Kinds Of Viruses Research Articles

Strategies to Overcome Homeless and Beggars with A Collaborative Approach in Makassar City

This research aims to provide an overview of the phenomena and opportunities for dealing with homeless and beggars in the city of Makassar, to further formulate a coping model through the formulation of effective policies, strategies and countermeasures. One of the crucial problems that the Indonesian government has been facing is the existence of homeless people and beggars, which are increasingly serious to overcome. This problem that sometimes has a relationship with the culture in one area is indeed a kind of virus or a disease that often recurs. The strategy to deal with vagrants and beggars that has been carried out by the Makassar City Government through the leading sector of related agencies has not been effective in solving the problem of vagrants and beggars. Then through exploratory data analysis, this research formulates an approach as an alternative solution to overcome homeless and beggars in the city of Makassar, by developing a holistic approach in the form of collaborative synergy between the government and the private sector.

Two strains model of infectious diseases for mathematical analysis and simulations

ABSTRACT In this study, we study a two-strain nonlinear model for the transmission of COVID-19 with a vaccinated class. Here, it is remarkable that the model we consider contains two kinds of viruses known as Omicron and Delta variants denoted by A and B , respectively. Also, the uninfected population is denoted by S , the vaccinated class by V and the recovered individuals by R . In the presented study, we consider the proposed model under conformable fractional order derivatives. The fundamental reproductive number and equilibrium points are computed. Moreover, we determine the existence and uniqueness of the solution to the suggested model using fixed-point theory. Furthermore, we provide a suitable methodology by applying the Euler numerical method to calculate the approximate solution of each compartment of the proposed model. Additionally, using MATLAB-16, we simulate the given results graphically for a variety of fractional orders using some real values of the parameters and initial conditions.

A novel fast hybrid capture sequencing method for high-efficiency common human coronavirus whole-genome acquisition.

Rapid and accurate sequencing of the entire viral genome, coupled with continuous monitoring of genetic changes, is crucial for understanding the epidemiology of coronaviruses. We designed a novel method called micro target hybrid capture system (MT-Capture) to enable whole-genome sequencing in a timely manner. The novel design of probes used in target binding exhibits a unique and synergistic "hand-in-hand" conjugation effect. The entire hybrid capture process is within 2.5 hours, overcoming the time-consuming and complex operation characteristics of the traditional liquid-phase hybrid capture (T-Capture) system. By designing specific probes for these coronaviruses, MT-Capture effectively enriched isolated strains and 112 clinical samples of coronaviruses with cycle threshold values below 37. Compared to multiplex PCR sequencing, it does not require frequent primer updates and has higher compatibility. MT-Capture is highly sensitive and capable of tracking variants.IMPORTANCEMT-Capture is meticulously designed to enable the efficient acquisition of the target genome of the common human coronavirus. Coronavirus is a kind of virus that people are generally susceptible to and is epidemic and infectious, and it is the virus with the longest genome among known RNA viruses. Therefore, common human coronavirus samples are selected to evaluate the accuracy and sensitivity of MT-Capture. This method utilizes innovative probe designs optimized through probe conjugation techniques, greatly shortening the time and simplifying the handwork compared with traditional hybridization capture processes. Our results demonstrate that MT-Capture surpasses multiplex PCR in terms of sensitivity, exhibiting a thousandfold increase. Moreover, MT-Capture excels in the identification of mutation sites. This method not only is used to target the coronaviruses but also may be used to diagnose other diseases, including various infectious diseases, genetic diseases, or tumors.

Biological characterization and genomic analysis of a novel methicillin-resistant Staphylococcus aureus phage, SauPS-28.

