Assessment of Proinflammatory Cytokines Among Patients with Middle East Respiratory Syndrome Coronavirus Infection.

Middle East respiratory syndrome coronavirus (MERS-CoV) is associated with significant morbidity and mortality. This study was performed to assess the proinflammatory cytokines profile among MERS-CoV patients. A total of 46 MERS-CoV-infected patients (27 symptomatic and 19 asymptomatic) were assessed and compared with 52 normal healthy controls for plasma levels of interleukin (IL)-1ß, tumor necrosis factor (TNF)-α, IL-17, IL-7, IL-6, interferon (IFN)-α, and IL-15 using a customized luminex kit. Whereas asymptomatic MERS-CoV patients and controls were no different; the mean plasma levels among MERS-CoV symptomatic patients were significantly higher than the normal controls: IL-1ß (16.89 ± 1.23 vs. 12.80 ± 0.59 pg/mL; p < 0.001), TNF-α (14.04 ± 0.93 vs. 10.35 ± 0.29 pg/mL; p < 0.0001), IL-17 (14.3 ± 0.89 vs. 11.47 ± 0.61 pg/mL; p < 0.001), IL-7 (21.56 ± 1.00 vs. 16.31 ± 0.30 pg/mL; p < 0.0001), IL-6 (156.5 ± 37.90 vs. 18.60 ± 1.59 pg/mL; p < 0.0001), and IFN-α (68.73 ± 13.06 vs. 23.57 ± 1.05 pg/mL; p < 0.0001). The mean plasma levels of IL-7 (24.81 ± 1.63 vs. 19.79 ± 0.94 pg/mL; p < 0.01), IL-6 (312.7 ± 94.67 vs. 101.2 ± 25.67 pg/mL; p < 0.01), and IFN-α (89.00 ± 18.97 vs. 51.05 ± 8.68 pg/mL; p < 0.05) were significantly elevated among MERS-CoV symptomatic patients with fatal outcome compared with MERS-CoV symptomatic patients who survived. Only IL-7 was found to have a higher risk ratio of mortality (4.76, 95% confidence interval: 1.5-14.94; p < 0.01). No differences were observed in IL-15 levels among the groups. Significantly elevated proinflammatory cytokines among symptomatic MERS-CoV-infected patients may contribute to manifestations of cytokine storm frequently observed among critically ill MERS-CoV patients and IL-7 may serve as a marker for disease activity.

COVID-19 effect on patients with noncommunicable diseases: A narrative review.

Background and Aims: On March 11, 2020, the WHO has declared COVID-19 a global pandemic, affecting our day-to-day lives. Physical distancing and lockdown made significant obstacles to populations, particularly healthcare systems. Most healthcare workers were reallocated to COVID-19 facilities. Noncommunicable disease patients were given low priority and are at a higher risk of severe COVID-19 infection, which disrupted the treatment and disease management of these patients. This review aimed to assess the effect of COVID-19 on different types of noncommunicable diseases and the severity it may cause to patients. Methods: We have conducted a review of the literature on COVID-19 and noncommunicable diseases from December 2019 until January 2022. The search was done in PubMed and Cochrane for relevant articles using variety of searching terms. Data for study variables were extracted. At the end of the selection process, 46 papers were selected for inclusion in the literature review. Result: The result from this review found that the COVID-19 pandemic has affected the efficiency of the patient's treatment indirectly by either delaying or canceling sessions, which solidified the need to rely more on telemedicine, virtual visits, and in-home visits to improve patient education and minimize the risk of exposure to the patients. The major and most common types of noncommunicable diseases are known to be related to the severe outcomes of COVID-19 infection. It is strongly recommended to prioritize these patients for vaccinations against COVID-19 to provide them with the protection that will neutralize the risk imposed by their comorbidities. Conclusion: We recommend conducting more studies with larger population samples to further understand the role of noncommunicable diseases (NCDs) in this pandemic. However, this pandemic has also affected the efficiency of NCDs treatment indirectly by delaying or canceling sessions and others.

Anti-SARS-CoV-2 IgG Antibodies Post-COVID-19 or Post-Vaccination in Libyan Population: Comparison of Four Vaccines.

