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Porcine viral diarrhea diseases affect the swine industry, resulting in significant economic losses. Porcine epidemic diarrhea virus (PEDV) genotypes G1 and G2, and groups A and C of the porcine rotavirus, are major etiological agents of severe gastroenteritis and profuse diarrhea, particularly among piglets, with mortality rates of up to 100%. Based on the high prevalence rate and frequent co-infection of PEDV, RVA, and RVC, close monitoring is necessary to avoid greater economic losses. We have developed a multiplex

The ongoing SARS (severe acute respiratory syndrome)-CoV (coronavirus)-2 pandemic has exposed major gaps in our knowledge on the origin, ecology, evolution, and spread of animal coronaviruses. Porcine epidemic diarrhea virus (PEDV) is a member of the genus Alphacoronavirus in the family Coronaviridae that may have originated from bats and leads to significant hazards and widespread epidemics in the swine population. The role of local and global trade of live swine and swine-related products in disseminating PEDV remains unclear, especially in developing countries with complex swine production systems. Here, we undertake an in-depth phylogeographic analysis of PEDV sequence data (including 247 newly sequenced samples) and employ an extension of this inference framework that enables formally testing the contribution of a range of predictor variables to the geographic spread of PEDV. Within China, the provinces of Guangdong and Henan were identified as primary hubs for the spread of PEDV, for which we estimate live swine trade to play a very important role. On a global scale, the United States and China maintain the highest number of PEDV lineages. We estimate that, after an initial introduction out of China, the United States acted as an important source of PEDV introductions into Japan, Korea, China, and Mexico. Live swine trade also explains the dispersal of PEDV on a global scale. Given the increasingly global trade of live swine, our findings have important implications for designing prevention and containment measures to combat a wide range of livestock coronaviruses. ispartof: MOLECULAR BIOLOGY AND EVOLUTION vol:39 issue:2 ispartof: location:United States status: published

Schwann cells (SCs) are PNS glia that play numerous support functions including myelination of axons. After PNS injury, SCs facilitate regeneration by phagocytosing cellular debris and providing physical and biochemical cues to guide axon growth. This reparative phenotype suggests SCs could be critical cellular targets for enhancing nerve regeneration. One method for altering cell morphology and motility is the application of direct current (DC) electric fields (EFs). Endogenous EFs have physiologic relevance during embryogenesis and serve as guidance and polarization cues. While much literature exists on EFs and CNS and PNS neurons, the effects of EFs on SCs have not been extensively studied. In this work, cell alignment, migration, and morphology of rat SCs were measured in response to several EF stimulation regimes including constant DC, 50% duty cycle DC and oscillating DC. SCs were found to re-orient perpendicular to field lines and respond to DC EFs as low as 75 mV/mm. EF exposure promoted directed migration, with travel towards the cathode at a mean rate of 7.5 µm/h. The data highlight the utility of EFs in modulating SC morphology, alignment and migration. Results may have implications for using EFs to attract and realign SCs at the site of PNS trauma.

The recent outbreak of COVID-19 in Wuhan turned into a public health emergency of international concern. With no antiviral drugs nor vaccines, and the presence of carriers without obvious symptoms, traditional public health intervention measures are significantly less effective. Here, we report the epidemiological and virological characteristics of the COVID-19 outbreak. Originated in bats, 2019-nCoV/ severe acute respiratory syndrome coronavirus (SARS-CoV)-2 likely experienced adaptive evolution in intermediate hosts before transfer to humans at a concentrated source of transmission. Similarities of receptor sequence binding to 2019-nCoV between humans and animals suggest a low species barrier for transmission of the virus to farm animals. We propose, based on the One Health model, that veterinarians and animal specialists should be involved in a cross-disciplinary collaboration in the fight against this epidemic.

Pair correlation functions provide a summary statistic which quantifies the amount of spatial correlation between objects in a spatial domain. While pair correlation functions are commonly used to quantify continuous-space point processes, the on-lattice discrete case is less studied. Recent work has brought attention to the discrete case, wherein on-lattice pair correlation functions are formed by normalizing empirical pair distances against the probability distribution of random pair distances in a lattice with Manhattan and Chebyshev metrics. These distance distributions are typically derived on an ad hoc basis as required for specific applications. Here we present a generalized approach to deriving the probability distributions of pair distances in a lattice with discrete Manhattan and Chebyshev metrics, extending the Manhattan and Chebyshev pair correlation functions to lattices in k dimensions. We also quantify the variability of the Manhattan and Chebyshev pair correlation functions, which is important to understanding the reliability and confidence of the statistic.

