Article
Biochemistry & Molecular Biology
Juan-Vicente Bou, Rafael Sanjuan
Summary: This study conducted a directed evolution experiment using coxsackievirus B3 to investigate the genetic basis and evolvability of membrane-associated viral shedding. The results showed that specific mutations in the viral capsid protein VP3, such as substitution N63H, significantly altered the ratio of membrane-associated to free viral particles. These findings open new avenues for understanding the mechanisms and implications of membrane-associated viral transmission.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Wenli Zhang, Jiaqi Wang, Yuxin Liu, Kaizhen Chen, Huibin Li, Yulin Duan, Wenbin Wu, Yun Shi, Wei Guo
Summary: This paper presents a deep-learning-based orange counting algorithm using video sequences to improve fruit detection accuracy and reduce double-counting issues. The algorithm includes OrangeYolo for fruit detection and OrangeSort for fruit tracking, achieving higher accuracy than existing standards.
HORTICULTURE RESEARCH
(2022)
Article
Virology
Rachelle Bester, Glynnis Cook, Hans J. Maree
Summary: High-throughput sequencing (HTS) has been successfully applied for virus discovery in agricultural crops, providing insights into virus population structure and differentiation among virus variants contributing differently to disease etiology. This study developed a bioinformatic pipeline for CTV genotype detection, with a 50% genome coverage cut-off identified for non-target read mappings, validating it as a CTV genotyping assay.
Article
Plant Sciences
Jianqiang Lu, Ruifan Yang, Chaoran Yu, Jiahan Lin, Wadi Chen, Haiwei Wu, Xin Chen, Yubin Lan, Weixing Wang
Summary: This study proposes a citrus green fruit detection method based on improved Mask-RCNN, which can effectively improve the detection accuracy through deep learning technology and is of great significance for the intelligent production of citrus.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Virology
Eva Varallyay, Jaroslava Pribylova, Zsuzsanna Nagyne Galbacs, Almash Jahan, Tunde Varga, Josef Spak, Ondrej Lenz, Jana Franova, Jiri Sedlak, Igor Koloniuk
Summary: This study used high-throughput sequencing to identify the presence of apple hammerhead viroid, apple luteovirus 1, and citrus concave gum-associated virus in apple germplasm collections and production orchards in the Czech Republic and Hungary. Further investigations and validations confirmed the widespread presence of these pathogens, with ALV-1 and CCGaV being transmitted from rootstocks to scions. The study also found that the rosy apple aphid could potentially act as a vector for ALV-1.
Article
Virology
Rachelle Bester, Glynnis Cook, Johannes H. J. Breytenbach, Chanel Steyn, Rochelle De Bruyn, Hans J. Maree
Summary: This study assessed the impact of different HTS protocols on pathogen detection, showing significant differences between data sets based on extraction methods and sequencing platforms. Illumina data combined with de novo assembly accurately generated virus scaffolds compared to Ion Torrent data.
Article
Plant Sciences
Chellappan Padmanabhan, Schyler Nunziata, M. Guillermo Leon, Yazmin Rivera, Vessela A. Mavrodieva, Mark K. Nakhla, Avijit Roy
Summary: Citrus leprosis (CiL) is an emerging viral disease of citrus in the Americas caused by Brevipalpus-transmitted viruses. The genetic diversity of viruses associated with CiL makes detection and diagnosis challenging, leading to the use of High-Throughput Sequencing (HTS) protocols. In this study, the HTS assay was used to detect and identify cileviruses infecting different host plants, leading to the discovery of a new strain of CiLV-C2 in hibiscus. These findings are important for citrus industry and further investigation is needed to understand the movement of the new strain from hibiscus to citrus.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Sun-Jung Kwon, Sohrab Bodaghi, Tyler Dang, Kiran R. Gadhave, Thien Ho, Fatima Osman, Maher Al Rwahnih, Ioannis E. Tzanetakis, Anne E. Simon, Georgios Vidalakis
Summary: Citrus yellow-vein disease (CYVD) is caused by a virus-like agent named citrus yellow-vein associated virus (CYVaV). The CYVaV RNA genome codes for two open reading frames, with ORF2 encoding the RNA-dependent RNA polymerase. Phylogenetic analysis shows that CYVaV is closely related to unclassified virus-like RNAs in the family Tombusviridae.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Plant Sciences
Maria Minutolo, Maria Cinque, Michela Chiumenti, Francesco Di Serio, Daniela Alioto, Beatriz Navarro
Summary: CCGaV is a negative-stranded RNA virus that can be detected in citrus and apple trees. The development of an anti-CCGaV polyclonal antiserum has allowed for sensitive and reliable detection of the virus in DAS-ELISA, revealing its relationships with different hosts.