Measurement of strength and durability of SARS-COV-2 antibody response is important to understand the waning dynamics of immune response to both vaccines and infection. The study aimed to evaluate the level of IgG antibodies against SARS-CoV-2 and their persistence in recovered, naïve, and vaccinated individuals. We investigated anti-spike RBD IgG antibody responses in 10,000 individuals, both following infection with SARS-CoV-2 and immunization with SARS-COV-2 AstraZeneca, Sputnik V, Sinopharm, and Sinovac. The mean levels of anti-spike IgG antibodies were higher in vaccinated participants with prior COVID-19 than in individuals without prior COVID-19. Overall, antibody titers in recovered vaccinee and naïve vaccinee persisted beyond 20 weeks. Vaccination with adenoviral-vector vaccines (AstraZeneca and Sputnik V) generates higher antibody titers than with killed virus vaccine (Sinopharm and Sinovac). Approximately two-thirds of asymptomatic unvaccinated individuals had developed virus-specific antibodies. A single dose of vaccine is likely to provide greater protection against SARS-CoV-2 infection in individuals with apparent prior SARS-CoV-2 infection, than in SARS-CoV-2-naive individuals. In addition, the high number of seropositivity among asymptomatic unvaccinated individuals showed that the number of infections are probably highly underestimated. Those vaccinated with inactivated vaccine may require more frequent boosters than those vaccinated with adenoviral vaccine. These findings are important for formulating public health vaccination strategies during COVID-19 pandemic.

Recreation as a Social Factor in Urban Development: A Response to Covid-19 Pandemic in Greater Jos, Nigeria

The importance of recreation cannot be overemphasised. Recreation refers to an activity that people engage in during their free time, and it is socially-inclined and has attendant values. Inaccessibility to recreational areas affects the social wellbeing of residents, who will not have a sense of belonging when it comes to community development, hence a response to Covid-19. Taking Greater Jos (Nigeria) as a case study, this paper assesses the social factors with regard to the provision of recreational facilities. The study also identified and mapped out recreational areas using the geographical positioning system. A questionnaire survey was conducted amongst the residents, age fifteen and above to authentically gauge their opinions on the study and, adopting stratified-random sampling considering the ten sectors according to the Greater Jos Master Plan. Results revealed that the residents had a good level of awareness of the presence of recreational facilities and high-quality recreational facilities, which were found mostly within the core of the city. The facilities fostered a high level of family and community bonding. However, the distance of recreational activity areas from their place of residence was what was rather disappointing for most people. Thus, the recent Covid-19 pandemic demand of social distancing negates social inclusion. The emphasis on social orientation and effective social inclusion of disadvantaged groups was conspicuously pronounced. Thus, appropriate and easy access to recreational facilities for all genders and ages must be provided closer to the people for effective services to promote their social lives and weaken the Covid-19 repulsive protocol. (C) 2022 Penerbit UTM Press. All rights reserved

HARNESSING IOT TECHNOLOGY FOR THE DEVELOPMENT OF WEARABLE CONTACT TRACING SOLUTIONS

Advancements in mobile computing and embedded system technologies show superiority in controlling the transmission of a virus during the COVID-19 pandemic. They provide rapid contact data compared to manual contact tracing and medical monitoring methodologies. Data tracing capabilities were achieved by existing technologies via the utilization of smartphone-based exposure notifications systems and proximity sensing tools based on Bluetooth/GPS. Such systems lack user privacy and data anonymization capabilities, it also requires that users have continuous access to smartphones. This paper proposes the development of a lightweight wearable prototype for contact tracing. The proposed system is based on the deployment of an IoT development board, incorporated with a Bluetooth chipset for proximity sensing. To overcome the problem of user-to-smartphone accessibility, the processing of contact data by the exposure notification system has been migrated from mobile computing to a contact tracer management server that is managed by the community. Daily contact exposures to the virus are recorded by each user's contact tracing system and stored in the user's blockchain. Data integrity and immunity against data injection attacks were achieved via the implementation of lightweight block chaining and validation schemes. Data anonymization was also supported via the utilization of the onboard AES crypto engine. Meanwhile, support for user anonymity was incorporated into the proposed system through the implementation of an anonymous authentication protocol based on the Zero-Knowledge Proof (ZKP) approach. Finally, we have analyzed the performance of the system in terms of power consumption under various systems settings, such as encryption key size and the required number of ZKP validation attempts per authentication session.

