Genomic and developmental characterisation of a novel bunyavirus infecting the crustacean Carcinus maenas

Virus discovery in cultured portunid crabs: Genomic, phylogenetic, histopathological and microscopic characterization of a reovirus and a new bunyavirus

Portunid crabs are distributed worldwide and highly valued in aquaculture. Viral infections are the main limiting factor for the survival of these animals and, consequently, for the success of commercial-scale cultivation. However, there is still a lack of knowledge about the viruses that infect cultured portunid crabs worldwide. Herein, the genome sequence and phylogeny of Callinectes sapidus reovirus 2 (CsRV2) are described, and the discovery of a new bunyavirus in Callinectes danae cultured in southern Brazil is reported. The CsRV2 genome sequence consists of 12 dsRNA segments (20,909 nt) encode 13 proteins. The predicted RNA-dependent RNA polymerase (RdRp) shows a high level of similarity with that of Eriocheir sinensis reovirus 905, suggesting that CsRV2 belongs to the genus Cardoreovirus. The CsRV2 particles are icosahedral, measuring approximately 65 nm in diameter, and exhibit typical non-turreted reovirus morphology. High throughput sequencing data revealed the presence of an additional putative virus genome similar to bunyavirus, called Callinectes danae Portunibunyavirus 1 (CdPBV1). The CdPBV1 genome is tripartite, consisting of 6,654 nt, 3,120 nt and 1,656 nt single-stranded RNA segments that each encode a single protein. Each segment has a high identity with European shore crab virus 1, suggesting that CdPBV1 is a new representative of the family Cruliviridae. The putative spherical particles of CdPBV1 measure ∼120 nm in diameter and present a typical bunyavirus morphology. The results of the histopathological analysis suggest that these new viruses can affect the health and, consequently, the survival of C. danae in captivity. Therefore, the findings reported here should be used to improve prophylactic and pathogen control practices and contribute to the development and optimization of the production of soft-shell crabs on a commercial scale in Brazil.

ICTV Virus Taxonomy Profile: Cruliviridae 2023

Cruliviridae is a family of negative-sense RNA viruses with genomes of 10.8-11.5 kb that have been found in crustaceans. The crulivirid genome consists of three RNA segments with ORFs that encode a nucleoprotein (NP), a glycoprotein (GP), a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain, and in some family members, a zinc-finger (Z) protein of unknown function. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Cruliviridae, which is available at ictv.global/report/cruliviridae.

Rift Valley Fever vaccine strategies: Enhanced stability of RVF Clone 13

Rift Valley Fever virus (RVFV) causes the zoonotic RVF disease, which results in substantial economic losses in livestock industries. Regular vaccination of livestock against RVF is necessary to generate long-term immunity and avoid the loss of livestock. The live attenuated vaccine based on Clone 13 virus strain has been used to reduce the negative impact of RVF disease. The vaccine strain is heat labile and requires stringent conditions for storage and handling. This research evaluated lactose and sucrose-based stabilizers coupled with lyophilisation to enhance stability of the RVF Clone 13 vaccine strain. The glass transition temperature (Tg) of the sucrose-RVF vaccine was 97.0 °C with average residual moisture of below 2 %. The lactose formulation was characterised with Tg of 83.5 °C and residual moisture of above 2 %. The RVF Clone 13 sucrose-based formulation maintained higher antigen titres during lyophilisation compared to the lactose-formulated vaccine. Cellular-mediated and humoral immunity was evaluated and compared for the two newly formulated vaccines. Pheroid® technology was also investigated as a potential adjuvant and its ability to further enhance the immunogenicity conferred by the RVF Clone 13 vaccine formulations in Merino sheep. No adverse reactions were observed following injection of the vaccine formulations in mice, guinea pigs and Merino sheep. Comparable protective humoral immune responses against RVF were obtained for all animals vaccinated with the lactose and sucrose-based stabilisers with and without the Pheroid® adjuvant. No proliferation of CD8+ and CD4+ T-cells as well as expression of IFN-γ was observed for all animals group vaccinated with Pheroid® only. Specific CD8+ IFN-γ+T-cells were expressed at higher levels compared to the CD4+ IFN-γ+T-cells in the RVF Clone 13 vaccines, suggesting that cellular immunity against RVF is through the Class I antigen presentation pathway.

