Identification and characterization of viral defective RNA genomes in influenza B virus.

Influenza B virus (FLUBV) is an important pathogen that infects humans and causes seasonal influenza epidemics. To date, little is known about defective genomes of FLUBV and their roles in viral replication. In this study, by using a next-generation sequencing approach, we analyzed total mRNAs extracted from A549 cells infected with B/Brisbane/60/2008 virus (Victoria lineage), and identified four defective FLUBV genomes with two (PB1∆A and PB1∆B) from the polymerase basic subunit 1 (PB1) segment and the other two (M∆A and M∆B) from the matrix (M) protein-encoding segment. These defective genomes contained significant deletions in the central regions with each having the potential for encoding a novel polypeptide. Significantly, each of the discovered defective RNAs can potently inhibit the replication of B/Yamanashi/166/98 (Yamagata lineage). Furthermore, PB1∆A was able to interfere modestly with influenza A virus (FLUAV) replication. In summary, our study provides important initial insights into FLUBV defective-interfering genomes, which can be further explored to achieve better understanding of the replication, pathogenesis and evolution of FLUBV.

Domestic pigs are susceptible to infection with influenza B viruses.

UNLABELLED: Influenza B virus (IBV) causes seasonal epidemics in humans. Although IBV has been isolated from seals, humans are considered the primary host and reservoir of this important pathogen. It is unclear whether other animal species can support the replication of IBV and serve as a reservoir. Swine are naturally infected with both influenza A and C viruses. To determine the susceptibility of pigs to IBV infection, we conducted a serological survey for U.S. Midwest domestic swine herds from 2010 to 2012. Results of this study showed that antibodies to IBVs were detected in 38.5% (20/52) of sampled farms, and 7.3% (41/560) of tested swine serum samples were positive for IBV antibodies. Furthermore, swine herds infected with porcine reproductive and respiratory syndrome virus (PRRSV) showed a higher prevalence of IBV antibodies in our 2014 survey. In addition, IBV was detected in 3 nasal swabs collected from PRRSV-seropositive pigs by real-time RT-PCR and sequencing. Finally, an experimental infection in pigs, via intranasal and intratracheal routes, was performed using one representative virus from each of the two genetically and antigenically distinct lineages of IBVs: B/Brisbane/60/2008 (Victoria lineage) and B/Yamagata/16/1988 (Yamagata lineage). Pigs developed influenza-like symptoms and lung lesions, and they seroconverted after virus inoculation. Pigs infected with B/Brisbane/60/2008 virus successfully transmitted the virus to sentinel animals. Taken together, our data demonstrate that pigs are susceptible to IBV infection; therefore, they warrant further surveillance and investigation of swine as a potential host for human IBV. IMPORTANCE: IBV is an important human pathogen, but its ability to infect other species, for example, pigs, is not well understood. We showed serological evidence that antibodies to two genetically and antigenically distinct lineages of IBVs were present among domestic pigs, especially in swine herds previously infected with PRRSV, an immunosuppressive virus. IBV was detected in 3 nasal swabs from PRRSV-seropositive pigs by real-time reverse transcription-PCR and sequencing. Moreover, both lineages of IBV were able to infect pigs under experimental conditions, with transmissibility of influenza B/Victoria lineage virus among pigs being observed. Our results demonstrate that pigs are susceptible to IBV infections, indicating that IBV is a swine pathogen, and swine may serve as a natural reservoir of IBVs. In addition, pigs may serve as a model to study the mechanisms of transmission and pathogenesis of IBVs.

Isolation of a novel swine influenza virus from Oklahoma in 2011 which is distantly related to human influenza C viruses.

Of the Orthomyxoviridae family of viruses, only influenza A viruses are thought to exist as multiple subtypes and has non-human maintenance hosts. In April 2011, nasal swabs were collected for virus isolation from pigs exhibiting influenza-like illness. Subsequent electron microscopic, biochemical, and genetic studies identified an orthomyxovirus with seven RNA segments exhibiting approximately 50% overall amino acid identity to human influenza C virus. Based on its genetic organizational similarities to influenza C viruses this virus has been provisionally designated C/Oklahoma/1334/2011 (C/OK). Phylogenetic analysis of the predicted viral proteins found that the divergence between C/OK and human influenza C viruses was similar to that observed between influenza A and B viruses. No cross reactivity was observed between C/OK and human influenza C viruses using hemagglutination inhibition (HI) assays. Additionally, screening of pig and human serum samples found that 9.5% and 1.3%, respectively, of individuals had measurable HI antibody titers to C/OK virus. C/OK virus was able to infect both ferrets and pigs and transmit to naive animals by direct contact. Cell culture studies showed that C/OK virus displayed a broader cellular tropism than a human influenza C virus. The observed difference in cellular tropism was further supported by structural analysis showing that hemagglutinin esterase (HE) proteins between two viruses have conserved enzymatic but divergent receptor-binding sites. These results suggest that C/OK virus represents a new subtype of influenza C viruses that currently circulates in pigs that has not been recognized previously. The presence of multiple subtypes of co-circulating influenza C viruses raises the possibility of reassortment and antigenic shift as mechanisms of influenza C virus evolution.

