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To study the outcome of natural selection using phylogenetic trees, we analyzed full-length genome sequences of porcine teschovirus (PTV). PTV belongs to the family Picornaviridae and has a positive-stranded RNA genome, the replication of which is carried out by the error-prone viral RNA-dependent RNA polymerase. The viral RNA encodes a single polyprotein that is cleaved into structural (i.e., L, VP4, VP2, VP3 and VP1) and nonstructural proteins (i.e., 2A, 2B, 2C, 3A, 3B, and 3C). A high degree of genetic diversity was found based on the pairwise nucleotide distances and on the mean ratio of the number of nonsynonymous (dN) and synonymous (dS) substitutions (dN/dS) in the structural genes. Conversely, the diversity of the nonstructural genes was lower. The differences in genetic diversity between the structural and nonstructural genomic regions were likely due to strong purifying selection; consequently, the estimates of phylogenies were also discordant among these genes. In particular, maximum-likelihood and Bayesian methods generated short-branched trees when loci that are under strong purifying selection were used. These findings indicate that even in an RNA virus with an intrinsically high mutation rate, a strong purifying selection will curb genetic diversity and should be considered an important source of bias in future studies based on phylogenetic methods. [ABSTRACT FROM AUTHOR]

A porcine teschovirus (PTV) was isolated from a dead piglet from a herd of 200 sows showing reproductive failure in Fuyu, Heilongjiang Province, China. Sequencing of most of the genome of this isolate, designated Fuyu/2009, revealed that is was a PTV-8 isolate, closely related to a previously identified Chinese PTV-8 strain (Jilin/2003). Both Chinese strains vary from the European PTV-8 strains by different clustering of the 3CD sequences. Infection with these viruses may be associated with pronounced diseases. [ABSTRACT FROM AUTHOR]

Pigeon paramyxovirus-1 (PPMV-1) is a strain of Newcastle disease virus (NDV) that has adapted to infect pigeons and poses a constant threat to the commercial poultry industry. Early detection via rapid and sensitive methods, along with timely preventative and mitigating actions, is important for reducing the spread of PPMV-1. Here, we report the development of a TaqMan loop-mediated isothermal amplification assay (TaqMan-LAMP) for rapid and specific detection of PPMV-1 based on the F gene. This system makes use of six novel primers and a TaqMan probe that targets nine distinct regions of the F gene that are highly conserved among PPMV-1 isolates. The results showed that the limit of detection was 10 copies μL-1 for PPMV-1 cDNA and 0.1 ng for PPMV-1 RNA. The reaction was completed within 25 min and was thus faster than conventional RT-PCR. Moreover, no cross-reactions with similar viruses or with peste des petits ruminants virus (PPRV) or NDV LaSota vaccine strains were observed under the same conditions. To evaluate the applicability of the assay, the TaqMan-LAMP assay and a commercial RT-PCR assay were compared using 108 clinical samples, and the concordance rate between two methods was found to be 96.3%. The newly developed PPMV-1 TaqMan-LAMP assay can therefore be used for simple, efficient, rapid, specific, and sensitive diagnosis of PPMV-1 infections. [ABSTRACT FROM AUTHOR]

Pseudorabies virus (PRV), the causative agent of Aujeszky's disease, has gained increased attention in China in recent years as a result of a recent outbreak of pseudorabies. The causative agent has a wide spectrum of hosts, including pigs, cattle, sheep, dogs, cats, bats, bears, and even some avian species. Although dog-related cases of pseudorabies have been reported regularly, many cases are overlooked, and few PRV strains are isolated because death occurs rapidly after PRV infection and veterinarians often do not test for PRV in dogs. Here, we performed a retrospective detection of PRV in dogs from July 2017 to December 2018. We found that PRV (including gE-deleted strains, classical strains, and variant strains) is prevalent in dogs regardless of season and region and that the epidemic PRV strains in dogs share high sequence similarity with gC and gE genes of swine epidemic strains and commercial vaccine strains. Collectively, our findings underscore the importance of PRV surveillance in dogs, which is beneficial for understanding the epidemiology of PRV in dogs and assists in efforts aimed at effectively controlling this disease. [ABSTRACT FROM AUTHOR]

In this study, we describe a novel and rapid method for the construction of a full-length infectious clone (pPPV). The constructed clone contained an engineered EcoRv site that served as a genetic marker and was shown to be infectious when transfected into a monolayer of PK-15 cells. The rescued virus (rPPV) of the infectious clone was found to be indistinguishable from wild-type virus BQ in terms of its biological properties. The generation of this PPV infectious clone provides a potentially powerful tool with which to elucidate the molecular pathogenesis of PPV. [ABSTRACT FROM AUTHOR]

The one-step polymerase chain reaction (one-step PCR) detection assay is an innovative PCR detection method, eliminating nucleic acid extraction steps, in which samples can be directly added to PCR reagents for testing. For simultaneous detection of CDV and CCoV, a sensitive and specific one-step duplex PCR (one-step dPCR) assay was developed with two pairs of primers that were designed based on H and M gene sequences of CDV and CCoV, respectively. The one-step dPCR with optimized detection conditions has high specificity and sensitivity; independent sequencing assays further verified these results. [ABSTRACT FROM AUTHOR]