Recent Advances in Agricultural-Associated Viruses

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closed (1 December 2023)

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Topic Information

Dear Colleagues,

Agricultural-associated viruses include viruses that rely on plants, fungi, oomycetes, protozoa, bacteria, nemotodes, and insect vectors of host diseases, which play critical ecological roles in agricultural and environmental ecosystems and are associated with food security, environmental safety, and sustainable development in a globalizing world. This Topic welcomes a wide variety of articles regarding emerging and re-emerging viruses in agricultural and environmental ecosystems, the development of routine and molecular detection tools for viruses, mechanisms of vector transmission, host–virus interactions regarding genetic, molecular, biochemistry, and biophysic aspects, the molecular mechanism of antiviral innate immunity, strategies for the generation of virus-resistant crops using routine and latest plant genome editing techniques, ecological roles and potential applications of persistent viruses in plants, fungi, oomycetes, bacteria, nemotodes, and vectors of host diseases, epidemiology, the risk assessment and integrated management of viruses and their caused diseases, and the viral modification of host functions affecting interactions with vectors and other organisms.

Prof. Dr. Cheng-Gui Han
Prof. Dr. Liying Sun
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Bacteria bacteria	-	-	2022	15.0 days *	CHF 1000
Biology biology	4.2	4.0	2012	18.7 Days	CHF 2700
Journal of Fungi jof	4.7	4.9	2015	18.4 Days	CHF 2600
Pathogens pathogens	3.7	5.1	2012	16.4 Days	CHF 2700
Viruses viruses	4.7	7.1	2009	13.8 Days	CHF 2600

* Median value for all MDPI journals in the second half of 2023.

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Published Papers (5 papers)

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All Bacteria Biology JoF Pathogens Viruses

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13 pages, 15255 KiB  

Open AccessArticle

Deleting the C84L Gene from the Virulent African Swine Fever Virus SY18 Does Not Affect Its Replication in Porcine Primary Macrophages but Reduces Its Virulence in Swine

by Jinjin Yang, Rongnian Zhu, Yanyan Zhang, Xintao Zhou, Huixian Yue, Qixuan Li, Junnan Ke, Yu Wang, Faming Miao, Teng Chen, Fei Zhang, Shoufeng Zhang, Aidong Qian and Rongliang Hu

Pathogens 2024, 13(2), 103; https://doi.org/10.3390/pathogens13020103 - 24 Jan 2024

Cited by 1 | Viewed by 827

Abstract

(1) Background: African swine fever (ASF) is a highly contagious disease that causes high pig mortality. Due to the absence of vaccines, prevention and control are relatively challenging. The pathogenic African swine fever virus (ASFV) has a complex structure and encodes over 160 [...] Read more.

(1) Background: African swine fever (ASF) is a highly contagious disease that causes high pig mortality. Due to the absence of vaccines, prevention and control are relatively challenging. The pathogenic African swine fever virus (ASFV) has a complex structure and encodes over 160 proteins, many of which still need to be studied and verified for their functions. In this study, we identified one of the unknown functional genes, C84L. (2) Methods: A gene deficient strain was obtained through homologous recombination and several rounds of purification, and its replication characteristics and virulence were studied through in vitro and in vivo experiments, respectively. (3) Results: Deleting this gene from the wild-type virulent strain SY18 did not affect its replication in porcine primary macrophages but reduced its virulence in pigs. In animal experiments, we injected pigs with a 10² TCID₅₀, 10⁵ TCID₅₀ deletion virus, and a 10² TCID₅₀ wild-type strain SY18 intramuscularly. The control group pigs reached the humane endpoint on the ninth day (0/5) and were euthanized. Two pigs in the 10² TCID₅₀(2/5) deletion virus group survived on the twenty-first day, and one in the 10⁵ TCID₅₀(1/5) deletion virus group survived. On the twenty-first day, the surviving pigs were euthanized, which was the end of the experiment. The necropsies of the survival group and control groups’ necropsies showed that the surviving pigs’ liver, spleen, lungs, kidneys, and submaxillary lymph nodes did not show significant lesions associated with the ASFV. ASFV-specific antibodies were first detected on the seventh day after immunization; (4) Conclusions: This is the first study to complete the replication and virulence functional exploration of the C84L gene of SY18. In this study, C84L gene was preliminarily found not a necessary gene for replication, gene deletion strain SY18ΔC84L has similar growth characteristics to SY18 in porcine primary alveolar macrophages. The C84L gene affects the virulence of the SY18 strain. Full article

