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1. Identification of Diverse Bacteriophages Associated with Bees and Hoverflies

   https://doi.org/10.3390/v17020201  

   Bandoo, Rohan A; Kraberger, Simona; Ozturk, Cahit; Lund, Michael C; Zhu, Qiyun; Cook, Chelsea; Smith, Brian; Varsani, Arvind (February 2025, Viruses)

   Bacteriophages are the most numerous, ubiquitous, and diverse biological entities on the planet. Prior studies have identified bacteriophages associated with pathogenic and commensal microbiota of honeybees. In this study we expand on what is known about bacteriophages from the lineages Caudoviricetes, Inoviridae, and Microviridae, which are associated with honeybees (Apidae, Apis mellifera), solitary bees of the genus Nomia (Halictidae, Nomia), and hoverflies (Syrphidae). The complete genomes of seven caudoviruses, seven inoviruses, and 288 microviruses were assembled from honeybees (n = 286) and hoverflies in Arizona (n = 2). We used bacterial host predictive software and sequence read mapping programs to infer the commensal and transient bacterial hosts of pollinating insects. Lastly, this study explores the phylogenetic relationships of microviruses sampled from bees, opportunistically sampled pollinating insects such as hoverflies, and blackflies. 

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2. Genome Sequences of Microviruses Associated with Coptotermes formosanus

   https://doi.org/10.1128/MRA.00185-19  

   Schmidlin, Kara; Kraberger, Simona; Fontenele, Rafaela S.; De Martini, Francesca; Chouvenc, Thomas; Gile, Gillian H.; Varsani, Arvind; Maresca, Julia A. (April 2019, Microbiology Resource Announcements)

   ABSTRACT Termites have a unique ability to effectively digest lignocellulose with the help of mutualistic symbionts. While gut bacteria and protozoa have been relatively well characterized in termites, the virome remains largely unexplored. Here, we report two genomes of microviruses (termite-associated microvirus-1 [TaMV-1] and termite-associated microvirus-2 [TaMV-2]) associated with the gut of Coptotermes formosanus . 

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3. The Effects of Packaged, but Misguided, Single-Stranded DNA Genomes Are Transmitted to the Outer Surface of the ϕX174 Capsid

   https://doi.org/10.1128/JVI.00883-21  

   Ogunbunmi, Elizabeth T.; Roznowski, Aaron P.; Fane, Bentley A. (August 2021, Journal of Virology)

   Sandri-Goldin, Rozanne M. (Ed.)

   ABSTRACT Most icosahedral viruses condense their genomes into volumetrically constrained capsids. However, concurrent genome biosynthesis and packaging are specific to single-stranded DNA (ssDNA) viruses. ssDNA genome packaging combines elements found in both double-stranded DNA (dsDNA) and ssRNA systems. Similar to dsDNA viruses, the genome is packaged into a preformed capsid. Like ssRNA viruses, there are numerous capsid-genome associations. In ssDNA microviruses, the DNA-binding protein J guides the genome between 60 icosahedrally ordered DNA binding pockets. It also partially neutralizes the DNA’s negative phosphate backbone. ϕX174-related microviruses, such as G4 and α3, have J proteins that differ in length and charge organization. This suggests that interchanging J proteins could alter the path used to guide DNA in the capsid. Previously, a ϕXG4J chimera, in which the ϕX174 J gene was replaced with the G4 gene, was characterized. It displayed lethal packaging defects, which resulted in procapsids being removed from productive assembly. Here, we report the characterization of another inviable chimera, ϕXα3J. Unlike ϕXG4J, ϕXα3J efficiently packaged DNA but produced noninfectious particles. These particles displayed a reduced ability to attach to host cells, suggesting that internal DNA organization could distort the capsid’s outer surface. Mutations that restored viability altered J-coat protein contact sites. These results provide evidence that the organization of ssDNA can affect both packaging and postpackaging phenomena. IMPORTANCE ssDNA viruses utilize icosahedrally ordered protein-nucleic acids interactions to guide and organize their genomes into preformed shells. As previously demonstrated, chaotic genome-capsid associations can inhibit ϕX174 packaging by destabilizing packaging complexes. However, the consequences of poorly organized genomes may extend beyond the packaging reaction. As demonstrated herein, it can lead to uninfectious packaged particles. Thus, ssDNA genomes should be considered an integral and structural virion component, affecting the properties of the entire particle, which includes the capsid’s outer surface. 

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4. 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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5. Shear Wave Splitting Across Antarctica: Implications for Upper Mantle Seismic Anisotropy

   https://doi.org/10.1029/2021JB023325  

   Lucas, Erica M.; Nyblade, Andrew A.; Accardo, Natalie J.; Lloyd, Andrew J.; Wiens, Douglas A.; Aster, Richard C.; Wilson, Terry J.; Dalziel, Ian W.; Stuart, Graham W.; O’Donnell, John Paul; et al (March 2022, Journal of Geophysical Research: Solid Earth)

   Abstract We examine upper mantle anisotropy across the Antarctic continent using 102 new shear wave splitting measurements obtained from teleseismic SKS, SKKS, and PKS phases combined with 107 previously published results. For the new measurements, an eigenvalue technique is used to estimate the fast polarization direction and delay time for each phase arrival, and high‐quality measurements are stacked to determine the best‐fit splitting parameters at each seismic station. The ensemble of splitting measurements shows largely NE‐SW‐oriented fast polarization directions across Antarctica, with a broadly clockwise rotation in polarization directions evident moving from west to east across the continent. Although the first‐order pattern of NE‐SW‐oriented polarization directions is suggestive of a single plate‐wide source of anisotropy, we argue the observed pattern of anisotropy more likely arises from regionally variable contributions of both lithospheric and sub‐lithospheric mantle sources. Anisotropy observed in the interior of East Antarctica, a region underlain by thick lithosphere, can be attributed to relict fabrics associated with Precambrian tectonism. In contrast, anisotropy observed in coastal East Antarctica, the Transantarctic Mountains (TAM), and across much of West Antarctica likely reflects both lithospheric and sub‐lithospheric mantle fabrics. While sub‐lithospheric mantle fabrics are best associated with either plate motion‐induced asthenospheric flow or small‐scale convection, lithospheric mantle fabrics in coastal East Antarctica, the TAM, and West Antarctica generally reflect Jurassic—Cenozoic tectonic activity. 

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