Biomarkers Selection for Population Normalization in SARS-CoV-2 Wastewater-based Epidemiology (preprint)

Wastewater-based epidemiology (WBE) has been one of the most cost-effective approaches to track the SARS-CoV-2 levels in the communities since the COVID-19 outbreak in 2020. Normalizing SARS-CoV-2 concentrations by the population biomarkers in wastewater can be critical for interpreting the viral loads, comparing the epidemiological trends among the sewersheds, and identifying the vulnerable communities. In this study, five population biomarkers, pepper mild mottle virus (pMMoV), creatinine (CRE), 5-hydroxyindoleacetic acid (5-HIAA), caffeine (CAF) and its metabolite paraxanthine (PARA) were investigated for their utility in normalizing the SARS-CoV-2 loads through developed direct and indirect approaches. Their utility in assessing the real-time population contributing to the wastewater was also evaluated. The best performed candidate was further tested for its capacity for improving correlation between normalized SARS-CoV-2 loads and the clinical cases reported in the City of Columbia, Missouri, a university town with a constantly fluctuated population. Our results showed that, except CRE, the direct and indirect normalization approaches using biomarkers allow accounting for the changes in wastewater dilution and differences in relative human waste input over time regardless flow volume and population at any given WWTP. Among selected biomarkers, PARA is the most reliable population biomarker in determining the SARS-CoV-2 load per capita due to its high accuracy, low variability, and high temporal consistency to reflect the change in population dynamics and dilution in wastewater. It also demonstrated its excellent utility for real-time assessment of the population contributing to the wastewater. In addition, the viral loads normalized by the PARA-estimated population significantly improved the correlation (rho=0.5878, p<0.05) between SARS-CoV-2 load per capita and case numbers per capita. This chemical biomarker offers an excellent alternative to the currently CDC-recommended pMMoV genetic biomarker to help us understand the size, distribution, and dynamics of local populations for forecasting the prevalence of SARS-CoV2 within each sewershed.

Anti-SARS-CoV-2 IgG antibodies after recovery from COVID-19 or vaccination in Libyan population: comparison of four vaccines (preprint)

Background: Natural and vaccine-induced immunity play an important role in controlling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Understanding humoral immunity to SARS-CoV-2 is of great importance for evaluating vaccine performance and inform public health decisions. Objective: We aimed to evaluate the level of IgG antibodies against SARS-CoV-2 and their persistence post infection or post-vaccination. Methods: A serological analysis (Immunoassay) to investigate the level of anti-spike IgG antibody responses following infection with SARS-CoV-2 or immunization with the first or second dose of the AstraZeneca, Sputnik, Sinovac and Sinopharm vaccines was performed. Results: A total of 9460 seropositive individuals were recruited. The mean levels of anti-spike IgG antibodies were higher in vaccinated participants with prior COVID-19 infections than in individuals without prior infection. Decline for IgG antibodies were faster in vaccinated individuals without previous COVID-19 infection compared to those with previous COVID-19 infection. Conclusion: A single dose of the vaccine is likely to provide greater protection against SARS-CoV-2 infection in subjects with prior SARS-CoV-2 infection, than in SARS-CoV-2-naive individuals. In addition, previous COVID-19 infection elicited robust and sustained levels of SARS-CoV-2 antibodies in vaccinated individuals.

Applying Fuzzy Logic and Neural Network in Sentiment Analysis for Fake News Detection: Case of Covid-19

The pandemic we witnessed starting from December 2019, was accompanied by a significant rise in internet usage, and the social media, in particular, people were asked to stay at home to limit the spreading of the Covid-19 virus, this isolation made fake news a dangerous weapon that can directly harm people’s wellbeing and encourage antagonism and racism. Considering the re-al danger of this misinformation and disinformation, fake news research witnessed a surge of contributions that apply machine learning models, deep learning, and sentiment analysis, but among these models and especially those that use sentiment analysis, we found that there is a lack of the integration of the fuzzy aspect of our language, which may give more details and accuracy to the detection of fake news. In this work, we extend the classification model from our previous work by combining a deep learning algorithm LSTM with fuzzy logic for sentiment-aware classification of fake news. We experiment with a dataset that contains over than 13 K of covid-19 text content al-ready labeled as being real or fake, and we compared the results of our model with the state-of-the-art methods that do not incorporate fuzzy logic and sentiment for fake news classification. and we observed that our approach yields better results. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Cardiovascular and haematological events post COVID-19 vaccination: A systematic review.

