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1. Bioconjugation Strategies for Tobacco Mild Green Mosaic Virus

   https://doi.org/10.1002/cbic.202200323  

   González‐Gamboa, Ivonne; Caparco, Adam A.; McCaskill, Justin M.; Steinmetz, Nicole F. (September 2022, ChemBioChem)
2. CRISPR/Cas9-mediated resistance to cauliflower mosaic virus

   https://doi.org/10.1002/pld3.47  

   Liu, Haijie; Soyars, Cara L.; Li, Jianhui; Fei, Qili; He, Guijuan; Peterson, Brenda A.; Meyers, Blake C.; Nimchuk, Zachary L.; Wang, Xiaofeng (March 2018, Plant Direct)
3. Opium Poppy Mosaic Virus Has an Xrn-Resistant, Translated Subgenomic RNA and a BTE 3′ CITE

   https://doi.org/10.1128/JVI.02109-20  

   Ilyas, Muhammad; Du, Zhiyou; Simon, Anne E. (April 2021, Journal of Virology)

   Dutch, Rebecca Ellis. (Ed.)

   ABSTRACT Opium poppy mosaic virus (OPMV) is a recently discovered umbravirus in the family Tombusviridae . OPMV has a plus-sense genomic RNA (gRNA) of 4,241 nucleotides (nt) from which replication protein p35 and p35 extension product p98, the RNA-dependent RNA polymerase (RdRp), are expressed. Movement proteins p27 (long distance) and p28 (cell to cell) are expressed from a 1,440-nt subgenomic RNA (sgRNA2). A highly conserved structure was identified just upstream from the sgRNA2 transcription start site in all umbraviruses, which includes a carmovirus consensus sequence, denoting generation by an RdRp-mediated mechanism. OPMV also has a second sgRNA of 1,554 nt (sgRNA1) that starts just downstream of a canonical exoribonuclease-resistant sequence (xrRNA D ). sgRNA1 codes for a 30-kDa protein in vitro that is in frame with p28 and cannot be synthesized in other umbraviruses. Eliminating sgRNA1 or truncating the p30 open reading frame (ORF) without affecting p28 substantially reduced accumulation of OPMV gRNA, suggesting a functional role for the protein. The 652-nt 3′ untranslated region of OPMV contains two 3′ cap-independent translation enhancers (3′ CITEs), a T-shaped structure (TSS) near its 3′ end, and a Barley yellow dwarf virus -like translation element (BTE) in the central region. Only the BTE is functional in luciferase reporter constructs containing gRNA or sgRNA2 5′ sequences in vivo , which differs from how umbravirus 3′ CITEs were used in a previous study. Similarly to most 3′ CITEs, the OPMV BTE links to the 5′ end via a long-distance RNA-RNA interaction. Analysis of 14 BTEs revealed additional conserved sequences and structural features beyond the previously identified 17-nt conserved sequence. IMPORTANCE Opium poppy mosaic virus (OPMV) is an umbravirus in the family Tombusviridae . We determined that OPMV accumulates two similarly sized subgenomic RNAs (sgRNAs), with the smaller known to code for proteins expressed from overlapping open reading frames. The slightly larger sgRNA1 has a 5′ end just upstream from a previously predicted xrRNA D site, identifying this sgRNA as an unusually long product produced by exoribonuclease trimming. Although four umbraviruses have similar predicted xrRNA D sites, only sgRNA1 of OPMV can code for a protein that is an extension product of umbravirus ORF4. Inability to generate the sgRNA or translate this protein was associated with reduced gRNA accumulation in vivo . We also characterized the OPMV BTE structure, a 3′ cap-independent translation enhancer (3′ CITE). Comparisons of 13 BTEs with the OPMV BTE revealed additional stretches of sequence similarity beyond the 17-nt signature sequence, as well as conserved structural features not previously recognized in these 3′ CITEs. 

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4. Engineering Tobacco Mosaic Virus and Its Virus‐Like‐Particles for Synthesis of Biotemplated Nanomaterials

   https://doi.org/10.1002/biot.202000311  

   Lee, Kok_Zhi; Basnayake_Pussepitiyalage, Vindula; Lee, Yu‐Hsuan; Loesch‐Fries, L_Sue; Harris, Michael_T; Hemmati, Shohreh; Solomon, Kevin_V (November 2020, Biotechnology Journal)

   Abstract Biomolecules are increasingly attractive templates for the synthesis of functional nanomaterials. Chief among them is the plant tobacco mosaic virus (TMV) due to its high aspect ratio, narrow size distribution, diverse biochemical functionalities presented on the surface, and compatibility with a number of chemical conjugations. These properties are also easily manipulated by genetic modification to enable the synthesis of a range of metallic and non‐metallic nanomaterials for diverse applications. This article reviews the characteristics of TMV and related viruses, and their virus‐like particle (VLP) derivatives, and how these may be manipulated to extend their use and function. A focus of recent efforts has been on greater understanding and control of the self‐assembly processes that drive biotemplate formation. How these features have been exploited in engineering applications such as, sensing, catalysis, and energy storage are briefly outlined. While control of VLP surface features is well‐established, fewer tools exist to control VLP self‐assembly, which limits efforts to control template uniformity and synthesis of certain templated nanomaterials. However, emerging advances in synthetic biology, machine learning, and other fields promise to accelerate efforts to control template uniformity and nanomaterial synthesis enabling more widescale industrial use of VLP‐based biotemplates. 

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5. Sugarcane Mosaic Virus Detection in Maize Using UAS Multispectral Imagery

   https://doi.org/10.3390/rs16173296  

   Bevers, Noah; Ohlson, Erik W; KC, Kushal; Jones, Mark W; Khanal, Sami (September 2024, Remote Sensing)

   One of the most important and widespread corn/maize virus diseases is maize dwarf mosaic (MDM), which can be induced by sugarcane mosaic virus (SCMV). This study explores a machine learning analysis of five-band multispectral imagery collected via an unmanned aerial system (UAS) during the 2021 and 2022 seasons for SCMV disease detection in corn fields. The three primary objectives are to (i) determine the spectral bands and vegetation indices that are most important or correlated with SCMV infection in corn, (ii) compare spectral signatures of mock-inoculated and SCMV-inoculated plants, and (iii) compare the performance of four machine learning algorithms, including ridge regression, support vector machine (SVM), random forest, and XGBoost, in predicting SCMV during early and late stages in corn. On average, SCMV-inoculated plants had higher reflectance values for blue, green, red, and red-edge bands and lower reflectance for near-infrared as compared to mock-inoculated samples. Across both years, the XGBoost regression model performed best for predicting disease incidence percentage (R2 = 0.29, RMSE = 29.26), and SVM classification performed best for the binary prediction of SCMV-inoculated vs. mock-inoculated samples (72.9% accuracy). Generally, model performances appeared to increase as the season progressed into August and September. According to Shapley additive explanations (SHAP analysis) of the top performing models, the simplified canopy chlorophyll content index (SCCCI) and saturation index (SI) were the vegetation indices that consistently had the strongest impacts on model behavior for SCMV disease regression and classification prediction. The findings of this study demonstrate the potential for the development of UAS image-based tools for farmers, aiming to facilitate the precise identification and mapping of SCMV infection in corn. 

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