Decoding bovine coronavirus immune targets:an epitope informatics approach

Bovine coronavirus(BCoV)poses a significant threat to the global cattle industry,causing both respiratory and gastrointestinal infections in cattle populations.This necessitates the development of efficacious vaccines.While several inactivated and live BCoV vaccines exist,they are predominantly limited to calves.The immunization of adult cattle is imperative for BCoV infection control,as it curtails viral transmission to calves and ameliorates the impact of enteric and respiratory ailments across all age groups within the herd.This study presents an in silico methodology for devising a multiepitope vaccine targeting BCoV.The spike glycoprotein(S)and nucleocapsid(N)proteins,which are integral elements of the BCoV structure,play pivotal roles in the viral infection cycle and immune response.We constructed a remarkably effective multiepitope vaccine candidate specifically designed to combat the BCoV population.Using immunoinformatics technology,B-cell and T-cell epitopes were predicted and linked together using linkers and adjuvants to efficiently trigger both cellular and humoral immune responses in cattle.The in silico construct was characterized,and assessment of its physicochemical properties revealed the formation of a stable vaccine construct.After 3D modeling of the vaccine construct,molecular docking revealed a stable interaction with the bovine receptor bTLR4.Moreover,the viability of the vaccine’s high expression and simple purification was demonstrated by codon optimization and in silico cloning expression into the pET28a(+)vector.By applying immunoinformatics approaches,researchers aim to better understand the immune response to bovine coronavirus,discover potential targets for intervention,and facilitate the development of diagnostic tools and vaccines to mitigate the impact of this virus on cattle health and the livestock industry.We anticipate that the design will be useful as a preventive treatment for BCoV sickness in cattle,opening the door for further laboratory studies.

Antigen epitopes of animal coronaviruses:a mini-review

Coronaviruses are widespread in nature and can infect mammals and poultry,making them a public health concern.Globally,prevention and control of emerging and re-emerging animal coronaviruses is a great challenge.The mecha-nisms of virus-mediated immune responses have important implications for research on virus prevention and control.The antigenic epitope is a chemical group capable of stimulating the production of antibodies or sensitized lympho-cytes,playing an important role in antiviral immune responses.Thus,it can shed light on the development of diagnos-tic methods and novel vaccines.Here,we have reviewed advances in animal coronavirus antigenic epitope research,aiming to provide a reference for the prevention and control of animal and human coronaviruses.

Efficacy and Safety of Lianhua Qingke Tablets in the Treatment of Long Coronavirus Disease (COVID) Cough: A Randomized, Double-Blind, Placebo-Controlled, Multicenter Clinical Study

Lianhua Qingke tablets,a patented traditional Chinese medicine that has validated clinical efficacy for treating cough caused by severe acute respiratory syndrome coronavirus 2 infection,lack rigorous evidence-based research evaluating their effect on long coronavirus disease(COVID)cough.A randomized,double-blind,placebo-controlled,multicenter clinical study was conducted among patients with long COVID cough from 19 hospitals and 23 community health centers in China.Patients were randomized 1:1 to receive either Lianhua Qingke tablets or placebo orally for 14 days(four tablets,1.84 g,three times a day).The primary endpoint indicator was the disappearance of cough,with the remission of cough also considered.Among 482 randomized patients,480(full analysis set 480;per-protocol set 470;safety set 480)were included in the primary analysis.According to the full analysis,the time until cough disappearance was significantly shorter in the trial group than in the control group,with a significant increase in the 14-day cough disappearance rate.Accordingly,the time to cough remission was significantly shorter in the trial group than in the control group.The change in the total symptom score was significantly greater in the trial group than in the control group on days 7 and 14,consistent with the results indicated by the visual analog scale(VAS)and cough evaluation test(CET)scores.No serious adverse events were recorded during the study.Lianhua Qingke tablets significantly improved the clinical symptoms of patients with long COVID cough.

