Early Stages Of Viral Infection Research Articles

Autophagy signaling pathway is a therapeutic target to inhibit GCRV replication

Autophagy is an evolutionarily conserved process that is thought to be essential for maintaining physiological homeostasis. However, the role of autophagy in host immune defense against viruses was poorly understood in fish. In this study, we found that although GCRV infection induced autophagy, increasing autophagy level by rapamycin significantly inhibited GCRV replication and increased cell viability, whereas 3-MA pretreatment significantly decreased cell viability and enhanced GCRV replication. Further investigation showed that GCRV invasion altered autophagy level, in which GCRV suppressed autophagy signaling at the early stage of viral infection but promoted autophagy at the late stage, to permit and promote viral replication. Moreover, overexpression of ATG12 and ATG5, as well as rapamycin, induced autophagy and synergistically restricted GCRV replication. Taken together, this study highlights the pivotal role of autophagy in anti-GCRV defense and provides a new therapeutic strategy against grass carp hemorrhagic disease targeting autophagy regulation.

Rapid field determination of SARS-CoV-2 by a colorimetric and fluorescent dual-functional lateral flow immunoassay biosensor

The rapid and accurate diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the early stage of virus infection can effectively prevent the spread of the virus and control the epidemic. Here, a colorimetric and fluorescent dual-functional lateral flow immunoassay (LFIA) biosensor was developed for the rapid and sensitive detection of spike 1 (S1) protein of SARS-CoV-2. A novel dual-functional immune label was fabricated by coating a single-layer shell formed by mixing 20 nm Au nanoparticles (Au NPs) and quantum dots (QDs) on SiO2 core to produce strong colorimetric and fluorescence signals and ensure good monodispersity and high stability. The colorimetric signal was used for visual detection and rapid screening of suspected SARS-CoV-2 infection on sites. The fluorescence signal was utilized for sensitive and quantitative detection of virus infection at the early stage. The detection limits of detecting S1 protein via colorimetric and fluorescence functions of the biosensor were 1 and 0.033 ng/mL, respectively. Furthermore, we evaluated the performance of the biosensor for analyzing real samples. The novel biosensor developed herein had good repeatability, specificity and accuracy, which showed great potential as a tool for rapidly detecting SARS-CoV-2.

Host-Viral Interactions in the Pathogenesis of Ulcerative Colitis.

Ulcerative colitis is characterized by relapsing and remitting colonic mucosal inflammation. During the early stages of viral infection, innate immune defenses are activated, leading to the rapid release of cytokines and the subsequent initiation of downstream responses including inflammation. Previously, intestinal viruses were thought to be either detrimental or neutral to the host. However, persisting viruses may have a role as resident commensals and confer protective immunity during inflammation. On the other hand, the dysregulation of gut mucosal immune responses to viruses can trigger excessive, pathogenic inflammation. The purpose of this review is to discuss virus-induced innate immune responses that are at play in ulcerative colitis.

The m6A RNA Demethylase ALKBH9B Plays a Critical Role for Vascular Movement of Alfalfa Mosaic Virus in Arabidopsis.

The N6-methyladenosine (m6A) pathway has been widely described as a viral regulatory mechanism in animals. We previously reported that the capsid protein (CP) of alfalfa mosaic virus (AMV) interacts with the Arabidopsis m6A demethylase ALKBH9B regulating m6A abundance on viral RNAs (vRNAs) and systemic invasion of floral stems. Here, we analyze the involvement of other ALKBH9 proteins in AMV infection and we carry out a detailed evaluation of the infection restraint observed in alkbh9b mutant plants. Thus, via viral titer quantification experiments and in situ hybridization assays, we define the viral cycle steps that are altered by the absence of the m6A demethylase ALKBH9B in Arabidopsis. We found that ALKBH9A and ALKBH9C do not regulate the AMV cycle, so ALKBH9B activity seems to be highly specific. We also define that not only systemic movement is affected by the absence of the demethylase, but also early stages of viral infection. Moreover, our findings suggest that viral upload into the phloem could be blocked in alkbh9b plants. Overall, our results point to ALKBH9B as a possible new component of phloem transport, at least for AMV, and as a potential target to obtain virus resistance crops.

