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Bilder CR, Hitt BD, Biggerstaff BJ, Tebbs JM, McMahan CS. binGroup2: Statistical Tools for Infection Identification via Group Testing. THE R JOURNAL 2023; 15:21-36. [PMID: 38818016 PMCID: PMC11139028 DOI: 10.32614/rj-2023-081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Group testing is the process of testing items as an amalgamation, rather than separately, to determine the binary status for each item. Its use was especially important during the COVID-19 pandemic through testing specimens for SARS-CoV-2. The adoption of group testing for this and many other applications is because members of a negative testing group can be declared negative with potentially only one test. This subsequently leads to significant increases in laboratory testing capacity. Whenever a group testing algorithm is put into practice, it is critical for laboratories to understand the algorithm's operating characteristics, such as the expected number of tests. Our paper presents the binGroup2 package that provides the statistical tools for this purpose. This R package is the first to address the identification aspect of group testing for a wide variety of algorithms. We illustrate its use through COVID-19 and chlamydia/gonorrhea applications of group testing.
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Affiliation(s)
- Christopher R Bilder
- University of Nebraska-Lincoln, Department of Statistics, Lincoln, NE 68583, USA
| | - Brianna D Hitt
- United States Air Force Academy, Department of Mathematical Sciences, Colorado Springs, CO 80840, USA
| | - Brad J Biggerstaff
- Centers for Disease Control and Prevention, Division of Vector-Borne Diseases, Fort Collins, CO 80521, USA
| | - Joshua M Tebbs
- University of South Carolina, Department of Statistics, Columbia, SC 29208, USA
| | - Christopher S McMahan
- Clemson University, School of Mathematical and Statistical Sciences, Clemson, SC 29634, USA
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Jeger M, Hamelin F, Cunniffe N. Emerging Themes and Approaches in Plant Virus Epidemiology. PHYTOPATHOLOGY 2023; 113:1630-1646. [PMID: 36647183 DOI: 10.1094/phyto-10-22-0378-v] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Plant diseases caused by viruses share many common features with those caused by other pathogen taxa in terms of the host-pathogen interaction, but there are also distinctive features in epidemiology, most apparent where transmission is by vectors. Consequently, the host-virus-vector-environment interaction presents a continuing challenge in attempts to understand and predict the course of plant virus epidemics. Theoretical concepts, based on the underlying biology, can be expressed in mathematical models and tested through quantitative assessments of epidemics in the field; this remains a goal in understanding why plant virus epidemics occur and how they can be controlled. To this end, this review identifies recent emerging themes and approaches to fill in knowledge gaps in plant virus epidemiology. We review quantitative work on the impact of climatic fluctuations and change on plants, viruses, and vectors under different scenarios where impacts on the individual components of the plant-virus-vector interaction may vary disproportionately; there is a continuing, sometimes discordant, debate on host resistance and tolerance as plant defense mechanisms, including aspects of farmer behavior and attitudes toward disease management that may affect deployment in crops; disentangling host-virus-vector-environment interactions, as these contribute to temporal and spatial disease progress in field populations; computational techniques for estimating epidemiological parameters from field observations; and the use of optimal control analysis to assess disease control options. We end by proposing new challenges and questions in plant virus epidemiology.