The potential role of Gegen Qinlian decoction in the treatment of coronavirus disease 2019 based on network pharmacology and validation of lipopolysaccharide-induced macrophages

Background:Coronavirus disease 2019(COVID-19)is caused by severe acute respiratory syndrome coronavirus 2,which has led to deaths and currently lacks an efficient treatment.Despite studies suggesting the potential of the Gegen Qinlian decoction(GQD)in preventing COVID-19,comprehensive analyses of its anti-COVID-19 potential are still lacking.Methods:GQD treatment was evaluated for its efficacy in ameliorating the early stage(24 hours)of lipopolysaccharide(LPS)-induced cytokine storm in vivo.Additionally,target genes of GQD were co-analyzed with COVID-19 signature genes to identify key ingredients and their pathways.Validation was also conducted using an LPS-induced macrophage model.Results:GQD treatment effectively ameliorated the early stage of LPS-induced cytokine storm in vivo.Key ingredients such as quercetin were found to be involved in multiple pathways,including inflammation,immunity,oxidative stress,cell proliferation,and apoptosis,through the AGE-RAGE signaling pathway and IL-17 signaling pathway.In the LPS-induced macrophage model,quercetin inhibited macrophage polarization(M1)and the secretion of inflammatory factors(IL-6,TNF-α,IL-17A).Conclusions:Our results indicate that GQD can be utilized in the treatment of cytokine storm induced by COVID-19 and has the potential to treat COVID-19 by suppressing the COVID-19 signature genes and macrophage polarization.

Impact of non-alcoholic fatty liver disease on coronavirus disease 2019: A systematic review

BACKGROUND Many studies have revealed a link between non-alcoholic fatty liver disease(NA-FLD)and coronavirus disease 2019(COVID-19),making understanding the relationship between these two conditions an absolute requirement.AIM To provide a qualitative synthesis on the currently present data evaluating COVID-19 and NAFLD.METHODS This systematic review was conducted in accordance with the guidelines pro-vided by preferred reporting items for systematic reviews and meta-analyses and the questionnaire utilized the population,intervention,comparison,and outcome framework.The search strategy was run on three separate databases,PubMed/MEDLINE,Scopus,and Cochrane Central,which were systematically searched from inception until March 2024 to select all relevant studies.In addition,ClinicalTrials.gov,Medrxiv.org,and Google Scholar were searched to identify grey literature.RESULTS After retrieval of 11 studies,a total of 39282 patients data were pooled.Mortality was found in 11.5%and 9.4%of people in NAFLD and non-NAFLD groups.In all,23.2%of NAFLD patients and 22%of non-NAFLD admissions diagnosed with COVID-19 were admitted to the intensive care unit,with days of stay varying.Ventilatory support ranged from 5%to 40.5%in the NAFLD cohort and from 3.1%to 20%in the non-NAFLD cohort.The incidence of acute liver injury showed significance.Clinical improvement on days 7 and 14 between the two classifications was significant.Hospitalization stay ranged from 9.6 days to 18.8 days and 7.3 days to 16.4 days in the aforementioned cohorts respectively,with 73.3%and 76.3%of patients being discharged.Readmission rates varied.CONCLUSION Clinical outcomes except mortality consistently showed a worsening trend in patients with NAFLD and concomitant COVID-19.Further research in conducting prospective longitudinal studies is essential for a more powerful conclusion.

Clinical Effect of Yinhuang Qingfei Capsules in Treatment of Asymptomatic and Mild/Common Severe Acute Respiratory Syndrome Coronavirus 2 Infection:An Analysis of 242 Cases

[Objectives]To investigate the clinical effect of Yinhuang Qingfei capsules in the treatment of asymptomatic and mild/common severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection.[Methods]A total of 362 patients with SARS-CoV-2 infection were divided into the treatment group with 242 patients and control group with 120 patients according to their treatment regimen.The patients in the control group were given standard treatment regimen and those in the treatment group were given Yinhuang Qingfei capsules in addition to the treatment in the control group.The two groups were observed in terms of average length of hospital stay,mean time for nucleic acid clearance,TCM syndrome score,and progression to severe/critical illness,and clinical outcome was compared between the two groups.[Results]There was a significant difference in the overall response rate between the treatment group and the control group[97.52%(236/242)vs 95.00%(114/120),P<0.05].Compared with the control group,the treatment group had significantly shorter length of hospital stay and time for nucleic acid clearance(P<0.05).After 7 days of treatment,both groups had a significant change in TCM syndrome score,and there was a significant difference in TCM syndrome score between the two groups(P<0.05);after 15 days of treatment,both groups had a TCM syndrome score of 0.Progression to severe/critical illness was not observed in either group.[Conclusions]Compared with the standard treatment regimen alone,standard treatment regimen combined with Yinhuang Qingfei capsules can effectively shorten the length of hospital stay and time for nucleic acid clearance and improve TCM symptoms in patients with asymptomatic and mild/common SARS-CoV-2 infection.