4′-(8-imidazole-octyloxy)-arctigenin efficiently inhibits spring viraemia of carp virus infection in vitro and in vivo

Spring viraemia of carp virus (SVCV), an important aquatic rhabdoviruses, causing devastating mortality in various carp species and other cultivated fish. In our previous studies, 4′-(8-Imidazole-octyloxy)-arctigenin (6A) with an eight carbon atoms of linker showed the higher activity against SVCV in EPC cells, based on the structure-activity relationship of 35 arctigenin derivatives. In this study, the antiviral activity and mechanism of 6A was further investigated both in vivo and in vitro. An analysis of survival curve of zebrafish indicated that 6A-treated group increased the survival rate by 23.4% and 20.0% following with 100 and 103 TCID50 doses of SVCV, respectively. Besides, 6A inhibited the gene expression of SVCV nucleoprotein and glycoprotein in brain, spleen, and liver at 4 and 7 d post-infection (dpi) by over 90% and 60%, respectively. Consistent with above results, there were no apparent signs of infection and inflammation in the brain, spleen and liver of the 6A-treated fish. However, we unexpectedly found an inability on 6A-treated zebrafish and EPC cells to mount a strong IFNф1 response to SVCV, which indicated that 6A inhibited SVCV replication not via the activation of IFNф1-related genes. Moreover, pre-treatment, co-treatment, and post-treatment of 6A with SVCV, 6A was observed to possess an intense antiviral response in the early stage of viral infection. Altogether, 6A was expected to be a therapeutic agent for the treatment of SVCV in aquaculture.

Highly efficient inhibition of infectious hematopoietic necrosis virus replication mediated by a novel synthesized coumarin derivative in vitro and in vivo

As an efficient pathogen resulting in economic impact in aquaculture, infectious hematopoietic necrosis virus (IHNV) causes devastating disease in salmons. In this study, we designed and synthesized a novel coumarin derivative, 7-((4-aminophenyl)diazenyl)-4-methyl-coumarin (AMC), to evaluate its in vitro and in vivo anti-IHNV effects. The results showed that up to 25 mg/L AMC inhibited the expression of six IHNV protein genes in epithelioma papulosum cyprini (EPC) cells, with a maximum inhibitory rate of >90%. Furthermore, AMC inhibited EPC cell apoptosis induced by IHNV and kept the normal cellular morphological structure, reflecting in the protection of EPC cells from cell swelling, the formation of apoptotic bodies, the disappearance of cellular morphology and nuclear fragmentation. For in vivo study, AMC exhibited an anti-IHNV effect in the virus-infected fish by substantially enhancing the survival rate. Consistent with above results, AMC repressed IHNV gene expression in virus sensitive tissues (brain, kidney and spleen) in the early stage of virus infection. Meanwhile, up-regulation of four interferon (IFN) related gene expressions demonstrated that AMC may activate IFN-related expressions for inhibiting IHNV replication during the early stage of viral infection, which is beneficial for the continuous antiviral action on controlling low viral loads in rainbow trout juvenile. Thus, AMC effectively regulated IHNV-induced undesirable conditions to be an excellent potential therapeutic agent against IHNV infection.

SPR-Based Kinetic Analysis of the Early Stages of Infection in Cells Infected with Human Coronavirus and Treated with Hydroxychloroquine.

