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1. Predictive Modeling of Virus Inactivation by UV

   https://doi.org/10.1021/acs.est.0c07814  

   Rockey, Nicole C.; Henderson, James B.; Chin, Kaitlyn; Raskin, Lutgarde; Wigginton, Krista R. (April 2021, Environmental Science & Technology)

   null (Ed.)

   UV254 disinfection strategies are commonly applied to inactivate pathogenic viruses in water, food, air, and on surfaces. There is a need for methods that rapidly predict the kinetics of virus inactivation by UV254, particularly for emerging and difficult-to-culture viruses. We conducted a systematic literature review of inactivation rate constants for a wide range of viruses. Using these data and virus characteristics, we developed and evaluated linear and nonlinear models for predicting inactivation rate constants. Multiple linear regressions performed best for predicting the inactivation kinetics of (+) ssRNA and dsDNA viruses, with cross-validated root mean squared relative prediction errors similar to those associated with experimental rate constants. We tested the models by predicting and measuring inactivation rate constants of a (+) ssRNA mouse coronavirus and a dsDNA marine bacteriophage; the predicted rate constants were within 7% and 71% of the experimental rate constants, respectively, indicating that the prediction was more accurate for the (+) ssRNA virus than the dsDNA virus. Finally, we applied our models to predict the UV254 rate constants of several viruses for which high-quality UV254 inactivation data are not available. Our models will be valuable for predicting inactivation kinetics of emerging or difficult-to-culture viruses. 

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2. A honey bee-associated virus remains infectious and quantifiable in postmortem hosts

   https://doi.org/10.1016/j.jip.2024.108258  

   Payne, Alexandria N; Prayugo, Vincent; Dolezal, Adam G (March 2025, Journal of Invertebrate Pathology)

   Corpse-mediated pathogen transmission is a viable route through which naïve hosts can become infected, but its likelihood for honey bee-associated viruses is largely unknown. While these viruses can be easily detected in deceased bees, it remains unclear if they stay infectious within postmortem hosts or if enough viral RNA degradation-and subsequently virus inactivation-occurs post-host death to render these viruses inviable. This knowledge gap has important implications for how researchers perform honey bee virus studies and for our general understanding of honey bee virus transmission. To better understand the resiliency of honey bee-associated viruses within deceased hosts, we first tested the hypothesis that postmortem specimens, stored in colony-normal temperature and humidity conditions, can be reliably used to quantify virus abundance. To determine this, we experimentally-infected adult honey bees with Israeli acute paralysis virus (IAPV) and then measured the virus levels of individuals sampled live or at different postmortem time points (4, 12, 24, and 48 hours post-death) using RT-qPCR and a standard curve absolute quantification method. We found no significant differences based on when bees were sampled, indicating that postmortem honey bees are statistically comparable to using live-sampled bees and can be reliably used to quantify absolute IAPV abundance. We then performed a follow-up experiment that determined whether or not the IAPV detected in postmortem bees remained infectious over time. We found that IAPV extracted from postmortem bees remained highly infectious for at least 48 hours post-death, indicating that any viral RNA degradation that may have occurred during the postmortem interval did not adversely affect IAPV's overall infectivity. The results from this study suggest that IAPV is more resilient to degradation than previously assumed, support the use of postmortem bees for downstream IAPV analyses, and indicate that postmortem hosts can act as sources of IAPV infection for susceptible individuals. 

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3. Population ecology and potential biogeochemical impacts of ssDNA and dsDNA soil viruses along a permafrost thaw gradient

   https://doi.org/10.1101/2023.06.13.544858  

   Trubl, Gareth; Roux, Simon; Borton, Mikayla A; Varsani, Arvind; Li, Yueh-Fen; Sun, Christine; Jang, Ho Bin; Woodcroft, Ben J; Tyson, Gene W; Wrighton, Kelly C; et al (June 2023, bioRxiv)

   Abstract Climate change is disproportionately warming northern peatlands, which may release large carbon stores via increased microbial activity. While there are many unknowns about such microbial responses, virus roles are especially poorly characterized with studies to date largely restricted to “bycatch” from bulk metagenomes. Here, we used optimized viral particle purification techniques on 20 samples along a highly contextualized peatland permafrost thaw gradient, extracted and sequenced viral particle DNA using two library kits to capture single-stranded (ssDNA) and double-stranded (dsDNA) virus genomes (40 total viromes), and explored their diversity and potential ecosystem impacts. Both kits recovered similar dsDNA virus numbers, but only one also captured thousands of ssDNA viruses. Combining these data, we explored population-level ecology using genomic representation from 9,560 viral operational taxonomic units (vOTUs); nearly a 4-fold expansion from permafrost-associated soils, and 97% of which were novel when compared against large datasets from soils, oceans, and the human gut.In silicopredictions identified putative hosts for 44% (4,149 dsDNA + 17 ssDNA) of the identified vOTUs spanning 2 eukaryotic, 12 archaeal, and 30 bacterial phyla. The recovered vOTUs encoded 1,684 putative auxiliary metabolic genes (AMGs) and other metabolic genes carried by ∼10% of detected vOTUs, of which 46% were related to carbon processing and 644 were novel. These AMGs grouped into five functional categories and 11 subcategories, and nearly half (47%) of the AMGs were involved in carbon utilization. Of these, 112 vOTUs encoded 123 glycoside hydrolases spanning 15 types involved in the degradation of polysaccharides (e.g., cellulose) to monosaccharides (e.g., galactose), or further monosaccharide degradation, which suggests virus involvement in myriad metabolisms including fermentation and central carbon metabolism. These findings expand the scope of viral roles in microbial carbon processing and suggest viruses may be critical for understanding the fate of soil organic carbon in peatlands. 

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4. Chloroviruses

   https://doi.org/10.3390/v12010020  

   Van Etten, James L.; Agarkova, Irina V.; Dunigan, David D. (January 2020, Viruses)

   Chloroviruses are large dsDNA, plaque-forming viruses that infect certain chlorella-like green algae; the algae are normally mutualistic endosymbionts of protists and metazoans and are often referred to as zoochlorellae. The viruses are ubiquitous in inland aqueous environments throughout the world and occasionally single types reach titers of thousands of plaque-forming units per ml of native water. The viruses are icosahedral in shape with a spike structure located at one of the vertices. They contain an internal membrane that is required for infectivity. The viral genomes are 290 to 370 kb in size, which encode up to 16 tRNAs and 330 to ~415 proteins, including many not previously seen in viruses. Examples include genes encoding DNA restriction and modification enzymes, hyaluronan and chitin biosynthetic enzymes, polyamine biosynthetic enzymes, ion channel and transport proteins, and enzymes involved in the glycan synthesis of the virus major capsid glycoproteins. The proteins encoded by many of these viruses are often the smallest or among the smallest proteins of their class. Consequently, some of the viral proteins are the subject of intensive biochemical and structural investigation. 

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5. 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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