Rediscovering "Baculovirus-A" (Johnson, 1976): The complete genome of 'Callinectes sapidus nudivirus'

Callinectes sapidus, or the 'blue crab', supports an extensive east-coast USA fishery and was one of the first crustacean species in which viruses were observed. Pioneering research by Dr Phyllis Johnson led to these initial discoveries, one of which included the discovery of a virus termed "Baculovirus-A". This virus was considered a potential member of the Baculoviridae, Nimaviridae, or Nudiviridae, in which all viral members are rod-shaped dsDNA viruses found in the nucleus of their host cell. With the availability of genomic and bioinformatic tools, such as Illumina HiSeq and assembly programs, it is now possible to assemble the genomes of viruses and gain additional genomic insight, which can shed light on viral taxonomy. Using these tools, alongside electron micrographs and histology slides, we reveal that the hepatopancreas-infecting 'Baculovirus-A' from Callinectes sapidus is a member of the Nudiviridae, resembling genetic and protein similarity to other crab and lobster infecting nudiviruses from the Gammanudivirus genus. Histologically, the virus causes nuclear hypertrophy as observed for other gammanuriviruses. The genome of the virus is circular, 122,436 bp in length, and encodes a predicted 98 protein coding genes, including all of the nudivirus core genes. The prevalence of virus from across Florida, USA, is provided alongside a genomic comparison of the new viral genome against other Gammanudivirus species, revealing the average prevalence to be 2.2% and that Callinectes sapidus nudivirus is distantly similar to the recently described Carcinus maenas nudivirus from Canada.

Pathology and genetic connectedness of the mangrove crab (Aratus pisonii) – a foundation for understanding mangrove disease ecology

Mangrove forests are productive ecosystems, acting as a sink for CO2, a habitat for a diverse array of terrestrial and marine species, and as a natural barrier to coastline erosion. The species that reside within mangrove ecosystems have important roles to play, including litter decomposition and the recycling of nutrients. Crustacea are important detritivores in such ecosystems and understanding their limitations (i.e. disease) is an important endeavour when considering the larger ecological services provided.

Histology and metagenomics were used to identify viral (Nudiviridae, Alphaflexiviridae), bacterial (Paracoccus sp., 'Candidatus Gracilibacteria sp.’, and Pseudoalteromonas sp.), protozoan, fungal, and metazoan diversity that compose the symbiome of the mangrove crab, Aratus pisonii. The symbiotic groups were observed at varying prevalence under histology: nudivirus (6.5%), putative gut epithelial virus (3.2%), ciliated protozoa (35.5%), gonad fungus (3.2%), gill ectoparasitic metazoan (6.5%). Metagenomic analysis of one specimen exhibiting a nudivirus infection provided the complete host mitochondrial genome (15,642 bp), nudivirus genome (108,981 bp), and the genome of a Cassava common mosaic virus isolate (6387 bp). Our phylogenetic analyses group the novel nudivirus with the Gammanudivirus and protein similarity searches indicate that Carcinus maenas nudivrius is the most similar to the new isolate. The mitochondrial genome were used to mine short fragments used in population genetic studies to gauge an idea of diversity in this host species across the USA, Caribbean, and central and southern America.

This study report several new symbionts based on their pathology, taxonomy, and genomics (where available) and discuss what effect they may have on the crab population. The role of mangrove crabs from a OneHealth perspective were explored, since their pathobiome includes cassava-infecting viruses. Finally, given that this species is abundant in mangrove forests and now boasts a well-described pathogen profile, we posit that A. pisonii is a valuable model system for understanding mangrove disease ecology.

2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

A Novel Bunyavirus Discovered in Oriental Shrimp (Penaeus chinensis)

Herein, we describe a novel bunyavirus, oriental wenrivirus 1 (OWV1), discovered in moribund oriental shrimp (Penaeus chinensis) collected from a farm in China in 2016. Like most bunyaviruses, OWV1 particles were enveloped, spherical- to ovoid-shaped, and 80-115 nm in diameter. However, its genome was found to comprise four segments of (-)ssRNA. These included an L RNA segment (6,317 nt) encoding an RNA-directed RNA polymerase (RdRp) of 2,052 aa, an M RNA segment (2,978 nt) encoding a glycoprotein precursor (GPC) of 922 aa, an S1 RNA segment (1,164 nt) encoding a nucleocapsid (N) protein of 243 aa, and an S2 RNA segment (1,382 nt) encoding a putative non-structural (NSs2) protein of 401 aa. All the four OWV1 RNA segments have complementary terminal decanucleotides (5'-ACACAAAGAC and 3'-UGUGUUUCUG) identical to the genomic RNA segments of uukuviruses and similar to those of phleboviruses and tenuiviruses in the Phenuiviridae. Phylogenetic analyses revealed that the RdRp, GPC, and N proteins of OWV1 were closely related to Wēnzhōu shrimp virus 1 (WzSV-1) and Mourilyan virus (MoV) that infect black tiger shrimp (P. monodon). Phylogenetic analyses also suggested that OWV1 could be classified into a second, yet to be established, species of the Wenrivirus genus in the Phenuiviridae. These wenriviruses also clustered with Wenling crustacean virus 7 from shrimps and bunya-like brown spot virus from white-clawed crayfish. Of note there were no homologs of the NSs2 of OWV1 and MoV/WzSV-1 in GenBank, and whether other crustacean phenuiviruses also possess a similar S2 RNA segment warrants further investigation. In addition, we established a TaqMan probe-based reverse-transcription quantitative PCR method for detection of OWV1, and it was detected as 1.17 × 102-1.90 × 107 copies/ng-RNA in gills of 23 out of 32 P. chinensis samples without an obvious gross sign. However, the discovery of OWV1 highlights the expanding genomic diversity of bunyaviruses.