Staphylococcus aureus, a representative gram-positive bacterium, is a common infectious pathogen widely present in the natural environment. The increasing application of antibiotics is witnessing an increment in the number of clinically resistant strains (such as methicillin-resistant S. aureus [MRSA]), which has posed a great challenge to antimicrobial therapy. In this study, a novel MRSA phage, SauPS-28, was isolated from the lake water of the Guangxi Zhuang Autonomous Region. This phage has an incubation period of approximately 30 min, a lysis period of approximately 40 min, and a burst size of approximately 25 PFU/cell. The isolated phage exhibited good biological stability at a pH range of 6.0-9.0 and temperature range of 4°C-37°C. In addition, the identification of an elongated tail using transmission electron microscopy confirmed that SauPS-28 belongs to the long-tailed phage family. Whole-genome sequencing analysis revealed that SauPS-28 has a 43,286-bp-long genome with 31.03% G + C content. Moreover, SauPS-28 exhibited 95.69% sequence identity with ECel-2020k, while the query coverage was only 66%, which is a newly discovered phage. Whole-genome functional annotation results revealed that SauPS-28 had 68 open reading frames (ORFs). Of these, 30 ORFs are unknown proteins. The results suggest that SauPS-28 could be a lysogenic phage strain. This study thus provides preliminary data to conduct further in-depth analysis of the mechanism of phage-host interaction and provides a reference value for phage therapy.IMPORTANCEIn recent years, drug-resistant bacterial infections have become increasingly serious. As a kind of virus with the ability to infect and lyse drug-resistant bacteria, phage is expected to be a new therapeutic method. In this study, we isolated and purified a new methicillin-resistant Staphylococcus aureus bacteriophage SauPS-28, studied a series of biological characteristics of the bacteriophage, analyzed the genome and structural proteome data of the bacteriophage, and provided reference data for further study of the interaction mechanism between bacteriophage and host bacteria and promoted new antibacterial strategies.

Biological Clock Rhythm Regulates Viral Resistance of Human Bodies

Virus has caused great distress to human health. Based on the lack of specific target sites and therapy of various viruses, this article highlights circadian rhythm, the biological clock that tells the body to do the correct thing according to the time, as a significant part in regulating human resistance to virus. Also, it summarizes how some core clock genes within human body regulate the intrusion and the replication of several kinds of viruses, together with the corresponding regulating methods to change the clock gene levels in dealing with the infection. After comparing the methods, it then comes to a conclusion which underlines the generality of REV-ERB in rejecting almost all of the viruses questioned. It regards applying REV-ERB enhancers like SR9009 and GSK4112 in a dose-dependent manner as an effective direction in designing relevant therapies. Besides, it puts circadian rhythm as an efficient researching direction for the later researches for other kinds of viruses.

Selenium compounds as promising antiviral agents

Selenium deficiency increases pathogenicity of RNA viruses. While dietary selenium supplementation has been practiced clinically, synthetic selenium compounds are under evaluation for their antiviral activity, important classes are discussed in this essay.

PREVALENCE OF SOME PATHOGENS DETECTED BY MULTIPLEX REAL-TIME PCR IN HOSPITALISED CHILDREN WITH ACUTE RESPIRATORY INFECTIONS IN BAC GIANG PROVINCIAL GENERAL HOSPITAL