Palmitoylation is required for intracellular trafficking of influenza B virus NB protein and efficient influenza B virus growth in vitro.

All influenza viruses bud and egress from lipid rafts within the apical plasma membrane of infected epithelial cells. As a result, all components of progeny virions must be transported to these lipid rafts for assembly and budding. Although the mechanism of transport for other influenza proteins has been elucidated, influenza B virus (IBV) glycoprotein NB subcellular localization and transport are not understood completely. To address the aforementioned properties of NB, a series of trafficking experiments were conducted. Here, we showed that NB co-localized with markers specific for the endoplasmic reticulum (ER) and Golgi region. The data from chemical treatment of NB-expressing cells by Brefeldin A, a fungal antibiotic and a known chemical inhibitor of the protein secretory pathway, further confirmed that NB is transported through the ER-Golgi pathway as it restricted NB localization to the perinuclear region. Using NB deletion mutants, the hydrophobic transmembrane domain was identified as being required for NB transport to the plasma membrane. Furthermore, palmitoylation was also required for transport of NB to the plasma membrane. Systematic mutation of cysteines to serines in NB demonstrated that cysteine 49, likely in a palmitoylated form, is also required for transport to the plasma membrane. Surprisingly, further analysis demonstrated that in vitro replication of NBC49S mutant virus was delayed relative to the parental IBV. The results demonstrated that NB is the third influenza virus protein to have been shown to be palmitoylated and together these findings may aid in future studies aimed at elucidating the function of NB.

Genomic and evolutionary characterization of a novel influenza-C-like virus from swine.

We recently described the isolation of a novel influenza virus from swine exhibiting respiratory disease in the United States that is distantly related to human influenza C virus. Based on genetic, biochemical and morphological analysis, the virus was provisionally classified as C/swine/Oklahoma/1334/2011 (C/OK). To further understand the genetics and evolution of this novel pathogen, we performed a comprehensive analysis of its sequence and phylogeny. The results demonstrated that C/OK and human influenza C viruses share a conserved array of predicted functional domains in the viral RNA genome replication and viral entry machinery but vary at key functional sites. Furthermore, our evolutionary analysis showed that homologous genes of C/OK and human influenza C viruses diverged from each other an estimated several hundred to several thousand years ago. Taken together, the findings described in this study support and extend our previous observations that C/OK is a genetically and evolutionarily distinct influenza virus in the family Orthomyxoviridae.

In vitro and in vivo replication of influenza A H1N1 WSN33 viruses with different M1 proteins.

The M1 protein is a major structural protein that has multiple functions in various steps within the life cycle of the influenza A virus (IAV). However, little is currently known about the role of M1 in IAV replication in vivo and the associated pathogenesis. In this study, six isogenic H1N1 WSN33 viruses, constructed to express unique M1 proteins derived from various strains, subtypes or WSN33 itself, were tested to determine in vitro and in vivo functional exchangeability of M1 proteins in the replication and pathogenesis of the WSN33 virus. Despite five chimeric M1 viruses replicating to levels similar to those of the parental WSN33 virus in cell cultures, all M1 chimeras exhibited improved replication and enhanced virulence in mice when compared with the WSN33 virus. Interestingly, M1 proteins derived from swine viruses caused more severe clinical diseases than those from human or quail. These data indicate that the M1 protein is an important determinant of viral replication and pathogenic properties in mice, although the functions of M1 observed in vivo are not adequately reflected in simple infections of cultured cells. Chimeric M1 viruses that are variable in their clinical manifestations described here will aid future understanding of the role of M1 in IAV pathogenesis.

A DNA vaccine (EG95-PT1/2/3-IL2) encoding multi-epitope antigen and IL-2 provokes efficient and long-term immunity to echinococcosis.

