Search Results (7)

Apple viruses pose significant threat to global apple production. In this study, HTS technology was used to investigate the apple virome in the Czech Republic. Previously reported viruses, including ACLSV, ASPV, ASGV, ApMV, AGCaV, and CCGaV, were confirmed, and near-complete genomes were assembled. Additionally, two novel viruses, ARWV1 and ARWV2 were identified for the first time in the Czech Republic. Phylogenetic analyses showed low genetic variability among ARWV2 isolates, suggesting a possible recent introduction or limited diversification. In contrast, ARWV1 isolates displayed distinct clustering in the coat protein coding region, separating symptomatic and asymptomatic samples, indicating a potential involvement of genetic determinants in symptom expression. Mixed infections were prevalent, with multiple molecular variants of ACLSV, ASPV, and AGCaV detected within individual samples, along with co-infections involving viruses from different families. Recombination analysis identified frequent recombination events in ACLSV and ASPV, often involving non-apple parental sequences, suggesting their potential for cross-host infections. Additionally, an interspecific recombination event was detected in an almond ApMV isolate, with PNRSV as a minor parent. These findings highlight the impact of agricultural practices on viral evolution and host adaptation. This study demonstrates the utility of HTS as a powerful tool for uncovering viral diversity, recombination events, and evolutionary dynamics. Full article

In this paper, we utilize the Advanced Research version of the Weather Research and Forecasting model (ARWv4) to explore how the fog is affected by the basin’s topography during a radiation fog event in the Sichuan Basin in December 2016 by setting up three sets of terrain tests. The simulation results demonstrate that the fog area in the expanded basin terrain emerges 40 min earlier than in the original topography control test (CTL), with the fog area extent marginally reduced. Conversely, the fog area in the reduced basin terrain emerges one hour earlier than in the CTL, with the fog area extent increased by 133.5%. Basin topography is an essential factor influencing the humidity, temperature, and dynamical fields. The expansion of basin topography was shown to be unfavorable for water vapor convergence. Moreover, the area exhibiting relative humidity levels exceeding 95% at the peak of the fog intensity was smaller than that observed in CTL. The impact of radiative cooling was diminished, and the thickness and intensity of the inversion layer were reduced compared to CTL. In addition, the wind speed in the marginal area exceeded 5 m s⁻¹, and the fog formation was observed only in the central portion of the basin, where wind speeds ranged from 0 to 3 m s⁻¹. In contrast, the change in the topography of the narrowed basin resulted in the opposite phenomenon overall. This work emphasizes the importance of basin topography in forming and developing the fog in the Sichuan Basin. Full article

Many viruses occur in apple (Malus domestica (Borkh.)), but no information is available on their seed transmissibility. Here, we report that six viruses infecting apple trees, namely, apple chlorotic leaf spot virus (ACLSV), apple green crinkle-associated virus (AGCaV), apple rubbery wood virus 2 (ARWV2), apple stem grooving virus (ASGV), apple stem pitting virus (ASPV), and citrus concave gum-associated virus (CCGaV) occur in seeds extracted from apple fruits produced by infected maternal trees. Reverse transcription polymerase chain reaction (RT-PCR) and quantitative RT-PCR (RT-qPCR) assays revealed the presence of these six viruses in untreated apple seeds with incidence rates ranging from 20% to 96%. Furthermore, ASPV was detected by RT-PCR in the flesh and peel of fruits produced by infected maternal trees, as well as from seeds extracted from apple fruits sold for fresh consumption. Finally, a large-scale seedling grow-out experiment failed to detect ACLSV, ASGV, or ASPV in over 1000 progeny derived from sodium hypochlorite surface sterilized seeds extracted from fruits produced by infected maternal trees, suggesting no detectable transmission via embryonic tissue. This is the first report on the seedborne nature of apple-infecting viruses. Full article

