Forty-nine metagenomic-assembled genomes from an aquatic virome expand Caudoviricetes by 45 potential new families and the newly uncovered Gossevirus of Bamfordvirae.

Twenty complete genomes (29-63 kb) and 29 genomes with an estimated completeness of over 90 % (30-90 kb) were identified for novel dsDNA viruses in the Yangshan Harbor metavirome. These newly discovered viruses contribute to the expansion of viral taxonomy by introducing 46 potential new families. Except for one virus, all others belong to the class Caudoviricetes. The exception is a novel member of the recently characterized viral group known as Gossevirus. Fifteen viruses were predicted to be temperate. The predicted hosts for the viruses appear to be involved in various aspects of the nitrogen cycle, including nitrogen fixation, oxidation and denitrification. Two viruses were identified to have a host of Flavobacterium and Tepidimonas fonticaldi, respectively, by matching CRISPR spacers with viral protospacers. Our findings provide an overview for characterizing and identifying specific viruses from Yangshan Harbor. The Gossevirus-like virus uncovered emphasizes the need for further comprehensive isolation and investigation of polinton-like viruses.

Hiding in plain sight: The discovery of complete genomes of 11 hypothetical spindle-shaped viruses that putatively infect mesophilic ammonia-oxidizing archaea.

The genome of a putative Nitrosopumilaceae virus with a hypothetical spindle-shaped particle morphology was identified in the Yangshan Harbour metavirome from the East China Sea through protein similarity comparison and structure analysis. This discovery was accompanied by a set of 10 geographically dispersed close relatives found in the environmental virus datasets from typical locations of ammonia-oxidizing archaeon distribution. Its host prediction was supported by iPHoP prediction and protein sequence similarity. The structure of the predicted major capsid protein, together with the overall N-glycosylation site, the transmembrane helices prediction, the hydrophilicity profile, and the docking simulation of the major capsid proteins, indicate that these viruses resemble spindle-shaped viruses. It suggests a similarly assembled structure and, consequently, a possibly spindle-shaped morphology of these newly discovered archaeal viruses.

Genomic Analysis and Taxonomic Characterization of Seven Bacteriophage Genomes Metagenomic-Assembled from the Dishui Lake.

Viruses in aquatic ecosystems exhibit remarkable abundance and diversity. However, scattered studies have been conducted to mine uncultured viruses and identify them taxonomically in lake water. Here, whole genomes (29-173 kbp) of seven uncultured dsDNA bacteriophages were discovered in Dishui Lake, the largest artificial lake in Shanghai. We analyzed their genomic signatures and found a series of viral auxiliary metabolic genes closely associated with protein synthesis and host metabolism. Dishui Lake phages shared more genes with uncultivated environmental viruses than with reference viruses based on the gene-sharing network classification. Phylogeny of proteomes and comparative genomics delineated three new genera within two known viral families of Kyanoviridae and Autographiviridae, and four new families in Caudoviricetes for these seven novel phages. Their potential hosts appeared to be from the dominant bacterial phyla in Dishui Lake. Altogether, our study provides initial insights into the composition and diversity of bacteriophage communities in Dishui Lake, contributing valuable knowledge to the ongoing research on the roles played by viruses in freshwater ecosystems.

Metavirome-assembled genome sequence of a new aquatic RNA virus expands the genus Locarnavirus.

RNA viruses in marine environments have long been recognized as major players in the virosphere. In this study, the complete genome sequence of an RNA virus from Yangshan Harbor, named marine RNA virus Yangshan-LWW (YS-LWW), was obtained based on metavirome assembly. The genome of YS-LWW is 8839 nt in length and contains two open reading frames (ORFs). Both RdRP- and whole-genome-based phylogenetic analysis showed that YS-LWW, together with 45 viral isolates with sequences in public datasets, represents a new species in the genus Locarnavirus of the family Marnaviridae. PCR and public dataset mining indicate that YS-LWW and YS-LWW-like viruses have been widely detected in coastal and freshwater environments, suggesting that they might play a significant role in aquatic ecosystems.

Fast VMAT planning for prostate radiotherapy: dosimetric validation of a deep learning-based initial segment generation method.

Objective. To develop and evaluate a deep learning based fast volumetric modulated arc therapy (VMAT) plan generation method for prostate radiotherapy.Approach. A customized 3D U-Net was trained and validated to predict initial segments at 90 evenly distributed control points of an arc, linked to our research treatment planning system (TPS) for segment shape optimization (SSO) and segment weight optimization (SWO). For 27 test patients, the VMAT plans generated based on the deep learning prediction (VMATDL) were compared with VMAT plans generated with a previously validated automated treatment planning method (VMATref). For all test cases, the deep learning prediction accuracy, plan dosimetric quality, and the planning efficiency were quantified and analyzed.Main results. For all 27 test cases, the resulting plans were clinically acceptable. TheV95%for the PTV2 was greater than 99%, and theV107%was below 0.2%. Statistically significant difference in target coverage was not observed between the VMATrefand VMATDLplans (P = 0.3243 > 0.05). The dose sparing effect to the OARs between the two groups of plans was similar. Small differences were only observed for the Dmean of rectum and anus. Compared to the VMATref, the VMATDLreduced 29.3% of the optimization time on average.Significance. A fully automated VMAT plan generation method may result in significant improvement in prostate treatment planning efficiency. Due to the clinically acceptable dosimetric quality and high efficiency, it could potentially be used for clinical planning application and real-time adaptive therapy application after further validation.