Echinococcosis is a highly prevalent global zoonosis, and vaccines are required. The commercial vaccine based on a protein-based subunit (EG95), however, is limited by its insufficient cellular immunity, a short protection period, and limited prevention against novel mutant strains. Herein, we applied bioinformatics to develop a DNA vaccine (pEG95-IL2) expressing both multi-epitope-based antigens (EG95-PT1/2/3) and an IL-2 adjuvant to regulate T cell differentiation and memory cell response. EG95-PT1/2/3 was screened with hierarchical structure prediction from the epitope conformation of B cells with high confidence across various species to guarantee immunogenicity. Importantly, cationic arginine-rich lipid nanoparticles (RNP) were utilized as a delivery vehicle to form lipoplexes that had a transfection efficiency of nearly two orders of magnitude greater than that of commercial reagents (Lipofectamine 2000 and polyethyleneimine) with both immune and nonimmune cells (DC2.4 and L929 cells, respectively). RNP/pEG95-IL2 lipoplexes displayed a robust and long-term antigen expression, as well as adjuvant effects during the immunization. Consequently, intramuscular injection of RNP/pEG95-IL2 elicited similar humoral immune responses and significantly greater cellular responses in mice when compared with those of the commercial vaccine. In addition, the inoculation protocol of RNP/pEG95-IL2 with sequential booster further strengthens cellular immunity in comparison with the homologous booster. Those findings provide a promising strategy for improving plasmid vaccine efficacy.

Meta-Analysis of the Prevalence of Echinococcus in Sheep in China From 1983 to 2020.

Echinococcosis is a zoonosis caused by the larval stage of cestode species that belong to the genus Echinococcus. The infection of hydatid in sheep is very common in China, especially in the northwestern China. Here, we conducted the first systematic review and meta-analysis of echinococcosis in sheep in China. Six databases (PubMed, ScienceDirect, Baidu Library, CNKI, Wanfang, and VIP Chinese Journal Database) were used to retrieve the literatures on echinococcosis in sheep in China from 1983 to 2020, and 74 studies. The random effects model was used in the "meta" package of the R software and the PFT was chosen for rate conversion. The research data were analyzed through subgroup analysis and univariate meta-regression analysis to reveal the factors that lead to research heterogeneity. The combined prevalence of Echinococcus in the selected period was estimated to be 30.9% (192,094/826,406). In the analysis of sampling year, the lowest positive rate was 13.9% (10,296/177,318) after 2011. The highest prevalence of Echinococcus was 51.1% (278/531) in the southwestern China. The highest infection rate in sheep was 20.1% (58,344/597,815) in the liver. The analysis based on age showed that the infection rate of elderly sheep was significantly higher than that in younger animals (P < 0.05). We also evaluated the effects of different geographic and climatic factors on the prevalence of Echinococcus in sheep. The results showed that the prevalence of Echinococcus was higher in high altitude, cold, humid, and high rainfall areas. It is necessary to carry out long-term monitoring and control of echinococcosis, cut off the infection route, and reduce the risk of infection in the high risk areas.

Next-Generation Sequencing Analysis of Cellular Response to Influenza B Virus Infection.

Influenza B virus (IBV) is a respiratory pathogen that infects humans and causes seasonal influenza epidemics. However, cellular response to IBV infection in humans and mechanisms of host-mediated restriction of IBV replication are not thoroughly understood. In this study, we used next-generation sequencing (NGS) to perform transcriptome profiling of IBV-infected human lung epithelial A549 cells at 0, 6, 12, and 24 h post infection (hpi) and characterized the cellular gene expression dynamics. We observed that more than 4000 host genes were differentially regulated during the study period, which included up regulation of genes encoding proteins, having a role in the innate antiviral immune responses, immune activation, cellular metabolism, autophagy, and apoptosis, as well as down regulation of genes involved in mitosis and cell proliferation. Further analysis of RNA-Seq data coupled with RT-qPCR validation collectively showed that double-strand RNA recognition pathways, including retinoic acid-inducible gene I (RIG-I) and Toll-like receptor 3 (TLR3), were substantially activated following IBV infection. Taken together, these results provide important initial insights into the intimate interaction between IBV and lung epithelial cells, which can be further explored towards elucidation of the cellular mechanisms in restriction or elimination of IBV infections in humans.

[Unnatural amino acid orthogonal translation: a genetic engineering technology for the development of new-type live viral vaccine].

Unnatural amino acid orthogonal translation machinery can insert unnatural amino acids at desired sites of protein through stop codon by means of foreign orthogonal translation system composed of aminoacyl-tRNA synthetase and orthogonal tRNA genes. This new genetic engineering technology is not only a new tool for biochemical researches of proteins, but also an epoch-making technology for the development of new-type live viral vaccines. The mutated virus containing premature termination codon in genes necessary for replication can be propagated in transgenic cells harboring unnatural amino acid orthogonal translation machinery in media with corresponding unnatural amino acid, but it cannot replicate in conventional host cells. This replication-deficient virus is a new-type of live viral vaccine that possesses advantages of high efficacy of traditional attenuated vaccine and high safety of killed vaccine. This article reviews the application and prospect of unnatural amino acid orthogonal translation machinery in the development of novel replication-deficient virus vaccines.