Cell-based assays are a valuable tool for examination of virus–host cell interactions and drug discovery processes, allowing for a more physiological setting compared to biochemical assays. Despite the fact that cell-based SPR assays are label-free and thus provide all the associated benefits, they have never been used to study viral growth kinetics and to predict drug antiviral response in cells. In this study, we prove the concept that the cell-based SPR assay can be applied in the kinetic analysis of the early stages of viral infection of cells and the antiviral drug activity in the infected cells. For this purpose, cells immobilized on the SPR slides were infected with human coronavirus HCov-229E and treated with hydroxychloroquine. The SPR response was measured at different time intervals within the early stages of infection. Methyl Thiazolyl Tetrazolium (MTT) assay was used to provide the reference data. We found that the results of the SPR and MTT assays were consistent, and SPR is a reliable tool in investigating virus–host cell interaction and the mechanism of action of viral inhibitors. SPR assay was more sensitive and accurate in the first hours of infection within the first replication cycle, whereas the MTT assay was not so effective. After the second replication cycle, noise was generated by the destruction of the cell layer and by the remnants of dead cells, and masks useful SPR signals.

Insights into Innate Immune Response Against SARS-CoV-2 Infection

Abstract The innate immune system is mandatory for the activation of antiviral host defense and eradication of the infection. In this regard, dendritic cells, natural killer cells, macrophages, neutrophils representing the cellular component, and cytokines, interferons, complement or Toll-Like Receptors, representing the mediators of unspecific response act together for both activation of the adaptive immune response and viral clearance. Of great importance is the proper functioning of the innate immune response from the very beginning. For instance, in the early stages of viral infection, the defective interferon response leads to uncontrolled viral replication and pathogen evasion, while hypersecretion during the later stages of infection generates hyperinflammation. This cascade activation of systemic inflammation culminates with cytokine storm syndrome and hypercoagulability state, due to a close interconnection between them. Thus an unbalanced reaction, either under- or over- stimulation of the innate immune system will lead to an uncoordinated response and unfavorable disease outcomes. Since both cellular and humoral factors are involved in the time-course of the innate immune response, in this review we aimed to address their gradual involvement in the antiviral response with emphasis on key steps in SARS-CoV-2 infection.

Mutations within the Open Reading Frame (ORF) including Ochre stop codon of the Surface Glycoprotein gene of SARS-CoV-2 virus erase potential seed location motifs of human non-coding microRNAs

MicroRNA are short and non-coding RNA, 18-25 nucleotides in length. They are produced at the early stage of viral infection. The roles played by cellular miRNAs and miRNA-mediated gene-silencing in the COVID-19 epidemic period is critical in order to develop novel therapeutics. We analyzed SARS-CoV-2 Surface Glycoprotein (S) nucleotide sequence originating from India as well as Iran, Australia, Germany, Italy, Russia, China, Japan and Turkey and identified mutation in potential seed location of several human miRNA. Seventy single nucleotide polymorphisms (SNP) were detected in the S gene out of which, 36, 32 and 2 were cases of transitions, transversions and deletions respectively. Eleven human miRNA targets were identified on the reference S gene sequence with a score >80 in the miRDB database. Mutation A845S erased a common binding site of 7 human miRNA (miR-195-5p, miR-16-5p, miR-15b-5p, miR-15a-5p, miR-497-5p, miR-424-5p and miR-6838-5p). A synonymous mutation altered the wild type Ochre stop codon within the S gene sequence (Italy) to Opal thereby changing the seed sequence of miR-511-3p. Similar (synonymous) mutations were detected at amino acid position 659 and 1116 of the S gene where amino acids serine and threonine were retained, abolishing potential seed location for miR-219a-1-3p and miR-20b-3p respectively. The significance of this finding in reference to the strategy to use synthetic miRNA combinations as a novel therapeutic tool is discussed.

Transcriptional Response of Wolbachia to Dengue Virus Infection in Cells of the Mosquito Aedes aegypti.