Since COVID-19 took a strong hold around the globe causing considerable morbidity and mortality, a lot of effort was dedicated to manufacturing effective vaccines against SARS-CoV-2. Many questions have since been raised surrounding the safety of the vaccines, and a lot of media attention to certain side effects. This caused a state of vaccine hesitancy that may prove problematic in the global effort to control the virus. This review was undertaken with the aim of putting together all the reported cardiovascular and haematological events post COVID-19 vaccination in published literature and to suggest possible mechanisms to explain these rare phenomena.

A Novel Model for Detection and Classification Coronavirus (COVID-19) Based on Chest X-Ray Images Using CNN-CapsNet

The coronavirus disease 2019 (COVID-19) first emerged in Wuhan China, and spread across the globe with unprecedented effect. It has became a major healthcare challenge threatening health of billions of humans. Due to absence of therapeutic drugs or vaccines for all, discovering this virus in the early stages will help in diagnosis, evaluation and fast recovery using one and most commonly of the key screening approaches being radiological imaging --Chest X-Ray--. With the advances in Artificial Intelligence algorithms and especially Deep Learning models, and within order to help the radiologists to analyze the vast amount of Chest X-Ray images, which can be crucial for diagnosis and detection of COVID-19. In this paper, we proposed an effective Chest X-Rays image classification model named CNN-CapsNet. Our main idea is to make full use of the merits of these two models: CNN and CapsNet. First, we used a CNN without fully connected layers are used as an initial feature maps extractor. In detail, we have used a pre-trained deep CNN model --VGG19-- that was fully trained on the ImageNet dataset is selected as a feature extractor. Then, we have fed the initial feature maps into a newly designed CapsNet to obtain the final classification result. The performance of our model was evaluated with the four metrics: Accuracy, Sensitivity, Precision and F1 Score. The result is based on the data available in the repositories of Kaggle and Mendeley. Where the experimental results demonstrate that the proposed method can lead to a competitive classification performance compared with the state-of-the-art methods, as achieved high accuracy of 94%. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Systemic inflammation in COVID-19 patients may induce various types of venous and arterial thrombosis: A systematic review.

COVID-19 is a global pandemic with a daily increasing number of affected individuals. Thrombosis is a severe complication of COVID-19 that leads to a worse clinical course with higher rates of mortality. Multiple lines of evidence suggest that hyperinflammation plays a crucial role in disease progression. This review compiles clinical data of COVID-19 patients who developed thrombotic complications to investigate the possible role of hyperinflammation in inducing hypercoagulation. A systematic literature search was performed using PubMed, Embase, Medline and Scopus to identify relevant clinical studies that investigated thrombotic manifestations and reported inflammatory and coagulation biomarkers in COVID-19 patients. Only 54 studies met our inclusion criteria, the majority of which demonstrated significantly elevated inflammatory markers. In the cohort studies with control, D-dimer was significantly higher in COVID-19 patients with thrombosis as compared to the control. Pulmonary embolism, deep vein thrombosis and strokes were frequently reported which could be attributed to the hyperinflammatory response associated with COVID-19 and/or to the direct viral activation of platelets and endothelial cells, two mechanisms that are discussed in this review. It is recommended that all admitted COVID-19 patients should be assessed for hypercoagulation. Furthermore, several studies have suggested that anticoagulation may be beneficial, especially in hospitalized non-ICU patients. Although vaccines against SARS-CoV-2 have been approved and distributed in several countries, research should continue in the field of prevention and treatment of COVID-19 and its severe complications including thrombosis due to the emergence of new variants against which the efficacy of the vaccines is not yet clear.

The psychological impact of the COVID-19 pandemic and confinement period on a tunisian sample

