•Systematically investigated the genetic evolution and biological characteristics of these viruses.•The genetic evolution and the reassortment of internal genes of all online H5N6 viruses were ...analyzed.•The pathogenicity differences of different genes reassortment H5N6 viruses in different hosts were analyzed.
Clade 2.3.4.4 of H5N6 subtype Avian Influenza Viruses (AIVs) has become dominant clade in South-East Asia. So far, a total of 16 cases of human infection, including 6 deaths, have been confirmed since 2014. In this study, we systematically investigated the genetic evolution and biological characteristics of these viruses. We first carried out phylogenetic and statistical analysis of all H5N6 viruses that were downloaded from Influenza Research Database, GISAID and isolates from our lab. We found that H5N6 AIVs continued to reassort with other AIVs subtypes since 2014. Among these H5N6 reassortments, four main gene types were identified: A (internal genes of H5N1-origin), B (PB2 of H6-origin, and others of H5N1-origin), C (internal genes of H9-origin) and D (PB2 of H6-origin and PB1of H3-origin, and others of H5N1). In addition, after several years of evolution, gene type D is currently the dominant gene type. To systematically compare the genetic and evolutionary characteristics and pathogenicity of these viruses, four H5N6 AIVs of different gene types were selected for further analysis. S4, XZ6, GD1602 and YZ587 virus represented gene type A, B, C and D, respectively. Their NA genes were all originated from H6 and their whole genome showed a high similarity with human isolates. All these isolates could both bind with SA-α2,3 Gal and SA-α2,6 Gal receptors. Pathogenicity test showed that these viruses were highly pathogenic in chickens, while YZ587 showed the lowest virulence. Moreover, XZ6 and S4 viruses were highly pathogenic in ducks and moderately pathogenic in mice, while GD1602 and YZ587 viruses were no-pathogenic in these animals. Interestingly, GD1602 and YZ587-like viruses were responsible for 4 and 2 human infection cases in 2016, respectively. Therefore, our study showed that the YZ587 virus which has mixed internal genes, showed lower virulence in avian species and mammals compared to other genotype viruses. Overall, our findings suggest that the H5N6 avian influenza virus is undergoing constantly evolving and reassortment. Thus, our study highlights the necessary of continued surveillance of the H5N6 AIVs in birds and paying close attention to the spread of these novel reassortment viruses.
Tuberculous meningitis (TBM) is a devastating form of tuberculosis (TB) causing high mortality and disability. TBM arises due to immune dysregulation, but the underlying immune mechanisms are ...unclear.
We performed single-cell RNA sequencing on peripheral blood mononuclear cells (PBMCs) and cerebrospinal fluid (CSF) cells isolated from children (n=6) with TBM using 10 xGenomics platform. We used unsupervised clustering of cells and cluster visualization based on the gene expression profiles, and validated the protein and cytokines by ELISA analysis.
We revealed for the first time 33 monocyte populations across the CSF cells and PBMCs of children with TBM. Within these populations, we saw that CD4_C04 cells with Th17 and Th1 phenotypes and Macro_C01 cells with a microglia phenotype, were enriched in the CSF. Lineage tracking analysis of monocyte populations revealed myeloid cell populations, as well as subsets of CD4 and CD8 T-cell populations with distinct effector functions. Importantly, we discovered that complement-activated microglial Macro_C01 cells are associated with a neuroinflammatory response that leads to persistent meningitis. Consistently, we saw an increase in complement protein (C1Q), inflammatory markers (CRP) and inflammatory factor (TNF-α and IL-6) in CSF cells but not blood. Finally, we inferred that Macro_C01 cells recruit CD4_C04 cells through CXCL16/CXCR6.
We proposed that the microglial Macro_C01 subset activates complement and interacts with the CD4_C04 cell subset to amplify inflammatory signals, which could potentially contribute to augment inflammatory signals, resulting in hyperinflammation and an immune response elicited by
-infected tissues.
Classical swine fever (CSF) continues to be a devastating infectious disease for the swine industry in China and commonly exists as wild or atypical types. From June 3rd to October 3rd, 2018, ...outbreaks of typical CSF cases with mortality rates of 42–86% occurred in 11 swine herds in five cities of Guangdong province, and were confirmed by RT-PCR. Phylogenetic analyses based on the nucleotide sequences of full-length E2 genes showed that the CSFV isolates collected in Guangdong, 2018 grouped into sub-subgenotype 2.1c and formed a separate clade from previously identified 2.1c isolates. Sequence comparison further confirmed the distance between the novel emergent and previously identified 2.1c isolates, with shared 94.5–98.2% and 97.8–99.7% identities at the nucleotide and amino acid levels respectively. Furthermore, 2.1c isolates collected in 2018 from Guangdong province contained a unique amino acid substitution (K174R) in the E2 protein in comparison with other 2.1c representative strains and CSFV 2.1, 2.2, 2.3 strains. Of note, the novel emergent 2.1c isolates are neutralized by sera from C-strain vaccinated sows, indicating that C-strain is still efficacious for protection against field isolates of CSFV.
