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King KM, Rajadhyaksha EV, Tobey IG, Van Doorslaer K. Synonymous nucleotide changes drive papillomavirus evolution. Tumour Virus Res 2022; 14:200248. [PMID: 36265836 PMCID: PMC9589209 DOI: 10.1016/j.tvr.2022.200248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Papillomaviruses have been evolving alongside their hosts for at least 450 million years. This review will discuss some of the insights gained into the evolution of this diverse family of viruses. Papillomavirus evolution is constrained by pervasive purifying selection to maximize viral fitness. Yet these viruses need to adapt to changes in their environment, e.g., the host immune system. It has long been known that these viruses evolved a codon usage that doesn't match the infected host. Here we discuss how papillomavirus genomes evolve by acquiring synonymous changes that allow the virus to avoid detection by the host innate immune system without changing the encoded proteins and associated fitness loss. We discuss the implications of studying viral evolution, lifecycle, and cancer progression.
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Affiliation(s)
- Kelly M King
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Esha Vikram Rajadhyaksha
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA; Department of Physiology and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Isabelle G Tobey
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA; Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, USA; The BIO5 Institute, The Department of Immunobiology, Genetics Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, Arizona, USA.
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Kraberger S, Austin C, Farkas K, Desvignes T, Postlethwait JH, Fontenele RS, Schmidlin K, Bradley RW, Warzybok P, Van Doorslaer K, Davison W, Buck CB, Varsani A. Discovery of novel fish papillomaviruses: From the Antarctic to the commercial fish market. Virology 2022; 565:65-72. [PMID: 34739918 PMCID: PMC8713439 DOI: 10.1016/j.virol.2021.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 01/04/2023]
Abstract
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.
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Affiliation(s)
- Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Charlotte Austin
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Kata Farkas
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene OR 97403, USA
| | | | - Rafaela S. Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Russell W. Bradley
- Santa Rosa Island Research Station, California State University Channel Islands, Camarillo CA 93012, USA
| | - Pete Warzybok
- Point Blue Conservation Science, Petaluma, California, CA 94954, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute; Department of Immunobiology; Cancer Biology Graduate Interdisciplinary Program; UA Cancer Center, University of Arizona, Tucson, AZ 85724, USA
| | - William Davison
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Christopher B. Buck
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA,corresponding authors Christopher B. Buck, Arvind Varsani
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925, Cape Town, South Africa,corresponding authors Christopher B. Buck, Arvind Varsani
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Agius JE, Phalen DN, Rose K, Eden JS. New insights into Sauropsid Papillomaviridae evolution and epizootiology: discovery of two novel papillomaviruses in native and invasive Island geckos. Virus Evol 2019; 5:vez051. [PMID: 31798966 PMCID: PMC6874027 DOI: 10.1093/ve/vez051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Papillomaviruses cause persistent infections in skin and mucosal membranes and, in at least one species, are also be able to infect a tissue of mesenchymal origin. Infections may either be subclinical or induce proliferative lesions. Of the known papillomaviruses, the majority that have been characterized are from humans and other mammals. Currently, only fifteen complete bird and reptile papillomavirus genomes have been described, and they have been found in birds (n = 11), turtles (n = 2), and snakes (n = 2). Using next-generation sequencing technologies and virus-specific PCR, we have identified two novel papillomavirus genomes, Hemidactylus frenatus Papillomavirus 1 and 2 (HfrePV1, HfrePV2), in the widely distributed and highly invasive Asian house gecko (H.frenatus) and mute gecko (Gehyra mutilata) on Christmas Island and Cocos (Keeling) Islands. HfrePV1 was also detected in critically endangered Lister’s geckos (Lepidodactylus listeri) in their captive breeding colony on Christmas Island. Tissue-containing virus included epidermis, oral mucosa, and liver (HfrePV1) and epidermis, liver, and colon (HfrePV2). Concurrent infections were found in both H.frenatus and G.mutilata. Invasive mourning geckos (Lepidodactylus lugubris) (n = 4), Sri Lankan house geckos (Hemidactylus parvimaculatus) (n = 3), flat-tailed house geckos (Hemidactylus platyurus) (n = 4) from the Cocos Islands, and blue-tailed skinks (Cryptoblepharus egeriae) (n = 10) from Christmas Island were also screened but were not found to be infected. The novel HfrePV1 and HfrePV2 genomes were 7,378 bp and 7,380 bp in length, respectively, and each contained the early (E1, E2, and E7), and late (L1 and L2) open-reading frames. Phylogenetic analysis of the concatenated E1, E2, and L1 proteins from both papillomaviruses revealed that they clustered with, but were basal to, the Sauropsida clade containing bird and reptile viruses. This study sheds light on the evolution of papillomaviruses and the distribution of pathogens in a highly invasive species impacting endangered populations of geckos.
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Affiliation(s)
- Jessica E Agius
- Faculty of Science, Sydney School of Veterinary Science, University of Sydney, Werombi Road, Camden, New South Wales 2570, Australia
| | - David N Phalen
- Faculty of Science, Sydney School of Veterinary Science, University of Sydney, Werombi Road, Camden, New South Wales 2570, Australia
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Bradleys Head Road, Mosman, New South Wales 2088, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, James Cook Drive, Townsville, Queensland 4814, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Faculty of Medicine and Health, Sydney School of Medicine, University of Sydney, Missenden Road, Camperdown, New South Wales 2006, Australia.,The Westmead Institute for Medical Research, Centre for Virus Research, Hawkesbury Rd, Westmead, New South Wales 2145, Australia
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