survey and exposure experiments, whereby PvPV positive krill caused clinical symptoms and histopathological lesions to P. vannamei and similarly, CMNV infection altered the swimming and feeding behavior of parent marine medaka Oryzias melastigma and caused tissue damage and even spinal curvature of the offspring. Results herein reveal, for the first time, the high abundance and taxonomic diversity of viruses in Antarctic krill while simultaneously highlighting the risk of an important virus reservoir to global aquaculture, and the potential impact on animals in the Antarctic ecosystem.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00270-w.

Viral metagenomic survey of Caspian seals

Introduction

Viral diseases of pinnipeds cause substantial mortality and morbidity and can influence population demography. Viral metagenomic studies can therefore play an important role in pinniped health assessments and disease surveillance relevant to both individual species and in a "One Health" context.

Methods

This study used a metagenomic approach with high throughput sequencing to make the first assessment of viral diversity in Caspian seals (Pusa caspica), the only marine mammal species endemic to the Caspian Sea.

Results

Sequencing libraries from 35 seals sampled 2009-2020 were analysed, finding sequences from the viral families Circoviridae, Parvoviridae, Herpesviridae, Papillomaviridae, Picornaviridae, Caliciviridae, Cruciviridae, Anelloviridae, Smacoviridae, and Orthomyxoviridae, with additional detection of Adenoviridae via PCR. The similarity of viral contigs from Caspian seal to sequences recovered from other pinnipeds ranged from 63.74% (San Miguel sea lion calicivirus) to 78.79% (Seal anellovirus 4).

Discussion

Some findings represent novel viral species, but overall, the viral repertoire of Caspian seals is similar to available viromes from other pinnipeds. Among the sequences recovered were partial contigs for influenza B, representing only the second such molecular identification in marine mammals. This work provides a foundation for further studies of viral communities in Caspian seals, the diversity of viromes in pinnipeds more generally, and contributes data relevant for disease risk assessments in marine mammals.

Diverse papillomaviruses identified from Antarctic fur seals, leopard seals and Weddell seals from the Antarctic

Papillomaviruses (family Papillomaviridae) are non-enveloped, circular, double-stranded DNA viruses known to infect squamous and mucosal epithelial cells. In the family Papillomaviridae there are 53 genera and 133 viral species whose members infect a variety of mammalian, avian, reptilian, and fish species. Within the Antarctic context, papillomaviruses (PVs) have been identified in Adélie penguins (Pygoscelis adeliae, 2 PVs), Weddell seals (Leptonychotes weddellii, 7 PVs), and emerald notothen (Trematomus bernacchii, 1 PV) in McMurdo Sound and Ross Island in eastern Antarctica. Here we identified 13 diverse PVs from buccal swabs of Antarctic fur seals (Arctocephalus gazella, 2 PVs) and leopard seal (Hydrurga leptonyx, 3 PVs) in western Antarctica (Antarctic Peninsula), and vaginal and nasal swabs of Weddell seals (8 PVs) in McMurdo Sound. These PV genomes group into four genera representing 11 new papillomavirus types, of which five are from two Antarctic fur seals and a leopard seal and six from Weddell seals.

Two Lineages of Papillomaviruses Identified from Caracals (Caracal caracal) in South Africa

Papillomaviruses (PV) infect epithelial cells and can cause hyperplastic or neoplastic lesions. In felids, most described PVs are from domestic cats (Felis catus; n = 7 types), with one type identified in each of the five wild felid species studied to date (Panthera uncia, Puma concolor, Leopardus wiedii, Panthera leo persica and Lynx rufus). PVs from domestic cats are highly diverse and are currently classified into three genera (Lambdapapillomavirus, Dyothetapapillomavirus, and Taupapillomavirus), whereas those from wild felids, although diverse, are all classified into the Lambdapapillomavirus genus. In this study, we used a metagenomic approach to identify ten novel PV genomes from rectal swabs of five deceased caracals (Caracal caracal) living in the greater Cape Town area, South Africa. These are the first PVs to be described from caracals, and represent six new PV types, i.e., Caracal caracal papillomavirus (CcarPV) 1-6. These CcarPV fall into two phylogenetically distinct genera: Lambdapapillomavirus, and Treisetapapillomavirus. Two or more PV types were identified in a single individual for three of the five caracals, and four caracals shared at least one of the same PV types with another caracal. This study broadens our understanding of wild felid PVs and provides evidence that there may be several wild felid PV lineages.