ABSTRACTAedes aegypti transmits one of the most significant mosquito‐borne viruses, dengue virus (DENV). The absence of effective vaccines and clinical treatments and the emergence of insecticide resistance in A. aegypti necessitate novel vector control strategies. A new approach uses the endosymbiotic bacterium Wolbachia pipientis to reduce the spread of arboviruses. However, the Wolbachia-mediated antiviral mechanism is not well understood. To shed light on this mechanism, we investigated an unexplored aspect of Wolbachia-virus-mosquito interaction. We used RNA sequencing to examine the transcriptional response of Wolbachia to DENV infection in A. aegypti Aag2 cells transinfected with the wAlbB strain of Wolbachia. Our results suggest that genes encoding an endoribonuclease (RNase HI), a regulator of sigma 70-dependent gene transcription (6S RNA), essential cellular, transmembrane, and stress response functions and primary type I and IV secretion systems were upregulated, while a number of transport and binding proteins of Wolbachia, ribosome structure, and elongation factor-associated genes were downregulated due to DENV infection. Furthermore, bacterial retrotransposon, transposable, and phage-related elements were found among the up- and downregulated genes. We show that Wolbachia elicits a transcriptional response to virus infection and identify differentially expressed Wolbachia genes mostly at the early stages of virus infection. These findings highlight Wolbachia’s ability to alter its gene expression in response to DENV infection of the host cell.IMPORTANCE Aedes aegypti is a vector of several pathogenic viruses, including dengue, Zika, chikungunya, and yellow fever viruses, which are of importance to human health. Wolbachia is an endosymbiotic bacterium currently used in transinfected mosquitoes to suppress replication and transmission of dengue viruses. However, the mechanism of Wolbachia-mediated virus inhibition is not fully understood. While several studies have shown mosquitoes’ transcriptional responses to dengue virus infection, none have investigated these responses in Wolbachia, which may provide clues to the inhibition mechanism. Our results suggest changes in the expression of a number of functionally important Wolbachia genes upon dengue virus infection, including those involved in stress responses, providing insights into the endosymbiont’s reaction to virus infection.

Development of an ultrasensitive fluorescent immunochromatographic assay based on multilayer quantum dot nanobead for simultaneous detection of SARS-CoV-2 antigen and influenza A virus

Rapid and accurate diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus (FluA) antigens in the early stages of virus infection is the key to control the epidemic spread. Here, we developed a two-channel fluorescent immunochromatographic assay (ICA) for ultrasensitive and simultaneous qualification of the two viruses in biological samples. A high-performance quantum dot nanobead (QB) was fabricated by adsorption of multilayers of dense quantum dots (QDs) onto the SiO2 surface and used as the highly luminescent label of the ICA system to ensure the high-sensitivity and stability of the assay. The combination of monodispersed SiO2 core (∼180 nm) and numerous carboxylated QDs formed a hierarchical shell, which ensured that the QBs possessed excellent stability, superior fluorescence signal, and convenient surface functionalization. The developed ICA biosensor achieved simultaneous detection of SARS-CoV-2 and FluA in one test within 15 min, with detection limits reaching 5 pg/mL for SARS-CoV-2 antigen and 50 pfu/mL for FluA H1N1. Moreover, our method showed high accuracy and specificity in throat swab samples with two orders of magnitude improvement in sensitivity compared with traditional AuNP-based ICA method. Hence, the proposed method is a promising and convenient tool for detection of respiratory viruses.