Objectives: Investigate the infection rate of some microorganisms using multiplex real-time PCR techniques in inpatient children with acute respiratory infection (ARI) in Bac Giang Provincial General Hospital.Subjects and methods: A retrospective cross-sectional descriptive study. There were 450 cases ARI children treated at the Pediatrics Department in Bac Giang Provincial General Hospital though medical records with multiplex real-time PCR results of nasopharyngeal swab testing using both RP1 and RP4 kitswere included in the study.Results: Among 450 ARI children, the age group of under 60 months old accounted for the largest rate (81.6%). Influenza virus and RSV caused infection for infant and all ages group, focus on 2-60 months old group. The rate of pathogens detection using RP1 kit was 23.8% and the influenza infection rate was13.6%, RSV was 10.2%. The rate of bacteria detected by RP4 kit was 40.0%. S. pneumonia, H. influenza infection were found across all age group, focus on children under 5 years old. The rate of S. pneumoniae infection was 24.4% and H. influenzae infection was 25.3%. M. pneumoniae infection was 2.4%, and such atypical pathogens mainly caused disease in the over 2 years old group. Some pathogens have low infection rate: B. pertusis (0.2%), L. pneumophila (0.2%), C. pneumoniae (0.2%). Combining RP1 and RP4 kits could enhance the detected rate of the ARI pathogens to 53.8%. 10.0% of co-infections were detected. Influenza infection rate was highest in spring (10.5%), decreased in summer and autumn, and gradually increased in winter (5.6%). RSV infection rate was highest winter (5.6%). S. pneumoniae and H. influenzae infections were distributed equally over the year but the peaks were found in November 2020 (7.1% - 6.0% respectively) and January 2021 (5.8% - 6.9% respectively). The highest rate of M. pneumoniae infection was in April 2021 (1.8%).Conclusions: Kit RP1 could detect 23.8% respiratory pathogens , of which 13.6% were influenza; 10.2% RSV. There were 40.0% positive for at least one pathogen in the RP4 kit, including 24.4% S.pneumoniae, 25.3% H. influenzae, 2.4% M. pneumoniae, 0.2% B. pertusis, 0.2% L. pneumophila, 0.2% C.pneumoniae. Combining RP1 and RP4 kit could enhance the positive rate to 53.8% including 13.8% were infected with 1 kind of virus, 30.0% were infected with 1 kind of bacteria and 10.0% were co-infection.The co-infection patterns still remain unclear and could be a result of random combination. Influenza,RSV and M. pneumoniae infections were significant affected by seasoning, while S. pneumoniae and H.influenzae infections were sporadic all over the time

Learning to Immunize Images for Tamper Localization and Self-Recovery.

Digital images are vulnerable to nefarious tampering attacks such as content addition or removal that severely alter the original meaning. It is somehow like a person without protection that is open to various kinds of viruses. Image immunization (Imuge) is a technology of protecting the images by introducing trivial perturbation, so that the protected images are immune to the viruses in that the tampered contents can be auto-recovered. This paper presents Imuge+, an enhanced scheme for image immunization. By observing the invertible relationship between image immunization and the corresponding self-recovery, we employ an invertible neural network to jointly learn image immunization and recovery respectively in the forward and backward pass. We also introduce an efficient attack layer that involves both malicious tamper and benign image post-processing, where a novel distillation-based JPEG simulator is proposed for improved JPEG robustness. Our method achieves promising results in real-world tests where experiments show accurate tamper localization as well as high-fidelity content recovery. Additionally, we show superior performance on tamper localization compared to state-of-the-art schemes based on passive forensics.

Intuitionistic SIR Technique with Double Parameters to Detect the Operative Vaccine of COVID-19

Since 2019, COVID disease threats the world. It originated in China, and due to its easy spread characteristics, it spreads quickly among all the countries. As the world faced a new kind of virus, the government could not control its spread, and the fatality rate had also hugely increased. In 2021, the vaccine for the virus was introduced by various countries, which aids in controlling the spread and mortality rate. The mutant form of this virus exhibits high efficiency. So, this study analyzes the effective of COVID vaccines released after 2020 against all COVID variants through the fuzzy superiority and inferiority ranking (SIR) decision-making method. The vaccines and variants are analyzed by the [Formula: see text] matrix pattern under the fuzzy SIR-integrated weight method. The disease variants are taken as criteria and that are assigned integrated weight based on subjective, objective weight approaches. The intuitionistic fuzzy set-double parameter (IFS-DP) handles the vagueness by strictly including only membership and non-membership functions with the condition [Formula: see text]. As a result, the vaccines Moderna and Covishield are attained top rank and have a high likelihood to combat all the COVID variants compared to other vaccines. The reached outcomes are corroborated through sensitivity and comparative analysis. The sensitivity and comparative studies are measured by increasing the order of IFS-DP and extant fuzzy MCDM methods, respectively. The comparison of these results with those obtained from the proposed method is similar to the sensitivity study, along with minor variations observed in the comparative study. Therefore, the proposed method generates an efficient outcome. Moreover, the testing hypothesis technique is applied to check the efficiency of proposed method.

Statistical Analysis of Common Respiratory Viruses Reveals the Binary of Virus-Virus Interaction.