Canis Familiaris Papillomavirus Type 26: A Novel Papillomavirus of Dogs and the First Canine Papillomavirus within the Omegapapillomavirus Genus

Domestic dogs are currently recognized as being infected by 25 different canine papillomavirus (CPV) types classified into three genera. A short sequence from a novel CPV type was amplified, along with CPV1, from a papilloma (wart) from the mouth of a dog. The entire 7499 bp genome was amplified, and CPV26 contained putative coding regions that were predicted to produce four early proteins and two late ones. The ORF L1 showed less than 62% similarity for all previously sequenced CPV types but over 69% similarity to multiple Omegapapillomavirus types from a variety of Caniform species including the giant panda, Weddel seal, and polar bear. Phylogenetic analysis confirmed CPV26 clusters within the Omegapapillomavirus genus. Specific primers were used to investigate the presence of CPV26 DNA within a series of 37 canine proliferative lesions. CPV26 DNA was amplified from one lesion, a cutaneous papilloma that also contained CPV6. This is the first time a PV type within the Omegapapillomavirus genus has been detected in a non-domestic species and this provides evidence that the omegapapillomaviruses infected a common ancestor of, and then co-evolved with, the Caniform species. Whether CPV26 causes disease is uncertain, but the absence of an E7 protein may suggest low pathogenicity.

A novel papillomavirus in a New Zealand fur seal (Arctocephalus forsteri) with oral lesions

Despite being the predominant seal species in the Australian-New Zealand region and serving as a key indicator of marine environmental health, little is known about infectious diseases in New Zealand fur seals (Long-nosed fur seal; Arctocephalus forsteri). Several papillomaviruses have been identified in earless seals and sea lions, with the latter linked to cutaneous plaques and invasive squamous cell carcinoma. To date, no papillomaviruses have been reported in fur seals. We used traditional veterinary diagnostic techniques and metatranscriptomic sequencing of tissue samples to investigate the virome of New Zealand fur seals. We identified a novel papillomavirus, provisionally termed A. forsteri papillomavirus 1 (AforPV1) in an animal with clinically and histologically identified oral papilloma-like lesions. RT-PCR confirmed the presence of AforPV1 only in oral papilloma samples from the affected individual. Phylogenetic analysis of the complete 7926 bp genome of AforPV1 revealed that it grouped with taupapillomaviruses found in related Carnivora species. These findings highlight the need for further research into the disease associations and impact of undiagnosed and novel viruses on New Zealand fur seals.

Active surveillance for influenza virus and coronavirus infection in Antarctic birds and mammals in environmental fecal samples, South Shetland Islands

Numerous Antarctic species are recognized as reservoirs for various pathogens, and their migratory behavior allows them to reach the Brazilian coast, potentially contributing to the emergence and circulation of new infectious diseases. To address the potential zoonotic risks, we conducted surveillance of influenza A virus (IAV) and coronaviruses (CoVs) in the Antarctic Peninsula, specifically focusing on different bird and mammal species in the region. During the summer of 2021/2022, as part of the Brazilian Antarctic Expedition, we collected and examined a total of 315 fecal samples to target these respiratory viruses. Although we did not detect the viruses of interest during this particular expedition, previous research conducted by our team has shown the presence of the H11N2 subtype of influenza A virus in penguin fecal samples from the same region. Given the continuous emergence of new viral strains worldwide, it is crucial to maintain active surveillance in the area, contributing to strengthening integrated One Health surveillance efforts.

Scavengers as Prospective Sentinels of Viral Diversity: the Snowy Sheathbill Virome as a Potential Tool for Monitoring Virus Circulation, Lessons from Two Antarctic Expeditions

Antarctica is a unique environment due to its extreme meteorological and geological conditions. In addition to this, its relative isolation from human influences has kept it undisturbed. This renders our limited understanding of its fauna and its associated microbial and viral communities a relevant knowledge gap to fill. This includes members of the order Charadriiformes such as snowy sheathbills. They are opportunistic predator/scavenger birds distributed on Antarctic and sub-Antarctic islands that are in frequent contact with other bird and mammal species. This makes them an interesting species for surveillance studies due to their high potential for the acquisition and transport of viruses. In this study, we performed whole-virome and targeted viral surveillance for coronaviruses, paramyxoviruses, and influenza viruses in snowy sheathbills from two locations, the Antarctic Peninsula and South Shetland. Our results suggest the potential role of this species as a sentinel for this region. We highlight the discovery of two human viruses, a member of the genus Sapovirus GII and a gammaherpesvirus, and a virus previously described in marine mammals. Here, we provide insight into a complex ecological picture. These data highlight the surveillance opportunities provided by Antarctic scavenger birds. IMPORTANCE This article describes whole-virome and targeted viral surveillance for coronaviruses, paramyxoviruses, and influenza viruses in snowy sheathbills from the Antarctic Peninsula and South Shetland. Our results suggest an important role of this species as a sentinel for this region. This species' RNA virome showcased a diversity of viruses likely tied to its interactions with assorted Antarctic fauna. We highlight the discovery of two viruses of likely human origin, one with an intestinal impact and another with oncogenic potential. Analysis of this data set detected a variety of viruses tied to various sources (from crustaceans to nonhuman mammals), depicting a complex viral landscape for this scavenger species.