Prevention and Nursing of Adverse Reactions of Novel Coronavirus Inactivated Vaccine (Vero Cells)

Objective:To discuss and analyze the causes of adverse reactions caused by the inactivated novel coronavirus vaccine(Vero cells),and to propose methods of prevention and care.Methods:A questionnaire was used to randomly select 229 adults who were vaccinated with the inactivated novel coronavirus vaccine(Vero cells)at Xi’an People’s Hospital(Xi’an Fourth Hospital).The adverse reactions were statistically analyzed.Results:Among the 229 adults vaccinated with the inactivated novel coronavirus vaccine(Vero cells),30 experienced vaccination reactions.The main reaction was local induration at the inoculation site,and dizziness was the primary systemic symptom.Conclusion:To reduce the incidence of adverse reactions to the inactivated novel coronavirus vaccine(Vero cells),it is necessary to effectively evaluate the health status of adults before vaccination,select the correct vaccination site,and strictly implement the rules of 3-inspections,7-checks,and 1-verification.Standardizing the operation process and providing thorough health education after vaccination can effectively reduce the occurrence of adverse reactions.

Serological survey on canine coronavirus antibodies in giant pandas by virus neutralization test

In order to survey the infectious situation of canine coronavirus (CCV) in giant panda population, a virus neutralization test detecting specific antibodies against CCV in giant panda抯 sera was established by using two-fold dilutions of serum and 100 TCID50 of the virus. The 62 sera samples of giant pandas, which were gathered from zoos and reserve region of Sichuan Province, China were detected. The neutralization antibody titer of 1:4 was recognized as the positive criterion, 8 sera samples were detected to be positive, and the positive rate was 12.9%. The titers of neutralizing antibody ranged from 1:8 to 1:32. It was the first comprehensive investigation on neutralization antibodies against CCV in giant panda population in China. The results of study showed that the infection of CCV in giant panda population was universal, which has posed a threat to the health of giant panda. Therefore, it is incumbent on us to study safe and effective vaccines to protect giant panda against CCV infection.

Site discrepancy of synonymous codon usage in SARS coronavirus and other viruses in Coronaviridae

The synonymous codon usage in the translational initiation and termination regions of genes of severe acute respiratory syndrome (SARS) coronavirus and five other viruses in Coronaviridae was systematically analyzed.The results indicate that most minor codons for these coronaviruses are preferentially used in the initial and terminal region.The minor codons preferentially used in the initial region are thought to have a negative effect on gene expression,which can be explained by the minor codon modulator hypothesis.It also indicates that the minor codons preferentially used in the terminal region may regulate the level of gene expression.The proposed results strongly imply that the minor codon modulator hypothesis can be applied to both some bacteria and some viruses.

Bat SARS coronavirus HKU3-1病毒株基因组及蛋白质的生物信息学分析

目的比较中国菊头蝠SARS冠状病毒(Bat SARS coronavirus)与人类及果子狸体内分离出来的SARS-Cov,分析它们是否存在一定的相似性。方法本文分析了Bat SARS coronavirus与已知冠状病毒Human SARS-CoV和civet SARS-CoV的系统进化关系,绘制了Bat SARS coronavirusHKU3-1的全基因序列图,同时预测了S蛋白和N蛋白的三维模型。结果对Bat SARS coronavirus HKU3-1的序列分析表明中国菊头蝠SARS-CoV与人和果子狸SARS-CoV非常相近。系统进化分析法显示Bat-SARS-CoV与SARS-CoV形成一个不同的群,称为group 2b CoV,与已知的group 2 CoV存在一定的距离。结论Bat SARS coronavirus HKU3-1不太可能是从人SARS-CoV传播过来的。另外,Bat SARS coronavirus与civet SARS-CoV可能具有共同的祖先,使得中国菊头蝠SARS病毒株同样具有感染人体的危险。

Evaluation of antiviral activities of Houttuynia cordata Thunb.extract,quercetin,quercetrin and cinanserin on murine coronavirus and dengue virus infection