Respiratory viruses may interfere with each other and affect the epidemic trend of the virus. However, the understanding of the interactions between respiratory viruses at the population level is still very limited. We here conducted a prospective laboratory-based etiological study by enrolling 14,426 patients suffered from acute respiratory infection (ARI) in Beijing, China during 2005 to 2015. All 18 respiratory viruses were simultaneously tested for each nasal and throat swabs collected from enrolled patients using molecular tests. The virus correlations were quantitatively evaluated, and the respiratory viruses could be divided into two panels according to the positive and negative correlations. One included influenza viruses (IFVs) A, B, and respiratory syncytial virus (RSV), while the other included human parainfluenza viruses (HPIVs) 1/3, 2/4, adenovirus (Adv), human metapneumovirus (hMPV), and enterovirus (including rhinovirus, named picoRNA), α and β human coronaviruses (HCoVs). The viruses were positive-correlated in each panel, while negative-correlated between panels. After adjusting the confounding factors by vector autoregressive model, positive interaction between IFV-A and RSV and negative interaction between IFV-A and picoRNA are still be observed. The asynchronous interference of IFV-A significantly delayed the peak of β human coronaviruses epidemic. The binary property of the respiratory virus interactions provides new insights into the viral epidemic dynamics in human population, facilitating the development of infectious disease control and prevention strategies. IMPORTANCE Systematic quantitative assessment of the interactions between different respiratory viruses is pivotal for the prevention of infectious diseases and the development of vaccine strategies. Our data showed stable interactions among respiratory viruses at human population level, which are season irrelevant. Respiratory viruses could be divided into two panels according to their positive and negative correlations. One included influenza virus and respiratory syncytial virus, while the other included other common respiratory viruses. It showed negative correlations between the two panels. The asynchronous interference between influenza virus and β human coronaviruses significantly delayed the peak of β human coronaviruses epidemic. The binary property of the viruses indicated transient immunity induced by one kind of virus would play role on subsequent infection, which provides important data for the development of epidemic surveillance strategies.

Sentiment Classification on tweets Based on LSTM with variants and BERT finetune

Covid-19 is a new type of epidemic, we performed sentiment classification tasks on Covid-19 tweets using different machine learning models. The famous pre-training models are not trained with the text relevant to COVID-19, a new kind of virus appearing at December 2019. The twitter posts with such a topic also have not been applied to test the performance of existing pre-training models and neural networks well. In our experiment, we used LSTM and Transformer to do the sentiment analysis (quinary classification) with a dataset including those twitter posts and tried different hyperparameters and models to improve the performance of classification. We finally found that the Transformer performs better than LSTM with an extra softmax layer in the encoder part, and the bidirectional transformer with 4 hidden layer and dropout 0.2 provides the best results among all hyperparameters we have tested. With the finetune of BERT,we got the best performance with the accuracy over 85%.

SARS-COV-2: THE SECONDARY EXTREMITY SUMMIT OF WHO

Covid-19 made all the countries to close their borders and locked down all citizens as the virus is widening around the globe with a steep speed. This is one of our enemies’ plots, dragging the countries to a shutdown. Nobody knew there'd be a pandemic or an epidemic of this proportion. But many who work in infectious disease knew a pandemic like this was coming. As far as the loss of life, a pandemic would match even the tremendous conflicts of the past. The economy will close down, the expense for humankind will be extraordinary, and no nation will be invulnerable from the issue this will create."We estimate there are around 1.5 million viruses in wildlife” that we don't yet know about. Any one of those could be spilling over into human population right now. Expansion of a virus from an animal to human society gives rise to zoonotic Virus, and for decades, these kinds of viruses which have been growing, spreading and causing outbreaks for the society. There's a risk with something like SARS or MERS, that it'll be something for which we're not ready. It is a coronavirus again? We know some pretty lethal ones, but we expect that there are others out there that are more lethal, that are better at being transmitted, where we've got no drugs and no vaccines which ultimately leads to a chancy.

Efficacy of Binary Ethylenimine in the Inactivation of Foot-and-Mouth Disease Virus for Vaccine Production in South Korea.