Characterization of a novel papillomavirus identified from a whale (Delphinapterus leucas) pharyngeal metagenomic library

Here, using viral metagenomic method, a novel whale papillomavirus (temporarily named wPV, GenBank accession number OP856597) was discovered in a whale (Delphinapterus leucas) pharyngeal metagenomic library. The complete genome size of wPV is 7179 bp, with GC content of 54.4% and a nucleotide composition of 23.4% A, 22.3% T, 28.4% G, and 25.9% C. The viral genome has a typical papillomavirus organization pattern, and five ORFs were predicted, including two late genes encoding L1 and L2, and three early genes encoding E1, E2, and E6. Pairwise sequence comparison and phylogenetic analysis based on the L1 gene sequence indicated that wPV may be a novel species within genus Dyodeltapapillomavirus. In addition, the E2 region of wPV was predicted to have a potential recombination event. The discovery of this novel papillomavirus increases our understanding of the viral ecology of marine mammals, providing insights into possible future infectious diseases.

Discovery of two novel Torque Teno viruses in Callithrix penicillata provides insights on Anelloviridae diversification dynamics

The development of high-throughput sequencing (HTS) technologies and metagenomics protocols deeply impacted the discovery of viral diversity. Moreover, the characterization of novel viruses in the Neotropical primates (NP) is central for the comprehension of viral evolution dynamics in those hosts, due to their evolutionary proximity to Old World primates, including humans. In the present work, novel anelloviruses were detected and characterized through HTS protocols in the NP Callithrix penicillata, the common black-tufted marmoset. De novo assembly of generated sequences was carried out, and a total of 15 contigs were identified with complete Anelloviridae ORF1 gene, two of them including a flanking GC-rich region, confirming the presence of two whole novel genomes of ~3 kb. The identified viruses were monophyletic within the Epsilontorquevirus genus, a lineage harboring previously reported anelloviruses infecting hosts from the Cebidae family. The genetic divergence found in the new viruses characterized two novel species, named Epsilontorquevirus callithrichensis I and II. The phylogenetic pattern inferred for the Epsilontorquevirus genus was consistent with the topology of their host species tree, echoing a virus-host diversification model observed in other viral groups. This study expands the host span of Anelloviridae and provides insights into their diversification dynamics, highlighting the importance of sampling animal viral genomes to obtain a clearer depiction of their long-term evolutionary processes.

Coevolutionary Analysis Implicates Toll-Like Receptor 9 in Papillomavirus Restriction

Upon infection, DNA viruses can be sensed by pattern recognition receptors (PRRs), leading to the activation of type I and III interferons to block infection. Therefore, viruses must inhibit these signaling pathways, avoid being detected, or both. Papillomavirus virions are trafficked from early endosomes to the Golgi apparatus and wait for the onset of mitosis to complete nuclear entry. This unique subcellular trafficking strategy avoids detection by cytoplasmic PRRs, a property that may contribute to the establishment of infection. However, as the capsid uncoats within acidic endosomal compartments, the viral DNA may be exposed to detection by Toll-like receptor 9 (TLR9). In this study, we characterized two new papillomaviruses from bats and used molecular archeology to demonstrate that their genomes altered their nucleotide compositions to avoid detection by TLR9, providing evidence that TLR9 acts as a PRR during papillomavirus infection. Furthermore, we showed that TLR9, like other components of the innate immune system, is under evolutionary selection in bats, providing the first direct evidence for coevolution between papillomaviruses and their hosts. Finally, we demonstrated that the cancer-associated human papillomaviruses show a reduction in CpG dinucleotides within a TLR9 recognition complex.

Discovery of novel fish papillomaviruses: From the Antarctic to the commercial fish market

Fish papillomaviruses form a newly discovered group broadly recognized as the Secondpapillomavirinae subfamily. This study expands the documented genomes of the fish papillomaviruses from six to 16, including one from the Antarctic emerald notothen, seven from commercial market fishes, one from data mining of sea bream sequence data, and one from a western gull cloacal swab that is likely diet derived. The genomes of secondpapillomaviruses are ∼6 kilobasepairs (kb), which is substantially smaller than the ∼8 kb of terrestrial vertebrate papillomaviruses. Each genome encodes a clear homolog of the four canonical papillomavirus genes, E1, E2, L1, and L2. In addition, we identified open reading frames (ORFs) with short linear peptide motifs reminiscent of E6/E7 oncoproteins. Fish papillomaviruses are extremely diverse and phylogenetically distant from other papillomaviruses suggesting a model in which terrestrial vertebrate-infecting papillomaviruses arose after an evolutionary bottleneck event, possibly during the water-to-land transition.

