New polyomavirus species identified in nutria, Myocastor coypus polyomavirus 1

Silva, M. S. da; Cibulski, Samuel Paulo; Alves, Christian Diniz Beduschi Travassos; Weber, Matheus Nunes; Budaszewski, R.F.; Silveira, Simone; Mósena, Ana Cristina Sbaraini; Mayer, Fabiana Quoos; Goltz, Laura Ver; Campos, Renata de Mendonça; Canal, Cláudio Wageck

doi:10.1007/s00705-018-3985-5

Cited by 5 publications

(5 citation statements)

References 19 publications

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“…In rodents, 45 PyVs have been described from 11 species originating from Europe, Asia, and Africa [ 30 ]. In South America, betapolyomaviruses were recently described in two Sigmodontinae (Cricetidae) species ( Akodon montensis and Calomys tener ), and an alphapolyomavirus in a Myocastoridae species ( Myocastor coypus ) [ 101 , 102 ]. We identified four PyV sequences in four species ( Figure 4 ).…”

Section: Discussionmentioning

confidence: 99%

The Influence of Habitat on Viral Diversity in Neotropical Rodent Hosts

Tirera

Thoisy

Donato

et al. 2021

Viruses

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Rodents are important reservoirs of numerous viruses, some of which have significant impacts on public health. Ecosystem disturbances and decreased host species richness have been associated with the emergence of zoonotic diseases. In this study, we aimed at (a) characterizing the viral diversity in seven neotropical rodent species living in four types of habitats and (b) exploring how the extent of environmental disturbance influences this diversity. Through a metagenomic approach, we identified 77,767 viral sequences from spleen, kidney, and serum samples. These viral sequences were attributed to 27 viral families known to infect vertebrates, invertebrates, plants, and amoeba. Viral diversities were greater in pristine habitats compared with disturbed ones, and lowest in peri-urban areas. High viral richness was observed in savannah areas. Differences in these diversities were explained by rare viruses that were generally more frequent in pristine forest and savannah habitats. Moreover, changes in the ecology and behavior of rodent hosts, in a given habitat, such as modifications to the diet in disturbed vs. pristine forests, are major determinants of viral composition. Lastly, the phylogenetic relationships of four vertebrate-related viral families (Polyomaviridae, Flaviviridae, Togaviridae, and Phenuiviridae) highlighted the wide diversity of these viral families, and in some cases, a potential risk of transmission to humans. All these findings provide significant insights into the diversity of rodent viruses in Amazonia, and emphasize that habitats and the host’s dietary ecology may drive viral diversity. Linking viral richness and abundance to the ecology of their hosts and their responses to habitat disturbance could be the starting point for a better understanding of viral emergence and for future management of ecosystems.

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Section: Discussionmentioning

confidence: 99%

The Influence of Habitat on Viral Diversity in Neotropical Rodent Hosts

Tirera

Thoisy

Donato

et al. 2021

Viruses

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“…4F ). In contrast, these key residues are not conserved in a recently discovered animal polyomavirus from nutria ( Myocastor coypus polyomavirus 1 [McoyPyV1]), which clusters in the phylogenetic tree based on the complete amino acid LTAg region ( 41 ).…”

Section: Resultsmentioning

confidence: 99%

“…The identification of shrew polyomaviruses (40) and McoyPyV1 in nutria (41), which are closely related in sequence to HPyV12, and studies reporting low seroprevalence rates and seroactivity for HPyV12, NJPyV, and LIPyV questioned the tropism of recently discovered human polyomaviruses (36). Further analyses are needed, but the presence of a functional core BC2 loop sialic acid-binding site in TSPyV nonetheless demonstrates the conservation of this site in a human-tropic virus (25).…”

Section: Discussionmentioning

confidence: 99%

“…However, other VP1-based analyses suggested close relationships of HPyV12 with sheep polyomavirus (ShPyV) found in commercially available sheep meat (2) and with avian viruses such as budgerigar fledgling disease polyomavirus (BFDPyV) and finch polyomavirus (FiPyV) (3,39). More recently, new polyomaviruses possessing especially high sequence identities with HPyV12 were detected in shrews and nutria, and thus, HPyV12 may be a variant of a nonhuman polyomavirus that naturally infects these animals (40,41). In contrast, a recent serological study with peak seroprevalence rates of 97.3% (35) indicates that HPyV12 or a related virus circulates widely in humans, outranging earlier and more recently reported seroprevalence rates of 20% (34) and 4% (36), respectively.…”