Foot-and-mouth disease (FMD) vaccines must be produced in a biosafety level 3 facility, so the FMD virus (FMDV) must be completely inactivated after amplification. The inactivation kinetics of FMDV during vaccine antigen production were assessed by evaluating whether the viral titer dropped below 10-7 TCID50/mL within 24 h of binary ethyleneimine (BEI) treatment. This study dealt with four FMD vaccine candidate strains for the efficacy of BEI treatment at different concentrations and temperatures to determine the optimal inactivation condition of each virus. Two domestic isolates, O/SKR/Boeun/2017 (O BE) and A/SKR/Yeoncheon/2017 (A YC), and two recombinant viruses, PAK/44/2008 (O PA-2) and A22/Iraq/24/64 (A22 IRQ), were investigated. The O BE and A22 IRQ required 2 mM BEI at 26 °C and 0.5 mM BEI at 37 °C for complete inactivation. The O PA-2 and A YC required 2 mM BEI at 26 °C and 1 mM BEI at 37 °C. Crucially, the yield of FMD virus particles (146S) in the viral infection supernatant was higher (>4.0 µg/mL) than those previously reported; additionally, there was little antigen loss, even after 24 h of treatment with 3 mM BEI. Overall, it is considered economical to produce FMD vaccines using these four kinds of viruses; therefore, these candidate strains will be prioritized for the manufacture of FMD vaccines in South Korea.

Natural Oncolysis of Enterovirus 71 in Antitumor Therapy of Colorectal Cancer.

Colorectal cancer (CRC) is an intestinal malignant tumor with high morbidity and mortality worldwide. Inoperability or resistanance to radiation and chemotherapy occur in the conventional treatments against CRC. Oncolytic viruses (OVs) are one kind of virus that selectively infects and lyses cancer cells, which is considered to be a new anticancer therapy with biological and immune-based approaches. Enterovirus 71 (EV71), belonging to the enterovirus genus in the family Picornaviridae, is a single positive-stranded RNA virus. EV71 is transmitted in a fetal-oral route and infects gastrointestinal tract in infants. Here, EV71 is exploited to be a novel oncolytic virus in colorectal cancer. It is revealed that EV71 infection can selectively cause colorectal cancer cells cytotoxicity but not primary intestinal epithelial cells. Consistently, EV71 injection significantly inhibits tumor growth in nude mice xenografted colorectal cancer cells. In detail, EV71 infects colorectal cancer cells to repress the expression of Ki67 and B-cell leukemia 2 (Bcl-2) leading to the inhibition of cell proliferation, while activating the cleavage of poly-adenosine diphosphatase-ribose polymerase and Caspase-3 protein resulting in the promotion of cell apoptosis. The findings demonstrate the oncolytic feature of EV71 in CRC treatment and may provide a potential clue for clinical anticancer therapy.

Prediction of target genes in community-acquired pneumonia based on the bioinformatics method.

To screen the related genes of community-acquired pneumonia (CAP) by bioinformatics technology, and to analyze the clinical value of key genes. Gene chip data sets containing CAP patients and normal controls were screened from the Gene Expression Omnibus (GEO) database. The downregulated differentially expressed genes (DEGs) were screened using a gene expression analysis tool (GEO2R). Simultaneously, gene set enrichment analysis (GSEA) was used to explore the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and core genes related to CAP. The candidate genes were then intersected with the genes reported in Online Mendelian Inheritance in Man (OMIM), and the clinical value of these candidate genes was examined based on a literature search. Finally, the clinical data of the CAP patients were retrospectively analyzed. Detect the type of pathogenic bacteria in bronchial-alveolar lavage fluid (BALF) using metagenomics next-generation sequencing (mNGS) high throughput sequencing technology, and detect the expression of key genes through liquid based cell immunohistochemistry to analyze the correlation between pathogenic bacteria and key genes. Through the intersection of Venn diagrams, 175 co-expressed downregulated DEGs related to CAP were identified. A total of 4 candidate genes, including ICOS, IL7R, ITK, and ZAP70, were obtained by constructing the protein mutual aid network and conducting a module analysis of the common differentially expressed genes. The core genes in the GSEA enrichment pathways were intersected with the CAP-related genes reported in the relevant literature retrieved from the OMIM database. In the Venn diagram, two genes that coexist with OMIM include IL7R and PIK3R1. After considering our findings and the relevant literature, we determined that the key gene related to the occurrence and development of CAP was IL7R. The mNGS detected 13 kinds of bacteria, 4 kinds of fungi, and 2 kinds of viruses. Based on immunohistochemical results, it was found that there were relatively more bacteria detected in the IL7R high expression group. The identification of the key gene IL7R and the related signaling pathways extend understanding of the pathogenesis of CAP and provide a theoretical basis for clinical targeted therapy research.

