ICTV Virus Taxonomy Profile: Solemoviridae 2021

The family Solemoviridae includes viruses with icosahedral particles (26–34 nm in diameter) assembled on T=3 symmetry with a 4–6 kb positive-sense, monopartite, polycistronic RNA genome. Transmission of members of the genera Sobemovirus and Polemovirus occurs via mechanical wounding, vegetative propagation, insect vectors or abiotically through soil; members of the genera Polerovirus and Enamovirus are transmitted by specific aphids. Most solemoviruses have a narrow host range. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Solemoviridae, which is available at ictv.global/report/solemoviridae.

Isolation of the Novel Phage PHB09 and Its Potential Use against the Plant Pathogen Pseudomonas syringae pv. actinidiae

Bacteriophages are viruses that specifically infect target bacteria. Recently, bacteriophages have been considered potential biological control agents for bacterial pathogens due to their host specificity. Pseudomonas syringae pv. actinidiae (Psa) is a reemerging pathogen that causes bacterial canker of kiwifruit (Actinidia sp.). The economic impact of this pest and the development of resistance to antibiotics and copper sprays in Psa and other pathovars have led to investigation of alternative management strategies. Phage therapy may be a useful alternative to conventional treatments for controlling Psa infections. Although the efficacy of bacteriophage φ6 was evaluated for the control of Psa, the characteristics of other DNA bacteriophages infecting Psa remain unclear. In this study, the PHB09 lytic bacteriophage specific to Psa was isolated from kiwifruit orchard soil. Extensive host range testing using Psa isolated from kiwifruit orchards and other Pseudomonas strains showed PHB09 has a narrow host range. It remained stable over a wide range of temperatures (4–50 °C) and pH values (pH 3–11) and maintained stability for 50 min under ultraviolet irradiation. Complete genome sequence analysis indicated PHB09 might belong to a new myovirus genus in Caudoviricetes. Its genome contains a total of 94,844 bp and 186 predicted genes associated with phage structure, packaging, host lysis, DNA manipulation, transcription, and additional functions. The isolation and identification of PHB09 enrich the research on Pseudomonas phages and provide a promising biocontrol agent against kiwifruit bacterial canker.

Species-Specific Inhibition of Necroptosis by HCMV UL36

Viral infection activates cellular antiviral defenses including programmed cell death (PCD). Many viruses, particularly those of the Herpesviridae family, encode cell death inhibitors that antagonize different forms of PCD. While some viral inhibitors are broadly active in cells of different species, others have species-specific functions, probably reflecting the co-evolution of the herpesviruses with their respective hosts. Human cytomegalovirus (HCMV) protein UL36 is a dual cell death pathway inhibitor. It blocks death receptor-dependent apoptosis by inhibiting caspase-8 activation, and necroptosis by binding to the mixed lineage kinase domain-like (MLKL) protein and inducing its degradation. While UL36 has been shown to inhibit apoptosis in human and murine cells, the specificity of its necroptosis-inhibiting function has not been investigated. Here we show that UL36 interacts with both human and murine MLKL, but has a higher affinity for human MLKL. When expressed by a recombinant mouse cytomegalovirus (MCMV), UL36 caused a modest reduction of murine MLKL levels but did not inhibit necroptosis in murine cells. These data suggest that UL36 inhibits necroptosis, but not apoptosis, in a species-specific manner, similar to ICP6 of herpes simplex virus type 1 and MC159 of molluscum contagiosum virus. Species-specific necroptosis inhibition might contribute to the narrow host range of these viruses.

Characterization and genome analysis of two novel Aeromonas hydrophila phages PZL-Ah1and PZL-Ah8

Aeromonas hydrophila (A.hydrophila) is an opportunistic pathogen of fish-human-livestock, which poses a seriously affects to the development of aquaculture. Phage therapy is considered as a process to alternatively control bacterial infections and contaminations. In this study, the genomes of two Aeromonas hydrophila- specific phages PZL-Ah1 and PZL-Ah8 were isolated, characterized and genomic sequence analyzed. Transmission electron microscopy showed that the two phages had been classified as the member of the Podoviridae family. Both the two phages in this study had relatively narrow host range with lytic activity against Aeromonas spp. strains. However, they could lyse 3 common A.hydrophila strain. As revealed from the whole genomic sequence analysis, PZL-Ah1 and PZL-Ah8 coverd the double-stranded genome of 38,641 bp and 40,855 bp in length, with the GC content of 53.68% and 51.89%, respectively. Through gene comparison in NCBI database revealed that PZL-Ah1 and PZL-Ah8 were 97.67% − 95.51% identical to Stenotrophomonas phage IME15 and Aeromonas Phage T7-Ah. Phylogenetic analysis showed that PZL-Ah8, PZL-Ah1 and other two phages belonged to the same genus. A total of 44 and 52 open reading frames (ORFs) were predicted in the PZL-Ah1 and PZL-Ah8 genome, respectively. In the process of gene annotation, 28 (63.6%) ORFs in PZL-Ah1 and 29 (55.8%) ORFs in PZL-Ah8 were known to functional proteins in NCBI database, while the remaining ORFs were classified as “hypothetical proteins”, whose functions were yet unknown. By comparing, ORF 02, ORF 29 and ORF 04 in PZL-Ah1, ORF24 in PZL-Ah8 were responsible for the host cell lysis. In conclusion, genomic studies of these two novel phages would lay the foundation for expanding the phage genome database and providing good candidates for phage typing applications.

