Construction and Identification of the Helper Plasmids for Reverse Genetic System of Rabies Virus Street Strain

To obtain the helper plasmids for a reverse genetics system of rabies virus, the cDNAs of the complete open reading frames of the N, P, G, and L genes of rabies street virus stain HN10 were each cloned into expression vector pVAX1, These four plasmids were identified by restriction enzyme digestion and gene sequencing. The plasmid encoding the N protein was selected to determine the expression effect of these plasmids in NA cells. The results showed that the helper plasmids for a reverse genetics system of rabies street virus strain HN10 had been successfully constructed.

Establishment of a Reverse Genetic System of Severe Fever with Thrombocytopenia Syndrome Virus Based on a C4 Strain

Severe fever with thrombocytopenia syndrome virus(SFTSV)is an emerging tick-borne bunyavirus that causes hemorrhagic fever-like disease(SFTS)in humans with a case fatality rate up to 30%.To date,the molecular biology involved in SFTSV infection remains obscure.There are seven major genotypes of SFTSV(C1-C4 and J1-J3)and previously a reverse genetic system was established on a C3 strain of SFTSV.Here,we reported successfully establishment of a reverse genetics system based on a SFTSV C4 strain.First,we obtained the 5’-and 3’-terminal untranslated region(UTR)sequences of the Large(L),Medium(M)and Small(S)segments of a laboratory-adapted SFTSV C4 strain through rapid amplification of cDNA ends analysis,and developed functional T7 polymerase-based L-,M-and S-segment minigenome assays.Then,fulllength cDNA clones were constructed and infectious SFTSV were recovered from co-transfected cells.Viral infectivity,growth kinetics,and viral protein expression profile of the rescued virus were compared with the laboratory-adapted virus.Focus formation assay showed that the size and morphology of the foci formed by the rescued SFTSV were indistinguishable with the laboratory-adapted virus.However,one-step growth curve and nucleoprotein expression analyses revealed the rescued virus replicated less efficiently than the laboratory-adapted virus.Sequence analysis indicated that the difference may be due to the mutations in the laboratory-adapted strain which are more prone to cell culture.The results help us to understand the molecular biology of SFTSV,and provide a useful tool for developing vaccines and antivirals against SFTS.

Establishment of an efficient reverse genetic system of Mumps virus S79 from cloned DNA

Background Mumps is a common type of respiratory infectious disease caused by mumps virus(MuV),and can be effectively prevented by vaccination.In this study,a reverse genetic system of MuV that can facilitate the rational design of safer,more efficient mumps vaccine candidates is established.Methods MuV-S79 cDNA clone was assembled into a full-length plasmid by means of the GeneArtTM High-Order Genetic Assembly System,and was rescued via reverse genetic technology.RT-PCR,sequencing,and immunofluorescence assays were used for rMuV-S79 authentication.Viral replication kinetics and in vivo experimental models were used to evaluate the replication,safety,and immunogenicity of rMuV-S79.Results A full-length cDNA clone of MuV-S79 in the assembly process was generated by a novel plasmid assemble strategy,and a robust reverse genetic system of MuV-S79 was successfully established.The established rMuV-S79 strain could reach a high virus titer in vitro.The average viral titer of rMuV-S79 in the lung tissues was 2.68±0.14 log10PFU/g lung tissue,and rMuV-S79 group did not induce inflammation in the lung tissues in cotton rats.Neutralizing antibody titers induced by rMuV-S79 were high,long-lasting and could provide complete protection against MuV wild strain challenge.Conclusion We have established a robust reverse genetic system of MuV-S79 which can facilitate the optimization of mumps vaccines.rMuV-S79 rescued could reach a high virus titer and the safety was proven in vivo.It could also provide complete protection against MuV wild strain challenge.

Reverse Genetic Analysis of Transcription Factor Os Hox9, a Member of Homeobox Family, in Rice

Homeobox transcription factors participate in the growth and development of plants by regulating cell differentiation, morphogenesis and environmental signal response. To reveal the functions of these transcription factors in rice, we constructed the RNAi vectors of OsHox9, a member of homeobox family, and analyzed the function of OsHox9 using reverse genetics. The plant height and tillering number of RNAi transgenic plants decreased compared with those of wild-type plants. Reverse transcdption-polymerase chain reaction analysis showed that OsHox9 expression reduced in the transgenic plants with phenotypic variance, whereas that in the transgenic plants without phenotypic variance was similar to that in the wild-type plants. This result suggests that the phenotypes of the transgenic plants were caused by RNAi effects. The tissue-specificity of OsHox9 expression indicated that it was expressed in different organs, with high expression in stem apical medstem and young panicles. Subcellular location of OsHox9 demonstrated that it was localized on the cell membrane.