Antiviral Activity of Cell Membrane-Bound Amphiphilic Polymers.

We demonstrate that cholesterol-modified polyethylene glycol has antiviral activity, exerted by anchoring to plasma membranes and sterically inhibiting viruses from entering cells. These polymers distribute sparsely on cell membranes even at binding saturation. However, the polymers have sufficient elastic repulsion energy to repel various kinds of viruses with sizes larger than the mean distances between anchored polymers, including SARS-CoV-2 pseudoparticles. Our strategy can be applied to protect the epithelium from viruses. When these polymers are applied to the epithelium, they localize on the apical surface due to the tight junction barriers, resulting in surface-only coating. Therefore, these polymers can prevent the entry of viruses into cells of the epithelium with minimal disturbance to lateral cell-cell interactions and organizations.

Applying T-classifier, binary classifiers, upon high-throughput TCR sequencing output to identify cytomegalovirus exposure history

With the continuous development of information technology and the running speed of computers, the development of informatization has led to the generation of increasingly more medical data. Solving unmet needs such as employing the constantly developing artificial intelligence technology to medical data and providing support for the medical industry is a hot research topic. Cytomegalovirus (CMV) is a kind of virus that exists widely in nature with strict species specificity, and the infection rate among Chinese adults is more than 95%. Therefore, the detection of CMV is of great importance since the vast majority of infected patients are in a state of invisible infection after the infection, except for a few patients with clinical symptoms. In this study, we present a new method to detect CMV infection status by analyzing high-throughput sequencing results of T cell receptor beta chains (TCRβ). Based on the high-throughput sequencing data of 640 subjects from cohort 1, Fisher’s exact test was performed to evaluate the relationship between TCRβ sequences and CMV status. Furthermore, the number of subjects with these correlated sequences to different degrees in cohort 1 and cohort 2 were measured to build binary classifier models to identify whether the subject was CMV positive or negative. We select four binary classification algorithms: logistic regression (LR), support vector machine (SVM), random forest (RF), and linear discriminant analysis (LDA) for side-by-side comparison. According to the performance of different algorithms corresponding to different thresholds, four optimal binary classification algorithm models are obtained. The logistic regression algorithm performs best when Fisher's exact test threshold is 10−5, and the sensitivity and specificity are 87.5% and 96.88%, respectively. The RF algorithm performs better at the threshold of 10−5, with a sensitivity of 87.5% and a specificity of 90.63%. The SVM algorithm also achieves high accuracy at the threshold value of 10−5, with a sensitivity of 85.42% and specificity of 96.88%. The LDA algorithm achieves high accuracy with 95.83% sensitivity and 90.63% specificity when the threshold value is 10−4. This is probably because the two-dimensional distribution of CMV data samples is linearly separable, and linear division models such as LDA are more effective, while the division effect of nonlinear separable algorithms such as random forest is relatively inaccurate. This new finding may be a potential diagnostic method for CMV and may even be applicable to other viruses, such as the infectious history detection of the new coronavirus.