Article
Agronomy
Bo Gu, Changji Wen, Xuanzhi Liu, Yingjian Hou, Yuanhui Hu, Hengqiang Su
Summary: This paper proposes a citrus detection model YOLO-DCA suitable for complex citrus orchard environments, which has high detection accuracy and small model space occupation. It achieves good detection effect in occlusion, light transformation, and motion change scenes, and can help improve the intelligence level of citrus-picking robots.
Article
Plant Sciences
Rachelle Bester, Chanel Steyn, Johannes H. J. Breytenbach, Rochelle de Bruyn, Glynnis Cook, Hans J. Maree
Summary: The credibility of high-throughput sequencing (HTS) as a pathogen detection assay for citrus viruses was assessed in this study. The results showed that HTS has good reproducibility and sensitivity, and its detection capability is comparable or more sensitive than the standard RT-PCR assays.
Article
Biology
Johan Rollin, Wei Rong, Sebastien Massart
Summary: This article introduces a bioinformatics tool called Cont-ID, which can detect cross-contamination by analyzing the relative abundance and duplication of virus sequencing reads in sequence metagenomic datasets. By using 273 real datasets, including 68 virus species from different hosts and several library preparation protocols, the study demonstrates that Cont-ID can accurately classify viral species detection into true infection or contamination, with an accuracy rate of 91%. This classification increases confidence in the detection results and facilitates the downstream interpretation and confirmation by prioritizing the virus detections that should be confirmed.
Article
Chemistry, Analytical
Bryan Vivas Apacionado, Tofael Ahamed
Summary: This study successfully utilized a low-cost home surveillance camera and deep learning algorithms to monitor and detect sooty mold infection on citrus canopy at night, showing great potential for real-time orchard disease monitoring.
Article
Entomology
Fengnian Wu, Mochi Huang, Eduardo G. P. Fox, Jiaquan Huang, Yijing Cen, Xiaoling Deng, Meirong Xu
Summary: Citrus tristeza virus (CTV) is a significant viral pathogen of citrus trees transmitted by several aphid species. This study shows that the Asian citrus psyllid D. citri is capable of acquiring and transmitting CTV, potentially serving as a vector for two major citrus diseases, Huanglongbing (HLB) and Citrus tristeza. The persistence and transmission ability of CTV in D. citri varied among different host plant species, with no transmission observed to orange jasmine plants.
Article
Virology
Aderito Tomas Pais da Cunha, Michela Chiumenti, Laurindo Chambula Ladeira, Raied Abou Kubaa, Giuliana Loconsole, Vitantonio Pantaleo, Angelantonio Minafra
Summary: Controlling CTV in nurseries is crucial, early detection and characterization of virus strains can help prevent outbreaks. High-throughput sequencing revealed a wide array of CTV strains in citrus-growing spots in Angola, with similarities to severe strains in other regions.