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confidence: 99%

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Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family

Stroh

Rustmeier

Blaum

et al. 2020

mBio

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Asymptomatic infections with polyomaviruses in humans are common, but these small viruses can cause severe diseases in immunocompromised hosts. New Jersey polyomavirus (NJPyV) was identified via a muscle biopsy in an organ transplant recipient with systemic vasculitis, myositis, and retinal blindness, and human polyomavirus 12 (HPyV12) was detected in human liver tissue. The evolutionary origins and potential diseases are not well understood for either virus. In order to define their receptor engagement strategies, we first used nuclear magnetic resonance (NMR) spectroscopy to establish that the major capsid proteins (VP1) of both viruses bind to sialic acid in solution. We then solved crystal structures of NJPyV and HPyV12 VP1 alone and in complex with sialylated glycans. NJPyV employs a novel binding site for a α2,3-linked sialic acid, whereas HPyV12 engages terminal α2,3- or α2,6-linked sialic acids in an exposed site similar to that found in Trichodysplasia spinulosa-associated polyomavirus (TSPyV). Gangliosides or glycoproteins, featuring in mammals usually terminal sialic acids, are therefore receptor candidates for both viruses. Structural analyses show that the sialic acid-binding site of NJPyV is conserved in chimpanzee polyomavirus (ChPyV) and that the sialic acid-binding site of HPyV12 is widely used across the entire polyomavirus family, including mammalian and avian polyomaviruses. A comparison with other polyomavirus-receptor complex structures shows that their capsids have evolved to generate several physically distinct virus-specific receptor-binding sites that can all specifically engage sialylated glycans through a limited number of contacts. Small changes in each site may have enabled host-switching events during the evolution of polyomaviruses. IMPORTANCE Virus attachment to cell surface receptors is critical for productive infection. In this study, we have used a structure-based approach to investigate the cell surface recognition event for New Jersey polyomavirus (NJPyV) and human polyomavirus 12 (HPyV12). These viruses belong to the polyomavirus family, whose members target different tissues and hosts, including mammals, birds, fish, and invertebrates. Polyomaviruses are nonenveloped viruses, and the receptor-binding site is located in their capsid protein VP1. The NJPyV capsid features a novel sialic acid-binding site that is shifted in comparison to other structurally characterized polyomaviruses but shared with a closely related simian virus. In contrast, HPyV12 VP1 engages terminal sialic acids in a manner similar to the human Trichodysplasia spinulosa-associated polyomavirus. Our structure-based phylogenetic analysis highlights that even distantly related avian polyomaviruses possess the same exposed sialic acid-binding site. These findings complement phylogenetic models of host-virus codivergence and may also reflect past host-switching events.

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“…Capsid-protected nucleic acids were extracted using a standard phenol-chloroform protocol (DNA) or TRIzol® (RNA). Viral DNA was enriched by multiple displacement amplification using phi29 DNA polymerase ( da Silva et al, 2018 ). RNA was converted to cDNA using SuperScript III reverse transcriptase and random-amplificated ( Clem et al, 2007 ).…”

Section: Methodsmentioning

confidence: 99%

A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil

et al. 2021

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A viral metagenomics study was conducted in beef, pork, and chicken sold in supermarkets from Southern Brazil. From chicken, six distinct gyroviruses (GyV) were detected, including GyV3 and GyV6, which for the first time were detected in samples from avian species, plus a novel smacovirus species and two highly divergent circular Rep-encoding ssDNA (CRESS-DNA) viruses. From pork, genomes of numerous anelloviruses, porcine parvovirus 5 (PPV5) and 6 (PPV6), two new genomoviruses and two new CRESS-DNA viruses were found. Finally, two new CRESS-DNA genomes were recovered from beef. Although none of these viruses have history of transmission to humans, the findings reported here reveal that such agents are inevitably consumed in diets that include these types of meat.

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New polyomavirus species identified in nutria, Myocastor coypus polyomavirus 1

Cited by 5 publications

References 19 publications

The Influence of Habitat on Viral Diversity in Neotropical Rodent Hosts

The Influence of Habitat on Viral Diversity in Neotropical Rodent Hosts

Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family

A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil

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