Sequencing and characterization of the full-length gene encoding the single-stranded DNA binding protein of a novel Chelonian herpesvirus

The Concurrent Detection of Chelonid Alphaherpesvirus 5 and Chelonia mydas Papillomavirus 1 in Tumoured and Non-Tumoured Green Turtles

Simple Summary

Characterised by benign tumours, fibropapillomatosis is a debilitating disease that predominantly afflicts the endangered green turtle (Chelonia mydas). A growing body of evidence has associated these tumours with a herpesvirus. However, a recent study detected both herpesvirus and papillomavirus in these tumours. This result challenged the idea that the herpesvirus is the sole virus associated with this disease. The present study aimed to better understand the co-occurrence of these viruses in turtles with fibropapillomatosis (in both tumour samples and non-tumoured skin samples), in addition to samples from non-tumoured turtles. Both viruses were detected in all sample types, with the 43.5% of tumours containing both herpesvirus and papillomavirus. Tumour samples were found to contain the most herpesvirus while the highest amount of papillomavirus was detected in non-tumoured skin from turtles with tumours. Collectively, these results pivot the way we think about this disease; as an infectious disease where two separate viruses may be at play.

Abstract

Characterised by benign tumours, fibropapillomatosis (FP) is a debilitating disease that predominantly afflicts the endangered green turtle (Chelonia mydas). A growing body of histological and molecular evidence has associated FP tumours with Chelonid alphaherpesvirus 5 (ChHV5). However, a recent study which detected both ChHV5 and Chelonia mydas papillomavirus 1 (CmPV1) DNA in FP tumour tissues has challenged this hypothesis. The present study aimed to establish a probe-based qPCR to assess the wider prevalence of CmPV1 and co-occurrence with ChHV5 in 275 marine turtles foraging in waters adjacent to the east coast of Queensland, Australia: three categories: Group A (FP tumours), Group B (non-tumoured skin from FP turtles) and Group C (non-tumoured skin from turtles without FP). Concurrent detection of ChHV5 and CmPV1 DNA is reported for all three categories, where Group A had the highest rate (43.5%). ChHV5 viral loads in Group A were significantly higher than loads seen in Group B and C. This was not the case for CmPV1 where the loads in Group B were highest, followed by Group A. However, the mean CmPV1 load for Group A samples was not significantly different to the mean load reported from Group B or C samples. Collectively, these results pivot the way we think about FP; as an infectious disease where two separate viruses may be at play.

Molecular evidence for horizontal transmission of chelonid alphaherpesvirus 5 at green turtle (Chelonia mydas) foraging grounds in Queensland, Australia

Fibropapillomatosis (FP) is a marine turtle disease recognised by benign tumours on the skin, eyes, shell, oral cavity and/or viscera. Despite being a globally distributed disease that affects an endangered species, research on FP and its likely causative agent chelonid alphaherpesvirus 5 (ChHV5) in Australia is limited. Here we present improved molecular assays developed for detection of ChHV5, in combination with a robust molecular and phylogenetic analysis of ChHV5 variants. This approach utilised a multi-gene assay to detect ChHV5 in all FP tumors sampled from 62 marine turtles found at six foraging grounds along the Great Barrier Reef. Six distinct variants of ChHV5 were identified and the distribution of these variants was associated with host foraging ground. Conversely, no association between host genetic origin and ChHV5 viral variant was found. Together this evidence supports the hypothesis that marine turtles undergo horizontal transmission of ChHV5 at foraging grounds and are unlikely to be contracting the disease at rookeries, either during mating or vertically from parent to offspring.

A review of fibropapillomatosis in Green turtles (Chelonia mydas)

Despite being identified in 1938, many aspects of the pathogenesis and epidemiology of fibropapillomatosis (FP) in marine turtles are yet to be fully uncovered. Current knowledge suggests that FP is an emerging infectious disease, with the prevalence varying both spatially and temporally, even between localities in close proximity to each other. A high prevalence of FP in marine turtles has been correlated with residency in areas of reduced water quality, indicating that there is an environmental influence on disease presentation. Chelonid herpesvirus 5 (ChHV5) has been identified as the likely aetiological agent of FP. The current taxonomic position of ChHV5 is in the family Herpesviridae, subfamily Alphaherpesvirinae, genus Scutavirus. Molecular differentiation of strains has revealed that a viral variant is typically present at specific locations, even within sympatric species of marine turtles, indicating that the disease FP originates regionally. There is uncertainty surrounding the exact path of transmission and the conditions that facilitate lesion development, although recent research has identified atypical genes within the genome of ChHV5 that may play a role in pathogenesis. This review discusses emerging areas where researchers might focus and theories behind the emergence of FP globally since the 1980s, which appear to be a multi-factorial interplay between the virus, the host and environmental factors influencing disease expression.