Objective:To evaluate the in vitro activities of the ethyl acetate(EA) fraction of Houttuynia cordata(H.cordata) Thunb.(Saururaceae) and three of its constituent flavonoids(quercetin.quercitrin and rutin) against murine coronavirus and dengue virus(DENV).Methods:The antiviral activities of various concentrations of the EA fraction of H.cordata and flavonoids were assessed using virus neutralization tests against mouse hepatitis virus(MHV) and DENV type 2(DENV-2).Cinanserin hydrochloride was also tested against MHV.The EA fraction of H.cordata was tested for acute oral toxicity in C57BL/6 mice.Results:The EA fraction of H.cordata inhibited viral infectivity up to 6 d.Cinanserin hydrochloride was able to inhibit MHV for only 2 d.The 50%inhibitory concentrations(IC_(50)) of the EA fraction of H.cordata added before the viral adsorption stage were 0.98 μg/mL for MHV and 7.50 μg/mL for DENV-2with absence of cytotoxicity.The mice fed with the EA fraction up to 2 000 mg/kg did not induce any signs of acute toxicity,with normal histological features of major organs.Certain flavonoids exhibited comparatively weaker antiviral activity,notably quercetin which could inhibit both MHV and DENV-2.This was followed by quercitrin which could inhibit DENV-2but not MHV,whereas rutin did not exert any inhibitory effect on either virus.When quercetin was combined with quercitrin,enhancement of anti-DENV-2 activity and reduced cytotoxicity were observed.However,the synergistic efficacy of the flavonoid combination was still less than that of the EA fraction.Conclusions:The compounds in H.cordata contribute to the superior antiviral efficacy of the EA fraction which lacked cytotoxicity in vitro and acute toxicity in vim.H.cordata has much potential for the development of antiviral agents against coronavirus and dengue infections.

Stability of SARS Coronavirus in Human Specimens and Environment and Its Sensitivity to Heating and UV Irradiation

Objective The causal agent for SARS is considered as a novel coronavirus that has never been described both in human and animals previously. The stability of SARS coronavirus in human specimens and in environments was studied. Methods Using a SARS coronavirus strain CoV-P9, which was isolated from pharyngeal swab of a probable SARS case in Beijing, its stability in mimic human specimens and in mimic environment including surfaces of commonly used materials or in household conditions, as well as its resistances to temperature and UV irradiation were analyzed. A total of 106 TCID50 viruses were placed in each tested condition, and changes of the viral infectivity in samples after treatments were measured by evaluating cytopathic effect (CPE) in cell line Vero-E6 at 48 h after infectionn. Results The results showed that SARS coronavirus in the testing condition could survive in serum, 1:20 diluted sputum and feces for at least 96 h, whereas it could remain alive in urine for at least 72 h with a low level of infectivity. The survival abilities on the surfaces of eight different materials and in water were quite comparable, revealing reduction of infectivity after 72 to 96 h exposure. Viruses stayed stable at 4℃, at room temperature (20℃) and at 37℃ for at least 2 h without remarkable change in the infectious ability in cells, but were converted to be non-infectious after 90-, 60- and 30-min exposure at 56℃, at 67℃ and at 75℃, respectively. Irradiation of UV for 60 min on the virus in culture medium resulted in the destruction of viral infectivity at an undetectable level. Conclusion The survival ability of SARS coronavirus in human specimens and in environments seems to be relatively strong. Heating and UV irradiation can efficiently eliminate the viral infectivity.

Coronavirus MHV-A59 infects the lung and causes severe pneumonia in C57BL/6 mice

It remains challenging to develop animal models of lung infection and severe pneumonia by severe acute respiratory syndrome coronavirus(SARS-CoV) and Middle East respiratory syndrome cornavirus(MERS-Co V) without high level of containment. This inevitably hinders understanding of virushost interaction and development of appropriate countermeasures. Here we report that intranasal inoculation of sublethal doses of murine coronavirus mouse hepatitis virus A-59(MHV-A59), a hepatic and neuronal tropic coronavirus, can induce acute pneumonia and severe lung injuries in C57BL/6 mice. Inflammatory leukocyte infiltrations, hemorrhages and fibrosis of alveolar walls can be observed 2-11 days after MHV-A59 infection. This pathological manifestation is associated with dramatical elevation of tissue IP-10 and IFN-γ and moderate increase of TNF-α and IL-1β, but inability of anti-viral type I interferon response. These results suggest that intranasal infection of MHV-A59 would serve as a surrogate mouse model of acute respiratory distress syndrome by SARS-CoV and MERS-CoV infections.