Prior to the emergence of H3N8 canine influenza virus (CIV) and the latest avian-origin H3N2 CIV, there was no evidence of a circulating canine-specific influenza virus. Molecular and epidemiological evidence suggest that H3N8 CIV emerged from H3N8 equine influenza virus (EIV). This host-range shift of EIV from equine to canine hosts and its subsequent establishment as an enzootic CIV is unique because this host-range shift was from one mammalian host to another. To further understand this host-range shift, we conducted a comprehensive phylodynamic analysis using all the available whole-genome sequences of H3N8 CIV. We found that (1) the emergence of H3N8 CIV from H3N8 EIV occurred in approximately 2002; (2) this interspecies transmission was by a reassortant virus of the circulating Florida-1 clade H3N8 EIV; (3) once in the canine species, H3N8 CIV spread efficiently and remained an enzootic virus; (4) H3N8 CIV evolved and diverged into multiple clades or sublineages, with intra and inter-lineage reassortment. Our results provide a framework to understand the molecular basis of host-range shifts of influenza viruses and that dogs are potential “mixing vessels” for the establishment of novel influenza viruses.

Objective To investigate the efficacy and safety of aceneuramic acid extended-release (Ace-ER), a treatment intended to replace deficient sialic acid, in patients with GNE myopathy. Methods UX001-CL301 was a phase 3, double-blind, placebo-controlled, randomized, international study evaluating the efficacy and safety of Ace-ER in patients with GNE myopathy. Participants who could walk ≥200 meters in a 6-minute walk test at screening were randomized 1:1, and stratified by sex, to receive Ace-ER 6 g/d or placebo for 48 weeks and assessed every 8 weeks. The primary endpoint was change in muscle strength over 48 weeks measured by upper extremity composite (UEC) score. Key secondary endpoints included change in lower extremity composite (LEC) score, knee extensor strength, and GNE myopathy–Functional Activity Scale (GNEM-FAS) mobility domain score. Safety assessments included adverse events (AEs), vital signs, and clinical laboratory results. Results Eighty-nine patients were randomized (Ace-ER n = 45; placebo n = 44). Change from baseline to week 48 for UEC score between treatments did not differ (least square mean [LSM] Ace-ER −2.25 kg vs placebo −2.99 kg; LSM difference confidence interval [CI] 0.74 [−1.61 to 3.09]; p = 0.5387). At week 48, there was no significant difference between treatments for the change in key secondary endpoints: LEC LSM difference (CI) −1.49 (−5.83 to 2.86); knee extension strength −0.40 (−2.38 to 1.58); and GNEM-FAS mobility domain score −0.72 (−2.01 to 0.57). Gastrointestinal events were the most common AEs. Conclusions Ace-ER was not superior to placebo in improving muscle strength and function in patients with GNE myopathy. Classification of evidence This study provides Class I evidence that for patients with GNE myopathy, Ace-ER does not improve muscle strength compared to placebo.

Human coronaviruses (HCoVs) were first described in the 1960s for patients with the common cold. Since then, more HCoVs have been discovered, including those that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), two pathogens that, upon infection, can cause fatal respiratory disease in humans. It was recently discovered that dromedary camels in Saudi Arabia harbor three different HCoV species, including a dominant MERS HCoV lineage that was responsible for the outbreaks in the Middle East and South Korea during 2015. In this review we aim to compare and contrast the different HCoVs with regard to epidemiology and pathogenesis, in addition to the virus evolution and recombination events which have, on occasion, resulted in outbreaks amongst humans., Trends Six coronaviruses (CoVs) are known to infect humans: 229E, OC43, SARS-CoV, NL63, HKU1, and MERS-CoV. Many CoVs are simultaneously maintained in nature, allowing for genetic recombination, resulting in novel viruses. Recombination of CoV in camels has resulted in a dominant MERS lineage that caused human outbreaks in 2015.