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Affiliation(s)
- Mike Jeger
- Department of Life Sciences, Imperial College London, Silwood Park, U.K
| | - Fred Hamelin
- IGEPP INRAE, University of Rennes, Rennes, France
| | - Nik Cunniffe
- Department of Plant Sciences, University of Cambridge, Cambridge, U.K
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Catto MA, Labadie PE, Jacobson AL, Kennedy GG, Srinivasan R, Hunt BG. Pest status, molecular evolution, and epigenetic factors derived from the genome assembly of Frankliniella fusca, a thysanopteran phytovirus vector. BMC Genomics 2023; 24:343. [PMID: 37344773 DOI: 10.1186/s12864-023-09375-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 05/13/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND The tobacco thrips (Frankliniella fusca Hinds; family Thripidae; order Thysanoptera) is an important pest that can transmit viruses such as the tomato spotted wilt orthotospovirus to numerous economically important agricultural row crops and vegetables. The structural and functional genomics within the order Thysanoptera has only begun to be explored. Within the > 7000 known thysanopteran species, the melon thrips (Thrips palmi Karny) and the western flower thrips (Frankliniella occidentalis Pergrande) are the only two thysanopteran species with assembled genomes. RESULTS A genome of F. fusca was assembled by long-read sequencing of DNA from an inbred line. The final assembly size was 370 Mb with a single copy ortholog completeness of ~ 99% with respect to Insecta. The annotated genome of F. fusca was compared with the genome of its congener, F. occidentalis. Results revealed many instances of lineage-specific differences in gene content. Analyses of sequence divergence between the two Frankliniella species' genomes revealed substitution patterns consistent with positive selection in ~ 5% of the protein-coding genes with 1:1 orthologs. Further, gene content related to its pest status, such as xenobiotic detoxification and response to an ambisense-tripartite RNA virus (orthotospovirus) infection was compared with F. occidentalis. Several F. fusca genes related to virus infection possessed signatures of positive selection. Estimation of CpG depletion, a mutational consequence of DNA methylation, revealed that F. fusca genes that were downregulated and alternatively spliced in response to virus infection were preferentially targeted by DNA methylation. As in many other insects, DNA methylation was enriched in exons in Frankliniella, but gene copies with homology to DNA methyltransferase 3 were numerous and fragmented. This phenomenon seems to be relatively unique to thrips among other insect groups. CONCLUSIONS The F. fusca genome assembly provides an important resource for comparative genomic analyses of thysanopterans. This genomic foundation allows for insights into molecular evolution, gene regulation, and loci important to agricultural pest status.
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Affiliation(s)
- Michael A Catto
- Department of Entomology, University of Georgia, Athens, GA, 30602, USA
| | - Paul E Labadie
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Alana L Jacobson
- Department of Entomology and Plant Pathology, Auburn University College of Agriculture, Auburn, AL, 36849, USA
| | - George G Kennedy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Brendan G Hunt
- Department of Entomology, University of Georgia, Griffin, GA, 30223, USA.
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Vector acquisition and co-inoculation of two plant viruses influences transmission, infection, and replication in new hosts. Sci Rep 2022; 12:20355. [PMID: 36437281 PMCID: PMC9701672 DOI: 10.1038/s41598-022-24880-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 11/22/2022] [Indexed: 11/28/2022] Open
Abstract
This study investigated the role of vector acquisition and transmission on the propagation of single and co-infections of tomato yellow leaf curl virus (TYLCV,) and tomato mottle virus (ToMoV) (Family: Geminiviridae, Genus: Begomovirus) by the whitefly vector Bemisia tabaci MEAM1 (Gennadius) in tomato. The aim of this research was to determine if the manner in which viruses are co-acquired and co-transmitted changes the probability of acquisition, transmission and new host infections. Whiteflies acquired virus by feeding on singly infected plants, co-infected plants, or by sequential feeding on singly infected plants. Viral titers were also quantified by qPCR in vector cohorts, in artificial diet, and plants after exposure to viruliferous vectors. Differences in transmission, infection status of plants, and titers of TYLCV and ToMoV were observed among treatments. All vector cohorts acquired both viruses, but co-acquisition/co-inoculation generally reduced transmission of both viruses as single and mixed infections. Co-inoculation of viruses by the vector also altered virus accumulation in plants regardless of whether one or both viruses were propagated in new hosts. These findings highlight the complex nature of vector-virus-plant interactions that influence the spread and replication of viruses as single and co-infections.