Fear can be more harmful than the severe acute respiratory syndrome coronavirus 2 in controlling the corona virus disease 2019 epidemic

The current corona virus disease 2019 outbreak caused by severe acute respiratory syndrome coronavirus 2 started in Wuhan,China in December 2019 and has put the world on alert.To safeguard Chinese citizens and to strengthen global health security,China has made great efforts to control the epidemic.Many in the global community have joined China to limit the epidemic.However,discrimination and prejudice driven by fear or misinformation have been flowing globally,superseding evidence and jeopardizing the anti-severe acute respiratory syndrome coronavirus 2 efforts.We analyze this phenomenon and its underlying causes and suggest practical solutions.

The origin, transmission and clinical therapies on coronavirus disease 2019(COVID-19) outbreak——an update on the status

An acute respiratory disease,caused by a novel coronavirus(SARS-CoV-2,previously known as 2019-nCoV),the coronavirus disease 2019(COVID-19)has spread throughout China and received worldwide attention.On 30 January 2020,World Health Organization(WHO)officially declared the COVID-19 epidemic as a public health emergency of international concern.The emergence of SARS-CoV-2,since the severe acute respiratory syndrome coronavirus(SARSCoV)in 2002 and Middle East respiratory syndrome coronavirus(MERS-CoV)in 2012,marked the third introduction of a highly pathogenic and large-scale epidemic coronavirus into the human population in the twenty-first century.As of 1 March 2020,a total of 87,137 confirmed cases globally,79,968 confirmed in China and 7169 outside of China,with 2977 deaths(3.4%)had been reported by WHO.Meanwhile,several independent research groups have identified that SARS-CoV-2 belongs toβ-coronavirus,with highly identical genome to bat coronavirus,pointing to bat as the natural host.The novel coronavirus uses the same receptor,angiotensin-converting enzyme 2(ACE2)as that for SARS-CoV,and mainly spreads through the respiratory tract.Importantly,increasingly evidence showed sustained human-tohuman transmission,along with many exported cases across the globe.The clinical symptoms of COVID-19 patients include fever,cough,fatigue and a small population of patients appeared gastrointestinal infection symptoms.The elderly and people with underlying diseases are susceptible to infection and prone to serious outcomes,which may be associated with acute respiratory distress syndrome(ARDS)and cytokine storm.Currently,there are few specific antiviral strategies,but several potent candidates of antivirals and repurposed drugs are under urgent investigation.In this review,we summarized the latest research progress of the epidemiology,pathogenesis,and clinical characteristics of COVID-19,and discussed the current treatment and scientific advancements to combat the epidemic novel coronavirus.

Novel coronavirus (2019-nCoV) update: What we know and what is unknown

The year 2020 was welcomed and characterized with a report of pneumonia of unknown etiology,which occurred primarily in Wuhan City of Hubei Province of China.Between 31 December 2019 and 3 January 2020,a total of 44 cases in human was reported to the World Health Organization(WHO)by the Chinese Health Authorities[1].By 3 February 2020,a total of 17391 cases have been confirmed globally with 2838 new cases(China:17238;2831 new cases and 361 deaths;Outside China:153 with 7 new cases and 1 death from 23 countries)[1].