A Data Analysis of D-Dimer & Interleukin-6 (IL-6) Test for Covid Patient

Various biomarkers, especially inflammatory markers like C-reactive protein (CRP), ferritin, fibrinogen, D-dimer and Interleukin 6 (IL-6) are associated with Covid-19 progression. Thrombosis prophylaxis with low molecular weight heparin has shown beneficial results in preventing coagulopathy a reducing risk of mortality due to thrombotic events. The COVID-19 patients highlighting the role of D-dimer, and Interleukin-6 (IL-6). During plasma coagulation soluble fibrin is generated by the influence of thrombin on fibrinogen. The soluble fibrin is crosslinked to the vessel walls by factor XIIIa. When splitting this cross linked fibrin, characteristic products called D-dimers are released. Increased D-dimer concentrations are found in thrombotic diseases and microthrombotic events (e.g. in case of disseminated intravascular coagulation, DIC). D-dimer determination is mainly used to exclude deep vein thrombosis of the leg and pulmonary embolism. D-Dimer levels rise during pregnancy and high levels are associated with complications. D-dimer is a fibrin degradation product that is often used to measure and assess clot formation. Amid the COVID-19 pandemic, elevated D-dimer levels have been associated with disease severity and mortality trends. Interleukin-6 (IL-6) is a pro-inflammatory cytokine secreted by T cells and macrophages to stimulate immune response to trauma, especially burns or other tissue damage leading to inflammation. IL-6 is also secreted by macrophages in response to specific microbial molecules, referred to as Pathogen Associated Molecular Patterns (PAMPs), which trigger the innate immune response and initiate inflammatory cytokine production. IL-6 is one of the most important mediators of fever and of the acute phase response. IL-6 is also called a “myokine”, a cytokine produced from muscle that increases in response to muscle contraction. Additionally, osteoblasts secrete IL-6 to stimulate osteoclast formation. The detection and control of pro-inflammatory response is crucial in the early stages of viral infection. COVID-19 is an emerging viral disease of global concern and optimal treatment has yet to be determined. Unknown response of treatment of COVID-19 is important during patient monitoring. IL-6 is one of the key cytokines after activated macrophages. Here we will present a laboratory data analysis of COVID-19 patients in different age group highlighting the role of positivity D-dimer and interleukin-6 (IL-6).

Bioactive Polyphenolic Compounds Showing Strong Antiviral Activities against Severe Acute Respiratory Syndrome Coronavirus 2.

Until now, there has been no direct evidence of the effectiveness of repurposed FDA-approved drugs against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections. Although curcumin, hesperidin, and quercetin have broad spectra of pharmacological properties, their antiviral activities against SARS-CoV-2 remain unclear. Our study aimed to assess the in vitro antiviral activities of curcumin, hesperidin, and quercetin against SARS-CoV-2 compared to hydroxychloroquine and determine their mode of action. In Vero E6 cells, these compounds significantly inhibited virus replication, mainly as virucidal agents primarily indicating their potential activity at the early stage of viral infection. To investigate the mechanism of action of the tested compounds, molecular docking studies were carried out against both SARS-CoV-2 spike (S) and main protease (Mpro) receptors. Collectively, the obtained in silico and in vitro findings suggest that the compounds could be promising SARS-CoV-2 Mpro inhibitors. We recommend further preclinical and clinical studies on the studied compounds to find a potential therapeutic targeting COVID-19 in the near future.

Profiling of T Cell Repertoire in SARS-CoV-2-Infected COVID-19 Patients Between Mild Disease and Pneumonia.

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a public health emergency. The most common symptoms of COVID-19 are fever, cough, and fatigue. While most patients with COVID-19 present with mild illness, some patients develop pneumonia, an important risk factor for mortality, at early stage of viral infection, putting these patients at increased risk of death. So far, little has been known about differences in the T cell repertoires between COVID-19 patients with and without pneumonia during SARS-CoV-2 infection. Herein, we aimed to investigate T cell receptor (TCR) repertoire profiles and patient-specific SARS-CoV-2-associated TCR clusters between COVID-19 patients with mild disease (no sign of pneumonia) and pneumonia. The TCR sequencing was conducted to characterize the peripheral TCR repertoire profile and diversity. The TCR clustering and CDR3 annotation were exploited to further discover groups of patient-specific TCR clonotypes with potential SARS-CoV-2 antigen specificities. Our study indicated a slight decrease in the TCR repertoire diversity and a skewed CDR3 length usage in patients with pneumonia compared to those with mild disease. The SARS-CoV-2-associated TCR clusters enriched in patients with mild disease exhibited significantly higher TCR generation probabilities and most of which were highly shared among patients, compared with those from pneumonia patients. Importantly, using similarity network-based clustering followed by the sequence conservation analysis, we found different patterns of CDR3 sequence motifs between mild disease- and pneumonia-specific SARS-CoV-2-associated public TCR clusters. Our results showed that characteristics of overall TCR repertoire and SARS-CoV-2-associated TCR clusters/clonotypes were divergent between COVID-19 patients with mild disease and patients with pneumonia. These findings provide important insights into the correlation between the TCR repertoire and disease severity in COVID-19 patients.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10875-021-01045-z.

