Identification of novel mammalian viruses in tree shrews(Tupaia belangeri chinensis)

The Chinese tree shrew(Tupaia belangeri chinensis),a member of the mammalian order Scandentia,exhibits considerable similarities with primates,including humans,in aspects of its nervous,immune,and metabolic systems.These similarities have established the tree shrew as a promising experimental model for biomedical research on cancer,infectious diseases,metabolic disorders,and mental health conditions.Herein,we used metatranscriptomic sequencing to analyze plasma,as well as oral and anal swab samples,from 105 healthy asymptomatic tree shrews to identify the presence of potential zoonotic viruses.In total,eight mammalian viruses with complete genomes were identified,belonging to six viral families,including Flaviviridae,Hepeviridae,Parvovirinae,Picornaviridae,Sedoreoviridae,and Spinareoviridae.Notably,the presence of rotavirus was recorded in tree shrews for the first time.Three viruses-hepacivirus 1,parvovirus,and picornavirus-exhibited low genetic similarity(<70%)with previously reported viruses at the whole-genome scale,indicating novelty.Conversely,three other viruses-hepacivirus 2,hepatovirus A and hepevirus-exhibited high similarity(>94%)to known viral strains.Phylogenetic analyses also revealed that the rotavirus and mammalian orthoreovirus identified in this study may be novel reassortants.These findings provide insights into the diverse viral spectrum present in captive Chinese tree shrews,highlighting the necessity for further research into their potential for crossspecies transmission.

Role of viruses in periodontitis:An extensive review of herpesviruses,human immunodeficiency virus,coronavirus-19,papillomavirus and hepatitis viruses

Periodontitis is the inflammation of the supporting structures around the dentition.Several microbial agents,mostly bacteria,have been identified as causative factors for periodontal disease.On the other hand,oral cavity is a rich reservoir for viruses since it contains a wide variety of cell types that can be targeted by viruses.Traditionally,the focus of research about the oral flora has been on bacteria because the most widespread oral diseases,like periodontitis and dental caries,are outcomes of bacterial infection.However,recently and especially after the emergence of coronavirus disease 2019,there is a growing tendency toward including viruses also into the scope of oral microbiome investigations.The global high prevalence of periodontitis and viral infections may point out to a concomitant or synergistic effect between the two.Although the exact nature of the mechanism still is not clearly understood,this could be speculated through the manipulation of the immune system by viruses;hence facilitating the furthermore colonization of the oral tissues by bacteria.This review provides an extensive and detailed update on the role of the most common viruses including herpes family(herpes simplex,varicella-zoster,Epstein-Barr,cytomegalovirus),Human papillomaviruses,Human immunodeficiency virus and severe acute respiratory syndrome coronavirus 2 in the initiation,progression and prognosis of periodontitis.

Substitutions of stem-loop subdomains in internal ribosome entry site of Senecavirus A:Impacts on rescue of sequence-modifying viruses

Senecavirus A(SVA)has a positive-sense,single-stranded RNA genome.Its 5´untranslated region harbors an internal ribosome entry site(IRES),comprising 10 larger or smaller stem-loop structures(including a pseudoknot)that have been demonstrated to be well conserved.However,it is still unclear whether each stem-loop subdomain,such as a single stem or loop,is also highly conserved.To clarify this issue in the present study,a set of 29 SVA cDNA clones were constructed by site-directed mutagenesis(SDM)on the IRES.The SDM-modified scenarios included:(1)stem-formed complementary sequences exchanging with each other;(2)loop transversion;(3)loop transition;and(4)point mutations.All cDNA clones were separately transfected into cells for rescuing viable viruses,whereas only four SVAs of interest could be recovered,and were genetically stable during 20 passages.One progeny grew significantly slower than the other three did.The dual-luciferase reporter assay showed that none of the SDM-modified IRESes significantly inhibited the IRES activity.Our previous study indicated that a single motif from any of the ten stem structures,if completely mutated,would cause the failure of virus recovery.Interestingly,our present study revealed three stem structures,whose individual complementary sequences could exchange with each other to rescue sequence-modifying SVAs.Moreover,one apical loop was demonstrated to have the ability to tolerate its own full-length transition,also having no impact on the recovery of sequence-modifying SVA.The present study suggested that not every stem-loop structure was strictly conserved in its conformation,while the full-length IRES itself was well conserved.This provides a new research direction on interaction between the IRES and many factors.

