Comparing Phylogenetic Codivergence between Polyomaviruses and Their Hosts

Conservation efforts to prevent the extinction of the endangered western barred bandicoot (Perameles bougainville) are currently hindered by a progressively debilitating cutaneous and mucocutaneous papillomatosis and carcinomatosis syndrome observed in captive and wild populations. In this study, we detected a novel virus, designated the bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1), in lesional tissue from affected western barred bandicoots using multiply primed rolling-circle amplification and PCR with the cutaneotropic papillomavirus primer pairs FAP59/FAP64 and AR-L1F8/AR-L1R9. Sequencing of the BPCV1 genome revealed a novel prototype virus exhibiting genomic properties of both the Papillomaviridae and the Polyomaviridae. Papillomaviral properties included a large genome size (ϳ7.3 kb) and the presence of open reading frames (ORFs) encoding canonical L1 and L2 structural proteins. The genomic organization in which structural and nonstructural proteins were encoded on different strands of the double-stranded genome and the presence of ORFs encoding the nonstructural proteins large T and small t antigens were, on the other hand, typical polyomaviral features. BPCV1 may represent the first member of a novel virus family, descended from a common ancestor of the papillomaviruses and polyomaviruses recognized today. Alternatively, it may represent the product of ancient recombination between members of these two virus families. The discovery of this virus could have implications for the current taxonomic classification of Papillomaviridae and Polyomaviridae and can provide further insight into the evolution of these ancient virus families.

Section: Downloaded Frommentioning

confidence: 99%

mentioning

confidence: 99%

A Novel Virus Detected in Papillomas and Carcinomas of the Endangered Western Barred Bandicoot ( Perameles bougainville ) Exhibits Genomic Features of both the Papillomaviridae and Polyomaviridae

Woolford

Rector

Ranst

et al. 2007

“…Though this might at first be seen as an argument in favor of the cospeciation hypothesis (42), two diverging interpretations of our phylogenetic trees can be made that end up with contrasting conclusions about the processes at play along MCPyVrelated PyV evolution. If three distinct MCPyV-related PyVs whose present descendants would be MCPyV, PtvPyV2/GggPyV1, and Ptv/PtsPyV1, respectively, are assumed to have been infecting the last common ancestor of African great apes, then the fact that along two of the corresponding evolutionary lineages (those leading to PtvPyV2/GggPyV1 and Ptv/PtsPyV1) species-specific patterns are not contradicted would indeed be consistent with the codivergence hypothesis.…”

Section: Discussionmentioning

confidence: 99%

African Great Apes Are Naturally Infected with Polyomaviruses Closely Related to Merkel Cell Polyomavirus

Leendertz

Scuda

Cameron

et al. 2011

The oncogenic Merkel cell polyomavirus (MCPyV) infects humans worldwide, but little is known about the occurrence of viruses related to MCPyV in the closest phylogenetic relatives of humans, great apes. We analyzed samples from 30 wild chimpanzees and one captive gorilla and identified two new groups of polyomaviruses (PyVs). These new viruses are by far the closest relatives to MCPyV described to date, providing the first evidence of the natural occurrence of PyVs related to MCPyV in wild great apes. Similar to MCPyV, the prevalence of these viruses is relatively high (>30%). This, together with the fact that humans in West and Central Africa frequently hunt and butcher primates, may point toward further MCPyV-like strains spreading to, or already existing in, our species.

“…While we have detected SaPyV1 in skin samples and found it associated with lymphocystis lesions in affected gilthead sea bream, there is currently little information available about the ability to cause disease, the host range, or the tissue tropism of the fish polyomaviruses, which will constitute important aspects in the study of this novel virus group. Because polyomavirus evolution is thought to occur, at least in part, by codivergent speciation with the host (40), the finding of polyomaviruses in fish suggests that further members of the family might be found in amphibians and reptiles, which split later than fish and before birds and mammals during vertebrate evolution (41).…”

Section: Discussionmentioning

confidence: 99%

Concurrence of Iridovirus, Polyomavirus, and a Unique Member of a New Group of Fish Papillomaviruses in Lymphocystis Disease-Affected Gilthead Sea Bream

López-Bueno

Mavian

Labella

et al. 2016

Lymphocystis disease is a geographically widespread disease affecting more than 150 different species of marine and freshwater fish. The disease, provoked by the iridovirus lymphocystis disease virus (LCDV), is characterized by the appearance of papillomalike lesions on the skin of affected animals that usually self-resolve over time. Development of the disease is usually associated with several environmental factors and, more frequently, with stress conditions provoked by the intensive culture conditions present in fish farms. In gilthead sea bream (Sparus aurata), an economically important cultured fish species in the Mediterranean area, a distinct LCDV has been identified but not yet completely characterized. We have used direct sequencing of the virome of lymphocystis lesions from affected S. aurata fish to obtain the complete genome of a new LCDV-Sa species that is the largest vertebrate iridovirus sequenced to date. Importantly, this approach allowed us to assemble the full-length circular genome sequence of two previously unknown viruses belonging to the papillomaviruses and polyomaviruses, termed Sparus aurata papillomavirus 1 (SaPV1) and Sparus aurata polyomavirus 1 (SaPyV1), respectively. Epidemiological surveys showed that lymphocystis disease was frequently associated with the concurrent appearance of one or both of the new viruses. SaPV1 has unique characteristics, such as an intron within the L1 gene, and as the first member of the Papillomaviridae family described in fish, provides evidence for a more ancient origin of this family than previously thought. IMPORTANCELymphocystis disease affects marine and freshwater fish species worldwide. It is characterized by the appearance of papillomalike lesions on the skin that contain heavily enlarged cells (lymphocysts). The causative agent is the lymphocystis disease virus (LCDV), a large icosahedral virus of the family Iridoviridae. In the Mediterranean area, the gilthead sea bream (Sparus aurata), an important farmed fish, is frequently affected. Using next-generation sequencing, we have identified within S. aurata lymphocystis lesions the concurrent presence of an additional LCDV species (LCDV-Sa) as well as two novel viruses. These are members of polyomavirus and papillomavirus families, and here we report them to be frequently associated with the presence of lymphocysts in affected fish. Because papillomaviruses have not been described in fish before, these findings support a more ancient origin of this virus family than previously thought and evolutionary implications are discussed. L ymphocystis is a widely distributed disease affecting over 150 different marine and freshwater fish species (1). It was initially described during the 19th century and is characterized by the appearance of papillomalike lesions on the skin and fins, which develop over prolonged periods of time ranging from weeks to months. Occasionally, lesions on internal organs have been described, but the condition is rarely life-threatening and the outgrowths usually self-r...