Coronaviruses: emerging and re-emerging pathogens in humans and animals

Origin and cross-species transmission of bat coronaviruses in China

Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. Here we use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 589 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal. We find that host-switching occurs more frequently and across more distantly related host taxa in alpha- than beta-CoVs, and is more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.

Symptom clusters and symptom networks of symptom experiences in patients with SARS-CoV-2 infection

Context

Symptom clusters and symptom networks can potentially enhance the precision in managing symptoms. However, limited research has been conducted on the symptom network experienced by patients infected with Severe Acute Respiratory Syndrome Coronavirus 2.

Objectives

To identify the composition of symptom clusters in SARS-CoV-2 infected patients, establish a symptom network to explore the centrality indices, and investigate independent risk factors influencing the occurrence of symptom clusters.

Methods

Between February 2022 and June 2023, a total of 418 patients diagnosed with SARS-CoV-2 infection were recruited in the Second Affiliated Hospital of Chongqing Medical University. A symptom questionnaire was utilized to assess three dimensions encompassing a comprehensive range of 40 symptoms. Principal component analysis was employed to identify distinct symptom clusters, while network analysis elucidated the interconnections among these symptoms. Univariate analysis and multiple linear regression analysis were conducted to investigate the factors influencing the manifestation of these symptom clusters.

Results

Eight symptom clusters were identified, namely the nasopharyngeal-related symptom cluster, the circulatory-related symptom cluster, the neural-related symptom cluster, the physical-related symptom cluster, the digestive-related symptom cluster, the respiratory-related symptom cluster, the fever-related symptom cluster, and the sensory-related symptom cluster. The three centrality indices with the highest values were chest tightness (rs = 7.84, rc = 0.013, rb = 6.99), muscle aches (rs = 7.32, rc = 0.013, rb = 2.72), and smell abnormality (rs = 6.56, rc = 0.011, rb = 4.58). Variables including age, gender, income, education, hyperlipidemia, chronic bronchitis, and tumor were associated with the occurrence of these eight symptom clusters.

Conclusion

The findings of this study highlight the necessity to explore symptom clusters and symptom networks in order to enhance the effectiveness of symptom management in patients with SARS-CoV-2 infection. Particularly crucial is the evaluation of centrality indices as an integral component of caring for such patients. Early detection of high-risk individuals within each symptom cluster can provide a scientific foundation for developing interventions that will optimize patient prognosis.

Repurposing antibiotics as potent multi-drug candidates for SARS-CoV-2 delta and omicron variants: molecular docking and dynamics

There is a daunting public health emergency due to the emergence and rapid global spread of the new omicron variants of SARS-CoV-2. The variants differ in many characteristics, such as transmissibility, antigenicity and the immune system of the human hosts' shifting responses. This change in characteristics raises concern, as it leads to unknown consequences and also raises doubts about the efficacy of the currently available vaccines. As of March 2022, there are five variants of SARS-CoV-2 disseminating: the alpha, the beta, the gamma, the delta and the omicron variant. The omicron variant has more than 30 mutations on the spike protein, which is used by the virus to enter the host cell and is also used as a target for the vaccines. In this work, we studied the possible anti-COVID-19 effect of two molecules by molecular docking using Autodock Vina and molecular dynamic simulations using Gromacs 2020 software. We docked amoxicillin and clavulanate to the main protease (Mpro), the RNA-dependent RNA polymerase (RdRp) and the spike protein receptor-binding domain (SRBD) of the wild type with the two variants (delta and omicron) of SARS-CoV-2. The docking results show that the ligands bound tightly with the SRBD of the omicron variant, while the dynamic simulation revealed the ability of amoxicillin to bind to the SRBD of both variants' delta and omicron. The high number of mutations that occurred in both variants increases the affinity of amoxicillin towards them.Communicated by Ramaswamy H. Sarma.

Characterization of Pharmacokinetics, Biotransformation and Elimination of Pomotrelvir Orally Administered in Healthy Male Adults Using Two [14C]-Labeled Microtracers with Separate Labeling Positions

Pomotrelvir is an orally bioavailable, target antiviral inhibitor of the main protease (Mpro) of coronaviruses, including severe acute respiratory syndrome coronavirus 2, the etiological agent of Coronavirus Disease 2019. The pharmacokinetics, metabolism and elimination of two [14C]-labeled microtracers of 5 µCi/700 mg pomotrelvir with separate labeling positions (isotopomers), [lactam carbonyl-14C-pomotelvir] and [benzene ring-U-14C-pomotrelvir], following a single oral dose in healthy adult males was evaluated in two separate cohorts. Pomotrelvir was rapidly absorbed and eliminated primarily through metabolism and subsequently excreted via urine and feces. There were no differences in pomotrelvir pharmacokinetics between the two cohorts. The mean total radioactive dose recovered was 93.8% (n = 8) in the lactam cohort (58% in urine and 36% in feces) and 94.2% (n = 8) in the benzene cohort (75% in urine and 19% in feces), with ≥80% of [14C] recovered within 96 hours after dosing. About 5% and 3% of the intact pomotrelvir was recovered in feces and urine, respectively. Eleven major metabolites were detected and characterized using liquid chromatography-accelerator mass spectrometry and liquid chromatography tandem mass spectrometry methods, with three and six different metabolites elucidated in the samples collected from lactam and benzene cohorts, respectively, and two metabolites observed in both cohorts. The major metabolism pathway of pomotrelvir is through hydrolysis of its peptide bonds followed by phase II conjugations. These results support that the application of two radiolabeled isotopomers provided a comprehensive metabolite profiling analysis and was a successful approach in identifying the major disposition pathways of pomotrelvir that has complex routes of metabolism. SIGNIFICANCE STATEMENT: An unconventional approach using two differentially labeled [14C] microtracers, [lactam carbonyl-14C-pomotrelvir] and [benzene ring-U-14C-pomotrelvir] evaluated the mass balance of orally administered pomotrelvir in healthy adult males in two separate cohorts. The radioactive dose recovered in excreta was about 94% for both cohorts. While the two isotopomers of the radiolabeled-pomotrelvir showed no major differences in pharmacokinetics overall, they allowed for differential detection of their radiolabeled metabolites and appropriate characterization of their plasma exposure and excretion in urine and feces.

Spatio-temporal multidisciplinary analysis of socio-environmental conditions to explore the COVID-19 early evolution in urban sites in South America

This study aimed to analyse how socio-environmental conditions affected the early evolution of COVID-19 in 14 urban sites in South America based on a spatio-temporal multidisciplinary approach. The daily incidence rate of new COVID-19 cases with symptoms as the dependent variable and meteorological-climatic data (mean, maximum, and minimum temperature, precipitation, and relative humidity) as the independent variables were analysed. The study period was from March to November of 2020. We inquired associations of these variables with COVID-19 data using Spearman's non-parametric correlation test, and a principal component analysis considering socio economic and demographic variables, new cases, and rates of COVID-19 new cases. Finally, an analysis using non-metric multidimensional scale ordering by the Bray-Curtis similarity matrix of meteorological data, socio economic and demographic variables, and COVID-19 was performed. Our findings revealed that the average, maximum, and minimum temperatures and relative humidity were significantly associated with rates of COVID-19 new cases in most of the sites, while precipitation was significantly associated only in four sites. Additionally, demographic variables such as the number of inhabitants, the percentage of the population aged 60 years and above, the masculinity index, and the GINI index showed a significant correlation with COVID-19 cases. Due to the rapid evolution of the COVID-19 pandemic, these findings provide strong evidence that biomedical, social, and physical sciences should join forces in truly multidisciplinary research that is critically needed in the current state of our region.