Genetic and biological properties of H10Nx influenza viruses in China

H10 subtype avian influenza viruses(AIV)have been circulating in China for 40 years.H10 AIVs in China have expanded their host range from wild birds to domestic poultry and mammals,even human.Most of the H10 subtype AIVs reported in China were isolate from the southeast part.We isolated an H10N3 AIV,A/Chicken/Liaoning/SY1080/2021(SY1080),from live poultry market(LPM)in Liaoning Province of the Northeast China.SY1080replicated efficiently in mice lungs and nasal turbinates without prior adaptation.We systematically compared SY1080 with other H10 subtype isolates in China.Phylogenetic analysis showed that SY1080 and most of the H10strains belonged to the Eurasian lineage.H10 AIVs in China have formed 63 genotypes.SY1080 as well as the H10N3 strains from human infections belonged to G60 genotype.H10Nx AIV acquired multiple mammalian adaptive and virulence related mutations during circulation and the recent reassortants derived internal genes from chicken H9N2 AIVs.The H10Nx subtypes AIVs posed potential threat to public health.These results suggested we should strengthen the surveillance and evaluation of H10 subtype strains.

Genetic and biological properties of H9N2 avian influenza viruses isolated in central China from2020 to 2022

The H9N2 subtype of avian influenza virus(AIV)is widely prevalent in poultry and wild birds globally,and has become the predominant subtype circulating in poultry in China.The H9N2 AIV can directly or indirectly(by serving as a"donor virus")infect humans,posing a significant threat to public health.Currently,there is a lack of in-depth research on the prevalence of H9N2 viruses in Shanxi Province,central China.In this study,we isolated 14 H9N2 AIVs from October 2020 to April 2022 in Shanxi Province,and genetic analysis revealed that these viruses belonged to 7 different genotypes.Our study on animals revealed that the H9N2 strains we identified displayed high transmission efficiency among chicken populations,and exhibited diverse replication abilities within these birds.These viruses could replicate efficiently in the lungs of mice,with one strain also demonstrating the capacity to reproduce in organs like the brain and kidneys.At the cellular level,the replication ability of different H9N2 strains was evaluated using plaque formation assays and multi-step growth curve assays,revealing significant differences in the replication and proliferation efficiency of the various H9N2 viruses at the cellular level.The antigenicity analysis suggested that these isolates could be classified into 2 separate antigenic clusters.Our research provides crucial data to help understand the prevalence and biological characteristics of H9N2 AIVs in central China.It also highlights the necessity of enhancing the surveillance of H9N2 AIVs.

Advance of the Research on Testing of Animal Viruses by LAMP Technology in Abroad

Loop-mediated isothermal amplification（LAMP） is an amplification method developed by Notomi et al and has been applied successfully for the detection of many viruses.This paper introduced the current status of LAMP and recent developments,and the method applying in the diagnosis of animal viruses in abroad.

Virion Proteomics of Large DNA Viruses

Large DNA viruses normally have complex structures with many of protein components derived from both viral and host origins. The development in proteomics, especially mass spectrometry identification techniques provide powerful tools for analyzing large viruses. In this review, we have summarized the recent achievements on proteomic studies of large DNA viruses, such as herpesvirus, poxvirus, nimavirus and baculoviruse. The proteomics of baculovirus occlusion-derived virions (ODV) were emphasized. Different mass spectrometry techniques used on various baculoviruses were introduced, and the identified structurally associated proteins of baculoviruses are summarized.

Molecular Characteristics of gp90 Gene of 14 Reticuloendotheliosis Viruses Isolated in China

[Objective] The paper was to study molecular characteristics of gp90 gene of 14 Reticuloendotheliosis viruses isolated in China.[Method] The surface envelop gene gp90 of 14 REV strains isolated from different commercial layer farms in China were amplified,and their nucleotide sequences were determined.[Result] Sequence analysis showes that 14 REV strains are more identical to the subtype 3 isolates than to the early Chinese REV isolates.In addition,14 REV strains have a high identity with some REV strains in US and Taiwan.[Conclusion] The study provided necessary information for further understanding the evolution of REV.