Generation of Recombinant Equine Influenza Vaccine Candidate RgH3N1 Virus by Reverse Genetics

The antigenic variation of influenza A virus hemagglutinin (HA) glycoproteins requires frequent changes in vaccine formulation. The new strategy of creating influenza seed strains for vaccine production is to generate 7 + 1 reassortants that contain seven genes from a high-yield virus A/Puerto Rico/8/34[A/PR/8/34](H1N1) and the HA gene from the circulating strains. By using this DNA-based cotransfection technique, we generated 7 + 1 reassortants rgH3N1 which had the antigenic determinants of influenza virus A/Songbird/HongKong/102/00[SB/HK/01](H3N8) and 7 other genes from A/PR/ 8/34. The hemagglutinin of A/Songbird/HongKong/102/00 is 96.3% homologous to that of A/Equine/Jilin/98[Eq/Jl/89] (H3N8). The resulting virus rgH3N1 grows to high HA titers in chicken embryonated eggs, allowing vaccine preparation in unconcentrated allantoic fluid. The rgH3N1 is stable after multiple passages in embryonated eggs. The reassortant rgH3N1 virus could be used as vaccine candidate to reduce the reemergence of equine influenza outbreaks.

Reverse genetics systems for SARS-CoV-2:Development and applications

The recent emergence of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)caused serious harm to human health and struck a blow to global economic development.Research on SARS-CoV-2 has greatly benefited from the use of reverse genetics systems,which have been established to artificially manipulate the viral genome,generating recombinant and reporter infectious viruses or biosafety level 2(BSL-2)-adapted non-infectious replicons with desired modifications.These tools have been instrumental in studying the molecular biological characteristics of the virus,investigating antiviral therapeutics,and facilitating the development of attenuated vaccine candidates.Here,we review the construction strategies,development,and applications of reverse genetics systems for SARS-CoV-2,which may be applied to other CoVs as well.

Genetic Analysis and Rescue of a Triple-reassortant H3N2 Influenza A Virus Isolated From Swine in Eastern China

One influenza H3N2 virus, A/swine/Shandong/3/2005 (Sw/SD/3/2005), was isolated from pigs with respiratory disease on a farm in eastern China. Genetic analysis revealed that Sw/SD/3/2005 was a triple-reassortant virus with a PB2 gene from human-like H1N1, NS from classical swine H1N1, and the remaining genes from human-like H3N2 virus. These findings further support the concept that swine can serve as reservoir or mixing vessels of influenza virus strains and maintain genetic and antigenic stability of viruses. Furthermore, we have successfully established a reverse genetics system based on eight plasmids and rescued Sw/SD/3/2005 through cell transfection. HI tests and RT-PCR confirmed that the rescued virus maintained the biological properties of the wild type Sw/SD/3/2005. The successful establishment of the reverse genetics system of Sw/SD/3/2005 will enable us to conduct extensive studies of the molecular evolution of H3N2 influenza viruses in swine.

An improved reverse genetics system for Newcastle disease virus genotype Ⅶ

Dear Editor, Newcastle disease virus （NDV）, also known as avian paramyxovirus serotype 1 （APMV-1）, is a member of the genus Avulavirus within the family Paramyxoviridae, or- der Mononegavirales （Miller et al., 2010）. Although all isolated NDV strains belong to a single serotype, epi- demiological studies have revealed that the genotype VII strain is currently the most prevalent circulating geno- type worldwide and is associated with many of the most recent outbreaks in China since 1997 （Liu et al., 2007）.

Identification of novel small-molecule inhibitors of SARS-CoV-2 by chemical genetics

There are only eight approved small molecule antiviral drugs for treating COVID-19.Among them,four are nucleotide analogues(remdesivir,JT001,molnupiravir,and azvudine),while the other four are protease inhibitors(nirmatrelvir,ensitrelvir,leritrelvir,and simnotrelvir-ritonavir).Antiviral resistance,unfavourable drug‒drug interaction,and toxicity have been reported in previous studies.Thus there is a dearth of new treatment options for SARS-CoV-2.In this work,a three-tier cell-based screening was employed to identify novel compounds with anti-SARS-CoV-2 activity.One compound,designated 172,demonstrated broad-spectrum antiviral activity against multiple human pathogenic coronaviruses and different SARS-CoV-2 variants of concern.Mechanistic studies validated by reverse genetics showed that compound 172 inhibits the 3-chymotrypsin-like protease(3CLpro)by binding to an allosteric site and reduces 3CLpro dimerization.A drug synergistic checkerboard assay demonstrated that compound 172 can achieve drug synergy with nirmatrelvir in vitro.In vivo studies confirmed the antiviral activity of compound 172 in both Golden Syrian Hamsters and K18 humanized ACE2 mice.Overall,this study identified an alternative druggable site on the SARS-CoV-23CLpro,proposed a potential combination therapy with nirmatrelvir to reduce the risk of antiviral resistance and shed light on the development of allosteric protease inhibitors for treating a range of coronavirus diseases.