Evolution and Control of COVID-19 Epidemic in Hong Kong

Hong Kong SAR has adopted universal masking, social distancing, testing of all symptomatic and high-risk groups for isolation of confirmed cases in healthcare facilities, and quarantine of contacts as epidemiological control measures without city lockdown or border closure. These measures successfully suppressed the community transmission of pre-Omicron SARS-CoV-2 variants or lineages during the first to the fourth wave. No nosocomial SARS-CoV-2 infection was documented among healthcare workers in the first 300 days. The strategy of COVID-19 containment was adopted to provide additional time to achieve population immunity by vaccination. The near-zero COVID-19 situation for about 8 months in 2021 did not enable adequate immunization of the eligible population. A combination of factors was identified, especially population complacency associated with the low local COVID-19 activity, together with vaccine hesitancy. The importation of the highly transmissible Omicron variant kickstarted the fifth wave of COVID-19, which could no longer be controlled by our initial measures. The explosive fifth wave, which was partially contributed by vertical airborne transmission in high-rise residential buildings, resulted in over one million cases of infection. In this review, we summarize the epidemiology of COVID-19 and the infection control and public health measures against the importation and dissemination of SARS-CoV-2 until day 1000.

Business or Hope? The Vaccine of the Day after, a Life Expectancy

This approach reflects the moments when humanity was infected by the new pandemic from a health point of view. The acceleration to find the vaccine that will protect us from the pandemic brings some interesting questions from the point of view of possible side effects and from the point of view of the economy. The growing interest in first producing the so-called ‘morning after’ vaccine calls into question whether this is a purely scientific act open to all countries of the world free of charge. Along the way, there are still the interests of many companies that have been favoured in one way or another to increase their profits. The analysis exposes the paradigm of health versus economy, of life expectancy versus business. Within this framework, humanity is discussed as a balance, perhaps taken advantage of by some of the biotechnology and pharmaceutical companies located in the strongest countries in the market, to the detriment of the weakest.

Identification and quantification of bioactive compounds suppressing SARS-CoV-2 signals in wastewater-based epidemiology surveillance

Recent SARS-CoV-2 wastewater-based epidemiology (WBE) surveillance have documented a positive correlation between the number of COVID-19 patients in a sewershed and the level of viral genetic material in the wastewater. Efforts have been made to use the wastewater SARS-CoV-2 viral load to predict the infected population within each sewershed using a multivariable regression approach. However, reported clear and sustained variability in SARS-CoV-2 viral load among treatment facilities receiving industrial wastewater have made clinical prediction challenging. Several classes of molecules released by regional industries and manufacturing facilities, particularly the food processing industry, can significantly suppress the SARS-CoV-2 signals in wastewater by breaking down the lipid-bilayer of the membranes. Therefore, a systematic ranking process in conjugation with metabolomic analysis was developed to identify the wastewater treatment facilities exhibiting SARS-CoV-2 suppression and identify and quantify the chemicals suppressing the SARS-COV-2 signals. By ranking the viral load per diagnosed case among the sewersheds, we successfully identified the wastewater treatment facilities in Missouri, USA that exhibit SARS-CoV-2 suppression (significantly lower than 5 × 1011 gene copies/reported case) and determined their suppression rates. Through both untargeted global chemical profiling and targeted analysis of wastewater samples, 40 compounds were identified as candidates of SARS-CoV-2 signal suppressors. Among these compounds, 14 had higher concentrations in wastewater treatment facilities that exhibited SARS-CoV-2 signal suppression compared to the unsuppressed control facilities. Stepwise regression analyses indicated that 4-nonylphenol, palmitelaidic acid, sodium oleate, and polyethylene glycol dioleate are positively correlated with SARS-CoV-2 signal suppression rates. Suppression activities were further confirmed by incubation studies, and the suppression kinetics for each bioactive compound were determined. According to the results of these experiments, bioactive molecules in wastewater can significantly reduce the stability of SARS-CoV-2 genetic marker signals. Based on the concentrations of these chemical suppressors, a correction factor could be developed to achieve more reliable and unbiased surveillance results for wastewater treatment facilities that receive wastewater from similar industries.

Impact of novel microbial secondary metabolites on the pharma industry

Microorganisms are remarkable producers of a wide diversity of natural products that significantly improve human health and well-being. Currently, these natural products comprise half of all the pharmaceuticals on the market. After the discovery of penicillin by Alexander Fleming 85 years ago, the search for and study of antibiotics began to gain relevance as drugs. Since then, antibiotics have played a valuable role in treating infectious diseases and have saved many human lives. New molecules with anticancer, hypocholesterolemic, and immunosuppressive activity have now been introduced to treat other relevant diseases. Smaller biotechnology companies and academic laboratories generate novel antibiotics and other secondary metabolites that big pharmaceutical companies no longer develop. The purpose of this review is to illustrate some of the recent developments and to show the potential that some modern technologies like metagenomics and genome mining offer for the discovery and development of new molecules, with different functions like therapeutic alternatives needed to overcome current severe problems, such as the SARS-CoV-2 pandemic, antibiotic resistance, and other emerging diseases. KEY POINTS: • Novel alternatives for the treatment of infections caused by bacteria, fungi, and viruses. • Second wave of efforts of microbial origin against SARS-CoV-2 and related variants. • Microbial drugs used in clinical practice as hypocholesterolemic agents, immunosuppressants, and anticancer therapy.

Public health and management

This chapter explains how hospital community health centers and nurseries home provide preventive curative, rehabilitation care for public health management. In this connection, it is explained how security professions, fire, ambulance providers and emergency medical services can be closely coordinated to increase the efficacy of health services. The authors want to develop awareness among doctors to mobilize other health service processions to manage the system under extreme climatic and disaster conditions to save life and social health stability. The last part of the chapter gives insight on systemic management of disease classification and under what circumstance a disease outbreak becomes epidemic and pandemic at the global level if inadequate management is taken. In this connection, the authors try to explain it with the example of the COVID-19 challenge and bring to the attention of the public to either eradicate or bring stability with the passing of time. So, it is necessary to develop a well-organized health-care system either temporarily or upgrade the existing health-care system to meet the demand in an emergency.