Growth in biological systems occurs as a consequence of cell proliferation fueled by a nutrient supply. In general, the nutrient gradient of the system will be nonconstant, resulting in biased cell proliferation. We develop a uniaxial discrete cellular automaton with biased cell proliferation using a probability distribution which reflects the nutrient gradient of the system. An explicit probability mass function for the displacement of any tracked cell under the cellular automaton model is derived and verified against averaged simulation results; this displacement distribution has applications in predicting cell trajectories and evolution of expected site occupancies.

H3N2 canine influenza virus (CIV) originated from avian species and emerged in dogs in Asia around 2005 where it became enzootic before reaching the USA in 2015. To investigate the key aspects of the evolution of H3N2 CIV regarding its emergence and adaptation in the canine host, we conducted an extensive analysis of all publicly available H3N2 CIV sequences spanning a 10-year period. We believe that H3N2 AIVs transferred to canines around 2002-2004. Furthermore, H3N2 CIVs could be divided into seven major clades with strong geographic clustering and some changed sites evidence of adaptive evolution. Most notably, the dN/dS of each H3N2 CIVs segment was higher than the correspondent of H3N2 AIVs and the U content of HA and NA was increasing over time, suggesting the idea that this avian-origin virus may be gradually adapting to the host. Our results provide a framework to elucidate a general mechanism for emergence of novel influenza viruses.

Interspecies transmission of equine influenza A(H3N8) virus has resulted in establishment of a canine influenza virus. To determine if something similar could happen with cats, we experimentally infected 14 cats with the equine influenza A(H3N8) virus. All showed clinical signs, shed virus, and transmitted the virus to a contact cohort.

Avian influenza A(H7N9) virus and mixed live poultry–animal markets in Guangdong province: a perfect storm in the making?

Mitogenic activity of UV-inactivated influenza viruses in cord blood lymphocytes (CBL), as measured by cytokine release, was investigated. Using prototype viruses of subtype H3N2 (A/Aichi/68), H2N2 (A/Japan/57), and H1N1 (A/Puerto Rico/34) for influenza A virus, and B/Lee/40 for influenza B virus, the results indicated that both Th1 and Th2 cytokines were induced. Stimulation indices were significantly higher for IFNγ, IL-4 and IL-10 by influenza A viruses than by influenza B virus. Stimulation indices for IL-2 and IL-6 were lower, as these two cytokines were spontaneously released by cord blood lymphocytes in culture. Alignment of the amino acid sequences of the HA for the viruses used in this study indicated that influenza B virus lacked sequence homology to the antigenic sites identified for influenza A virus. Therefore, the antigenic sites may play a role in the mitogenic property, and cord blood lymphocytes could provide a system to compare this property for clinical isolates of influenza virus.

Phylogenetic and antigenic analyses indicate that recent circulating equine-2 influenza viruses in the United States have been alternating between two genetic and antigenic distinct lineages since 1996. The evolution rates for these two lineages, the Kentucky and the Florida lineage, are very similar. For the earlier isolates in the Kentucky lineage, there are multiple and sequential nonsynonymous substitutions at antigenic sites B and D. However, there are no changes at any of these antigenic sites for KY98 and OK00. In the Florida lineage, except for NY99 with one amino acid substitution at antigenic site B, viruses in this lineage do not have nonsynonymous substitutions at any of the antigenic sites. The lack of amino acid substitutions at these antigenic sites suggests a mechanism other than immune selection is responsible for the maintenance of these viral lineages. Serological analysis indicates that these two lineages are antigenic distinct, and the pattern of reactivity of horse sera towards these two lineages alternates in consecutive years, parallel to the "switching" of virus lineage seen in the phylogenetic tree. This alternate circulation may play a role in the maintenance of these two lineages of equine-2 influenza virus.

