Genetic diversity and evolution of the emerging picornavirus Senecavirus A.

Senecavirus A (SVA) is an emerging picornavirus that causes vesicular disease (VD) in swine. The virus has been circulating in swine in the United Stated (USA) since at least 1988, however, since 2014 a marked increase in the number of SVA outbreaks has been observed in swine worldwide. The factors that led to the emergence of SVA remain unknown. Evolutionary changes that accumulated in the SVA genome over the years may have contributed to the recent increase in disease incidence. Here we compared full-genome sequences of historical SVA strains (identified before 2010) from the USA and global contemporary SVA strains (identified after 2011). The results from the genetic analysis revealed 6.32 % genetic divergence between historical and contemporary SVA isolates. Selection pressure analysis revealed that the SVA polyprotein is undergoing selection, with four amino acid (aa) residues located in the VP1 (aa 735), 2A (aa 941), 3C (aa 1547) and 3D (aa 1850) coding regions being under positive/diversifying selection. Several aa substitutions were observed in the structural proteins (VP1, VP2 and VP3) of contemporary SVA isolates when compared to historical SVA strains. Some of these aa substitutions led to changes in the surface electrostatic potential of the structural proteins. This work provides important insights into the molecular evolution and epidemiology of SVA.

Mycobacterium paratuberculosis sheep type strain in Uruguay: Evidence for a wider geographic distribution in South America.

Johne's disease (JD) is an economically important disease of ruminants caused by Mycobacterium avium paratuberculosis (MAP), which also infects other species including humans. Two major MAP strain types are currently recognized: sheep (S) and cattle (C) types. Information on JD prevalence and MAP types infecting small ruminants in South America is limited, and all but one of the MAP types reported from this region are of the C type. This study describes clinicopathological, molecular and microbiological findings in 11 cases of JD caused by a type S MAP strain, and estimated true within-flock prevalence in a ~735-sheep operation in Uruguay. Postmortem examination and histology (hematoxylin-eosin and Ziehl-Neelsen stains) of samples from 41 selected sheep revealed lymphohistiocytic/granulomatous enteritis and mesenteric lymphadenitis in 11 animals, with moderate/severe multibacillary lesions in 6 clinical cases, and minimal/mild paucibacillary lesions in 5 sub-clinical cases. Immunohistochemistry using an antibody against Mycobacterium bovis that cross-reacts with MAP (2 cases), and transmission electron microscopy (1 case), revealed myriads of intrahistiocytic mycobacteria. MAP was isolated in one case and detected by PCR in 6 cases. The S type of MAP was identified using a multiplex PCR that distinguishes between S and C types, and PCR-REA. The estimated true within-flock prevalence was ≤ 2.3%. This represents the first communication on within-flock prevalence of JD associated with a type S MAP strain in South America and the second documentation of this strain in the subcontinent. Additional studies are required to better understand the molecular epidemiology of the different MAP types in the region.

A porcine enterovirus G associated with enteric disease contains a novel papain-like cysteine protease.

Identification of unknown pathogens in pigs displaying enteric illness is difficult due to the large diversity of bacterial and viral species found within faecal samples. Current methods often require bacterial or viral isolation, or testing only a limited number of known species using quantitative PCR analysis. Herein, faeces from two 25-day-old piglets with diarrhoea from Texas, USA, were analysed by metagenomic next-generation sequencing to rapidly identify possible pathogens. Our analysis included a bioinformatics pipeline of rapid short-read classification and de novo genome assembly which resulted in the identification of a porcine enterovirus G (EV-G), a complete genome with substantial nucleotide differences (>30 %) among current sequences, and a novel non-structural protein similar in sequence to the Torovirus papain-like cysteine protease (PLpro). This discovery led to the identification and circulation of an EV-G with a novel PLpro in the USA that has not been previously reported.