Novel coronavirus pathogen in humans and animals: an overview on its social impact, economic impact, and potential treatments

In the light of thousands of infections and deaths, the World Health Organization (WHO) has declared the outbreak of coronavirus disease (COVID-19) a worldwide pandemic. It has spread to about 22 million people worldwide, with a total of 0.45 million expiries, limiting the movement of most people worldwide in the last 6 months. However, COVID-19 became the foremost health, economic, and humanitarian challenge of the twenty-first century. Measures intended to curb the pandemic of COVID-19 included travel bans, lockdowns, and social distances through shelter orders, which will further stop human activities suddenly and eventually impact the world and the national economy. The viral disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). After SARS-CoV-2 virus and Middle East respiratory syndrome (MERS)-related CoV, COVID-19 is the third most significant lethal disease to humans. According to WHO, COVID-19 mortality exceeded that of SARS and MERS since COVID-19 was declared an international public health emergency. Genetic sequencing has recently established that COVID-19 is close to SARS-CoV and bat coronavirus which has not yet been recognized as the key cause of this pandemic outbreak, its transmission, and human pathogen mechanism. This review focuses on a brief introduction of novel coronavirus pathogens, including coronavirus in humans and animals, its taxonomic classification, symptoms, pathogenicity, social impact, economic impact, and potential treatment therapy for COVID-19.

The real-time reproduction number, impact of interventions and prediction of the epidemic size of COVID-19 in the center of Iran

Background:

The monitoring of reproduction number over time provides feedback on the effectiveness of interventions and on the need to intensify control efforts. Hence, we aimed to compute basic (R₀) and real-time (Rt) reproduction number and predict the trend and the size of the coronavirus disease 2019 (COVID-19) outbreak in the center of Iran.

Materials and Methods:

We used the 887 confirmed cases of COVID-19 from February 20, 2020, to April 17, 2020 in the center of Iran. We considered three scenarios for serial intervals (SIs) with gamma distribution. R_t was calculated by the sequential Bayesian and time-dependent methods. Based on a branching process using the Poisson distributed number of new cases per day, the daily incidence and cumulative incidence for the next 30 days were predicted. The analysis was applied in R packages 3.6.3 and STATA 12.0.

Results:

The model shows that the R_t of COVID-19 has been decreasing since the onset of the epidemic. According to three scenarios based on different distributions of SIs in the past 58 days from the epidemic, R_t has been 1.03 (0.94, 1.14), 1.05 (0.96, 1.15), and 1.08 (0.98, 1.18) and the cumulative incidence cases will be 360 (180, 603), 388 (238, 573), and 444 (249, 707) for the next 30 days, respectively.

Conclusion:

Based on the real-time data extracted from the center of Iran, R_t has been decreasing substantially since the beginning of the epidemic, and it is expected to remain almost constant or continue to decline slightly in the next 30 days, which is consequence of the schools and universities shutting down, reduction of working hours, mass screening, and social distancing.

Development of the Inactivated QazCovid-in Vaccine: Protective Efficacy of the Vaccine in Syrian Hamsters

In March 2020, the first cases of the human coronavirus disease COVID-19 were registered in Kazakhstan. We isolated the SARS-CoV-2 virus from clinical materials from some of these patients. Subsequently, a whole virion inactivated candidate vaccine, QazCovid-in, was developed based on this virus. To develop the vaccine, a virus grown in Vero cell culture was used, which was inactivated with formaldehyde, purified, concentrated, sterilized by filtration, and then adsorbed on aluminum hydroxide gel particles. The formula virus and adjuvant in buffer saline solution were used as the vaccine. The safety and protective effectiveness of the developed vaccine were studied in Syrian hamsters. The results of the studies showed the absolute safety of the candidate vaccine in the Syrian hamsters. When studying the protective effectiveness, the developed vaccine with an immunizing dose of 5 μg/dose specific antigen protected animals from a wild homologous virus at a dose of 10⁴.⁵ TCID_50/mL. The candidate vaccine induced the formation of virus-neutralizing antibodies in vaccinated hamsters at titers of 3.3 ± 1.45 log2 to 7.25 ± 0.78 log2, and these antibodies were retained for 6 months (observation period) for the indicated titers. No viral replication was detected in vaccinated hamsters, protected against the development of acute pneumonia, and ensured 100% survival of the animals. Further, no replicative virus was isolated from the lungs of vaccinated animals. However, a virulent virus was isolated from the lungs of unvaccinated animals at relatively high titers, reaching 4.5 ± 0.7 log TCID₅₀/mL. After challenge infection, 100% of unvaccinated hamsters showed clinical symptoms (stress state, passivity, tousled coat, decreased body temperature, and body weight, and the development of acute pneumonia), with 25 ± 5% dying. These findings pave the way for testing the candidate vaccine in clinical human trials.

Potential Effects of Coronaviruses on the Liver: An Update

The coronaviruses that cause notable diseases, namely, severe acute respiratory syndrome (SARS), middle east respiratory syndrome (MERS) and coronavirus disease 2019 (COVID-19), exhibit remarkable similarities in genomic components and pathogenetic mechanisms. Although coronaviruses have widely been studied as respiratory tract pathogens, their effects on the hepatobiliary system have seldom been reported. Overall, the manifestations of liver injury caused by coronaviruses typically involve decreased albumin and elevated aminotransferase and bilirubin levels. Several pathophysiological hypotheses have been proposed, including direct damage, immune-mediated injury, ischemia and hypoxia, thrombosis and drug hepatotoxicity. The interaction between pre-existing liver disease and coronavirus infection has been illustrated, whereby coronaviruses influence the occurrence, severity, prognosis and treatment of liver diseases. Drugs and vaccines used for treating and preventing coronavirus infection also have hepatotoxicity. Currently, the establishment of optimized therapy for coronavirus infection and liver disease comorbidity is of significance, warranting further safety tests, animal trials and clinical trials.

Incorporating Time Delays in the Mathematical Modelling of the Human Immune Response in Viral Infections

Mathematical modelling helps to describe the functional and causal relationships between objects in the physical world. The complexity of these models increases as more components and variables are added to maintain and observe. Differential equations are regularly used in these models, as they are able to display the interactions between several variables and describe non-linear behaviour. Differential equations are commonly used in immune response mathematical models to help describe these complex and dynamic interactions within the immune system of the organism. Time delays in the immune system are common and are often disregarded due to the low-resolution of models, which provide limited description of the specific section of immune system being studied. The few models that incorporate time delays are mostly at the epidemiological level, to track the spread of the virus in the population. In this paper we review the applications of the models based on differential equations and describe their potential utilization for the studies of immune response in SARS-CoV-2.