Microarrays of virus-specific oligonucleotides may provide a method of screening samples for the presence or absence of a large variety of viruses simultaneously. Influenza viruses are ideal for evaluating such microarrays because of their genetic and host diversity, and the availability of an extensive sequence database. A collection of 476 influenza virus-specific oligonucleotides was spotted onto glass slides as probes. Viral RNAs were reverse transcribed and amplified by PCR, and the products were labeled with cyanine dyes. The presence of viruses and their identities were determined by hybridization. The fluorescence intensities of oligonucleotide spots were highly reproducible within each slide and satisfactorily proportional between experiments. However, the intensities of probe spots completely complementary to target sequences varied from background to saturation. The variations did not correlate with base composition, nucleotide sequence, or internal secondary structures. Therefore, thresholds for determining whether hybridization to a spot should be judged as positive were assigned individually. Considering only positive spots from probes predicted to be monospecific for influenza virus species, subtype, host source, or gene segment, this method made correct identifications at the species, hemagglutinin subtype, and gene segment levels. Monospecific neuraminidase (NA) subtype probes were insufficiently diverse to allow confident NA subtype assignment. Incorporating positive spots from polyspecific probes into the identification scheme gave similar results. Overall, the results demonstrate the potential of microarray-based oligonucleotide hybridization for multiple virus detection.

Zoonotic transmission of pathogenic avian influenza virus (AIV) is a potential public health threat ([1][1], [2][2]), as the virus may acquire human-to-human transmissibility through mutations or by reassortment with seasonal influenza viruses (e.g., H3N2 and H1N1). The recent outbreak of novel H7N9

The hemagglutination-inhibition (HI) titers of a panel of 25 mouse monoclonal antibodies (MAbs) against 44 isolates of highly pathogenic avian influenza virus H5N1 were determined. A two-dimensional antigenic dendrogram was constructed by hierarchical clustering of HI titers. Viruses with similar reactivity patterns were clustered horizontally, whereas MAbs were clustered vertically. In this 2-D dendrogram, with 40% similarity as a cut-off, four virus clusters and four MAbs clusters were identified. A phylogenetic tree based on the deduced amino acid sequence of the hemagglutinin gene of tested viruses was constructed and its topology was compared to the antigenic dendrogram. Interestingly, viruses with high genetic homology in the phylogenetic tree also had high similarity in their reactivity patterns, as indicated by their relatedness in the tree and close clustering in the dendrogram, respectively. However, the reverse and the converse were also true. Of the five pairs of viruses in the dendrogram with bootstrap values higher than 75, four pairs were in concordance with their genetic relatedness. However, one pair contained viruses belong to two distinct genetic clades. These results were discussed in the context of antigenic variation, genetic polymorphism, and the potential application of MAbs in antigenic analysis., link_to_OA_fulltext

Interactions between host factors and the viral replication complex play important roles in host adaptation and regulation of influenza virus replication. A cellular protein, nuclear factor 90 (NF90), was copurified with H5N1 viral nucleoprotein (NP) from human cells in which NP was transiently expressed and identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis. In vitro coimmunoprecipitation of NF90 and NP coexpressed in HEK 293T cells or individually expressed in bacterial and HEK 293T cells, respectively, confirmed a direct interaction between NF90 and NP, independent of other subunits of the ribonucleoprotein complex. This interaction was prevented by a mutation, F412A, in the C-terminal region of the NP, indicating that the C-terminal of NP is required for NF90 binding. RNase V treatment did not prevent coprecipitation of NP and NF90, which demonstrates that the interaction is RNA binding independent. After small interfering RNA knockdown of NF90 expression in A549 and HeLa cells, viral polymerase complex activity and virus replication were significantly increased, suggesting that NF90 negatively affects viral replication. Both NP and NF90 colocalized in the nucleus of virus-infected cells during the early phase of infection, suggesting that the interaction between NF90 and NP is an early event in virus replication. Quantitative reverse transcription-PCR showed that NF90 downregulates both viral genome replication and mRNA transcription in infected cells. These results suggest that NF90 inhibits influenza virus replication during the early phase of infection through direct interaction with viral NP. Copyright © 2009, American Society for Microbiology. All Rights Reserved., link_to_OA_fulltext

