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1. Metagenomic identification of novel viruses of maize and teosinte in North America

   Lappe RR, Elmore MG (November 2022, BMC genomics)

   Background: Maize-infecting viruses are known to inflict significant agronomic yield loss throughout the world annually. Identification of known or novel causal agents of disease prior to outbreak is imperative to preserve food security via future crop protection efforts. Toward this goal, a large-scale metagenomic approach utilizing high throughput sequencing (HTS) was employed to identify novel viruses with the potential to contribute to yield loss of graminaceous species, particularly maize, in North America. Results: Here we present four novel viruses discovered by HTS and individually validated by Sanger sequencing. Three of these viruses are RNA viruses belonging to either the Betaflexiviridae or Tombusviridae families. Additionally, a novel DNA virus belonging to the Geminiviridae family was discovered, the first Mastrevirus identified in North Ameri- can maize. Conclusions: Metagenomic studies of crop and crop-related species such as this may be useful for the identifica- tion and surveillance of known and novel viral pathogens of crops. Monitoring related species may prove useful in identifying viruses capable of infecting crops due to overlapping insect vectors and viral host-range to protect food security. 

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2. Characterization of Diverse Anelloviruses, Cressdnaviruses, and Bacteriophages in the Human Oral DNA Virome from North Carolina (USA)

   https://doi.org/10.3390/v15091821  

   Paietta, Elise N; Kraberger, Simona; Custer, Joy M; Vargas, Karla L; Espy, Claudia; Ehmke, Erin; Yoder, Anne D; Varsani, Arvind (September 2023, Viruses)

   The diversity of viruses identified from the various niches of the human oral cavity—from saliva to dental plaques to the surface of the tongue—has accelerated in the age of metagenomics. This rapid expansion demonstrates that our understanding of oral viral diversity is incomplete, with only a few studies utilizing passive drool collection in conjunction with metagenomic sequencing methods. For this pilot study, we obtained 14 samples from healthy staff members working at the Duke Lemur Center (Durham, NC, USA) to determine the viral diversity that can be identified in passive drool samples from humans. The complete genomes of 3 anelloviruses, 9 cressdnaviruses, 4 Caudoviricetes large bacteriophages, 29 microviruses, and 19 inoviruses were identified in this study using high-throughput sequencing and viral metagenomic workflows. The results presented here expand our understanding of the vertebrate-infecting and microbe-infecting viral diversity of the human oral virome in North Carolina (USA). 

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3. OUP accepted manuscript

   https://doi.org/10.1093/bioinformatics/btaa490  

   Antipov, Rayko (May 2020, Bioinformatics)

   metaviralSPAdes: Assembly of Viruses From Metagenomic Data Abstract Motivation: Although the set of currently known viruses has been steadily expanding, only a tiny fraction of the Earth's virome has been sequenced so far. Shotgun metagenomic sequencing provides an opportunity to reveal novel viruses but faces the computational challenge of identifying viral genomes that are often difficult to detect in metagenomic assemblies. Results: We describe a metaviralSPAdes tool for identifying viral genomes in metagenomic assembly graphs that is based on analyzing variations in the coverage depth between viruses and bacterial chromosomes. We benchmarked metaviralSPAdes on diverse metagenomic datasets, verified our predictions using a set of virus-specific Hidden Markov Models, and demonstrated that it improves on the state-of-the-art viral identification pipelines. Availability: metaviralSPAdes includes viralAssembly, viralVerify, and viralComplete modules that are available as standalone packages: https://github.com/ablab/spades/tree/metaviral_publication, https://github.com/ablab/viralVerify/ and https://github.com/ablab/viralComplete/. Supplementary information: Supplementary data are available at Bioinformatics online. 

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4. Metagenomics and the development of viral water quality tools

   https://doi.org/10.1038/s41545-019-0032-3  

   Bibby, Kyle; Crank, Katherine; Greaves, Justin; Li, Xiang; Wu, Zhenyu; Hamza, Ibrahim A.; Stachler, Elyse (March 2019, npj Clean Water)

   Abstract Human exposure to pathogenic viruses in environmental waters results in a significant global disease burden. Current microbial water quality monitoring approaches, mainly based on fecal indicator bacteria, insufficiently capture human health impacts posed by pathogenic viruses in water. The emergence of the ‘microbiome era’ and high-throughput metagenome sequencing has led to the discovery of novel human-associated viruses, including both pathogenic and commensal viruses in the human microbiome. The discovery of novel human-associated viruses is often followed by their detection in wastewater, highlighting the great diversity of human-associated viruses potentially present in the water environment. Novel human-associated viruses provide a rich reservoir to develop viral water quality management tools with diverse applications, such as regulating wastewater reuse and monitoring agricultural and recreational waters. Here, we review the pathway from viral discovery to water quality monitoring tool, and highlight select human-associated viruses identified by metagenomics and subsequently detected in the water environment (namely Bocavirus, Cosavirus, CrAssphage, Klassevirus, and Pepper Mild Mottle Virus). We also discuss research needs to enable the application of recently discovered human-associated viruses in water quality monitoring, including investigating the geographic distribution, environmental fate, and viability of potential indicator viruses. Examples suggest that recently discovered human pathogens are likely to be less abundant in sewage, while other human-associated viruses (e.g., bacteriophages or viruses from food) are more abundant but less human-specific. The improved resolution of human-associated viral diversity enabled by metagenomic tools provides a significant opportunity for improved viral water quality management tools. 

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5. The Presence of Ancient Core Genes Reveals Endogenization from Diverse Viral Ancestors in Parasitoid Wasps

   https://doi.org/10.1093/gbe/evab105  

   Burke, Gaelen R; Hines, Heather M; Sharanowski, Barbara J (July 2021, Genome Biology and Evolution)

   Wayne, Marta (Ed.)

   Abstract The Ichneumonoidea (Ichneumonidae and Braconidae) is an incredibly diverse superfamily of parasitoid wasps that includes species that produce virus-like entities in their reproductive tracts to promote successful parasitism of host insects. Research on these entities has traditionally focused upon two viral genera Bracovirus (in Braconidae) and Ichnovirus (in Ichneumonidae). These viruses are produced using genes known collectively as endogenous viral elements (EVEs) that represent historical, now heritable viral integration events in wasp genomes. Here, new genome sequence assemblies for 11 species and 6 publicly available genomes from the Ichneumonoidea were screened with the goal of identifying novel EVEs and characterizing the breadth of species in lineages with known EVEs. Exhaustive similarity searches combined with the identification of ancient core genes revealed sequences from both known and novel EVEs. One species harbored a novel, independently derived EVE related to a divergent large double-stranded DNA (dsDNA) virus that manipulates behavior in other hymenopteran species. Although bracovirus or ichnovirus EVEs were identified as expected in three species, the absence of ichnoviruses in several species suggests that they are independently derived and present in two younger, less widespread lineages than previously thought. Overall, this study presents a novel bioinformatic approach for EVE discovery in genomes and shows that three divergent virus families (nudiviruses, the ancestors of ichnoviruses, and Leptopilina boulardi Filamentous Virus-like viruses) are recurrently acquired as EVEs in parasitoid wasps. Virus acquisition in the parasitoid wasps is a common process that has occurred in many more than two lineages from a diverse range of arthropod-infecting dsDNA viruses. 

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