Characterization of Blf4, an Archaeal Lytic Virus Targeting a Member of the Methanomicrobiales

Today, the number of known viruses infecting methanogenic archaea is limited. Here, we report on a novel lytic virus, designated Blf4, and its host strain Methanoculleus bourgensis E02.3, a methanogenic archaeon belonging to the Methanomicrobiales, both isolated from a commercial biogas plant in Germany. The virus consists of an icosahedral head 60 nm in diameter and a long non-contractile tail of 125 nm in length, which is consistent with the new isolate belonging to the Siphoviridae family. Electron microscopy revealed that Blf4 attaches to the vegetative cells of M. bourgensis E02.3 as well as to cellular appendages. Apart from M. bourgensis E02.3, none of the tested Methanoculleus strains were lysed by Blf4, indicating a narrow host range. The complete 37 kb dsDNA genome of Blf4 contains 63 open reading frames (ORFs), all organized in the same transcriptional direction. For most of the ORFs, potential functions were predicted. In addition, the genome of the host M. bourgensis E02.3 was sequenced and assembled, resulting in a 2.6 Mbp draft genome consisting of nine contigs. All genes required for a hydrogenotrophic lifestyle were predicted. A CRISPR/Cas system (type I-U) was identified with six spacers directed against Blf4, indicating that this defense system might not be very efficient in fending off invading Blf4 virus.

A temperate phage 5W infecting multidrug-resistant Acinetobacter baumannii

We isolated 5W, a temperate phage that infects multidrug-resistant Acinetobacter baumannii from pond water, using an enrichment method that involves the addition of host bacteria. 5W is a long-tailed phage with a narrow host range lysed four of 19 A. baumannii clinical isolates tested, and complete lysis was observed for A. baumannii clinical isolate Ab1. 5W adsorbed rapidly to its Ab1 host and > 80% adsorption was observed after 2 min of mixing. The one-step growth curve showed that 5W has a 20 min latent period and a ~ 100 min rise period, with a burse size of ~ 180 PFU/cell. 5W contains a dsDNA genome 43,032 bp in length, with 61 open reading frames and a GC content of 39.85%. The genome lacks any known virulence and drug resistance genes, but encodes an N-acetyl-β-D-muramidase with numerous positively charged amino acids at its C-terminus that belongs to the GH_108 family. The M/S subunits of the restriction endonuclease are inserted in the lysogenic gene cluster. The first and second halves of the 5W genome are highly homologous with prophages phiABCR01-03 and phiABCR01-02 in the A. baumannii ABCR01 genome, respectively, which suggests that 5W may be a product of recombination between the two prophages.

Complete Genome Sequence of vB_EcoP_SU7, a Podoviridae Coliphage with the Rare C3 Morphotype

Enterotoxigenic Escherichia coli (ETEC) strains are an important cause of bacterial diarrheal illness in humans and animals. Infections arising from ETEC could potentially be treated through the use of bacteriophage (phage) therapy, as phages encode for enzymes capable of bacterial cell lysis. vB_EcoP_SU7 was isolated from the Käppala wastewater treatment plant in Stockholm, Sweden, and propagated on an ETEC strain exhibiting the O:139 serovar. Transmission electron microscopy confirmed that vB_EcoP_SU7 belongs to the Podoviridae family and has the rare C3 morphotype of an elongated head. Bioinformatic analyses showed that the genome was 76,626 base pairs long and contained 35 genes with predicted functions. A total of 81 open reading frames encoding proteins with hypothetical function and two encoding proteins of no significant similarity were also found. A putative tRNA gene, which may aid in vB_EcoP_SU7’s translation, was also identified. Phylogenetic analyses showed that compared to other Podoviridae, vB_EcoP_SU7 is a rare Kuravirus and is closely related to E. coli phages with the uncommon C3 morphotype, such as ECBP2, EK010, vB_EcoP_EcoN5, and vB_EcoP_SU10. Phage vB_EcoP_SU7 has a narrow host range, infecting 11 out of the 137 E. coli strains tested, a latency period of 30 min, a burst size of 12 PFU/cell, and an adsorption rate of 8.78 × 10−9 mL/min five minutes post infection. With a limited host range and poor infection kinetics, it is unlikely that SU7 can be a standalone phage used for therapeutic purposes; rather, it must be used in combination with other phages for broad-spectrum therapeutic success.