(This article belongs to the Topic Recent Advances in Agricultural-Associated Viruses)

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20 pages, 5884 KiB  

Open AccessArticle

Genome-Wide Analysis of Q-Type C2H2 ZFP Genes in Response to Biotic and Abiotic Stresses in Sugar Beet

by Menglin Li, Xuanyu Dong, Guozhang Long, Zongying Zhang, Chenggui Han and Ying Wang

Biology 2023, 12(10), 1309; https://doi.org/10.3390/biology12101309 - 04 Oct 2023

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Abstract

A plant’s Q-type C2H2-type ZFP plays key roles in plant growth and development and responses to biotic and abiotic stresses. Sugar beet (Beta vulgaris L.) is an important crop for sugar production. Salt stress and viral infection significantly reduce the root yield [...] Read more.

A plant’s Q-type C2H2-type ZFP plays key roles in plant growth and development and responses to biotic and abiotic stresses. Sugar beet (Beta vulgaris L.) is an important crop for sugar production. Salt stress and viral infection significantly reduce the root yield and sugar content of sugar beet. However, there is a lack of comprehensive genome-wide analyses of Q-type C2H2 ZFPs and their expression patterns in sugar beet under stress. In this study, 35 sugar beet Q-type C2H2 ZFPs (BvZFPs) containing at least one conserved “QALGGH” motif were identified via bioinformatics techniques using TBtools software. According to their evolutionary relationship, the BvZFPs were classified into five subclasses. Within each subclass, the physicochemical properties and motif compositions showed strong similarities. A Ka/Ks analysis indicated that the BvZFPs were conserved during evolution. Promoter cis-element analysis revealed that most BvZFPs are associated with elements related to phytohormone, biotic or abiotic stress, and plant development. The expression data showed that the BvZFPs in sugar beet are predominantly expressed in the root. In addition, BvZFPs are involved in the response to abiotic and biotic stresses, including salt stress and viral infection. Overall, these results will extend our understanding of the Q-type C2H2 gene family and provide valuable information for the biological breeding of sugar beet against abiotic and biotic stresses in the future. Full article

(This article belongs to the Topic Recent Advances in Agricultural-Associated Viruses)

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14 pages, 2170 KiB  

Open AccessArticle

A Longitudinal Cohort Study of Risk Factors Associated with Small Ruminant Lentivirus Seropositivity in Intensively Reared Dairy Ewes in Greece

by Aphrodite I. Kalogianni, Ilias Bouzalas, Ioannis Bossis and Athanasios I. Gelasakis

Pathogens 2023, 12(10), 1200; https://doi.org/10.3390/pathogens12101200 - 27 Sep 2023

Cited by 2 | Viewed by 669

Abstract

A two-year longitudinal cohort study was conducted on a total of 407 purebred Chios and Lacaune ewes from four intensive dairy sheep farms to assess potential risk factors for small ruminant lentiviruses (SRLVs) seropositivity. Ewes were serologically tested semiannually at pre-mating and pre-lambing, [...] Read more.

A two-year longitudinal cohort study was conducted on a total of 407 purebred Chios and Lacaune ewes from four intensive dairy sheep farms to assess potential risk factors for small ruminant lentiviruses (SRLVs) seropositivity. Ewes were serologically tested semiannually at pre-mating and pre-lambing, and their age, breed, and body condition score (BCS) were recorded. Εwes were categorized as constantly seronegative, constantly seropositive, seroconverted, seroreverted, or animals with an intermittent presence of antibodies. Mixed binary logistic regression models were used to estimate the adjusted relative risks of the studied risk factors for (i) the individual ewes’ seropositivity, (ii) the manifestation of specific serological patterns, and (iii) the occurrence of seroconversion and seroreversion incidents. Increased age was associated with seropositivity and constantly seropositive status (p < 0.001 in both cases). On the other hand, age was negatively associated with constantly seronegative pattern, seroconversion incident, and the intermittent presence of antibodies (p < 0.05 in all cases). Moreover, breed was recognized as a risk factor: Lacaune ewes demonstrated increased seropositivity, whereas Chios ewes were more likely to demonstrate an intermittent presence of antibodies (p < 0.01 in both cases). Seropositive status (p < 0.001), seropositivity in animals with an intermittent presence of antibodies (p = 0.001), and seroconversion incidents (p < 0.001) were significantly increased at pre-lambing compared to pre-mating. The risk factors recognized in our study contribute to a better understanding of SRLVs epidemiology and the evidence-based designation of SRLVs’ control programs in intensive dairy sheep farms in Greece. Full article