Sequence Analysis of HA Genes from Three H9N2 Subtype Avian Influenza Viruses

[ Objective] The study aimed to understand the genetic characters of H9N2 subtype avian influenza viruses isolated in Belling area. [ Method] HA genes of three H9N2 subtype avian influenza viruses A/Chicken/Beijing/xu/00, A/Chicken/Beijing/bei/00 and A/Chicken/Beijing/ liu/00 were amplified by RT-PCR and then sequenced. [ Result] The results of phylogenetic analysis showed that A/Chicken/Beijing/xu/00, A/ Chicken/Beijing/bei/00 and A/Chicken/Beijing/liu/00 shared the nucleotide homologies of 84.8% （ Dk/HK/Y439/97 ） -98.0% （ Ck/GX17/00 ）, 85.1% （Dk/HK/Y439/97） - 99.1% （ Ck/GXl 7/00）, 90.7% （ Ck/BJ/3/01 ） - 99.1% （Ck/GX17/00） with the isolates from Hongkong and other are- as of Chinese Mainland respectively. At the same time, the analysis of amino acid indicated that the three isolates belonged to low pathogenic H9N2 isolates of avian origin. The 226^th amino acid of them were L （ Leu）, suggesting their high binding affinity to human cells. There were seven glyco- sylation sites in HA protein, five from HA1 and two from HA2. [ Cenclusien] By analysis at molecular level, it could be concluded that A/Chicken/ Beijing/xu/00, A/Chicken/Beijing/bei/00 and A/Chicken/Beijing/liu/00 were low pathogenic H9N2 isolates of avian origin.

Could autophagy dysregulation link neurotropic viruses to Alzheimer’s disease?

Neurotropic herpesviruses have been associated with the onset and progression of Alzheimer’s disease,a common form of dementia that afflicts a large percentage of elderly individuals.Interestingly,among the neurotropic herpesviruses,herpes simplex virus-1,human herpesvirus-6A,and human herpesvirus-6B have been reported to infect several cell types present in the central nervous system and to dysregulate autophagy,a process required for homeostasis of cells,especially neurons.Indeed autophagosome accumulation,indicating an unbalance between autophagosome formation and autophagosome degradation,has been observed in neurons of Alzheimer’s disease patients and may play a role in the intracellular and extracellular accumulation of amyloidβand in the altered protein tau metabolism.Moreover,herpesvirus infection of central nervous system cells such as glia and microglia can increase the production of oxidant species through the alteration of mitochondrial dynamics and promote inflammation,another hallmark of Alzheimer’s disease.This evidence suggests that it is worth further investigating the role of neurotropic herpesviruses,particularly human herpesvirus-6A/B,in the etiopathogenesis of Alzheimer’s disease.

Human hepatitis viruses-associated cutaneous and systemic vasculitis

Human hepatitis viruses(HHVs)include hepatitis A virus,hepatitis B virus(HBV),hepatitis C virus(HCV),hepatitis delta virus,and hepatitis E virus and can cause liver inflammation in their common human host.Usually,HHV is rapidly cleared by the immune system,following acute HHV invasion.The morbidities associated with hepatitis A virus and hepatitis E virus infection occur shortly after their intrusion,in the acute stage.Nevertheless,the viral infectious process can persist for a long period of time,especially in HBV and HCV infection,leading to chronic hepatitis and further progressing to hepatic cirrhosis and liver cancer.HHV infection brings about complications in other organs,and both acute and chronic hepatitis have been associated with clinical presentations outside the liver.Vascular involvement with cutaneous and systemic vasculitis is a well-known extrahepatic presentation;moreover,there is growing evidence for a possible causal relationship between viral pathogens and vasculitis.Except for hepatitis delta virus,other HHVs have participated in the etiopathogenesis of cutaneous and systemic vasculitis via different mechanisms,including direct viral invasion of vascular endothelial cells,immune complex-mediated vessel wall damage,and autoimmune responses with stimulation of autoreactive B-cells and impaired regulatory T-cells.Cryoglobulinemic vasculitis and polyarteritis nodosa are recognized for their association with chronic HHV infection.Although therapeutic guidelines for HHV-associated vasculitis have not yet been established,antiviral therapy should be initiated in HBV and HCV-related systemic vasculitis in addition to the use of corticosteroids.Plasma exchange and/or combined cyclophosphamide and corticosteroid therapy can be considered in patients with severe life-threatening vasculitis manifestations.

Multiplex qPCR for serodetection and serotyping of hepatitis viruses: A brief review

The present review describes the current status of multiplex quantitative real time polymerase chain reaction(q PCR) assays developed and used globally for detection and subtyping of hepatitis viruses in body fluids. Several studies have reported the use of multiplex q PCR for the detection of hepatitis viruses, including hepatitis A virus(HAV), hepatitis B virus(HBV), hepatitis C virus(HCV), hepatitis D virus(HDV), and hepatitis E virus(HEV). In addition, multiplex q PCR has also been developed for genotyping HBV, HCV, and HEV subtypes. Although a single step multiplex q PCR assay for all six hepatitis viruses, i.e., A to G viruses, is not yet reported, it may be available in the near future as the technologies continue to advance. All studies use a conserved region of the viral genome as the basis of amplification and hydrolysis probes as the preferred chemistries for improved detection. Based on a standard plot prepared using varying concentrations of template and the observed threshold cycle value, it is possible to determine the linear dynamic range and to calculate an exact copy number of virus in the specimen. Advantages of multiplex q PCR assay over singleplex or other molecular techniques in samples from patients with co-infection include fast results, low cost, and a single step investigation process.