Immune responses and protective efficacy on 4-(2-methoxyphenyl)-3,4-dihydro-2H-chromeno[4,3-d] pyrimidine-2,5 (1H)-dione against spring viremia of carp virus in vivo

Spring viremia of carp virus (SVCV) is a highly pathogenic sprivivirus that continues to cause outbreaks in cyprinidae characterized by high mortality. Currently, few therapeutics have approved for use in aquaculture against SVCV infection. Previously, we reported that 4-(2-methoxyphenyl)-3,4-dihydro-2H-chromeno[4,3-d] pyrimidine-2,5(1H)-dione-phenylpropanoid (S3) inhibits SVCV proliferation. It was first appeared in the S5 series of compounds. Compared with S5, S3 is easier to synthesize and has a higher yield. Here, in order to further evaluate the practical application potential of S3 in aquaculture, common carp as a model organism was carried out relevant experiments. In this study, we evaluated toxicity of S3 in vivo. The results showed that the dose below 100 μg/mL is safe, and there was a significant toxicity if it exceeds this dose. In pathogenicity tested of SVCV, the 50% lethal dose (LD50) of the present SVCV isolate to present common carp was approximately 101.6-fold TCID50/fish. Subsequently, further data suggested that S3 was stability with a prolonged inhibitory half-life in the early stage of virus infection (1–4 days). Importantly, intraperitoneal (i.p.) therapy of S3 markedly decreased fish mortality and reduced virus copies in both spleen and kidney. Mechanically, S3 enhanced the levels of IFN-related genes demonstrated that S3 indirectly activated IFNs for the clearance of SVCV in common carp. Additionally, the results of HE staining showed that S3 may be able to attenuate inflammation symptoms in SVCV infected fish. Therefore, the phenylpropanoid derivative S3 has potential to be used as an anti-SVCV therapeutics against fish viral diseases.

Cloning, analysis, and anti–duck Tembusu virus innate immune response of Cherry Valley duck tripartite motif-containing 32

Tripartite motif-containing 32 (TRIM32) is an E3 ubiquitin ligase with multiple functions. In this study, we amplified TRIM32 gene from the Cherry Valley duck, and its cDNA sequence contained an open reading frame of 1,950 bp that encodes 649 amino acids. Duck TRIM32 (duTRIM32) mRNA was expressed in all tissues tested. A series of immune-related genes that were induced by viral infection, including interferon alfa, IL-1β, retinoic acid–inducible gene-I, Mx, and OAS, were regulated by duTRIM32 expression. DuTRIM32 overexpression inhibits duck Tembusu virus (DTMUV) replication in the early stages of viral infection. Knockdown of duTRIM32 expression by siRNA reduced the ability of duck embryo fibroblast cells to mount a type Ⅰ interferon response to DTMUV. Therefore, our results suggest that the duTRIM32-mediated signal pathway plays an essential role in DTMUV infection-induced innate immune response.

IoT Enabled Wearable Device for COVID Safety and Emergencies

The worldwide outbreak of COVID-19 has significantly changed the mindset of the people and over the period they started practicing healthy lifestyle to contain the spread of the virus. Despite this, increase in the number of cases and death rates across the globe are major cause of concern. In addition to maintaining the healthy lifestyle it is also essential to exploit the technological advancements in the field of Internet of Things (IoT) in designing a cost-effective wearable device which could possibly indicate the early stages of virus infection. In this work, a low cost IoT enabled wearable device is designed which generates alerts in case of any of the measured parameter goes out of the normal range besides sending notifications.

