Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7)

Salmon pancreas disease virus, more commonly known as salmonid alphavirus (SAV), is a single-stranded positive sense RNA virus and the causative agent of pancreas disease and sleeping disease in salmonids. In this study, a unique strain of SAV previously isolated from ballan wrasse was subjected to whole genome sequencing using nanopore sequencing. In order to accurately examine the evolutionary history of this strain in comparison to other SAV strains, a partitioned phylogenetic analysis was performed to account for variation in the rate of evolution for both individual genes and codon positions. Partitioning the genome alignments almost doubled the observed branch lengths in the phylogenetic tree when compared to the more common approach of applying one model of substitution across the genome and significantly increased the statistical fit of the best-fitting models of nucleotide substitution. Based on the genomic data, a valid case can be made for the viral strain examined in this study to be considered a new SAV genotype. In addition, this study adds to a growing number of studies in which SAV has been found to infect non-salmonid fish, and as such we have suggested that the viral species name be amended to the more inclusive ‘piscine alphavirus’.

Ultrasound Diagnosis of Nonalcoholic Fatty Pancreas Disease in Children and Its Clinical Significance

Background The purpose of this study was to investigate the incidence of non-alcoholic fatty pancreatic disease (NAFPD) diagnosed by ultrasound in children and the related factors of NAFPD in children. Methods 326 children (2–14 years old) were selected as the study subjects. All statistical analyses were performed using SPSS software 23.0 (SPSS Inc., Chicago, IL, USA). Results A total of 41 cases (12.6%) of the 326 children had NAFPD. The two experimental groups showed statistically significant differences in age, height, WHtR, TC, LDL, ALT, AST and GGT (p < 0.05), among which age and height were negatively correlated with NAFPD. Univariate analysis and multivariate analysis showed that WHtR > 0.472(p = 0.007), TC > 5.3 mmol/L༈p < 0.001༉, LDL > 2.49 mmol/L༈p = 0.002༉and ALT > 23.8 U/L( p = 0.018) were independent risk factors for occurrence of NAFPD. Conclusions (1) The high incidence of NAFPD in children was worthy of attention; (2) WHtR was an independent risk factor for NAFPD; (3) WHtR might be an sensitive index which could early screen children MetS and used in epidemiological investigation; (4) NAFPD was closely related to obesity and metabolic syndrome, and ultrasound could be used as the preferred imaging diagnosis method for NAFPD.