Genetic Diversity and Population Structure of the Xanthomonas campestris pv. campestris Strains Affecting Cabbages in China Revealed by MLST and Rep-PCR Based Genotyping

<i>Xanthomonas campestris</i> pv. <i>campestris</i> (<i>Xcc</i>) is the causal agent of black rot for cruciferous vegetables worldwide, especially for the cole crops such as cabbage and cauliflower. Due to the lack of resistant cabbage cultivars, black rot has brought about considerable yield losses in recent years in China. Understanding of the pathogen features is a key step for disease prevention, however, the pathogen diversity, population structure, and virulence are largely unknown. In this study, we studied 50 <i>Xcc</i> strains including 39 <i>Xcc</i> isolates collected from cabbage in 20 regions across China, using multilocus sequence genotyping (MLST), repetitive DNA sequence-based PCR (rep-PCR), and pathogenicity tests. For MLST analysis, a total of 12 allelic profiles (AP) were generated, among which the largest AP was AP1 containing 32 strains. Further cluster analysis of rep-PCR divided all strains into 14 DNA groups, with the largest group DNA I comprising of 34 strains, most of which also belonged to AP1. Inoculation tests showed that the representative <i>Xcc</i> strains collected from diverse regions performed differential virulence against three brassica hosts compared with races 1 and 4. Interestingly, these results indicated that AP1/DNA I was not only the main pathotype in China, but also a novel group that differed from the previously reported type races in both genotype and virulence. To our knowledge, this is the first extensive genetic diversity survey for <i>Xcc</i> strains in China, which provides evidence for cabbage resistance breeding and opens the gate for further cabbage-<i>Xcc</i> interaction studies.

Patterns of Exposure and Infection with Microparasites in Iberian Wild Carnivores: A Review and Meta-Analysis

We use a suite of meta-analytic and comparative methods to derive fundamental insights into how sampling effort, pathogen richness, infection prevalence, and seroprevalence vary across Carnivora taxa and Iberian geography. The red fox was the most studied species, the wolf and Iberian lynx were disproportionally studied, and the Arctoidea were understudied. Sampling effort was higher in Mediterranean areas, but central Spain showed the higher pathogen richness. Excluding studies analyzing fecal samples, 53 different pathogens have been detected in Iberian carnivores, including 16 viruses, 27 bacteria, and 10 protozoa but no fungi. Sampling effort and pathogen diversity were generally more similar among closely related carnivore species. Seropositivity to viruses was lower and higher in the Mustelinae and the Canidae, respectively, and seropositivity to protozoa was higher in both taxa. Canine distemper virus exposure was greatest in canids and mustelids. Carnivore protoparvovirus-1 exposure was greatest in the Atlantic regions, and the Felidae and the Musteloidea had lower infection prevalence. A subclade of the Mustelidae had a greater prevalence of Leishmania infection. We observed no relationships between host phylogenetic distance and pathogen sharing among species. Lastly, we identify important research pitfalls and future directions to improve the study of infectious disease in Iberian wild carnivore communities.

Detection of Cacao Mild Mosaic Virus (CaMMV) Using Nested PCR and Evidence of Uneven Distribution in Leaf Tissue

Distribution of improved germplasm of Theobroma cacao is essential for meeting the increased demand for cocoa beans. In cacao, the introduction of new diseases is prevented by exchanging material through a national and international quarantine system. In 2020, virus symptoms were observed on plants in a quarantine greenhouse, and Cacao mild mosaic virus (CaMMV) was detected in one plant using published diagnostic primers. However, no virus was detected in other symptomatic plants. To address high pathogen diversity and low virus titer in recently infected plants, a nested PCR test was developed based on 15 CaMMV sequences from Trinidad and Puerto Rico. The test was validated on a subset (n = 30) of plants in the greenhouse, of which 29 tested positive. Most infections are thought to have occurred during the later stage of the quarantine period, possibly due to spread by mealybugs. However, phylogenetic analysis revealed the presence of three strains, suggesting that it was introduced on scionwood from multiple sources. Results of PCR assays on different leaf tissues indicate that the virus is unevenly distributed and that petiole tissue should be used in molecular diagnostics. The movement of infected scionwood is a major dissemination pathway for CaMMV but can be managed through careful screening.