Comparison of Porcine Airway and Intestinal Epithelial Cell Lines for the Susceptibility and Expression of Pattern Recognition Receptors upon Influenza Virus Infection.

Influenza viruses infect the epithelial cells of the swine respiratory tract. Cell lines derived from the respiratory tract of pigs could serve as an excellent in vitro model for studying the pathogenesis of influenza viruses. In this study, we examined the replication of influenza viruses in the MK1-OSU cell line, which was clonally derived from pig airway epithelium. MK1-OSU cells expressed both cytokeratin and vimentin proteins and displayed several sugar moieties on the cell membrane. These cells also expressed both Sial2-3Gal and Sial2-6Gal receptors and were susceptible to swine influenza A, but not to human B and C viruses. Interestingly, these cells were also permissive to infection by influenza D virus that utilized 9-O-acetylated glycans. To study the differences in the expression of pattern recognition receptors (PRRs) upon influenza virus infection in the respiratory and digestive tract, we compared the protein expression of various PRRs in MK1-OSU cells with that in the SD-PJEC cell line, a clonally derived cell line from the porcine jejunal epithelium. Toll-like receptor 7 (TLR-7) and melanoma differentiation-associated protein 5 (MDA5) receptors showed decreased expression in influenza A infected MK1-OSU cells, while only TLR-7 expression decreased in SD-PJEC cells. Further research is warranted to study the mechanism behind the virus-mediated suppression of these proteins. Overall, this study shows that the porcine respiratory epithelial cell line, MK1-OSU, could serve as an in-vitro model for studying the pathogenesis and innate immune responses to porcine influenza viruses.

[Recovery of an infectious virus from the full-length cDNA of PRRSV BJ-4].

Six recombinant plasmids covering cDNA of porcine reproductive and respiratory syndrome virus BJ-4 were sequenced, respectively, and 23 point mutations were reverted with site-directed mutagenesis kit. The full-length cDNA clone pWSK-DCBA was assembled and re-sequenced. The capped viral genomic RNA was transcribed in vitro, mixed with liposome and transfected into MARC-145 cells, and an infectious virus (designated rV68) was rescued. The rescued virus was able to induce CPE typical of PRRSV on MARC-145 and stably propagated in vitro . Growth kinetics curve of the rV68 exhibited a delayed replication in MARC-145 cell, namely its peak titer time was 12h later than that of parental virus. However, there was no significant difference between the peak titers of the rescued and parental virus (P > 0.05). These results suggest that the full-length cDNA clone pWSK-DCBA of PRRSV BJ-4 is infectious, which provide a basis for further study on molecular pathogenicity and immunity, as well as developing novel vaccine of PRRSV.

In vitro reassortment between endemic H1N2 and 2009 H1N1 pandemic swine influenza viruses generates attenuated viruses.

The pandemic H1N1 (pH1N1) influenza virus was first reported in humans in the spring of 2009 and soon thereafter was identified in numerous species, including swine. Reassortant viruses, presumably arising from the co-infection of pH1N1 and endemic swine influenza virus (SIV), were subsequently identified from diagnostic samples collected from swine. In this study, co-infection of swine testicle (ST) cells with swine-derived endemic H1N2 (MN745) and pH1N1 (MN432) yielded two reassortant H1N2 viruses (R1 and R2), both possessing a matrix gene derived from pH1N1. In ST cells, the reassortant viruses had growth kinetics similar to the parental H1N2 virus and reached titers approximately 2 log(10) TCID(50)/mL higher than the pH1N1 virus, while in A549 cells these viruses had similar growth kinetics. Intranasal challenge of pigs with H1N2, pH1N1, R1 or R2 found that all viruses were capable of infecting and transmitting between direct contact pigs as measured by real time reverse transcription PCR of nasal swabs. Lung samples were also PCR-positive for all challenge groups and influenza-associated microscopic lesions were detected by histology. Interestingly, infectious virus was detected in lung samples for pigs challenged with the parental H1N2 and pH1N1 at levels significantly higher than either reassortant virus despite similar levels of viral RNA. Results of our experiment suggested that the reassortant viruses generated through in vitro cell culture system were attenuated without gaining any selective growth advantage in pigs over the parental lineages. Thus, reassortant influenza viruses described in this study may provide a good system to study genetic basis of the attenuation and its mechanism.