(This article belongs to the Topic Recent Advances in Agricultural-Associated Viruses)

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18 pages, 2999 KiB  

Open AccessArticle

In Silico Virome Analysis of Chinese Narcissus Transcriptomes Reveals Diverse Virus Species and Genetic Diversity at Different Flower Development Stages

by Hoseong Choi, Yeonhwa Jo and Won Kyong Cho

Biology 2023, 12(8), 1094; https://doi.org/10.3390/biology12081094 - 05 Aug 2023

Cited by 2 | Viewed by 1174

Abstract

Viromes of Chinese narcissus flowers were explored using transcriptome data from 20 samples collected at different flower development stages. Quality controlled raw data underwent de novo assembly, resulting in 5893 viral contigs that matched the seven virus species. The most abundant viruses were [...] Read more.

Viromes of Chinese narcissus flowers were explored using transcriptome data from 20 samples collected at different flower development stages. Quality controlled raw data underwent de novo assembly, resulting in 5893 viral contigs that matched the seven virus species. The most abundant viruses were narcissus common latent virus (NCLV), narcissus yellow stripe virus (NYSV), and narcissus mottling-associated virus (NMaV). As flower development stages advanced, white tepal plants showed an increase in the proportion of viral reads, while the variation in viral proportion among yellow tepal plants was relatively small. Narcissus degeneration virus (NDV) dominated the white tepal samples, whereas NDV and NYSV prevailed in the yellow tepal samples. Potyviruses, particularly NDV, are the primary infectious viruses. De novo assembly generated viral contigs for five viruses, yielding complete genomes for NCLV, NDV, narcissus late season yellow virus (NLSYV), and NYSV. Phylogenetic analysis revealed genetic diversity, with distinct NCLV, NMaV, NDV, NLSYV, and NYSV groups. This study provides valuable insights into the viromes and genetic diversity of viruses in Chinese narcissus flowers. Full article

(This article belongs to the Topic Recent Advances in Agricultural-Associated Viruses)

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17 pages, 2263 KiB  

Open AccessArticle

Transcriptomic and Proteomic Analyses of Myzus persicae Carrying Brassica Yellows Virus

by Meng-Jun He, Deng-Pan Zuo, Zong-Ying Zhang, Ying Wang and Cheng-Gui Han

Biology 2023, 12(7), 908; https://doi.org/10.3390/biology12070908 - 25 Jun 2023

Viewed by 1114

Abstract

Viruses in the genus Polerovirus infect a wide range of crop plants and cause severe economic crop losses. BrYV belongs to the genus Polerovirus and is transmitted by Myzus persicae. However, the changes in transcriptome and proteome profiles of M. persicae during [...] Read more.

Viruses in the genus Polerovirus infect a wide range of crop plants and cause severe economic crop losses. BrYV belongs to the genus Polerovirus and is transmitted by Myzus persicae. However, the changes in transcriptome and proteome profiles of M. persicae during viral infection are unclear. Here, RNA-Seq and TMT-based quantitative proteomic analysis were performed to compare the differences between viruliferous and nonviruliferous aphids. In total, 1266 DEGs were identified at the level of transcription with 980 DEGs being upregulated and 286 downregulated in viruliferous aphids. At the protein level, among the 18 DEPs identified, the number of upregulated proteins in viruliferous aphids was twice that of the downregulated DEPs. Enrichment analysis indicated that these DEGs and DEPs were mainly involved in epidermal protein synthesis, phosphorylation, and various metabolic processes. Interestingly, the expressions of a number of cuticle proteins and tubulins were upregulated in viruliferous aphids. Taken together, our study revealed the complex regulatory network between BrYV and its vector M. persicae from the perspective of omics. These findings should be of great benefit to screening key factors involved in the process of virus circulation in aphids and provide new insights for BrYV prevention via vector control in the field. Full article

(This article belongs to the Topic Recent Advances in Agricultural-Associated Viruses)

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