SARS-CoV-2 and its new variants: a comprehensive review on nanotechnological application insights into potential approaches

SARS-CoV-2 (COVID-19) spreads and develops quickly worldwide as a new global crisis which has left deep socio-economic damage and massive human mortality. This virus accounts for the ongoing outbreak and forces an urgent need to improve antiviral therapeutics and targeted diagnosing tools. Researchers have been working to find a new drug to combat the virus since the outbreak started in late 2019, but there are currently no successful drugs to control the SARS-CoV-2, which makes the situation riskier. Very recently, new variant of SARS-CoV-2 is identified in many countries which make the situation very critical. No successful treatment has yet been shown although enormous international commitment to combat this pandemic and the start of different clinical trials. Nanomedicine has outstanding potential to solve several specific health issues, like viruses, which are regarded a significant medical issue. In this review, we presented an up-to-date drug design strategy against SARS-CoV-2, including the development of novel drugs and repurposed product potentials were useful, and successful drugs discovery is a constant requirement. The use of nanomaterials in treatment against SARS-CoV-2 and their use as carriers for the transport of the most frequently used antiviral therapeutics are discussed systematically here. We also addressed the possibilities of practical applications of nanoparticles to give the status of COVID-19 antiviral systems.

Immunoinformatics based prediction of recombinant multi-epitope vaccine for the control and prevention of SARS-CoV-2

The emergence of SARS-CoV-2 has been reported during December 2019, in the city of Wuhan, China. The transmission of this virus via human to human interaction has already been described. The novel virus has become pandemic and declared as a comprehensive emergency worldwide by World Health Organization due to its exponential spread within and outside China. There is a need of time to create a therapeutic agent and a vaccine to cure and control this lethal SARS-CoV-2. Conventionally, the vaccine development process is time taking, tiresome and requires more economical inputs with manpower. However, bioinformatics offers a key solution to compute the possibilities. The present study focuses on the utilization of bioinformatics platforms to forecast B and T cell epitopes that belong to SARS-CoV-2 spike glycoprotein. The protein is thought to have an involvement in triggering of momentous immune response. NCBI database was explored to collect the surface glycoprotein sequence and was analyzed to determine the immunogenic epitopes. This prediction analysis was carried out using IEDB web based server and the prediction of protein structure was done by homology modeling approach. This study resulted in prediction of 5T cell and 13B cell epitopes. Moreover, GPGPG linker was used to make these predicted epitopes a single peptide prior to further analysis. Afterwards, a 3D model of the final vaccine peptide was constructed, and the structure quality of the final construct was checked by Ramachandran Plot analysis and ProSA-web. Moreover, docking analysis highlighted three interactions of epitope against HLA-B7 including Lys 178, Gol 303 and Thr 31 residues. In conclusion, the predicted multi epitope peptide can be suggested as therapeutic or prophylactic candidate vaccine against SARS-CoV-2 after further confirmation by immunological assays.

Contribution of Syndecans to the Cellular Entry of SARS-CoV-2

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel emerging pathogen causing an unprecedented pandemic in 21st century medicine. Due to the significant health and economic burden of the current SARS-CoV-2 outbreak, there is a huge unmet medical need for novel interventions effectively blocking SARS-CoV-2 infection. Unknown details of SARS-CoV-2 cellular biology hamper the development of potent and highly specific SARS-CoV-2 therapeutics. Angiotensin-converting enzyme-2 (ACE2) has been reported to be the primary receptor for SARS-CoV-2 cellular entry. However, emerging scientific evidence suggests the involvement of additional membrane proteins, such as heparan sulfate proteoglycans, in SARS-CoV-2 internalization. Here, we report that syndecans, the evolutionarily conserved family of transmembrane proteoglycans, facilitate the cellular entry of SARS-CoV-2. Among syndecans, the lung abundant syndecan-4 was the most efficient in mediating SARS-CoV-2 uptake. The S1 subunit of the SARS-CoV-2 spike protein plays a dominant role in the virus's interactions with syndecans. Besides the polyanionic heparan sulfate chains, other parts of the syndecan ectodomain, such as the cell-binding domain, also contribute to the interaction with SARS-CoV-2. During virus internalization, syndecans colocalize with ACE2, suggesting a jointly shared internalization pathway. Both ACE2 and syndecan inhibitors exhibited significant efficacy in reducing the cellular entry of SARS-CoV-2, thus supporting the complex nature of internalization. Data obtained on syndecan specific in vitro assays present syndecans as novel cellular targets of SARS-CoV-2 and offer molecularly precise yet simple strategies to overcome the complex nature of SARS-CoV-2 infection.

Machine learning techniques applied to the drug design and discovery of new antivirals: a brief look over the past decade

Introduction: Drug design and discovery of new antivirals will always be extremely important in medicinal chemistry, taking into account known and new viral diseases that are yet to come. Although machine learning (ML) have shown to improve predictions on the biological potential of chemicals and accelerate the discovery of drugs over the past decade, new methods and their combinations have improved their performance and established promising perspectives regarding ML in the search for new antivirals.Areas covered: The authors consider some interesting areas that deal with different ML techniques applied to antivirals. Recent innovative studies on ML and antivirals were selected and analyzed in detail. Also, the authors provide a brief look at the past to the present to detect advances and bottlenecks in the area.Expert opinion: From classical ML techniques, it was possible to boost the searches for antivirals. However, from the emergence of new algorithms and the improvement in old approaches, promising results will be achieved every day, as we have observed in the case of SARS-CoV-2. Recent experience has shown that it is possible to use ML to discover new antiviral candidates from virtual screening and drug repurposing.

Global prevalence and determinants of mortality among patients with COVID-19: A systematic review and meta-analysis

BACKGROUND

The challenge of COVID-19 is very high globally due to a lack of proven treatment and the complexity of its transmission. The prevalence of in-hospital mortality among patients with COVID-19 was very high which ranged from 1 to 52% of hospital admission. The prevalence of mortality among intensive care patients with COVID-19 was very high which ranged from 6% to 86% of admitted patients.

METHODS

A three-stage search strategy was conducted on PubMed/Medline; Science direct Cochrane Library. The Heterogeneity among the included studies was checked with forest plot, χ2 test, I2 test, and the p-values. Publication bias was checked with a funnel plot and the objective diagnostic test was conducted with Egger's correlation, Begg's regression tests.

RESULT

The Meta-Analysis revealed that the pooled prevalence of in-hospital mortality in patients with coronavirus disease was 15% (95% CI: 13 to 17). Prevalence of in-hospital mortality in patients with COVID-19 was strongly related to different factors. Patients with Acute respiratory distress syndrome were eight times more likely to die as compared to those who didn't have, RR = 7.99(95% CI: 4.9 to 13).

CONCLUSION

The review revealed that more than fifteen percent of patients admitted to the hospital with coronavirus died. This presages the health care stakeholders to manage morbidity and mortality among patients with coronavirus through the mobilization of adequate resources and skilled health care providers.

REGISTRATION

This systematic review and meta-analysis was registered in research registry with UIN of reviewregistry1093.

Immunotherapeutics for Covid-19 and post vaccination surveillance

Severe acute respiratory syndrome coronavirus (SARS-CoV-2) has emerged as a pandemic and named as novel coronavirus disease (nCOVID-19). SARS-CoV-2 is different from other known viruses due to multiple mutations on the sites of nonstructural proteins (NSP) 2 and 3, and the varying nature of virulence between different persons. Immunotherapies such as vaccines and monoclonal antibodies have a protective effect on the patients bringing them to the front of the line of potential treatments. The present review intends to cover the development of 20 different vaccine candidates categorized under live attenuated vaccines, inactivated vaccines, subunit vaccines, viral vector-based vaccines, and nucleic acid vaccines. Formulation of these vaccine candidates by various companies in collaboration with global organizations and their status of clinical trials were addressed. On the other hand, various approaches for post-vaccination surveillance using nucleic acid and protein biomarkers imbued on suitable platforms were also highlighted to sum up the immune therapeutics for Covid-19.