Design and Development of KPRI RSCM Employee Presence Attendance Application Using Android-Based QR Code

RSCM KPRI Services Cooperative is a cooperative that operates in 2 initial tasks, namely providing loans to members with light services and carrying out the distribution of basic goods from the government to members of each company or agency. make attendance. attendance attendance is part of the most important role in every body of work. Where attendance is one of the main supports that can motivate and support all work activities to be carried out in it, using the finger print system in attendance at the Cooperative office which is in the Dr. Cipto Mangunkusumo National General Hospital (RSCM) environment is very at risk of being exposed to various kinds of virus, and one of them is the Corona Virus which is still a pandemic, so that the KPRI RSCM Service Cooperative innovates in the employee attendance system by using a presence system using an Android-based QR Code, so that cooperative employees can take attendance using their personal cell phones. explains how to use the designed application system, namely the KPRI RSCM Employee Presence Application. It is hoped that this application can make it easier for employees to make attendance, and the Personnel section can more easily monitor the attendance of their employees utilizing the Android system as a tool or attendance system that makes it easier for companies and employees, especially at the KPRI RSCM Service Cooperative so that it reduces contact that can cause risk of exposure to the coronavirus.

Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.

Comprehensive identification of possible target cells for viruses is crucial for understanding the pathological mechanism of virosis. The susceptibility of cells to viruses depends on many factors. Besides the existence of receptors at the cell surface, effective expression of viral genes is also pivotal for viral infection. The regulation of viral gene expression is a multilevel process including transcription, translational initiation and translational elongation. At the translational elongation level, the translational efficiency of viral mRNAs mainly depends on the match between their codon composition and cellular translational machinery (usually referred to as codon adaptation). Thus, codon adaptation for viral ORFs in different cell types may be related to their susceptibility to viruses. In this study, we selected the codon adaptation index (CAI) which is a common codon adaptation-based indicator for assessing the translational efficiency at the translational elongation level to evaluate the susceptibility to two-pandemic viruses (HIV-1 and SARS-CoV-2) of different human cell types. Compared with previous studies that evaluated the infectivity of viruses based on codon adaptation, the main advantage of our study is that our analysis is refined to the cell-type level. At first, we verified the positive correlation between CAI and translational efficiency and strengthened the rationality of our research method. Then we calculated CAI for ORFs of two viruses in various human cell types. We found that compared to high-expression endogenous genes, the CAIs of viral ORFs are relatively low. This phenomenon implied that two kinds of viruses have not been well adapted to translational regulatory machinery in human cells. Also, we indicated that presumptive susceptibility to viruses according to CAI is usually consistent with the results of experimental research. However, there are still some exceptions. Finally, we found that two viruses have different effects on cellular translational mechanisms. HIV-1 decouples CAI and translational efficiency of endogenous genes in host cells and SARS-CoV-2 exhibits increased CAI for its ORFs in infected cells. Our results implied that at least in cases of HIV-1 and SARS-CoV-2, CAI can be regarded as an auxiliary index to assess cells' susceptibility to viruses but cannot be used as the only evidence to identify viral target cells.

The TRIM25 Gene in Ducks: Cloning, Characterization and Antiviral Immune Response.

TRIM25, as a significant member of the TRIM family, has been frequently demonstrated in regulating the host's antiviral response by activating innate immunity. Ducks are often asymptomatic carriers of influenza A viruses, but the beneficial roles of TRIM25 in modulating the immune response remain largely unknown in ducks. In this study, we characterized the TRIM25, which contains a 16 bp 5'-UTR, a 279 bp 3'-UTR and a 2052 bp ORF that encodes 683 amino acid residues. In addition, we found that duTRIM25 transcripts were widely expressed in the 10 tissues tested, with higher expression levels in the kidney, liver, muscle and spleen and lower expression levels in the duodenum and blood. In addition, the six kinds of virus- or bacteria-mimicking stimuli were transfected into DEFs, and duTRIM25 was induced significantly with 5'ppp dsRNA stimulation. Furthermore, overexpression of duTRIM25 followed by treatment with 5'ppp dsRNA resulted in an increase in IFN-β. The SPRY domain of duTRIM25 contributed to promoting IFN-β activity in DEFs challenged with 5'ppp dsRNA. Taken together, our findings suggest that duck TRIM25 can induce the production of IFN-β against double-stranded RNA virus stimuli and that the SPRY domain of duTRIM25 was critical for the infection.