•CSFV sub-subgenotype 2.1c is dominant in Guangdong province.•The novel identified 2.1c isolates contained a unique substitution K174R in the E2 proteins.•The emergent 2.1c isolates can still be neutralized by sera from vaccinated pigs.
H3 subtype avian influenza virus (AIV) poses a great threat to public health, and so investigating its epidemiology is of great importance. A novel reassortant H3N2 AIV strain was isolated from a ...live poultry market in eastern China. The strain's genes originated from H1N1, H3, and H7 AIVs. Thus, the genome information of the H3N2 isolate will help to investigate further the epidemiology of H3 subtype AIVs in China.
Many new astroviruses have been identified in humans and other animals in recent years, but only a few have been successfully isolated for extensive biological study. Here, we report an unusual ...isolation of a porcine astrovirus 5 (PAstV5) strain from a clinical classical swine fever virus (CSFV)-infected tissue sample. Incubation of porcine PK-15 cells with an extract of the CSFV-positive tissue resulted in unexpected cytopathic effects (CPEs), and high-throughput viromic sequencing identified PAstV5 and porcine circovirus type 2 (PCV2) as well as CSFV in the culture. After clearance of CSFV and PCV2, a pure PAstV5 strain, named PAstV5-AH29-2014, was obtained. Analysis revealed virus of typical astroviral morphology with a genome of 6,448 nucleotides, sharing 84.3 to 88.9% nucleotide identity with previously published PAstV5 strains. A mechanistic study showed that CSFV coinfection was likely an important factor for successful isolation by significantly enhancing PAstV5 replication in PK-15 cells via suppression of a type I interferon response. Altogether, PAstV5-AH29-2014, as the first isolated PAstV5 strain, will provide critical material for the investigation of the biological and pathogenic properties of this virus as well as for future development of relevant biological and diagnostic reagents.
Porcine astroviruses are mainly associated with gastroenteritis and neurological diseases in pigs, and five genotypes have been identified (PAstV1-5). However, the clinical manifestations of genotypes other than PAstV1 have not yet been determined because of the failure of
virus isolation. Here, we report a surprising isolation of a PAstV5 strain from a clinical classical swine fever virus (CSFV)-infected tissue sample, which can stably passage in PK-15 cells, and coinfection with CSFV significantly enhanced the replication of PAstV5, possibly through suppression of beta interferon production. Thus, the first isolated PAstV5 strain will be useful for investigating the biological and pathogenic properties of this virus, and the findings obtained in this study provide new insights into defining the interaction mechanism between CSFV and PAstV5.
Getah virus (GETV) is a mosquito‐borne virus that is widely distributed in Asian countries including China, in which the first case of equine GETV infection was reported in Guangdong province in ...August 2018. In this study, GETVs were detected in two classical swine fever virus‐positive samples collected from swine herds in Foshan city, Guangdong province, 2018. Infection of porcine PK‐15 cells produced rapid cytopathic effects (CPEs), including shrinking, rounding and detaching, and peak titre of 109.3 TCID50/ml occurred at 24 hr post‐infection. Electron microscopy and ultra‐thin sectioning revealed spherical GETV particles of 70 nm diameter with an isometric interior and are found to be lining the outer membrane of infected cells. Whole‐genome analysis showed that the two GETV isolates are identical to each other and cluster with Group III strains of GETV, sharing 96.1%–99.7% nucleotide sequence identity with all available reference strains. The most closely relative of the obtained GETV isolates was porcine strain HNJZ‐S2 from Henan province (99.7%), with 98.6% sequence identity shared with equine GETV strain GZ201808 first identified in Guangdong province, indicating different sources for porcine and equine GETV infections in this region. No evidence of GETV infection was found in 497 archived porcine samples collected between 1990 and 2018 in Guangdong province.
Senecavirus A (SVA), an emerging swine pathogen, has been reported in many provinces of China since the first outbreak in 2015 in Guangdong province. In this study, 10 lymph nodes positive for SVA, ...collected between 2018 and 2019 from slaughterhouses in Guangdong province, were subjected to virus isolation. Rapid and evident cytopathic effects (CPEs) were observed in SVA-infected PK-15 cells, including shrinking, rounding and detaching, with peak titers being reached at 24 h post infection (hpi). Electron microscopy showed that SVA particles are spherical and approximately 30 nm in diameter, and exist as crystalline lattices in cytoplasm revealed by ultra-thin sectioning. Phylogenetic analysis based on the whole genome sequences of all available isolates showed that SVA globally can be divided into two groups with each being further divided into two subgroups (Ia-b and IIa-b), and with the Guangdong isolates obtained here and other Chinese strains belonging to subgroups IIa and IIb. Evolutionary analysis showed that the mean substitution rate of SVA was 2.696 × 10−3 per site per year based on whole genomic sequences, with subgroup IIb isolates having evolved faster than those of subgroup IIa. Analysis of efficient population size showed that the outbreak point of SVA worldwide occurred at the end of 2013 with that of subgroup IIb, the current dominant group, in mid 2014.