Rapid Recovery of Classical Swine Fever Virus Directly from Cloned cDNA

The reverse genetics for classical swine fever virus （CSFV） is currently based on the transfection of in vitro transcribed RNA from a viral genomic cDNA clone, which is inefficient and time-consuming. This study was aimed to develop an improved method for rapid recovery of CSFV directly from cloned cDNA. Full-length genomic cDNA from the CSFV Shimen strain, which was flanked by a T7 promoter, the hepatitis delta virus ribozyme and T7 terminator sequences, was cloned into the low- copy vector pOK12, producing pOKShimen-RzTФ. Direct transfection of pOKShimen-RzTqb into PK/T7 cells, a PK-15- derived cell line stably expressing bacteriophage T7 RNA polymerase, allowed CSFV to be rescued rapidly and efficiently, i.e., at least 12 h faster and 31.6-fold greater viral titer when compared with the in vitro transcription-based rescue system. Furthermore, the progeny virus rescued from PK/T7 cells was indistinguishable, both in vitro and in vivo, from its parent virus and the virus rescued from classical reverse genetics. The reverse genetics based on intracellular transcription is efficient, convenient and cost-effective. The PK/T7 cell line can be used to rescue CSFV directly from cloned cDNA and it can also be used as an intracellular transcription and expression system for studying the structure and function of viral genes.

Reverse Genetic Approaches in Zebrafish

Zebrafish（Danio rerio） is a well-established vertebrate animal model.A comprehensive collection of reverse genetics tools has been developed for studying gene function in this useful organism.Morpholino is the most widely used reagent to knock down target gene expression post-transcriptionally.For a long time,targeted genome modification has been heavily relied on large-scale traditional forward genetic screens,such as ENU（N-ethyl-N-nitrosourea） mutagenesis derived TILLING（Targeting Induced Local Lesions IN Genomes） strategy and pseudo-typed retrovirus mediated insertional mutagenesis.Recently,engineered endonucleases,including ZFNs（zinc finger nucleases） and TALENs（transcription activator-like effector nucleases）,provide new and efficient strategies to directly generate site-specific indel mutations by inducing double strand breaks in target genes.Here we summarize the major reverse genetic approaches for loss-of-function studies used and emerging in zebrafish,including strategies based on genome-wide mutagenesis and methods for site-specific gene targeting.Future directions and expectations will also be discussed.

Insertion site of FLAG on foot-and-mouth disease virus VP1 G-H loop affects immunogenicity of FLAG

The G-H loop of the foot-and-mouth disease virus（FMDV） virion contains certain dominant immunogenic epitopes, as well as an arginine-glycine-aspartic acid（RGD） motif that is recognized by cell surface integrin receptors. Previous experiments indicate that it is critical to maintain virus structural integrity when inserting an exogenous epitope into the surface of an FMDV structural protein. However, it remains to be determined how factors such as different insertion positions affect interactions among the virus, cells and host immune system. In this study, one infectious c DNA clone of the swine FMDV Cathay topotype strain O/CHA/90 was constructed. Then, a FLAG marker（DYKDDDDK） was inserted upstream（–4） or downstream（＋10） of the RGD motif to generate tagged viruses vFLAG-O/CHA/90 or vO/CHA/90-FLAG, investigating the possibility of expressing foreign antigen and effect on its immunogenicity. Compared to the parental virus, both tagged viruses exhibited similar plaque phenotypes, suckling mouse pathogenicity and antigenicity. Additionally, the FLAGtag insertion position did not change the use of integrin-mediated cell entry by the tagged viruses. Interestingly, both tagged vaccines protected pigs against challenge with the parental virus O/CHA/90 and induced immune responses against FMDV in BALB/c mice and pigs, but only vaccination with vFLAG-O/CHA/90 generated anti-FLAG antibodies. Our findings demonstrated that two sites（RGD–4 and RGD＋10） tolerated the insertion of an exogenous gene in the swine FMDV O/CHA/90 strain. However, only RGD–4 was a novel and appropriate inserting site which could tolerate exogenous FLAG. The resultant tagged virus is a promising candidate for FMD vaccine which can be differentiating infected from vaccinated animals（DIVA）.