Horizontal gene transfers with or without cell fusions in all categories of the living matter

This article reviews the history of widespread exchanges of genetic segments initiated over 3 billion years ago, to be part of their life style, by sphero-protoplastic cells, the ancestors of archaea, prokaryota, and eukaryota. These primordial cells shared a hostile anaerobic and overheated environment and competed for survival. "Coexist with, or subdue and conquer, expropriate its most useful possessions, or symbiose with it, your competitor" remain cellular life's basic rules. This author emphasizes the role of viruses, both in mediating cell fusions, such as the formation of the first eukaryotic cell(s) from a united crenarchaeon and prokaryota, and the transfer of host cell genes integrated into viral (phages) genomes. After rising above the Darwinian threshold, rigid rules of speciation and vertical inheritance in the three domains of life were established, but horizontal gene transfers with or without cell fusions were never abolished. The author proves with extensive, yet highly selective documentation, that not only unicellular microorganisms, but the most complex multicellular entities of the highest ranks resort to, and practice, cell fusions, and donate and accept horizontally (laterally) transferred genes. Cell fusions and horizontally exchanged genetic materials remain the fundamental attributes and inherent characteristics of the living matter, whether occurring accidentally or sought after intentionally. These events occur to cells stagnating for some 3 milliard years at a lower yet amazingly sophisticated level of evolution, and to cells achieving the highest degree of differentiation, and thus functioning in dependence on the support of a most advanced multicellular host, like those of the human brain. No living cell is completely exempt from gene drains or gene insertions.

The order Herpesvirales

The taxonomy of herpesviruses has been updated by the International Committee on Taxonomy of Viruses (ICTV). The former family Herpesviridae has been split into three families, which have been incorporated into the new order Herpesvirales. The revised family Herpesviridae retains the mammal, bird and reptile viruses, the new family Alloherpesviridae incorporates the fish and frog viruses, and the new family Malacoherpesviridae contains a bivalve virus. Three new genera have been created in the family Herpesviridae, namely Proboscivirus in the subfamily Betaherpesvirinae and Macavirus and Percavirus in the subfamily Gammaherpesvirinae. These genera have been formed by the transfer of species from established genera and the erection of new species, and other new species have been added to some of the established genera. In addition, the names of some nonhuman primate virus species have been changed. The family Alloherpesviridae has been populated by transfer of the genus Ictalurivirus and addition of the new species Cyprinid herpesvirus 3. The family Malacoherpesviridae incorporates the new genus Ostreavirus containing the new species Ostreid herpesvirus 1.

Localization of fibropapilloma-associated turtle herpesvirus in green turtles (Chelonia mydas) by in-situ hybridization

Fibropapilloma-associated turtle herpesvirus (FPTHV) is the presumed aetiological agent of sea turtle fibropapillomatosis (FP). Intralesional DNA and RNA of the virus have been detected by polymerase chain reaction (PCR) and reverse transcriptase-PCR (RT-PCR), respectively, but the exact location and distribution of the virus within the tumours have not been addressed. In this study, in-situ hybridization (ISH) was used to investigate viral transcriptional activity and localization of FPTHV. Twenty-five tumours were obtained from the skin or conjunctiva of 105 green turtles (Chelonia mydas) examined on two islands in Puerto Rico (Culebra and Culebrita). These lesions comprised 19 fibropapillomas and six fibromas. FPTHV mRNA transcripts were detected by ISH in three fibropapillomas, with positive reactions confined to the nuclei of clusters of epithelial cells. Viral DNA was detected by riboprobe ISH combined with denaturation in 14 tumours, including both fibropapillomas and fibromas. Signals were confined to the nuclei of acanthotic epithelial cells and were not seen in the subepithelial fibrous areas of the tumours. These results suggest that FPTHV is present in epithelial cells and transcriptionally active in fibropapillomas.