PopCover-2.0. Improved Selection of Peptide Sets With Optimal HLA and Pathogen Diversity Coverage

The use of minimal peptide sets offers an appealing alternative for design of vaccines and T cell diagnostics compared to conventional whole protein approaches. T cell immunogenicity towards peptides is contingent on binding to human leukocyte antigen (HLA) molecules of the given individual. HLA is highly polymorphic, and each variant typically presents a different repertoire of peptides. This polymorphism combined with pathogen diversity challenges the rational selection of peptide sets with broad immunogenic potential and population coverage. Here we propose PopCover-2.0, a simple yet highly effective method, for resolving this challenge. The method takes as input a set of (predicted) CD8 and/or CD4 T cell epitopes with associated HLA restriction and pathogen strain annotation together with information on HLA allele frequencies, and identifies peptide sets with optimal pathogen and HLA (class I and II) coverage. PopCover-2.0 was benchmarked on historic data in the context of HIV and SARS-CoV-2. Further, the immunogenicity of the selected SARS-CoV-2 peptides was confirmed by experimentally validating the peptide pools for T cell responses in a panel of SARS-CoV-2 infected individuals. In summary, PopCover-2.0 is an effective method for rational selection of peptide subsets with broad HLA and pathogen coverage. The tool is available at https://services.healthtech.dtu.dk/service.php?PopCover-2.0.

Direct and indirect viral associations predict coexistence in wild plant virus communities

Integration of community ecology with disease biology is viewed as a promising avenue for uncovering determinants of pathogen diversity, and for predicting disease risks. Plant-infecting viruses represent a vastly underestimated component of biodiversity with potentially important ecological and evolutionary roles. We performed hierarchal spatial analysis of wild plant populations to characterise the diversity and coexistence structure of within-host virus communities, and their predictors. Our results show that these virus communities are characterised by single infections of few, dominating virus taxa as well as diverse, non-random coinfections. Using a novel graphical modelling framework we demonstrate that after accounting for environmental heterogeneity at the level of both individual host plants and populations, most virus co-occurrence patterns can be attributed to virus-virus associations. Moreover, we show that conditioning variables changed virus association networks especially through their indirect effects. This highlights a previously underestimated mechanism of how human-driven environmental change can influence disease risks.

Phony peach disease: past and present impact on the peach industry in the southeastern U.S.A

Background Phony peach disease (PPD) is caused by the plant pathogenic bacterium Xylella fastidiosa subsp. multiplex (Xfm). Historically, the disease has caused severe yield loss in Georgia and elsewhere in the southeastern United States, with millions of PPD trees being removed from peach orchards over the last century. The disease remains a production constraint, and management options are few. Limited research has been conducted on PPD since the 1980s, but the advent of new technologies offers the opportunity for new, foundational research to form a basis for informed management of PPD in the U.S. Furthermore, considering the global threat of Xylella to many plant species, preventing import of Xfm to other regions, particularly where peach is grown, should be considered an important phytosanitary endeavor. Main topics We review PPD, its history and impact on peach production, and the eradication efforts that were conducted for 42 years. Additionally, we review the current knowledge of the pathogen, Xfm, and how that knowledge relates to our understanding of the peach—Xylella pathosystem, including the epidemiology of the disease and consideration of the vectors. Methods used to detect the pathogen in peach are discussed, and ramifications of detection in relation to management and control of PPD are considered. Control options for PPD are limited. Our current knowledge of the pathogen diversity and disease epidemiology are described, and based on this, some potential areas for future research are also considered. Conclusion There is a lack of recent foundational research on PPD and the associated strain of Xfm. More research is needed to reduce the impact of this pathogen on peach production in the southeastern U.S., and, should it spread internationally, wherever peaches are grown.

Diversity of Botryosphaeriaceae species associated with Chinese hickory tree (Carya cathayensis) trunk cankers

Tree trunk cankers (TRC) represent serious fungal diseases that pose significant threats to Chinese hickory trees (Carya cathayensis). To characterize the pathogen diversity associated with, diseased tissues were collected between 2016 and 2018 from the primary Chinese hickory plantation regions. A total of 97 cultures were isolated from trees in six towns (Longgang, Qingliangfeng, Changhua, Tuankou, Taiyang Town, and Lin’an urban area) within the Linan district, where 60% of Chinese hickory tree yields originate. The isolated cultures caused cankers on Chinese hickory tree branches, but infections did not occur on fruits or leaves under tested conditions. Combined morphological observations and phylogenetic analysis of multiple genes (ITS, β-tublin, and EF) indicated that five Botryosphaeriaceae species were recovered, including 89 isolates of Botryosphaeria dothidea, four isolates of B. fabicerciana, one isolate of B. qingyuanensis, one isolate of B. corticis, and two isolates of Lasiodiplodia theobromae. B. dothidea was the most prevalent, and this is the first report of B. corticis, B. qingyuanensis, and L. theobromae infections in Chinese hickory trees. We investigated the mycelial growth, spore germination, and pathogenicity of these species at different temperatures. L. theobromae grew the fastest and B. cortices grew the slowest on PDA. The optimum temperature of spore germination for all species was 30°C. L. theobromae was the most virulent species, followed by B. dothidea and B. qingyuanensis, then B. fabicerciana, and finally B. cortices. These new insights into fungal pathogen diversity provide critical new information to understand and manage TRC of Chinese hickory.