Reverse genetics in virology:A double edged sword

Reverse genetics via targeted modification of gene sequences to obtain a phenotype and the inference of a gene's function or regulatory mechanism is widely used as a potent tool in viral biology and application.However,while reverse genetics has contributed significantly to our understanding of molecular biology and the pathogenesis of viruses,its accessibility(operation)and openness(data)have raised many concerns regarding biosafety and biosecurity.In this review,we retrospectively examine the development of reverse genetics and its applications in virology,then emphasize global biosafety and biosecurity concerns regarding reverse genetics,and summarize global regulations,governance,and laws on reverse genetics.This review seeks to enhance our understanding and rational application of reverse genetics technology for the benefit of humankind.

Development and Assessment of Two Highly Pathogenic Avian Influenza(HPAI) H5N6 Candidate Vaccine Viruses for Pandemic Preparedness

Objective In China, 24 cases of human infection with highly pathogenic avian influenza(HPAI) H5 N6 virus have been confirmed since the first confirmed case in 2014. Therefore, we developed and assessed two H5 N6 candidate vaccine viruses(CVVs).Methods In accordance with the World Health Organization(WHO) recommendations, we constructed two reassortant viruses using reverse genetics(RG) technology to match the two different epidemic H5 N6 viruses. We performed complete genome sequencing to determine the genetic stability. We assessed the growth ability of the studied viruses in MDCK cells and conducted a hemagglutination inhibition assay to analyze their antigenicity. Pathogenicity attenuation was also evaluated in vitro and in vivo.Results The results showed that no mutations occurred in hemagglutinin or neuraminidase, and both CVVs retained their original antigenicity. The replication capacity of the two CVVs reached a level similar to that of A/Puerto Rico/8/34 in MDCK cells. The two CVVs showed low pathogenicity in vitro and in vivo, which are in line with the WHO requirements for CVVs.Conclusion We obtained two genetically stable CVVs of HPAI H5N6 with high growth characteristics,which may aid in our preparedness for a potential H5N6 pandemic.

Anti-tumor Effect of Newcastle Disease Virus Expressing IL-2 in Lung Cancer Model

Recombinant Newcastle disease virus(rNDV)has shown an anti-cancer effect in preclinical studies,but has never been tested for lung cancer models.This study explored the anti-cancer activity of genetically modified NDV expressing IL-2(rNDV–IL-2)in lung cancer models.This study used Lewis lung carcinoma cell line(LLC)to create tumor models in C57 female mice,the tumor-bearing mice were treated with rNDV-IL-2,rNDV and phosphate-buffered saline(PBS),respectively.In vitro results revealed that rNDV effectively infected malignant cells and expressed IL-2,in vivo results revealed that rNDV expressing IL-2 was highly efficient in inhibiting lung cancer tumors,with an average tumor size of 291.255 mm^3 in rNDV-IL-2 group compared to 763.068 mm^3 in rNDV group and 1101.68 mm^3 in PBS group.For the survival studies,treatment with rNDV-IL-2 enhanced the survival rates of tumor-bearing mice by 36%compared to those of rNDV treated mice and by 80%compared to those of vehicle-treated mice(survival rate:12 out of 15 for rNDV-IL-2 group;seven out of 15 for rNDV group and zero out of 15 for vehicle group).These results demonstrated that rNDV-expressed IL-2 enhanced the intrinsic anti-tumor ability of Newcastle disease virus in lung cancer models by further restrain of lung tumor growth and improvement of the survival rates of the tumor-bearing mice.The genetically modified rNDV-IL-2 was a good candidate for lung cancer therapy.

Construction and characterization of a full-length infectious clone of Getah virus in vivo

Getah virus(GETV)is a mosquito-borne virus of the genus Alphavirus in the family Togaviridae and,in recent years,it has caused several outbreaks in animals.The molecular basis for GETV pathogenicity is not well understood.Therefore,a reverse genetic system of GETV is needed to produce genetically modified viruses for the study of the viral replication and its pathogenic mechanism.Here,we generated a CMV-driven infectious cDNA clone based on a previously isolated GETV strain,GX201808(pGETV-GX).Transfection of pGETV-GX into BHK-21 cells resulted in the recovery of a recombinant virus(rGETV-GX)which showed similar growth characteristics to its parental virus.Then three-day-old mice were experimentally infected with either the parental or recombinant virus.The recombinant virus showed milder pathogenicity than the parental virus in the mice.Based on the established CMV-driven cDNA clone,subgenomic promoter and two restriction enzyme sites(BamHI and EcoRI)were introduced into the region between E1 protein and 3’UTR.Then the green fluorescent protein(GFP),red fluorescent protein(RFP)and improved light-oxygen-voltage(iLOV)genes were inserted into the restriction enzyme sites.Transfection of the constructs carrying the reporter genes into BHK-21 cells proved the rescue of the recombinant reporter viruses.Taken together,the establishment of a reverse genetic system for GETV provides a valuable tool for the study of the virus life cycle,and to aid the development of genetically engineered GETVs as vectors for foreign gene expression.

