https://zenodo.org/record/1259447/files/article.pdf

Evolutionary genomics of Nucleo-Cytoplasmic Large DNA Viruses

Coronaviruses can infect a variety of animals including poultry, livestock, and humans and are currently classified into three groups. The interspecies transmissions of coronaviruses between different hosts form a complex ecosystem of which little is known. The outbreak of severe acute respiratory syndrome (SARS) and the recent identification of new coronaviruses have highlighted the necessity for further investigation of coronavirus ecology, in particular the role of bats and other wild animals. In this study, we sampled bat populations in 15 provinces of China and reveal that approximately 6.5% of the bats, from diverse species distributed throughout the region, harbor coronaviruses. Full genomes of four coronavirues from bats were sequenced and analyzed. Phylogenetic analyses of the spike, envelope, membrane, and nucleoprotein structural proteins and the two conserved replicase domains, putative RNA-dependent RNA polymerase and RNA helicase, revealed that bat coronaviruses cluster in three different groups: group 1, another group that includes all SARS and SARS-like coronaviruses (putative group 4), and an independent bat coronavirus group (putative group 5). Further genetic analyses showed that different species of bats maintain coronaviruses from different groups and that a single bat species from different geographic locations supports similar coronaviruses. Thus, the findings of this study suggest that bats may play an integral role in the ecology and evolution of coronaviruses.

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Prevalence and Genetic Diversity of Coronaviruses in Bats from China

Publisher Summary This chapter focuses on the advances in iridovirus research over the past decade. It summarizes salient features of the iridovirus research studies, and discusses their importance to future work. As knowledge of iridovirus biology increases, so does the understanding of the taxonomic structure of the family. A new genus (Megalocytivirus) has recently been created to accommodate a number of viruses isolated from diseased fish in Southeast Asia, and an established one (Chloriridovirus) is about to be validated following the sequencing of the genome of the mosquito pathogen IIV-3. Genomic sequencing projects have clarified evolutionary relationships between iridoviruses and other families of large, nucleocytoplasmic DNA viruses. Iridoviruses appear situated at the center of a clade of DNA viruses that include the poxviruses, phycodnaviruses,ASFV, ascoviruses, and possibly a new giant virus of amoebae (mimivirus). Not all iridovirus infections result in mortal disease. The recognition that many iridovirus infections are chronic, especially among insects, should stimulate studies on the importance of such illnesses on host fitness. Sublethal effects have been demonstrated in infected insects, and theoretical studies suggest such effects have a major influence on the dynamics of host populations. However, the consequences of chronic disease on the demography (fecundity, fertility, death rate, etc.) of infected amphibian and fish populations are notable by their absence. The ability to detect iridovirus infections has advanced markedly with the adoption of highly sensitive loop-mediated isothermal amplification and multiplex polymerase chain reaction techniques for rapid diagnosis of infected individuals.

A decade of advances in iridovirus research.

Members of the family Iridoviridae infect a diverse array of invertebrate and cold-blooded vertebrate hosts and are currently viewed as emerging pathogens of fish and amphibians. Iridovirid replication is unique and involves both nuclear and cytoplasmic compartments, a circularly permuted, terminally redundant genome that, in the case of vertebrate iridoviruses, is also highly methylated, and the efficient shutoff of host macromolecular synthesis. Although initially neglected largely due to the perceived lack of health, environmental, and economic concerns, members of the genus Ranavirus, and the newly recognized genus Megalocytivirus, are rapidly attracting growing interest due to their involvement in amphibian population declines and their adverse impacts on aquaculture. Herein we describe the molecular and genetic basis of viral replication, pathogenesis, and immunity, and discuss viral ecology with reference to members from each of the invertebrate and vertebrate genera.

/pdf/family-iridoviridae-poor-viral-relations-no-longer-3ume8f68kv.pdf

Family Iridoviridae: Poor Viral Relations No Longer

During the last several decades corals have been in decline and at least one-third of all coral species are now threatened with extinction. Coral disease has been a major contributor to this threat, but little is known about the responsible pathogens. To date most research has focused on bacterial and fungal diseases; however, viruses may also be important for coral health. Using a combination of empirical viral metagenomics and real-time PCR, we show that Porites compressa corals contain a suite of eukaryotic viruses, many related to the Herpesviridae. This coral-associated viral consortium was found to shift in response to abiotic stressors. In particular, when exposed to reduced pH, elevated nutrients, and thermal stress, the abundance of herpes-like viral sequences rapidly increased in 2 separate experiments. Herpes-like viral sequences were rarely detected in apparently healthy corals, but were abundant in a majority of stressed samples. In addition, surveys of the Nematostella and Hydra genomic projects demonstrate that even distantly related Cnidarians contain numerous herpes-like viral genes, likely as a result of latent or endogenous viral infection. These data support the hypotheses that corals experience viral infections, which are exacerbated by stress, and that herpes-like viruses are common in Cnidarians.

/pdf/metagenomic-analysis-indicates-that-stressors-induce-47cbs8v3v3.pdf

Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa

Here we report the complete genome sequence of Singapore grouper iridovirus (SGIV). Sequencing of the random shotgun and restriction endonuclease genomic libraries showed that the entire SGIV genome consists of 140,131 nucleotide bp. One hundred sixty-two open reading frames (ORFs) from the sense and antisense DNA strands, coding for lengths varying from 41 to 1,268 amino acids, were identified. Computer-assisted analyses of the deduced amino acid sequences revealed that 77 of the ORFs exhibited homologies to known virus genes, 23 of which matched functional iridovirus proteins. Forty-two putative conserved domains or signatures were detected in the National Center for Biotechnology Information CD-Search database and PROSITE database. An assortment of enzyme activities involved in DNA replication, transcription, nucleotide metabolism, cell signaling, etc., were identified. Viruses were cultured on a cell line derived from the embryonated egg of the grouper Epinephelus tauvina, isolated, and purified by sucrose gradient ultracentrifugation. The protein extract from the purified virions was analyzed by polyacrylamide gel electrophoresis followed by in-gel digestion of protein bands. Matrix-assisted laser desorption ionization-time of flight mass spectrometry and database searching led to identification of 26 proteins. Twenty of these represented novel or previously unidentified genes, which were further confirmed by reverse transcription-PCR (RT-PCR) and DNA sequencing of their respective RT-PCR products.

https://jvi.asm.org/content/jvi/78/22/12576.full.pdf

Jin Qiu

Papers

Functional Genomics Analysis of Singapore Grouper Iridovirus: Complete Sequence Determination and Proteomic Analysis