Symbionts of invasive and native crabs, in Argentina: The most recently invaded area on the Southwestern Atlantic coastline

Biological invasions have the capacity to introduce non-native parasites. This study aimed to determine whether the invasive green crab population, Carcinus spp., on the Southwestern Atlantic coast of Argentina harbours any symbionts, and whether these may spillover or spillback between native crabs, Cyrtograpsus altimanus and C. angulatus. Macroscopy, histology, and molecular analyses of some parasites were used to describe and compare their diversity across the three species of crab. We also evaluated the susceptibility of invasive Carcinus spp. to a native digenean, Maritrema madrynense, via experimental infections (exposure and cohabitation). Our results revealed that the green crab pathobiome included similar symbiotic groups to native crabs. This included putative viral, bacterial, and protozoan parasites. Haplosporidium-like observations were recorded in all crab species, and a single green crab was found to be parasitized by an Agmasoma-like microsporidium. Metagenomic analysis of one individual revealed additional symbiotic diversity (46 bacteria, 5 eukaryotic species). The green crabs were infected by more microparasite taxa than the native crabs (5:3). Wild populations of Carcinus spp. were free of metazoan parasites and are shown not to be susceptible to M. madryense under experimental conditions. Our results suggest a reduction/escape of macroparasites (trematode Maritrema madrynense; acanthocephalan Profilicollis chasmagnathi) in invasive Carcinus spp. compared to their native competitors.

Invasive Non-Native Crustacean Symbionts: Diversity and Impact

Invasive non-native species (INNS) pose a risk as vectors of parasitic organisms (Invasive Parasites). Introducing invasive parasites can result in ecological disturbances, leading to biodiversity loss and native species illness/mortality, but occasionally can control INNS limiting their impact. Risks to human health and the economy are also associated with INNS and invasive parasites; however, we understand little about the diversity of symbiotic organisms co-invading alongside INNS. This lack of clarity is an important aspect of the 'One Health' prerogative, which aims to bridge the gap between human, wildlife, and ecosystem health. To explore symbiont diversity associated with the invasive crustacean group (including: crab, lobster, crayfish, shrimp, amphipod, isopod, copepod, barnacle, other) (n = 323) derived from 1054 aquatic invertebrates classed as INNS across databases, we compile literature (year range 1800-2017) from the native and invasive range to provide a cumulative symbiont profile for each species. Our search indicated that 31.2% of INN crustaceans were known to hold at least one symbiont, whereby the remaining 68.8% had no documented symbionts. The symbiont list mostly consisted of helminths (27% of the known diversity) and protists (23% of the known diversity), followed by bacteria (12%) and microsporidians (12%). Carcinus maenas, the globally invasive and extremely well-studied green crab, harboured the greatest number of symbionts (n = 72). Additional screening is imperative to become more informed on invasive symbiont threats. We reveal that few studies provide truly empirical data that connect biodiversity loss with invasive parasites and suggest that dedicated studies on available systems will help to provide vital case studies. Despite the lack of empirical data, co-invasive parasites of invasive invertebrates appear capable of lowering local biodiversity, especially by causing behavioural change and mortality in native species. Alternatively, several invasive parasites appear to protect ecosystems by controlling the impact and population size of their invasive host. We provide a protocol that could be followed to explore symbiont diversity in invasive groups as part of our case studies. The consequence of limited parasite screening of INNS, in addition to the impacts invasive parasites impart on local ecologies, are explored throughout the review. We conclude in strong support of the 'One Health' prerogative and further identify a need to better explore disease in invasion systems, many of which are accountable for economic, human health and ecological diversity impacts.