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Determinants of Virus Variation, Evolution, and Host Adaptation. Pathogens 2022; 11:pathogens11091039. [PMID: 36145471 PMCID: PMC9501407 DOI: 10.3390/pathogens11091039] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Virus evolution is the change in the genetic structure of a viral population over time and results in the emergence of new viral variants, strains, and species with novel biological properties, including adaptation to new hosts. There are host, vector, environmental, and viral factors that contribute to virus evolution. To achieve or fine tune compatibility and successfully establish infection, viruses adapt to a particular host species or to a group of species. However, some viruses are better able to adapt to diverse hosts, vectors, and environments. Viruses generate genetic diversity through mutation, reassortment, and recombination. Plant viruses are exposed to genetic drift and selection pressures by host and vector factors, and random variants or those with a competitive advantage are fixed in the population and mediate the emergence of new viral strains or species with novel biological properties. This process creates a footprint in the virus genome evident as the preferential accumulation of substitutions, insertions, or deletions in areas of the genome that function as determinants of host adaptation. Here, with respect to plant viruses, we review the current understanding of the sources of variation, the effect of selection, and its role in virus evolution and host adaptation.
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Chen Y, Liu Y, Wang L, Li H, Linghu T, Chen Y, Tian H, Lin S, Zheng X, Wei H. The Infection Route of Tomato Zonate Spot Virus in the Digestive System of Its Insect Vector Frankliniella occidentalis. Front Microbiol 2022; 13:911751. [PMID: 35836419 PMCID: PMC9274000 DOI: 10.3389/fmicb.2022.911751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
Tomato zonate spot virus (TZSV) is a phytopathogen of the genus Orthotospovirus (Bunyaviridae) that is widespread in many areas of Southwest China. TZSV is mainly transmitted by Frankliniella occidentalis, but its exact infection route remains unclear. To explore this issue, we detected the nucleocapsid protein of TZSV in the digestive systems of first-instar F. occidentalis nymphs fed with TZSV-infected pepper leaves. TZSV infection in the F. occidentalis digestive system begins within 4 h post-first access to diseased plants: The foregut is likely the primary site of infection, and primary salivary glands (PSGs) are the destination. There are three potential routes for TZSV transmission from the alimentary canal to the PSGs: (1) virus dissemination from the midgut to hemocoel followed by movement to the PSGs; (2) accumulation in midgut epithelial cells and arrival at PSGs via tubular salivary glands and efferent ducts; and (3) arrival at epitheliomuscular cells of the forepart of the midgut and movement along the ligament to the PSGs. We tested the transmission efficiency of F. occidentalis in second-instar nymphs and female and male adults. TZSV was transmitted in a persistent-propagative mode by both nymphs and adults, with adults appearing to show slightly higher transmission efficiency than nymphs. We confirmed the presence of all three routes for TZSV transmission in F. occidentalis and determined that like other Orthotospoviruses, TZSV is transmitted in a persistent-propagative manner. These results should facilitate the control of TZSV-related diseases and further our understanding of the transmission biology of Orthotospoviruses in general.
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Affiliation(s)
- Yong Chen
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of Ministry of Agriculture, Fujian Engineering Research Center for Green Pest Management, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuyan Liu
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of Ministry of Agriculture, Fujian Engineering Research Center for Green Pest Management, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Liang Wang
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of Ministry of Agriculture, Fujian Engineering Research Center for Green Pest Management, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Heng Li
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of Ministry of Agriculture, Fujian Engineering Research Center for Green Pest Management, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Tingting Linghu
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of Ministry of Agriculture, Fujian Engineering Research Center for Green Pest Management, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yixin Chen
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of Ministry of Agriculture, Fujian Engineering Research Center for Green Pest Management, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Houjun Tian
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of Ministry of Agriculture, Fujian Engineering Research Center for Green Pest Management, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Shuo Lin
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of Ministry of Agriculture, Fujian Engineering Research Center for Green Pest Management, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xue Zheng
- Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Hui Wei
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou Scientific Observing and Experimental Station of Crop Pests of Ministry of Agriculture, Fujian Engineering Research Center for Green Pest Management, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Hui Wei,
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