Attenuated MuV-S79 as vector stably expressing foreign gene

Background To describe mumps virus(MuV)used as a vector to express enhanced green fluorescent protein(EGFP)or red fluorescent protein(RFP)genes.Methods Molecular cloning technique was applied to establish the cDNA clones of recombinant mumps viruses(rMuVs).rMuVs were recovered based on our reverse genetic system of MuV-S79.The properties of rMuVs were determined by growth curve,plaque assay,fluorescent microscopy and determination of fluorescent intensity.Results Three recombinant viruses replicated well in Vero cells and similarly as parental rMuV-S79,expressed heterologous genes in high levels,and were genetically stable in at least 15 passages.Conclusion rMuV-S79 is a promising platform to accommodate foreign genes like marker genes,other antigens and immunomodulators for addressing various diseases.

Efficient and Specific Modifications of the Drosophila Genome by Means of an Easy TALEN Strategy

Technology development has always been one of the forces driving breakthroughs in biomedical research. Since the time of Thomas Morgan, Drosophilists have, step by step, developed powerful genetic tools for manipulating and functionally dissecting the Drosophila genome, but room for improving these technologies and developing new techniques is still large, especially today as biologists start to study systematically the functional genomics of different model organisms, including humans, in a high-throughput manner. Here, we report, for the first time in Drosophila, a rapid, easy, and highly specific method for modifying the Drosophila genome at a very high efficiency by means of an improved transcription activator-like effector nuclease （TALEN） strategy. We took advantage of the very recently developed ＂unit assembly＂ strategy to assemble two pairs of specific TALENs designed to modify the yellow gene （on the sex chromosome） and a novel autosomal gene. The mRNAs of TALENs were subsequently injected into Drosophila embryos. From 31.2% of the injected Fo fertile flies, we detected inheritable modification involving the yellow gene. The entire process from construction of specific TALENs to detection of inheritable modifications can be accomplished within one month. The potential applications of this TALEN-mediated genome modification method in Drosophila are discussed.

Phytochrome-regulated Gene Expression

Identification of all genes involved in the phytochrome （phy）-medieted responses of plants to their light environment is an important goal in providing an overall understanding of light-regulated growth end development. This article highlights end integrates the central findings of two recent comprehensive studies in Arabidopsis that have identified the genome-wide set of phy-reguleted genes that respond rapidly to red-light signals upon first exposure of dark-grown seedlings, and have tested the functional relevance to normal seedling photomorphogenesis of an Initial subset of these genes. The data： （a） reveal considerable complexity in the channeling of the light signals through the different phy-femily members （phyA to phyE） to responsive genes; （b） identify a diversity of transcription-factor-encoding genes as major early, if not primary, targets of phy signaling, end, therefore, as potentially important regulators in the transcriptional-network hierarchy; and （c） identify auxin-related genes as the dominant class among rapidly-regulated, hormone-related genes. However, reverse-genetic functional profiling of a selected subset of these genes reveals that only a limited fraction are necessary for optimal phy-induced seedling deetioletion.

Construction of Non-infectious SARS-CoV-2 Replicons and Their Application in Drug Evaluation

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has caused a devastating pandemic worldwide.Vaccines and antiviral drugs are the most promising candidates for combating this global epidemic,and scientists all over the world have made great efforts to this end.However,manipulation of the SARS-CoV-2 should be performed in the biosafety level3 laboratory.This makes experiments complicated and time-consuming.Therefore,a safer system for working with this virus is urgently needed.Here,we report the construction of plasmid-based,non-infectious SARS-CoV-2 replicons with turbo-green fluorescent protein and/or firefly luciferase reporters by reverse genetics using transformation-associated recombination cloning in Saccharomyces cerevisiae.Replication of these replicons was achieved simply by direct transfection of cells with the replicon plasmids as evident by the expression of reporter genes.Using SARS-CoV-2 replicons,the inhibitory effects of E64-D and remdesivir on SARS-CoV-2 replication were confirmed,and the halfmaximal effective concentration(EC50)value of remdesivir and E64-D was estimated by different quantification methods respectively,indicating that these SARS-CoV-2 replicons are useful tools for antiviral drug evaluation.