Gene editing in tree and clonal crops: progress and challenges

Because of the limitations inherent in conventional breeding of trees and clonally propagated crops, gene editing is of great interest. Dozens of published papers attest to the high efficiency of CRISPR-based systems in clonal crops and trees. The opportunity for “clean” edits is expected to avoid or reduce regulatory burdens in many countries and may improve market acceptance. To date, however, nearly all studies in trees and clonal crops retained all of the gene editing machinery in the genome. Despite high gene editing efficiency, technical and regulatory obstacles are likely to greatly limit progress toward commercial use. Technical obstacles include difficult and slow transformation and regeneration, delayed onset of flowering or clonal systems that make sexual segregation of CRISPR-associated genes difficult, inefficient excision systems to enable removal of functional (protein- or RNA-encoding) transgenic DNA, and narrow host range or limited gene-payload viral systems for efficient transient editing. Regulatory obstacles include those such as in the EU where gene-edited plants are regulated like GMO crops, and the many forms of method-based systems that regulate stringently based on the method vs. product novelty and thus are largely applied to each insertion event. Other major obstacles include the provisions of the Cartagena Protocol with respect to international trade and the need for compliance with the National Environmental Policy Act in the USA. The USDA SECURE act has taken a major step toward a more science- and risk-based—vs. method and insertion event based—system, but much further regulatory and legal innovation is needed in the USA and beyond.

Characterization of a Bacteriophage Isolated from a River water against a Local Field Strain Multi-Drug Resistant Staphylococcus Aureus

It is becoming increasingly difficult in combating Multi-drug resistant (MDR) bacteria. MDR Staphylococcus aureus particularly methicillin-resistant S. aureus is one such notorious pathogen in clinical settings and the food industry. With increasing incidences of drug resistance and slow progress in developing new antibiotics, bacteriophages against pathogenic S. aureus are promising as antibacterial. We isolated Four local field MDR S. aureus from wastewater samples. We got a bacteriophage against an MDR S. aureus from a river-water sample. The bacteriophage was lytic and was stable at various temperatures ranging from − 20°C to 37°C. the bacteriophage was stable at a highly alkaline PH and had a narrow host range. Through genomic analysis, the bacteriophage DNA encodes 52 genes, and all predicted genes are on one strand, it also encodes a phage RNA polymerase; although it does not show similarity to any known staphylococcal bacteriophage, it shows similarity (91%) to Enterobacteriaceae phages. When surveying the research articles about Staphylococcal phages, we could find about the unclassified and Singleton-Staphylococcal phages.

Ciboria carunculoides Suppresses Mulberry Immune Responses Through Regulation of Salicylic Acid Signaling

Ciboria carunculoides is the dominant causal agent of mulberry sclerotial disease, and it is a necrotrophic fungal pathogen with a narrow host range that causes devastating diseases in mulberry fruit. However, little is known about the interaction between C. carunculoides and mulberry. Here, our transcriptome sequencing results showed that the transcription of genes in the secondary metabolism and defense-related hormone pathways were significantly altered in infected mulberry fruit. Due to the antimicrobial properties of proanthocyanidins (PAs), the activation of PA biosynthetic pathways contributes to defense against pathogens. Salicylic acid (SA) and jasmonic acid (JA) are major plant defense hormones. However, SA signaling and JA signaling are antagonistic to each other. Our results showed that SA signaling was activated, while JA signaling was inhibited, in mulberry fruit infected with C. carunculoides. Yet SA mediated responses are double-edged sword against necrotrophic pathogens, as SA not only activates systemic acquired resistance (SAR) but also suppresses JA signaling. We also show here that the small secreted protein CcSSP1 of C. carunculoides activates SA signaling by targeting pathogenesis-related protein 1 (PR1). These findings reveal that the infection strategy of C. carunculoides functions by regulating SA signaling to inhibit host defense responses.