Stability and infectivity of coronaviruses in inanimate environments

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)is a highly contagious virus that can transmit through respiratory droplets,aerosols,or contacts.Frequent touching of contaminated surfaces in public areas is therefore a potential route of SARS-CoV-2 transmission.The inanimate surfaces have often been described as a source of nosocomial infections.However,summaries on the transmissibility of coronaviruses from contaminated surfaces to induce the coronavirus disease 2019 are rare at present.This review aims to summarize data on the persistence of different coronaviruses on inanimate surfaces.The literature was systematically searched on Medline without language restrictions.All reports with experimental evidence on the duration persistence of coronaviruses on any type of surface were included.Most viruses from the respiratory tract,such as coronaviruses,influenza,SARS-CoV,or rhinovirus,can persist on surfaces for a few days.Persistence time on inanimate surfaces varied from minutes to up to one month,depending on the environmental conditions.SARSCoV-2 can be sustained in air in closed unventilated buses for at least 30 min without losing infectivity.The most common coronaviruses may well survive or persist on surfaces for up to one month.Viruses in respiratory or fecal specimens can maintain infectivity for quite a long time at room temperature.Absorbent materials like cotton are safer than unabsorbent materials for protection from virus infection.The risk of transmission via touching contaminated paper is low.Preventive strategies such as washing hands and wearing masks are critical to the control of coronavirus disease 2019.

Clinical Characteristics of Children with Coronavirus Disease 2019 in Hubei, China

Since December 2019,COVID-19 has occurred unexpectedly and emerged as a health problem worldw ide.Despite the rapidly increasing number of cases in subsequent weeks,the clinical characteristics of pediatric cases are rarely described.A cross-sectional multicenter study was carried out in 10 hospitals across Hubei province.A total of 25 confirmed pediatric cases of COVID-19 were collected.The demographic data,epidemiological history,underlying discascs,clinical mani festations,laboratory and radiological data,treatments,and outcomes were analyzcd.Of 25 hospitalized patients with COVID-19,the boy to girl ratio was 1.27:1.The median age was 3 years.COVID-19 cases in children aged<3 years,3-6 years,and≥6-years patients were 10(40%),6(24%),and 9(36%),respectively.The most common symptoms at onset of ilness were fever(13[52%]),and dry cough(11[44%]).Chest CT images showed essential normal in 8 cases(33.3%),unilateral involvement of lungs in 5 cases(20.8%),and bilateral involvement in 11 cases(45.8%).Clinical diagnoses included upper respiratory tract infection(n=8),mild pneumonia(n=15),and critical cases(n=2).Two critical cases(8%)were given invasive mechanical ventilation,corticosteroids,and immunoglobulin.The symptoms in 24(96%)of 25 patients were alleviated and one patient had been discharged.It was concluded that children were susceptible to COVID-19 like adults,while the clinical presentations and outcomes were more favorable in children.However,children less than 3 years old accounted for majority cases and critical cases lied in this age group,which demanded extra attentions during home caring and hospitalization treatment.

Intelligent Forecasting Model of COVID-19 Novel Coronavirus Outbreak Empowered with Deep Extreme Learning Machine

An epidemic is a quick and widespread disease that threatens many lives and damages the economy.The epidemic lifetime should be accurate so that timely and remedial steps are determined.These include the closing of borders schools,suspension of community and commuting services.The forecast of an outbreak effectively is a very necessary but difficult task.A predictive model that provides the best possible forecast is a great challenge for machine learning with only a few samples of training available.This work proposes and examines a prediction model based on a deep extreme learning machine(DELM).This methodology is used to carry out an experiment based on the recent Wuhan coronavirus outbreak.An optimized prediction model that has been developed,namely DELM,is demonstrated to be able to make a prediction that is fairly best.The results show that the new methodology is useful in developing an appropriate forecast when the samples are far from abundant during the critical period of the disease.During the investigation,it is shown that the proposed approach has the highest accuracy rate of 97.59%with 70%of training,30%of test and validation.Simulation results validate the prediction effectiveness of the proposed scheme.

Recent advances and perspectives of nucleic acid detection for coronavirus

The recent pneumonia outbreak caused by a novel coronavirus(SARS-CoV-2)is posing a great threat to global public health.Therefore,rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments,saving people's lives and preventing epidemics.It is important to establish a quick standard diagnostic test for the detection of the infectious disease(COVID-19)to prevent subsequent secondary spread.Polymerase chain reaction(PCR)is regarded as a gold standard test for the molecular diagnosis of viral and bacterial infections with high sensitivity and specificity.Isothermal nucleic acid amplification is considered to be a highly promising candidate method due to its fundamental advantage in quick procedure time at constant temperature without thermocycler opera-tion.A variety of improved or new approaches also have been developed.This review summarizes the currently available detection methods for coronavirus nucleic acid.It is anticipated that this will assist researchers and clinicians in developing better techniques for timely and effective detection of coro-navirus infection.