Biological Control of Tortricidae in Tea Fields in Japan Using Insect Viruses and Parasitoids

Tea is a perennial and evergreen plant. Cultivated tea trees provide a habitat for insect pests and their natural enemies. In Japan, granuloviruses (GVs) have successfully controlled two of the most important pests of tea, Adoxophyes honmai and Homona magnanima (Tortricidae: Lepidoptera). The GVs are produced in vivo and a single application sustains pesticidal efficacy throughout a year, which encompasses 4 to 5 discrete generations of both species. A. honmai and H. magnanima also have various natural enemies, especially hymenopteran parasitoids. Such resident natural enemies also play a role in reducing the pest density in virus-controlled fields, but the effect of virus infection on parasitoids sharing the same host larva has not been well studied. Survival of one of the major parasitoids of A. honmai, Ascogaster reticulata (Braconidae: Hymenoptera), is reduced by virus infection of the host. Viruses, including GV and entomopoxvirus (EPV), and certain koinobiont endoparasitoids, including A. reticulata, are both known to regulate host endocrinology. However, the GV and EPV have distinct host regulation mechanisms, and consequently have different impacts on the survival of A. retuculata, when A. reticulata parasitizes a host that is infected with either GV or EPV. These additional effects on host regulation displayed by both viruses and parasitoids affect the outcome of virus-parasitoid interactions.

High-resolution 3D Structures Reveal the Biological Functions of Reoviruses

Viruses in the family Reoviridae are non-enveloped particles comprising a segmented double-stranded RNA genome surrounded by a two-layered or multi-layered icosahedral protein capsid.These viruses are classified into two sub-families based on their particle structural organization.Recent studies have focused on high-resolution three-dimensional structures of reovirus particles by using cryo-electron microscopy (cryo-EM) to approach the resolutions seen in X-ray crystallographic structures.The results of cryo-EM image reconstructions allow tracing of most of the protein side chains,and thus permit integration of structural and functional information into a coherent mechanism for reovirus assembly and entry.

Labeling of influenza viruses with synthetic fluorescent and biotin-labeled lipids

Direct labeling of virus particles is a powerful tool for the visualization of virus–cell interaction events. However, this technique involves the chemical modification of viral proteins that affects viral biological properties. Here we describe an alternative approach of influenza virus labeling that utilizes Function-Spacer-Lipid(FSL) constructs that can be gently inserted into the virus membrane. We assessed whether labeling with fluorescent(fluo-Ad-DOPE) or biotin-labeled(biot-CMG2-DOPE) probes has any deleterious effect on influenza virus hemagglutinin(HA) receptor specificity, neuraminidase(NA) activity, or replicative ability in vitro. Our data clearly show that neither construct significantly affected influenza virus infectivity or viral affinity to sialyl receptors. Neither construct influenced the NA activities of the influenza viruses tested, except the A/Puerto Rico/8/34(H1N1) strain. Our data indicate that lipid labeling provides a powerful tool to analyze influenza virus infection in vitro.

Human Monoclonal Antibodies as Candidate Therapeutics Against Emerging Viruses and HIV-1

More than 40 monoclonal antibodies (mAbs) have been approved for a number of disease indications with only one of these (Synagis) - for a viral disease, and not for therapy but for prevention. However, in the last decade novel potent mAbs have been discovered and characterized with potential as therapeutics against viruses of major importance for public health and biosecurity including Hendra virus (HeV), Nipah virus (NiV), severe acute respiratory syndrome coronavirus (SARS-CoV), Ebola virus (EBOV), West Nile virus (WNV), influenza virus (IFV) and human immunodeficiency virus type 1 (HIV-1). Here, we review such mAbs with an emphasis on antibodies of human origin, and highlight recent results as well as technologies and mechanisms related to their potential as therapeutics.