SARS-CoV, MERS-CoV, and 2019-nCoV viruses: an overview of origin, evolution, and genetic variations

Coronaviruses are single stranded RNA viruses usually present in bats (reservoir hosts), and are generally lethal, highly transmissible, and pathogenic viruses causing sever morbidity and mortality rates in human. Several animals including civets, camels, etc. have been identified as intermediate hosts enabling effective recombination of these viruses to emerge as new virulent and pathogenic strains. Among the seven known human coronaviruses SARS-CoV, MERS-CoV, and SARS-CoV-2 (2019-nCoV) have evolved as severe pathogenic forms infecting the human respiratory tract. About 8096 cases and 774 deaths were reported worldwide with the SARS-CoV infection during year 2002; 2229 cases and 791 deaths were reported for the MERS-CoV that emerged during 2012. Recently ~ 33,849,737 cases and 1,012,742 deaths (data as on 30 Sep 2020) were reported from the recent evolver SARS-CoV-2 infection. Studies on epidemiology and pathogenicity have shown that the viral spread was potentially caused by the contact route especially through the droplets, aerosols, and contaminated fomites. Genomic studies have confirmed the role of the viral spike protein in virulence and pathogenicity. They target the respiratory tract of the human causing severe progressive pneumonia affecting other organs like central nervous system in case of SARS-CoV, severe renal failure in MERS-CoV, and multi-organ failure in SARS-CoV-2. Herein, with respect to current awareness and role of coronaviruses in global public health, we review the various factors involving the origin, evolution, and transmission including the genetic variations observed, epidemiology, and pathogenicity of the three potential coronaviruses variants SARS-CoV, MERS-CoV, and 2019-nCoV.

Analysis of partial sequences of the RNA-dependent RNA polymerase gene as a tool for genus and subgenus classification of coronaviruses

The recent reclassification of the Riboviria, and the introduction of multiple new taxonomic categories including both subfamilies and subgenera for coronaviruses (family Coronaviridae, subfamily Orthocoronavirinae), represents a major shift in how official classifications are used to designate specific viral lineages. While the newly defined subgenera provide much-needed standardization for commonly cited viruses of public health importance, no method has been proposed for the assignment of subgenus based on partial sequence data, or for sequences that are divergent from the designated holotype reference genomes. Here, we describe the genetic variation of a 387 nt region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the most used partial sequence loci for both detection and classification of coronaviruses in molecular epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus sequences and examine clade groupings relative to all subgenus holotype sequences. Our phylogenetic analyses are largely coherent with whole-genome analyses based on designated holotype members for each subgenus. Distance measures between sequences form discrete clusters between taxa, offering logical threshold boundaries that can attribute subgenus or indicate sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus propose that partial RdRp sequence data of coronaviruses are sufficient for the attribution of subgenus-level taxonomic classifications and we supply the R package, MyCoV, which provides a method for attributing subgenus and assessing the reliability of the attribution.

Lysine 164 is critical for SARS-CoV-2 Nsp1 inhibition of host gene expression

The emerging pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused social and economic disruption worldwide, infecting over 9.0 million people and killing over 469 000 by 24 June 2020. Unfortunately, no vaccine or antiviral drug that completely eliminates the transmissible disease coronavirus disease 2019 (COVID-19) has been developed to date. Given that coronavirus nonstructural protein 1 (nsp1) is a good target for attenuated vaccines, it is of great significance to explore the detailed characteristics of SARS-CoV-2 nsp1. Here, we first confirmed that SARS-CoV-2 nsp1 had a conserved function similar to that of SARS-CoV nsp1 in inhibiting host-protein synthesis and showed greater inhibition efficiency, as revealed by ribopuromycylation and Renilla luciferase (Rluc) reporter assays. Specifically, bioinformatics and biochemical experiments showed that by interacting with 40S ribosomal subunit, the lysine located at amino acid 164 (K164) was the key residue that enabled SARS-CoV-2 nsp1 to suppress host gene expression. Furthermore, as an inhibitor of host-protein expression, SARS-CoV-2 nsp1 contributed to cell-cycle arrest in G0/G1 phase, which might provide a favourable environment for virus production. Taken together, this research uncovered the detailed mechanism by which SARS-CoV-2 nsp1 K164 inhibited host gene expression, laying the foundation for the development of attenuated vaccines based on nsp1 modification.

Current approaches used in treating COVID-19 from a molecular mechanisms and immune response perspective

Coronavirus disease 2019 (COVID-19), which is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared by the World Health Organization (WHO) as a global pandemic on March 11, 2020. SARS-CoV-2 targets the respiratory system, resulting in symptoms such as fever, headache, dry cough, dyspnea, and dizziness. These symptoms vary from person to person, ranging from mild to hypoxia with acute respiratory distress syndrome (ARDS) and sometimes death. Although not confirmed, phylogenetic analysis suggests that SARS-CoV-2 may have originated from bats; the intermediary facilitating its transfer from bats to humans is unknown. Owing to the rapid spread of infection and high number of deaths caused by SARS-CoV-2, most countries have enacted strict curfews and the practice of social distancing while awaiting the availability of effective U.S. Food and Drug Administration (FDA)-approved medications and/or vaccines. This review offers an overview of the various types of coronaviruses (CoVs), their targeted hosts and cellular receptors, a timeline of their emergence, and the roles of key elements of the immune system in fighting pathogen attacks, while focusing on SARS-CoV-2 and its genomic structure and pathogenesis. Furthermore, we review drugs targeting COVID-19 that are under investigation and in clinical trials, in addition to progress using mesenchymal stem cells to treat COVID-19. We conclude by reviewing the latest updates on COVID-19 vaccine development. Understanding the molecular mechanisms of how SARS-CoV-2 interacts with host cells and stimulates the immune response is extremely important, especially as scientists look for new strategies to guide their development of specific COVID-19 therapies and vaccines.

Effects of the severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV) on the nervous system. What can we expect from SARS -CoV-2?

Coronaviruses cause respiratory and gastrointestinal disorders in animals and humans. The current SARS-CoV-2, the COVID-19 infectious agent, belongs to a subgroup called betacoronavirus including the SARS-CoV and MERS-CoV responsible for epidemics in 2002 and 2012, respectively. These viruses can also infect the nervous system due to their affinity for the human angiotensin-converting enzyme 2 (ACE2) expressed in neurons and glial cells. Infections with SARS-CoV, MERS-CoV, and now SARS-CoV-2 also produce neurological signs such as acute cerebrovascular disease, impaired consciousness, and muscle injury, as well as dizziness, hypogeusia, hyposmia, hypoxia, neuralgia, and hypoxic encephalopathy. For this reason, close attention should be paid to the neurological manifestations of COVID-19 patients.