Circoviruses and cycloviruses identified in Weddell seal fecal samples from McMurdo Sound, Antarctica

Circoviridae is a family of circular single-stranded DNA viruses whose members infect a wide variety of hosts. While well characterized in avian and mammalian hosts, little is known about circoviruses associated with Antarctic animals. From 48 Weddell seal (Leptonychotes weddellii) fecal samples collected on the sea ice in McMurdo between Nov 2014 and Dec 2014, we identified and determined the genomes of novel viruses that fall within two genera of the family Circoviridae, i.e. Circovirus (n = 7) and Cyclovirus (n = 45). We named these viruses as werosea circovirus (WerCV) and werosea cyclovirus (WerCyV). The genomes of WerCV and WerCyV share ~63-64% genome-wide pairwise identity with classified circoviruses and cycloviruses, respectively. Based on the species demarcation threshold of 80% for members of the Circoviridae, the genomes of WerCV and WerCyV represent new species in their respective genera. Evidence indicated recombination in five of the 45 WerCyV genomes identified in this study. These are the first circoviruses found associated with Antarctic pinnipeds, adding to those recently identified associated with Adélie (Pygoscelis adeliae) and chinstrap penguins (P. antarcticus).

Identification of a Novel Papillomavirus Type (MfoiPV1) Associated with Acrochordon in a Stone Marten (Martes foina)

Papillomaviruses (PVs) are an extremely large group of viruses that cause skin and mucosal infections in humans and various domestic and wild animals. Nevertheless, there is limited knowledge about PVs in wildlife hosts, including mustelid species. This study describes a case in stone marten (Martes foina) with a clinical manifestation of skin tumor, which is rather atypical for infections with PVs. The result of the papillomavirus PCR performed on the skin tumor sample was positive, and the complete PV genome was determined in the studied sample using next-generation sequencing technology. The analysis of the PV genome revealed infection of the stone marten with a putative new PV type belonging to the Dyonupapillomavirus genus. The proposed new stone marten PV type was named MfoiPV1.

Molecular characterization of a novel Camelus dromedarius papillomavirus

Papillomaviruses affect both human and non-human hosts. In camels, papillomatosis is caused by Camelus dromedarius papillomavirus type 1 and 2 (CdPV1 and CdPV2, respectively). In late 2018, an outbreak of camelpox occurred in a herd of fattening camels in Egypt. Several animals were found to be co-infected with camelpox and camel papillomaviruses. The morbidity with papillomatosis was 35 %. The infection was confirmed by PCR then Illumina sequencing revealed the presence of a complete genome of two CdPVs. One of these was CdPV1 (MT130101) and the other was a putative novel virus, tentatively named as CdPV3 (MT130100). Seven ORFs and a long upstream regulatory region were identified in the genomes of both viruses. Pairwise comparisons of L1 gene revealed 98.92 % nt identity between MT130101/CdPV1/Egypt/2018 and HQ912790/CdPV1/Sudan/2009 with 100 % coverage. However, MT130100/CdPV3/ Egypt/2018 showed only 68.99 % nt identity with the closest genome HQ912791/CdPV2/Sudan/2009. Phylogenetic analyses indicated that CdPV1 and CdPV3 belonged to the genus Deltapapillomavirus. These results should be useful for future CdPVs molecular surveillance and construction of evolutionary characteristics of this virus.

Single-Stranded DNA Viruses in Antarctic Cryoconite Holes

Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular molecules encoding either a Rep, a capsid protein gene, or other unidentified but viral-like open reading frames were identified. The samples from which the genomes were identified show a strong gradient in microbial diversity and abundances, and the number of viral genomes detected in each sample mirror that gradient. Additionally, one of the CRESS genomes assembled here shares ~90% genome-wide pairwise identity with a virus identified from a freshwater pond on the McMurdo Ice Shelf (Antarctica). Otherwise, the similarity of these viruses to those previously identified is relatively low. Together, these patterns are consistent with the presence of a unique regional virome present in fresh water host populations of the McMurdo Dry Valley region.

Genome Sequence of a Gyrovirus Associated with Ashy Storm-Petrel

Ashy storm-petrels (order Procellariiformes) are seabirds that are found along the coast of California to Baja Mexico. A novel gyrovirus was identified from a cloacal swab of an ashy storm-petrel, which is the second gyrovirus to be identified in sea birds, the first being found in the related northern fulmar.