Family Level Phylogenies Reveal Relationships of Plant Viruses within the Order Bunyavirales

Bunyavirales are negative-sense segmented RNA viruses infecting arthropods, protozoans, plants, and animals. This study examines the phylogenetic relationships of plant viruses within this order, many of which are recently classified species. Comprehensive phylogenetic analyses of the viral RNA dependent RNA polymerase (RdRp), precursor glycoprotein (preGP), the nucleocapsid (N) proteins point toward common progenitor viruses. The RdRp of Fimoviridae and Tospoviridae show a close evolutional relationship while the preGP of Fimoviridae and Phenuiviridae show a closed relationship. The N proteins of Fimoviridae were closer to the Phasmaviridae, the Tospoviridae were close to some Phenuiviridae members and the Peribunyaviridae. The plant viral movement proteins of species within the Tospoviridae and Phenuiviridae were more closely related to each other than to members of the Fimoviridae. Interestingly, distal ends of 3′ and 5′ untranslated regions of species within the Fimoviridae shared similarity to arthropod and vertebrate infecting members of the Cruliviridae and Peribunyaviridae compared to other plant virus families. Co-phylogeny analysis of the plant infecting viruses indicates that duplication and host switching were more common than co-divergence with a host species.

Mycosis is a Disease State Encountered Rarely in Shore Crabs, Carcinus maenas

There is a paucity of knowledge regarding the diversity and impact(s) of disease-causing fungi in marine animals, especially shellfish. In efforts to address this knowledge gap for the shore crab Carcinus maenas, a year-long disease screen was carried out across two sites in Swansea Bay (Wales, UK) with a view to characterising putative fungal infections. Crabs were sampled between November 2017 and October 2018, and screened systematically for disease signatures using haemolymph (blood) preparations, targeted PCR and tissue histopathology. Strikingly, mycosis was confirmed in ~0.4% of total crabs tested (n = 1191) and restricted to one location only (Mumbles Pier). Clinical infections were observed in four out of four infected crabs. In these animals, the gills and hepatopancreas were congested with fungal morphotypes. In addition, some evidence indicates haemocyte (immune cell) reactivity toward the fungi. Phylogenetic placement of the partial internal transcribed spacer (ITS1) gene regions amplified from three mycotic crabs revealed the causative agent to be related to hypocrealean fungi, thereby representing a novel species.

Exploration of the virome of the European brown shrimp (Crangon crangon)

Crangon crangon is economically a very important species. Recently, promising culture attempts have been made, but a major problem is the uncontrollable mortality during the grow-out phase. As of yet, the life cycle of C. crangon is not closed in captivity so wild-caught individuals are used for further rearing. Therefore, it is important to investigate the virome of C. crangon both in wild-caught animals as in cultured animals. In recent years, next-generation-sequencing (NGS) technologies have been very important in the unravelling of the virome of a wide range of environments and matrices, such as soil, sea, potable water, but also of a wide range of animal species. This will be the first report of a virome study in C. crangon using NGS in combination with the NetoVIR protocol. The near complete genomes of 16 novel viruses were described, most of which were rather distantly related to unclassified viruses or viruses belonging to the Picornavirales, Bunyavirales Nudiviridae, Parvoviridae, Flaviviridae, Hepeviridae, Tombusviridae, Narnaviridae, Nodaviridae, Sobemovirus. A difference in virome composition was observed between muscle and hepatopancreatic tissue, suggesting a distinct tissue tropism of several of these viruses. Some differences in the viral composition were noted between the cultured and wild shrimp, which could indicate that in sub-optimal aquaculture conditions some viruses become more abundant. This research showed that a plethora of unknown viruses is present in C. crangon and that more research is needed to determine which virus is potentially dangerous for the culture of C. crangon.

Life History and Population Dynamics of Green Crabs (Carcinus maenas)

Carcinus maenas (the “shore crab” or “European green crab”) is a very proficient invader (considered to be one of the world’s 100 worst invaders by the IUCN) due to its phenotypic plasticity, wide temperature and salinity tolerance, and an extensive omnivorous diet. Native to Atlantic Europe, it has established two well-studied nonindigenous populations in the northwestern Atlantic and northeastern Pacific and less-studied populations in Australia, Argentina and South Africa. Green crabs are eurythermal and euryhaline as adults, but they are limited to temperate coastlines due to more restrictive temperature requirements for breeding and larval development. They cannot tolerate wave-swept open shores so are found in wave-protected sheltered bays, estuaries and harbors. Carcinus maenas has been the subject of numerous papers, with over 1000 published in the past decade. This review provides an up-to-date account of the current published information on the life history and population dynamics of this very important species, including genetic differentiation, habitat preferences, physical parameter tolerances, reproduction and larval development, sizes of crabs, densities of populations, sex ratios, ecosystem dynamics and ecological impacts in the various established global populations of green crabs.