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Synonymous codon bias in the viral genome affects protein translation and gene expression, suggesting that the synonymous codon mutant plays an essential role in influencing virulence and evolution. However, how the recessive mutant form contributes to virus evolvability remains elusive. In this paper, we characterize how the Senecavirus A (SVA), a picornavirus, utilizes synonymous codon mutations to influence its evolution, resulting in the adaptive evolution of the virus to adverse environments. The phylogenetic tree and Median-joining (MJ)-Network of these SVA lineages worldwide were constructed to reveal SVA three-stage genetic development clusters. Furthermore, we analyzed the codon bias of the SVA genome of selected strains and found that SVA could increase the GC content of the third base of some amino acid synonymous codons to enhance the viral RNA adaptive evolution. Our results highlight the impact of recessive mutation of virus codon bias on the evolution of the SVA and uncover a previously underappreciated evolutionary strategy for SVA. They also underline the importance of understanding the genetic evolution of SVA and how SVA adapts to the adverse effects of external stress. [ABSTRACT FROM AUTHOR]

The eastern margin of the Qinghai-Tibet Plateau is an extreme topography transition zone, and characterized by significant vegetation zonation, in addition to geographic features (such as enormous topographic relief and active tectonics) that control the occurrence of debris flows, which are rapid, surging flows of water-charged clastic sediments moving along a steep channel and are one of the most dangerous mountain hazards in this region. There is thus an urgent need in this region to conduct a regional-scale debris flow susceptibility assessment to determine the spatial likelihood of a debris flow occurrence and guarantee the safety of people and property, in addition to the smooth operation of the Sichuan-Tibet transport corridor. It is, however, a challenging task to estimate the region's debris flow susceptibility while taking into consideration the comprehensive impacts of vegetation on the occurrence of debris flows, such as the positive effect of root anchoring and the negative effect of vegetation weight loads. In this study, a novel regional-scale susceptibility assessment method was constructed by integrating state-of-the-art machine learning algorithms (such as support vector classification (SVC), random forest (RF), and eXtreme Gradient Boosting (XGB)) with the removing outliers (RO) algorithm and particle swarm optimization (PSO), allowing the impacts of vegetation on debris flow initiation to be integrated with the topographical conditions, hydrological conditions, and geotechnical conditions. This method is finally applied to assess the regional-scale susceptibility of debris flows in the Dadu River basin on the eastern margin of the Qinghai-Tibet Plateau. The study results show that (i) all hybrid machine learning techniques can effectively predict the occurrence of debris flows in the extreme topography transition zone; (ii) the hybrid machine learning technique RO-PSO-SVC has the best performance, and its accuracy (ACC) is 0.946 and the area under the ROC curve (AUC) is 0.981; (iii) the RO-PSO algorithm improves SVC, RF, and XGB performance (according to the ACC value) by 3.84%, 2.59%, and 5.94%, respectively; and (iv) the contribution rate of ecology-related variables is almost only one-tenth that of topography- and hydrology-related factors, according to the factor important analysis for RO-PSO-SVC. Furthermore, debris flow susceptibility maps for the Dadu River basin were created, which can be used to assess and mitigate debris flow hazards. [ABSTRACT FROM AUTHOR]

Background: Senecavirus A (SVA), a member of the family Picornaviridae , is newly discovered, which causes vesicular lesions, lameness in swine, and even death in neonatal piglets. SVA has rapidly spread worldwide in recent years, especially in Asia., Objectives: We conducted a global meta-analysis and systematic review to determine the status of SVA infection in pigs., Methods: Through PubMed, VIP Chinese Journals Database, China National Knowledge Infrastructure, and Wanfang Data search data from 2014 to July 26, 2020, a total of 34 articles were included in this analysis based on our inclusion criteria. We estimated the pooled prevalence of SVA in pigs by the random effects model. A risk of bias assessment of the studies and subgroup analysis to explain heterogeneity was undertaken., Results: We estimated the SVA prevalence to be 15.90% (1,564/9,839; 95% confidence interval [CI], 44.75-65.89) globally. The prevalence decreased to 11.06% (945/8,542; 95% CI, 28.25-50.64) after 2016. The highest SVA prevalence with the VP1-based RT-PCR and immunohistochemistry assay was 58.52% (594/1,015; 95% CI, 59.90-83.96) and 85.54% (71/83; 95% CI, 76.68-100.00), respectively. Besides, the SVA prevalence in piglet herds was the highest at 71.69% (119/166; 95% CI, 68.61-98.43) ( p < 0.05). Moreover, our analysis confirmed that the subgroups, including country, sampling year, sampling position, detected gene, detection method, season, age, and climate, could be the heterogeneous factors associated with SVA prevalence., Conclusions: The results indicated that SVA widely exists in various countries currently. Therefore, more prevention and control policies should be proposed to enhance the management of pig farms and improve breeding conditions and the environment to reduce the spread of SVA., Competing Interests: The authors declare no conflicts of interest., (© 2023 The Korean Society of Veterinary Science.)