•SVA particles are spherical and approximately 30 nm in diameter, and exist as crystalline lattices in cytoplasm.•SVA isolates can be divided into two groups with each being further divided into two subgroups (Ia-b and IIa-b).•SVA subgroup IIb isolates are currently dominant in China.
<p><b>Offers Timely and Comprehensive Coverage of Dynamic System Reliability Theory</b> <p>This book focuses on hot issues in dynamic system reliability, systematically ...introducing the reliability modeling and analysis methods for systems with imperfect fault coverage, systems with function dependence, systems subject to deterministic or probabilistic common&#45;cause failures, systems subject to deterministic or probabilistic competing failures, and dynamic standby sparing systems. It presents recent developments of such extensions involving reliability modeling theory, reliability evaluation methods, and features numerous case studies based on real&#45;world examples. The presented dynamic reliability theory can enable a more accurate representation of actual complex system behavior, thus, more effectively guiding the reliable design of real&#45;world critical systems. <p><i>Dynamic System Reliability: Modeling and Analysis of Dynamic and Dependent</i> <i>Behaviors</i> begins by describing the evolution from the traditional static reliability theory to the dynamic system reliability theory, and provides a detailed investigation of dynamic and dependent behaviors in subsequent chapters. Although written for those with a background in basic probability theory and stochastic processes, the book includes a chapter reviewing the fundamentals that readers need to know in order to understand contents of other chapters which cover advanced topics in reliability theory and case studies. <ul> <li>The first book systematically focusing on dynamic system reliability modeling and analysis theory</li> <li>Provides a comprehensive treatment on imperfect fault coverage &#40;single&#45;level/ multi&#45;level or modular&#41;, function dependence, common cause failures &#40;deterministic and probabilistic&#41;, competing failures &#40;deterministic and probabilistic&#41;, and dynamic standby sparing</li> <li>Includes abundant illustrative examples and case studies based on real&#45;world systems</li> <li>Covers recent advances in combinatorial models and algorithms for dynamic system reliability analysis</li> <li>Offers a rich set of references, providing helpful resources for readers to pursue further research and study of the topics</li> </ul> <p><i>Dynamic System Reliability: Modeling and Analysis of Dynamic and Dependent Behaviors</i> is an excellent book for undergraduate and graduate students, engineers and researchers in reliability and related disciplines.
PICKLE
(
PKL
), a putative CHD3 chromatin remodeling factor, has been suggested to be involved in multiple processes in
Arabidopsis
. Here, we confirmed the late-flowering phenotype caused by
pkl
...mutation with
pkl
mutants in two different ecotypes, and investigated the possible mechanisms that account for PKL regulation of flowering time. Quantitative RT-PCR and RNA-seq assays showed that expression of the
LEAFY
gene (
LFY
) and a number of LFY-regulated floral homeotic genes were down-regulated in seedlings of the
pkl
mutants. As predicted, overexpression of
LFY
restored normal flowering time of
pkl
mutants. Our results suggest that PKL may be involved in regulating flowering time via
LFY
expression. To uncover the underlying mechanism, ChIP-PCR using anti-PKL was performed on materials from three developmental stages of seedlings. Our results showed that PKL associated with the genomic sequences of
LFY
, particularly at 10-day and 25-day after germination. We also showed that loss of
PKL
affected H3K27me3 level at the promoter of
LFY
. Taken together, our data suggest that transcriptional regulation of
LFY
at the chromatin level by PKL may at least partially account for the late-flowering phenotype of
pkl
mutants.
•Common cause failures are modeled and analyzed for non-repairable phased-mission systems.•Combinatorial methods based on multiple-valued decision diagrams are proposed.•An explicit method and two ...implicit methods are compared.•All three methods are applicable to arbitrary distribution types for component time-to-failure.
Due to a shock or shared root cause, multiple system components may fail at the same time contributing significantly to the entire system failure. Such dependent component failures are referred to as common cause failures (CCFs). A rich body of research has been conducted for addressing effects of CCFs in reliability analysis of diverse types of systems. This paper first adapts multiple-valued decision diagrams (MDDs) for analyzing reliability of a non-repairable phased-mission system (PMS) subject to CCFs caused by external shocks. An explicit method and two implicit methods based on MDDs are proposed and compared. While the three MDD-based methods differ in terms of space and computation complexities, examples show that all these methods offer low computational complexity while addressing dynamics and dependencies caused by CCFs and phased operations.
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