A colorimetric IsoPCR for the rapid and sensitive visual detection of high-risk HPV16 in clinical samples with hydroxynaphthol blue

HPV16 infection is found in more than 50 % of cervical cancer cases worldwide, triggering the development of numerous molecular techniques for viral diagnosis. The present study focuses on the development of a colorimetric IsoPCR for HPV16 DNA detection. The methodology combines the advantages of PCR and LAMP, while the most significant aspect of the new established methodology is the visual detection of amplification products through hydroxynapthol blue dye, thus minimizing the time and labor needed. An experimental cut-off value was tested through reconstitution experiments, while the specificity was evaluated by assessing clinical samples. The analytical sensitivity of the new colorimetric IsoPCR was found to be 0.1 viral DNA copy per reaction, while the specificity was 100 % for the detection of HPV16 DNA. The assay enabled the amplification of viral DNA in cases with viral load lower than 1 copy. In conclusion, the new established colorimetric IsoPCR can be regarded as an attractive molecular tool that facilitates the specific, rapid and highly sensitive visual detection of HPV16 DNA even at the very early stages of viral infection.

Genome composition and genetic characterization of SARS-CoV-2.

SARS-CoV-2 is a type of Betacoronaviruses responsible for COVID-19 pandemic disease, with more than 1.745 million fatalities globally as of December-2020. Genetically, it is considered the second largest genome of all RNA viruses with a 5′ cap and 3′ poly-A tail. Phylogenetic analyses of coronaviruses reveal that SARS-CoV-2 is genetically closely related to the Bat-SARS Like-Corona virus (Bat-SL-Cov) with 96% whole-genome identity. SARS-CoV-2 genome consists of 15 ORFs coded into 29 proteins. At the 5′ terminal of the genome, we have ORF1ab and ORF1a, which encode the 1ab and 1a polypeptides that are proteolytically cleaved into 16 different nonstructural proteins (NSPs). The 3′ terminal of the genome represents four structural (spike, envelope, matrix, and nucleocapsid) and nine accessory (3a, 3b, 6, 7a, 7b, 8b, 9a, 9b, and orf10) proteins. As the number of COVID-19 patients increases dramatically worldwide, there is an urgent need to find a quick and sensitive diagnostic tool for controlling the outbreak of SARS-CoV-2 in the community. Today, molecular testing methods utilizing viral genetic material (e.g., PCR) represent the crucial diagnostic tool for the SARS-CoV-2 virus despite its low sensitivity in the early stage of viral infection. This review summarizes the genome composition and genetic characterization of the SARS-CoV-2.

Critical role of Syk-dependent STAT1 activation in innate antiviral immunity

The JAK/STAT1 pathway is generally activated by cytokines, providing essential antiviral defense. Here, we identify that STAT1 activation is independent of cytokines and JAKs at the early infection stage of some viruses, including influenza A virus (IAV). Instead, STAT1 is activated mainly through spleen tyrosine kinase (Syk) downstream of retinoic acid-inducible gene-I/mitochondrial antiviral-signaling protein (RIG-I/MAVS) signaling. Syk deletion profoundly impairs immediate innate immunity, as evidenced by the finding that Syk deletion attenuates tyrosine phosphorylation of STAT1 and reduces the expressions of interferon-stimulated genes (ISGs) invitro and invivo. The antiviral response to IAV infection is also significantly suppressed in the STAT1Y701F knockin mice. The results demonstrate that STAT1 activation is dependent on Syk rather than the cytokine-activated JAK signaling at the early stage of viral infection, which is critical for initial antiviral immunity. Our finding provides insights into the complicated mechanisms underlying host immune responses to viral infection.