Wind speed is an important meteorological parameter, whose simulation is influenced by various physical process parameterizations. However, the impact of cumulus parameterization schemes (CPSs) on wind speed simulation at the climate scale has not been sufficiently investigated in previous studies. Using the Advanced Research version of the Weather Research and Forecasting model (ARWv3) and hydrostatic wind speed change equation, we assessed the effects of four CPSs on a 10 m wind speed simulation over mainland China in the summer of 2003. In general, different CPSs can reproduce the wind speed distribution. Meanwhile, the sensitivity of wind speed simulation to CPSs was found to be the highest in East and southern China, followed by the Tibetan Plateau, and then Northwest China. We found that the main physical processes influencing wind speed (i.e., the pressure gradient (PRE), diffusion (DFN), and convection (CON) terms) vary greatly with sub-regions. CPSs mainly affect the secondary CON that regulates the balance between the dominant terms PRE and DFN, and also has a significant effect on PRE. For example, for CON, the difference index (DIF) between the Kain–Fritsch (KF) and previous KF (pKF) CPSs is larger than 20%, corresponding to a PRE DIF of about 14%. The term of local wind speed change (V_t) is significantly more sensitive to the CPSs than the other terms with a DIF of 283% over the Tibetan Plateau, suggesting high CPS sensitivity of the simulated wind speed. In addition, we explained the causes of the CPS-induced sensitivities. This work helps understand the Weather Research and Forecasting model (WRF) performance and emphasizes the importance of the CPS choice in simulating/forecasting wind speed. Full article

Apple rubbery wood virus 2 (ARWV-2) and citrus virus A (CiVA) belong to a recently approved family Phenuiviridae in the order Bunyavirales and possess negative-sense single-stranded RNA genomes. In this study, the genome sequence of three ARWV-2 isolates (S17E2, LYC2, and LYXS) and a CiVA isolate (CiVA-P) infecting pear trees grown in China were characterized using high-throughput sequencing combined with conventional reverse-transcription PCR (RT-PCR) assays. The genome-wide nt sequence identities were above 93.6% among the ARWV-2 isolates and above 93% among CiVA isolates. Sequence comparisons showed that sequence diversity occurred in the 5′ untranslated region of the ARWV-2 genome and the intergenic region of the CiVA genome. For the first time, this study revealed that ARWV-2 proteins Ma and Mb displayed a plasmodesma subcellular localization, and the MP of CiVA locates in cell periphery and can interact with the viral NP in bimolecular fluorescence complementation assays. RT-PCR tests disclosed that ARWV-2 widely occurs, while CiVA has a low incidence in pear trees grown in China. This study presents the first complete genome sequences and incidences of ARWV-2 and CiVA from pear trees and the obtained results extend our knowledge of the viral pathogens of pear grown in China. Full article

Although land surface influences atmospheric processes significantly, insufficient studies have been conducted on the ensemble forecasts using the breeding of growing modes (BGM) with perturbed land surface variables. To investigate the practicability of perturbed land variables for ensemble forecasting, we used the ARWv3 mesoscale model to generate ensembles for an event of 24 h heavy rainfall with perturbed atmospheric and land variables by the BGM method. Results show that both atmospheric and land variables can generate initial perturbations with BGM, except that they differ in time and saturation characteristics, e.g., saturation is generally achieved in approximately 30 h with a growth rate of ~1.30 for atmospheric variables versus 102 h and growth rate of 1.02 for land variables. With the increase in precipitation, the importance of the perturbations of land variables also increases as compared to those of atmospheric variables. Moreover, the influence of the perturbations of land variables on simulated precipitation is still relatively large, although smaller than that of atmospheric variables, e.g., the spreads of perturbed atmospheric and land subsets were 7.3 and 3.8 mm, respectively. The benefits of perturbed initialisation can also be observed in terms of probability forecast. All findings indicate that the BGM method with perturbed land variables has the potential to ensemble forecasts for precipitation. Full article

Citrus concave gum-associated virus (CCGaV) is a negative-stranded RNA virus, first reported a few years ago in citrus trees from Italy. It has been reported in apple trees in the USA and in Brazil, suggesting a wider host range and geographic distribution. Here, an anti-CCGaV polyclonal antiserum to specifically detect the virus has been developed and used in a standard double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) that has been validated as a sensitive and reliable method to detect this virus both in citrus and apple trees. In contrast, when the same antiserum was used in direct tissue-blot immunoassay, CCGaV was efficiently detected in citrus but not in apple. Using this antiserum, the first apple trees infected by CCGaV were identified in Italy and the presence of CCGaV in several apple cultivars in southern Italy was confirmed by field surveys. High-throughput sequencing (HTS) allowed for the assembling of the complete genome of one CCGaV Italian apple isolate (CE-c3). Phylogenetic analysis of Italian CCGaV isolates from apple and citrus and those available in the database showed close relationships between the isolates from the same genus (Citrus or Malus), regardless their geographical origin. This finding was further confirmed by the identification of amino acid signatures specific of isolates infecting citrus or apple hosts. Analysis of HTS reads also revealed that the CE-c3 Italian apple tree, besides CCGaV, was simultaneously infected by several viruses and one viroid, including apple rubbery wood virus 2 which is reported for the first time in Italy. The complete or almost complete genomic sequences of the coinfecting agents were determined. Full article