A novel class of herpesvirus with bivalve hosts

Ostreid herpesvirus 1 (OsHV-1) is the only member of the Herpesviridae that has an invertebrate host and is associated with sporadic mortality in the Pacific oyster (Crassostrea gigas) and other bivalve species. Cryo-electron microscopy of purified capsids revealed the distinctive T=16 icosahedral structure characteristic of herpesviruses, although the preparations examined lacked pentons. The gross genome organization of OsHV-1 was similar to that of certain mammalian herpesviruses (including herpes simplex virus and human cytomegalovirus), consisting of two invertible unique regions (U(L), 167.8 kbp; U(S), 3.4 kbp) each flanked by inverted repeats (TR(L)/IR(L), 7.6 kbp; TR(S)/IR(S), 9.8 kbp), with an additional unique sequence (X, 1.5 kbp) between IR(L) and IR(S). Of the 124 unique genes predicted from the 207 439 bp genome sequence, 38 were members of 12 families of related genes and encoded products related to helicases, inhibitors of apoptosis, deoxyuridine triphosphatase and RING-finger proteins, in addition to membrane-associated proteins. Eight genes in three of the families appeared to be fragmented. Other genes that did not belong to the families were predicted to encode DNA polymerase, the two subunits of ribonucleotide reductase, a helicase, a primase, the ATPase subunit of terminase, a RecB-like protein, additional RING-like proteins, an ion channel and several other membrane-associated proteins. Sequence comparisons showed that OsHV-1 is at best tenuously related to the two classes of vertebrate herpesviruses (those associated with mammals, birds and reptiles, and those associated with bony fish and amphibians). OsHV-1 thus represents a third major class of the herpesviruses.

Nucleotide sequence of an ICP18.5 assembly protein (UL28) gene of green turtle herpesvirus pathogenically associated with green turtle fibropapilloma

Because newly identified green turtle herpesvirus (GTHV) is associated pathogenically with marine turtle fibropapillomatosis (FP) and it has not been isolated in vitro, molecular sequencing and analysis of the genomic DNA of this putative reptilian herpesvirus will enhance the current understanding of GTHV in causing the FP disease. An inverse polymerase chain reaction (IPCR) genomic walking technique was developed to obtain new DNA sequences based on a portion of known genomic sequence. Through two genomic walks, a 2169 bp DNA fragment of GTHV was cloned and sequenced. Sequence analysis shows that this DNA fragment contains the entire gene of the UL28, as well as the partial genomic sequence of the UL27 gene. The UL28 gene is 2250 bp long and encodes a 750-amino acid peptide known as ICP18.5 assembly protein of herpesviruses. Phylogenetic analysis of the GHTV UL28 gene showed a high sequence homology with the UL28 homologs of other herpesviruses and supports the current classification of GTHV to be a member of Alphaherpesvirinae. Identification of the genomic sequences of GTHV provides a molecular base for the development of diagnostic immunoassay and also for the determination of the pathogenic role of GTHV infection.

Genomic variation of the fibropapilloma-associated marine turtle herpesvirus across seven geographic areas and three host species

Fibropapillomatosis (FP) of marine turtles is an emerging neoplastic disease associated with infection by a novel turtle herpesvirus, fibropapilloma-associated turtle herpesvirus (FPTHV). This report presents 23 kb of the genome of an FPTHV infecting a Hawaiian green turtle (Chelonia mydas). By sequence homology, the open reading frames in this contig correspond to herpes simplex virus genes UL23 through UL36. The order, orientation, and homology of these putative genes indicate that FPTHV is a member of the Alphaherpesvirinae. The UL27-, UL30-, and UL34-homologous open reading frames from FPTHVs infecting nine FP-affected marine turtles from seven geographic areas and three turtle species (C. mydas, Caretta caretta, and Lepidochelys olivacea) were compared. A high degree of nucleotide sequence conservation was found among these virus variants. However, geographic variations were also found: the FPTHVs examined here form four groups, corresponding to the Atlantic Ocean, West pacific, mid-Pacific, and east Pacific. Our results indicate that FPTHV was established in marine turtle populations prior to the emergence of FP as it is currently known.

Integrating reptilian herpesviruses into the family herpesviridae

The phylogeny of reptilian herpesviruses (HVs) relative to mammalian and avian HVs was investigated by using available gene sequences and by alignment of encoded amino acid sequences and derivation of trees by maximum-likelihood and Bayesian methods. Phylogenetic loci were obtained for green turtle HV (GTHV) primarily on the basis of DNA polymerase (POL) and DNA binding protein sequences, and for lung-eye-trachea disease-associated HV (LETV) primarily from its glycoprotein B sequence; both have nodes on the branch leading to recognized species in the Alphaherpesvirinae subfamily and should be regarded as new members of that subfamily. A similar but less well defined locus was obtained for an iguanid HV based on a partial POL sequence. On the basis of short POL sequences (around 60 amino acid residues), it appeared likely that GTHV and LETV belong to a private clade and that three HVs of gerrhosaurs (plated lizards) are associated with the iguanid HV. Based on phylogenetic branching patterns for mammalian HV lineages that mirror those of host lineages, we estimated a date for the HV tree's root of around 400 million years ago. Estimated dates for branching events in the development of reptilian, avian, and mammalian Alphaherpesvirinae lineages could plausibly be accounted for in part but not completely by ancient coevolution of these virus lines with reptilian lineages and with the development of birds and mammals from reptilian progenitors.