Tidal effects on diel variations of picoplankton and viruses in the Changjiang estuary

Spatial distributions and seasonal variations of picoplankton (i.e. Synechococcus spp., Prochlorococcus spp., picoeukaryotes and heterotrophic bacteria) and viruses in the Changjiang estuary have been reported in the past. However, short-term variations (e.g. at a tidal timescale) of these organisms and their regulating factors remain unclear. We determined the time-series of fluctuations of picoplankton and viruses with tide simultaneously in flow cytometry in the Changjiang estuary during a cruise in June 2006, in which a tidal model based rectangle equation was applied. The results indicate that high cell abundances of picoplankton and viruses occurred during flood tide and low cell abundances during ebb tide. The period of the surface cell abundance variations was about 13 h, suggesting the surface cell abundances in the Changjiang estuary were largely regulated by tide. However, cell abundances in middle and bottom waters varied in different periods due to influences of tidal induced physical forces such as resuspension and stratification. Therefore, tidal action is an important factor for the diel variations of picoplankton and viruses in the Changjiang estuary.

Laboratory biosafety for handling emerging viruses

Emerging viruses are viruses whose occurrence has risen within the past twenty years,or whose presence is likely to increase in the near future.Diseases caused by emerging viruses are a major threat to global public health.In spite of greater awareness of safety and containment procedures,the handling of pathogenic viruses remains a likely source of infection,and mortality,among laboratory workers.There is a steady increase in both the number of laboratories and scientist handling emerging viruses for diagnostics and research.The potential for harm associated to work with these infectious agents can be minimized through the application of sound biosafety concepts and practices.The main factors to the prevention of laboratory-acquired infection are well-trained personnel who are knowledgable and biohazard aware,who are perceptive of the various ways of transmission,and who are professional in safe laboratory practice management.In addition,we should emphasize that appropriate facilities,practices and procedures are to be used by the laboratory workers for the handling of emerging viruses in a safe and secure manner.This review is aimed at providing researchers and laboratory personnel with basic biosafety principles to protect themselves from exposure to emerging viruses while working in the laboratory.This paper focuses on what emerging viruses are,why emerging viruses can cause laboratory-acquired infection,how to assess the risk of working with emerging viruses,and how laboratory-acquired infection can be prevented.Control measures used in the laboratory designed as such that they protect workers from emerging viruses and safeguard the public through the safe disposal of infectious wastes are also addressed.

A duplex RT-PCR assay for detection of H9 subtype avian influenza viruses and infectious bronchitis viruses

H9 s ubtype avian influenza virus（AIV） and infectious bronchitis virus（IBV） are major pathogens circulating in poultry and have resulted in great economic losses due to respiratory disease and reduced egg production. As similar symptoms are elicited by the two pathogens, it is difficult for their differential diagnosis. So far, no reverse transcription-polymerase chain reaction（RT-PCR） assay has been found to differentiate between H9 AIV and IBV in one reaction. Therefore, developing a sensitive and specific method is of importance to simultaneously detect and differentiate H9 AIV and IBV. In this study, a duplex RT-PCR（d RT-PCR） was established. Two primer sets target the hemagglutinin（HA） gene of H9 AIV and the nucleocapsid（N） gene of IBV, respectively. Spec ific PCR products were obtained from all tested H9 AIVs and IBVs belonging to the major clades circulating in China, but not from AIVs of other subtypes or other infectious avian viruses. The sensitivity of the d RT-PCR assay corresponding to H9 AIV, IBV and mixture of H9 AIV and IBV were at a concentration of 1×10^1, 1.5×10^1 and 1.5×10^1 50% egg infective doses（EID_（50）） m L^–1, respectively. The concordance rates between the d RT-PCR and virus isolation were 99.1 and 98.2%, respectively, for detection of samples from H9N2 AIV or IBV infected chickens, while the concordance rate was 99.1% for detection of samples from H9N2 AIV and IBV co-infected chickens. Thus, the d RT-PCR assay reported herein is specific and sensitive, and suitable for the differential diagnosis of clinical infections and survei llance of H9 AIVs and IBVs.

Innate and adaptive immune responses against picornaviruses and their counteractions: An overview

Picornaviruses, small positive-stranded RNA viruses, cause a wide range of diseases which is based on their differential tissue and cell type tropisms. This diversity is reflected by the immune responses, both innate and adaptive, induced after infection, and the subsequent interactions of the viruses with the immune system. The defense mechanisms of the host and the countermeasures of the virus significantly contribute to the pathogenesis of the infections. Important human pathogens are poliovirus, coxsackievirus, human rhinovirus and hepatitis A virus. These viruses are the beststudied members of the family, and in this review we want to present the major aspects of the reciprocal effects between the immune system and these viruses.