Ayurveda and Allopathic Therapeutic Strategies in Coronavirus Pandemic Treatment 2020

Purpose of Review

In the last month of 2019, i.e., December, COVID-19 hit Wuhan city in China. Since then, it has infected more than 210 countries and nearly about 33.4 million people with one million deaths globally. It is a viral disease with flu-like symptoms; hence, prevention and management is the best option to be adopted for its cure.

Recent Findings

Many healthcare systems, scientists, and researchers are fighting for the cure of this pandemic. Ayurvedic and allopathic treatments have been studied extensively and approached for the cure of COVID-19. In addition to ayurvedic treatments, the Ministry of Ayush, India, has also recommended many remedies to boost up immunity. Allopathic studies involved several antiviral drugs which were used in different combinations for the treatment of COVID-19.

Summary

Comparative analysis of Ayurveda and allopathic treatment strategies were carried out in the present study. Depending upon the patient's conditions and symptoms, Ayurveda is useful for the treatment of COVID-19. Allopathic treatments inhibit viral infection by targeting majorly endocytosis, and angiotensin-converting enzyme (Ace) receptor signaling. In this article, we summarize different ayurvedic and allopathic medicines and treatment strategies which have been used for the treatment of COVID-19, a global pandemic.

Coronaviruses in wastewater processes: Source, fate and potential risks

The last 17 years have seen three major outbreaks caused by coronaviruses, with the latest outbreak, COVID-19, declared a pandemic by the World Health Organization. The frequency of these outbreaks, their mortality and associated disruption to normal life calls for concerted efforts to understand their occurrence and fate in different environments. There is an increased interest in the occurrence of coronaviruses in wastewater from the perspective of wastewater-based epidemiology. However, there is no comprehensive review of the knowledge on coronavirus occurrence, fate and potential transmission in wastewater. This paper, provides a review of the literature on the occurrence of coronaviruses in wastewater treatment processes. We discuss the presence of viral RNA in feces as a result of diarrhoea caused by gastrointestinal infections. We also reviewed the literature on the presence, survival and potential removal of coronaviruses in common wastewater treatment processes. The detection of infectious viral particles in feces of patients raises questions on the potential risks of infection for people exposed to untreated sewage/wastewater. We, therefore, highlighted the potential risk of infection with coronaviruses for workers in wastewater treatment plants and the public that may be exposed through faulty plumbing or burst sewer networks. The mortalities and morbidities associated with the current COVID-19 pandemic warrants a much more focused research on the role of environments, such as wastewater and surface water, in disease transmission. The current wealth of knowledge on coronaviruses in wastewater based on the reviewed literature is scant and therefore calls for further studies.

Considerations for future novel human-infecting coronavirus outbreaks

Up until, June 13, 2020, >7,500,000 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and >400,000 deaths, across 216 countries, have been confirmed by the World Health Organization (WHO). With reference to the two previous beta-CoV outbreaks (SARS-CoV and middle east respiratory syndrome [MERS]), this paper examines the pathophysiological and clinical similarities seen across all three CoVs, with a special interest in the neuroinvasive capability and subsequent consequences for patients with primary or metastatic brain tumors. More widely, we examine the lessons learned from the management of such large-scale crises in the past, specifically looking at the South Korean experience of MERS and the subsequent shift in disaster management response to SARS-CoV-2, based on prior knowledge gained. We assess the strategies with which infection prevention and control can, or perhaps should, be implemented to best contain the spread of such viruses in the event of a further likely outbreak in the future.

Origin and cross-species transmission of bat coronaviruses in China

Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. Here we use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 630 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal. We find that host-switching occurs more frequently and across more distantly related host taxa in alpha- than beta-CoVs, and is more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.

Molecular biology of coronaviruses: current knowledge

The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) late December 2019 in Wuhan, China, marked the third introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. The constant spillover of coronaviruses from natural hosts to humans has been linked to human activities and other factors. The seriousness of this infection and the lack of effective, licensed countermeasures clearly underscore the need of more detailed and comprehensive understanding of coronavirus molecular biology. Coronaviruses are large, enveloped viruses with a positive sense single-stranded RNA genome. Currently, coronaviruses are recognized as one of the most rapidly evolving viruses due to their high genomic nucleotide substitution rates and recombination. At the molecular level, the coronaviruses employ complex strategies to successfully accomplish genome expression, virus particle assembly and virion progeny release. As the health threats from coronaviruses are constant and long-term, understanding the molecular biology of coronaviruses and controlling their spread has significant implications for global health and economic stability. This review is intended to provide an overview of our current basic knowledge of the molecular biology of coronaviruses, which is important as basic knowledge for the development of coronavirus countermeasures.

COVID-19 Pandemic: from Molecular Biology, Pathogenesis, Detection, and Treatment to Global Societal Impact

PURPOSE OF REVIEW

In December 2019, there was an outbreak of viral disease in Wuhan, China which raised the concern across the whole world. The viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or novel coronavirus or COVID-19 (CoV-19) is known as a pandemic. After SARS-CoV and Middle East respiratory syndrome (MERS)-related CoV, COVID-19 is the third most pathogenic virus, hazardous to humans which have raised worries concerning the capacity of current security measures and the human services framework to deal with such danger.

RECENT FINDINGS

According to WHO, the mortality rate of COVID-19 exceeded that of SARS and MERS in view of which COVID-19 was declared as public health emergency of international concern. Coronaviruses are positive-sense RNA viruses with single stranded RNA and non-segmented envelopes. Recently, genome sequencing confirmed that COVID-19 is similar to SARS-CoV and bat coronavirus, but the major source of this pandemic outbreak, its transmission, and mechanisms related to its pathogenicity to humans are not yet known.

SUMMARY

In order to prevent the further pandemic and loss to humanity, scientists are studying the development of therapeutic drugs, vaccines, and strategies to cure the infections. In this review, we present a brief introduction to emerging and re-emerging pathogens, i.e., coronavirus in humans and animals, its taxonomic classification, genome organization, its replication, pathogenicity, impact on socioeconomic growth, and drugs associated with COVID-19.

Rate of Intensive Care Unit admission and outcomes among patients with coronavirus: A systematic review and Meta-analysis

BACKGROUND

The rate of ICU admission among patients with coronavirus varied from 3% to 100% and the mortality was as high as 86% of admitted patients. The objective of the systematic review was to investigate the rate of ICU admission, mortality, morbidity, and complications among patients with coronavirus.

METHODS

A comprehensive strategy was conducted in PubMed/Medline; Science direct and LILACS from December 2002 to May 2020 without language restriction. The Heterogeneity among the included studies was checked with forest plot, χ2 test, I2 test, and the p-values. All observational studies reporting rate of ICU admission, the prevalence of mortality and its determinants among ICU admitted patients with coronavirus were included and the rest were excluded.