The expression of hepatitis B virus (HBV) DNA in the liver was studied by nonisotopic in situ hybridization and correlated with liver histology, different phases in the natural evolution of chronic hepatitis B, and hepatic expression of HBV antigens in 251 Chinese patients with chronic HBV infection. A good correlation was found between the detection of HBV-DNA by in situ hybridization and serum HBV-DNA (P < .01). Chronic active hepatitis had the highest HBV-DNA detected in cytoplasm and nuclei, compared with livers showing minimal change, chronic persistent hepatitis, cirrhosis, and hepatocellular carcinoma. HBV-DNA in cytoplasm exceeded HBV-DNA in nucleus in all patients except in livers with hepatocellular carcinoma. Hepatic HBV-DNA correlated with disease activity (P < .02) and the correlation was highly significant with intralobular activity (P < .001). Patients in the early viral replicative phase of infection had higher levels of cytoplasmic and nuclear HBV-DNA compared with the late viral nonreplicative phase. Cytoplasmic and nuclear HBV-DNA correlated with hepatic expression of HBcAg and HBsAg (P < .05 in both cases), but not with HBeAg. These data indicate that hepatic expression of HBV-DNA follows the natural history of chronic HBV infection and is associated with active liver disease.

Persistent viral infections in vitro are useful systems to study the coevolution of virus and cell populations. Persistent infection of mouse Friend erythroleukemic cells (FEL) with vaccinia virus results in profound changes of the virus as well as of the cells. To investigate phenotypic changes of other cell types, we have established a persistent infection with vaccinia virus in a human leukemic cell line (K562). This cell line can be induced to differentiate along the erythroid pathway synthesizing embryonic and fetal globins, thus providing a system in which specific genes can be stimulated. After serial passage, the persistently infected cells (K562vac) became spontaneously differentiated, as shown by the increase in the number of cells producing hemoglobin (benzidine positive cells), and resistant to superinfection. These phenotypic changes of the cells were not accompanied by changes in the viral population. Hybridization of cellular RNA with cloned embryonic and fetal globin genes indicated that uninduced K562 cells do not express these genes, whereas cells induced by hemin or butyrate express G gamma (fetal globin) epsilon and zeta (embryonic globins) genes. By contrast vaccinia infected cells spontaneously express the G gamma gene. These results demonstrate that persistent infection with vaccinia virus elicited phenotypic changes in the infected cell population; in this case the constitutive expression of fetal hemoglobin.

Persistent viral infections in vitro are useful to study the evolution of virus populations in the absence of immunological pressure. Several deletion mutants have been isolated in this laboratory from Friend erythroleukemia cells persistently infected with vaccinia virus strain IHD-W, designated SQA vac . Two of the mutants, which remain stable after serial passage in L cells, have been characterized. The deletion which range between 20 to 22 kb, has been localized at the left terminus comprising Hin dIII fragments C and N. In addition, H in dIII B fragment lost the sequences that hybridize to pAG5, a plasmid containing the 3.5 kb terminal sequences and acquired different restriction sites. Phenotypic characterization of these mutants revealed that they were not replication defective since they grew in all cell lines tested and produced plaques of the same size as the wild-type. However, they were less effective in suppressing host protein synthesis. The LD 50 for the mutants titered in NIH Swiss female mice was greater than 10 9 PFU as compared to 10 6 PFU for the wild-type, indicating reduced virulence in vivo. These mutants, which display different properties to previously described mutants with deletions at the left terminus, provide another valuable system to study the molecular basis of virulence of vaccinia.

Understanding the molecular basis of virulence in poxvirus is of great importance for the development of recombinant vaccines using vaccinia virus as a vector. We have previously described mutants of vaccinia virus with deletions ranging from 20 to 21 kb at the left terminus and with attenuated phenotype. The virulence of these mutants was studied, using different routes of inoculation, for protection from wild-type challenge in mice and for replication in vivo. Regardless of the route of inoculation, the LD50 of the deletion mutants is at least 1000-fold higher than that of the wild-type. Results from protection experiments using viable and ultraviolet-inactivated viruses, and from determination of infectivity in different organs, indicated that the mutants were unable to replicate in vivo. Southern blot hybridization of viral DNA with pSC16, a plasmid containing the vaccinia growth factor (VGF) gene, revealed that in the IHD-W strain of vaccinia virus this gene is localized at the left terminus exclusively and that the mutants lack this gene. The results suggest that absence of the VGF gene is correlated with inability to replicate in vivo and decreased virulence.