Article
Biochemical Research Methods
Nandlal Choudhary, G. Wei, A. Govindarajulu, Avijit Roy, Wenbin Li, Deric D. Picton, M. K. Nakhla, L. Levy, R. H. Brlansky
JOURNAL OF VIROLOGICAL METHODS
(2015)
Article
Plant Sciences
Avijit Roy, Andrew L. Stone, Jonathan Shao, Gabriel Otero-Colina, Gang Wei, Nandlal Choudhary, Diann Achor, Laurene Levy, Mark K. Nakhla, John S. Hartung, William L. Schneider, Ronald H. Brlansky
Article
Biochemical Research Methods
Nandlal Choudhary, Avijit Roy, M. G. Leon, G. Wei, M. K. Nakhla, L. Levy, R. H. Brlansky
JOURNAL OF VIROLOGICAL METHODS
(2017)
Article
Biochemical Research Methods
Nandlal Choudhary, Avijit Roy, Leon M. Guillermo, D. D. Picton, G. Wei, M. K. Nakhla, L. Levy, R. H. Brlansky
JOURNAL OF VIROLOGICAL METHODS
(2013)
Article
Biochemical Research Methods
Nandlal Choudhary, Avijit Roy, A. Govindarajulu, M. K. Nakhla, L. Levy, R. H. Brlansky
JOURNAL OF VIROLOGICAL METHODS
(2014)
Article
Plant Sciences
G. Ananthakrishnan, N. Choudhary, Avijit Roy, V. G. Sengoda, E. Postnikova, J. S. Hartung, A. L. Stone, V. D. Damsteegt, W. L. Schneider, J. E. Munyaneza, R. H. Brlansky
Article
Plant Sciences
Avijit Roy, Nandlal Choudhary, John S. Hartung, R. H. Brlansky
Article
Computer Science, Information Systems
Chandrasen Pandey, Neeraj Baghel, Malay Kishore Dutta, Ashish Srivastava, Nandlal Choudhary
Summary: Viral infection in crops can lead to significant losses without known recovery methods. Early diagnosis of viral growth is challenging for farmers, but can be identified using automatic tools based on artificial intelligence.
MULTIMEDIA TOOLS AND APPLICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Damini Jaiswal, V. Kavi Sidharthan, Susheel Kumar Sharma, Richa Rai, Nandlal Choudhary, Amalendu Ghosh, Virendra Kumar Baranwal
Summary: The study investigated the gene circulation of citrus greening disease pathogen CLas in the Asian citrus psyllid ACP, revealing differential gene expression in response to CLas and potential targets for sustainable management of ACP and CLas.
Article
Ecology
Rakesh Chandra Joshi, Manoj Kaushik, Malay Kishore Dutta, Ashish Srivastava, Nandlal Choudhary
Summary: Various viral diseases adversely affect plant growth, leading to the need for automatic detection methods to monitor viral infections in crops. The proposed deep-learning-based method in this study is able to automatically detect viral infections in Vigna mungo, providing real-time classification on different categories of leaf images.
ECOLOGICAL INFORMATICS
(2021)
Review
Biotechnology & Applied Microbiology
Nandlal Choudhary, M. L. Lodha, V. K. Baranwal
Article
Entomology
Guillermo M. Leon, Avijit Roy, Nandlal Choudhary, Ronald Brlansky
REVISTA COLOMBIANA DE ENTOMOLOGIA
(2017)
Meeting Abstract
Plant Sciences
A. Roy, N. Choudhary, G. Otero-Colina, G. Wei, A. Stone, D. Achor, J. Shao, L. Levy, M. K. Nakhla, C. R. Hollingsworth, J. S. Hartung, W. Schneider, R. H. Brlansky
Article
Microbiology
Avijit Roy, Andrew Stone, Gabriel Otero-Colina, Gang Wei, Nandlal Choudhary, Diann Achor, Jonathan Shao, Laurene Levy, Mark K. Nakhla, Charla R. Hollingsworth, John S. Hartung, William L. Schneider, Ronald H. Brlansky
GENOME ANNOUNCEMENTS
(2013)