RESULT

A total of 646 articles were identified from different databases and 50 articles were selected for evaluation. Thirty-seven Articles with 24983 participants were included. The rate of ICU admission was 32% (95% CI: 26 to 38, 37 studies and 32, 741 participants). The Meta-Analysis revealed that the pooled prevalence of mortality in patients with coronavirus disease in ICU was 39% (95% CI: 34 to 43, 37 studies and 24, 983 participants).

CONCLUSION

The Meta-Analysis revealed that approximately one-third of patients admitted to ICU with severe Coronavirus disease and more than thirty percent of patients admitted to ICU with a severe form of COVID-19 for better care died which warns the health care stakeholders to give attention to intensive care patients.

REGISTRATION

This Systematic review and Meta-Analysis was registered in Prospero international prospective register of systemic reviews (CRD42020177095) on April 9/2020.

Emerging coronavirus diseases and future perspectives

Coronavirus related infectious diseases seems to be biggest challenge of 21 century that have been constantly emerging and threating public health around the globe. Coronavirus disease-19 (COVID-19) that was detected as cause of respiratory tract infection in China by end the December 2019 impelled World Health Organization to declare in January 2020 public health emergency of international concern and consequently pandemic in March 2020. Over a past six months COVID-19 pandemic has wrapped up all continents except Antarctica. Scientists around the globe are finding way to tackle and reduce the ultimate risk and size of pandemic with lower morbidity and mortality rates. In this context, technologies such as sequencing, Crispr and artificial intelligence are playing vital role in diagnosis and management of infectious disease in contrast to conventional methods. Despite of this, there is a need to have rapid and early diagnostic tools and systems that recognize infectious disease in asymptotic condition. Here we provide an overview on the recent CoV outbreak and contribution of technologies with the emphasis on the future management for detection of such infectious diseases.

Origin and cross-species transmission of bat coronaviruses in China

Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. We used a Bayesian statistical framework and sequence data from all known bat-CoVs (including 630 novel CoV sequences) to study their macroevolution, cross-species transmission, and dispersal in China. We find that host-switching was more frequent and across more distantly related host taxa in alpha-than beta-CoVs, and more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus . Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.

Cross-Species Transmission of Deltacoronavirus and the Origin of Porcine Deltacoronavirus

Deltacoronavirus is the last identified Coronaviridae subfamily genus. Differing from other coronavirus (CoV) genera, which mainly infect birds or mammals, deltacoronaviruses (δ‐CoVs) reportedly infect both animal types. Recent studies show that a novel δ‐CoV, porcine deltacoronavirus (PDCoV), can also infect calves and chickens with the potential to infect humans, raising the possibility of cross‐species transmission of δ‐CoVs. Here, we explored the deep phylogenetic history and cross‐species transmission of δ‐CoVs. Virus–host cophylogenetic analyses showed that δ‐CoVs have undergone frequent host switches in birds, and sparrows may serve as the unappreciated hubs for avian to mammal transmission. Our molecular clock analyses show that PDCoV possibly originated in Southeast Asia in the 1990s and that the PDCoV cluster shares a common ancestor with Sparrow‐CoV of around 1,810. Our findings contribute valuable insights into the diversification, evolution, and interspecies transmission of δ‐CoVs and the origin of PDCoV, providing a model for exploring the relationships of δ‐CoVs in birds and mammals.

Coronavirus Disease 2019 (COVID-19) Pandemic and Economic Impact

In less than two decades, the world has experienced three outbreaks of deadly Coronaviruses, including the recent pandemic of Coronavirus Disease 2019 (COVID-19) in China. COVID-19 posed an emergency of international concerns, and cases have been reported in more than 200 countries/regions that resulted in health, lives, and economic losses. China’s economic growth is projected to fall to 5.6% this year, the International Monetary Fund (IMF) projected that policy investment and tax policies to implement $3.3 trillion and contributes further $4.5 trillion. IMF forecasts grow from 3.7% of global gross domestic product (GDP) in 2019 to 9.9% in 2020. GDP ratio projected from 3.0% in 2019 to grow 10.7% in 2020, the US ratio expected to increase from 5.8% to 15.7%. France, Germany, Italy, Japan, and the United Kingdom (UK) each reported public sector funding programs totalling > 10% of their yearly GDP. There is a dire need for regional and international co-operation to extend hands to prevent further spreading of COVID-19.

Quantifying the role of social distancing, personal protection and case detection in mitigating COVID-19 outbreak in Ontario, Canada

Public health interventions have been implemented to mitigate the spread of coronavirus disease 2019 (COVID-19) in Ontario, Canada; however, the quantification of their effectiveness remains to be done and is important to determine if some of the social distancing measures can be relaxed without resulting in a second wave. We aim to equip local public health decision- and policy-makers with mathematical model-based quantification of implemented public health measures and estimation of the trend of COVID-19 in Ontario to inform future actions in terms of outbreak control and de-escalation of social distancing. Our estimates confirm that (1) social distancing measures have helped mitigate transmission by reducing daily infection contact rate, but the disease transmission probability per contact remains as high as 0.145 and case detection rate was so low that the effective reproduction number remained higher than the threshold for disease control until the closure of non-essential business in the Province; (2) improvement in case detection rate and closure of non-essential business had resulted in further reduction of the effective control number to under the threshold. We predict the number of confirmed cases according to different control efficacies including a combination of reducing further contact rates and transmission probability per contact. We show that improved case detection rate plays a decisive role to reduce the effective reproduction number, and there is still much room in terms of improving personal protection measures to compensate for the strict social distancing measures.

Middle East Respiratory Syndrome Coronavirus and the One Health concept

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is one of the major threats to the healthcare systems in some countries, especially in the Arabian Peninsula. MERS-CoV is considered an ideal example of the One Health concept. This is due to the animals, especially dromedary camels, play important roles in the transmission and sustainability of the virus, and the virus can be transmitted through aerosols of infected patients into the environment. However, there is some debate regarding the origin of MERS-CoV either from bats or other unknown reservoirs. The dromedary camel is the only identified animal reservoir to date. These animals play important roles in sustaining the virus in certain communities and may act as an amplifier of the virus by secreting it in their body fluids, especially in nasal and rectal discharges. MERS-CoV has been detected in the nasal and rectal secretions of infected camels, and MERS-CoV of this origin has full capacity to infect human airway epithelium in both in vitro and in vivo models. Other evidence confirms the direct transmission of MERS-CoV from camels to humans, though the role of camel meat and milk products has yet to be well studied. Human-to-human transmission is well documented through contact with an active infected patient or some silently infected persons. Furthermore, there are some significant risk factors of individuals in close contact with a positive MERS-CoV patient, including sleeping in the same patient room, removing patient waste (urine, stool, and sputum), and touching respiratory secretions from the index case. Outbreaks within family clusters have been reported, whereby some blood relative patients were infected through their wives in the same house were not infected. Some predisposing genetic factors favor MERS-CoV infection in some patients, which is worth investigating in the near future. The presence of other comorbidities may be another factor. Overall, there are many unknown/confirmed aspects of the virus/human/animal network. Here, the most recent advances in this context are discussed, and the possible reasons behind the emergence and sustainability of MERS-CoV in certain regions are presented. Identification of the exact mechanism of transmission of MERS-CoV from camels to humans and searching for new reservoir/s are of high priority. This will reduce the shedding of the virus into the environment, and thus the risk of human infection can be mitigated.

Viruses in bats and potential spillover to animals and humans

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Bats are a very important source of emerging viruses.

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Bat coronavirus, filovirus, paramyxovirus and reovirus are known zoonotic viruses.

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Many of the emergent bat viruses are highly lethal in livestock and humans.

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Past incidents and viral genetic features predict bat coronaviruses as the highest risk.

In the last two decades, several high impact zoonotic disease outbreaks have been linked to bat-borne viruses. These include SARS coronavirus, Hendra virus and Nipah virus. In addition, it has been suspected that ebolaviruses and MERS coronavirus are also linked to bats. It is being increasingly accepted that bats are potential reservoirs of a large number of known and unknown viruses, many of which could spillover into animal and human populations. However, our knowledge into basic bat biology and immunology is very limited and we have little understanding of major factors contributing to the risk of bat virus spillover events. Here we provide a brief review of the latest findings in bat viruses and their potential risk of cross-species transmission.

Detection of Bovine Coronavirus in Healthy and Diarrheic Dairy Calves

Background

BCoV is identified in both healthy and diarrheic calves, complicating its assessment as a primary pathogen.

Objectives

To investigate the detection rates of bovine coronavirus (BCoV) in feces of healthy and diarrheic calves and to describe the usefulness of a pancoronavirus reverse transcriptase (RT) PCR (PanCoV‐RT‐PCR) assay to identify BCoV in samples of diarrheic calves.

Animals

Two hundred and eighty‐six calves <21 days. Calves with liquid or semiliquid feces, temperature >39.5°C, and inappetence were considered as cases, and those that had pasty or firm feces and normal physical examination were designated as controls.

Methods

Prospective case–control study. A specific BCoV‐RT‐PCR assay was used to detect BCoV in fecal samples. Association between BCoV and health status was evaluated by exact and random effect logistic regression. Fecal (n = 28) and nasal (n = 8) samples from diarrheic calves were tested for the presence of BCoV by both the PanCoV‐RT‐PCR and a specific BCoV‐RT‐PCR assays. A Kappa coefficient test was used to assess the level of agreement of both assays.

Results

BCoV was detected in 55% (157/286) of calves; 46% (66/143), and 64% (91/143) of healthy and diarrheic calves, respectively. Diarrheic calves had higher odds of BCoV presence than healthy calves (OR: 2.16, 95% CI: 1.26 to 3.83, P = 0.004). A good agreement between PanCoV‐RT‐PCR and BCoV‐RT‐PCR to detect BCoV was identified (κ = 0.68, 95% CI: 0.392 to 0.967; P < 0.001).

Conclusions and Clinical Importance

BCoV was more likely to be detected in diarrheic than healthy calves. The PanCoV‐RT‐PCR assay can be a useful tool to detect CoV samples from diarrheic calves.

MERS-CoV papain-like protease (PLpro): expression, purification, and spectroscopic/thermodynamic characterization

Within a decade, MERS-CoV emerged with nearly four times higher case fatality rate than an earlier outbreak of SARS-CoV and spread out in 27 countries in short span of time. As an emerging virus, combating it requires an in-depth understanding of its molecular machinery. Therefore, conformational characterization studies of coronavirus proteins are necessary to advance our knowledge of the matter for the development of antiviral therapies. In this study, MERS-CoV papain-like protease (PL^pro) was recombinantly expressed and purified. Thermal folding pathway and thermodynamic properties were characterized using dynamic multimode spectroscopy (DMS) and thermal shift assay. DMS study showed that the PL^pro undergoes a single thermal transition and follows a pathway of two-state folding with T_m and van’t Hoff enthalpy values of 54.4 ± 0.1 °C and 317.1 ± 3.9 kJ/mol, respectively. An orthogonal technique based on intrinsic tryptophan fluorescence also showed that MERS-CoV PL^pro undergoes a single thermal transition and unfolds via a pathway of two-state folding with a T_m value of 51.4 °C. Our findings provide significant understandings of the thermodynamic and structural properties of MERS-CoV PL^pro.

Lower respiratory tract viral infections: Diagnostic role of exfoliative cytology

Viral lower respiratory tract infections (VLRTI) remain one of the most common causes of morbidity and mortality worldwide. For many years, the diagnosis of VLRTI was based on laboratory techniques such as viral isolation in cell culture, antigen detection by direct fluorescent antibody staining, and rapid enzyme immunoassay. Radiological imaging and morphology also play an important role in diagnosing these infections. Exfoliative cytology provides a simple, rapid, inexpensive, and valuable means to diagnose and manage VLRTI. Here we review viral‐associated cytomorphological changes seen in exfoliated cells of the lower respiratory tract. Diagn. Cytopathol. 2017;45:614–620. © 2017 Wiley Periodicals, Inc.

Global research trends of Middle East respiratory syndrome coronavirus: a bibliometric analysis

BACKGROUND

Middle East respiratory syndrome coronavirus (MERS-CoV) is a virus that causes severe viral pneumonia in humans, known to have a high mortality rate and a similarity in clinical symptoms with severe acute respiratory syndrome coronavirus. It was first isolated in Kingdom of Saudi Arabia (KSA) in 2012 and after that, MERS-CoV exhibited outbreaks in several regions of the world. This study aimed to assess the characteristics of publications involving MERS-CoV at global level by using a bibliometric analysis.

METHODS

Scopus database was searched on March 4, 2016 for MERS-CoV publications published between 2012 and 2015. It was performed on the same day in order to avoid the possible bias came from update on the database because the metrics are changing over time. All publication types were considered; however publications as errata were excluded. Analysis parameters include year of publication, publication type, patterns of international collaboration, research institutions, journals, impact factor, h-index, language, and times cited.

RESULTS

A total of 883 MERS-CoV research publications were published across the world. The MERS-CoV-associated publications were originated from 92 countries/territories, indicating the international spread of MERS-CoV research. The USA was the largest contributor, with 319 articles published over 4 years, followed by KSA (113 articles). The total number of citations for these publications has already achieved 8,015, with an average of 9.01 citations per each publication. The h-index for MERS-CoV-associated publications was 48. The USA also have the highest h-index (32), followed by KSA (26) and UK (22). Netherland produced the greatest proportion of publications with international research collaboration (72.7 %) followed by the UK (71 %) and Germany (69.1 %) out of the total number of publications for each country.

CONCLUSIONS

There is a rapid increase in research activities related to MERS-CoV from 2012 to 2015. This study demonstrates that the MERS-CoV related literature has grown to be more extensive and global over the past 4 years. The bulk of publications in the field of MERS-CoV research are published by high-income countries such as the USA. Furthermore, the USA, the UK and KSA may have higher quality of articles according to the value of h-index.