IntroductionCoronavirus disease 2019, is now a global pandemic that has spread rapidly causing many deaths. Most countries have opted for compulsory confinement which had repercussions on mental health and well-being.ObjectivesThe purpose of this study is to assess mental health consequences during the confinement period.MethodsThis is a cross-sectional descriptive study of 360 Tunisians in April and May 2020. We used an anonymous E-questionnaire that included a socio-demographic fact sheet, The HAD questionnaire, and a Q-EDD questionnaire to explore eating disorders.ResultsThe subjects of our sample were mostly males with a mean age of 31. The body mass index was 25.5 (range 16.10 -46.24), 15% suffered from obesity. Half of the subjects were single and 6.7% spent the confinement time alone. 11.1% were smokers while 4.4% were alcohol users. The HAD-A and the HAD-D scores had an average of 9.1 and 8.48 respectively.A pathological threshold of anxiety and depression was found in 20% and 30% of the sample respectively.15% had an eating disorder: 76% had binge eating, 20% had bulimia and 17% had anorexia. In our study, we found an association between eating disorder and obesity, single marital status (p=0.007), living alone (p=0.001), history of depression (p=0.046), anxiety (p=0.049) and depression (p=0.038).ConclusionsReduced social interactions, decreased physical activity and increased stress are potentially harmful causes for our brain. Confining the population for several weeks has a negative impact on our physical and mental health. A crisis unit has been formed in Tunisia to help subjects overcome these psychological difficulties.

Kidney Transplant Recipients Infected With Coronavirus Disease 2019: Retrospective Qatar Experience.

BACKGROUND: This study aimed to evaluate the incidence of coronavirus disease 2019 (COVID-19) infection on kidney transplant, mortality, and risk factors associated with infection acquisition and severe illness in kidney transplant recipients with COVID-19. METHODS: Of 693 kidney transplant recipients who reported to our center, 249 were tested for COVID-19 by throat and nasal swab reverse transcription polymerase chain reaction. Of these, 43 recipients tested positive and 206 recipients tested negative. Among the 43 positive recipients, 9 were treated within an isolation facility, 25 were admitted to the hospital, and 9 were admitted to the intensive care unit (ICU). Risk factors associated with positive results and ICU admission were evaluated. RESULTS: COVID-19 was found in 6% of transplant recipients. Asian ethnicity (p = .003), history of hypertensive nephropathy (p = .01), AB blood group (P = .04), and higher tacrolimus trough levels (P = .007) were more frequent in the COVID-19 positive than in the COVID-19 negative group. ICU admission was more frequent in recipients presenting with fever, shortness of breath, and acute allograft dysfunction. Renal replacement therapy was required in 3 (7%) of 43 recipients, and mortality was reported in 1 (2.3%) recipient. Acute allograft dysfunction was an independent risk factor for severe COVID-19 (odds ratio, 93.7; 95% confidence interval, 2.37-3710.94; P = .02). CONCLUSIONS: Higher tacrolimus targets may be associated with COVID-19 development. Acute kidney injury during the COVID-19 course may be a sign of severe disease. Prognostication of COVID-19 severity in kidney transplant recipients is crucial for early recognition of critical illness and may ensure early intervention.

Systemic Inflammation May Induce Cardiac Injury in COVID-19 Patients Including Children and Adolescents Without Underlying Cardiovascular Diseases: A Systematic Review.

Coronavirus disease 2019(COVID-19) is an ongoing global pandemic with a daily increasing number of affected individuals and a relatively high mortality rate. COVID-19 patients that develop cardiac injury are at increased risk of a worse clinical course with higher rates of mortality. Increasing amounts of evidence suggest that a system-wide inflammatory response and a cytokine storm mediated type syndrome plays a crucial role in disease progression. This systematic review investigates the possible role of hyperinflammation in inducing cardiac injury as one of the severe complications of COVID-19. A systematic literature search was performed using PubMed, Embase and Scopus databases to identify relevant clinical studies that investigated cardiovascular injury manifestations and reported inflammatory and cardiac biomarkers in COVID-19 patients. Only 29 studies met our inclusion criteria and the majority of these studies demonstrated significantly elevated inflammatory and cardiac blood markers. It was evident that underlying cardiovascular diseases may increase the risk of developing cardiac injury. However, many COVID-19 patients included in this review, developed different types of cardiac injury without having any underlying cardiovascular diseases. Furthermore, many of these patients were either children or adolescents. Therefore, age and comorbidities may not always be the two main risk factors that dictate the severity and outcome of COVID-19. Further investigations are required to understand the underlying mechanisms of pathogenicity as an urgent requirement to develop the appropriate treatment and prevention strategies. These strategies may specifically target hyperinflammation as a suspected driving factor for some of the severe complications of COVID-19.

Smart wearable devices in cardiovascular care: where we are and how to move forward.

Technological innovations reach deeply into our daily lives and an emerging trend supports the use of commercial smart wearable devices to manage health. In the era of remote, decentralized and increasingly personalized patient care, catalysed by the COVID-19 pandemic, the cardiovascular community must familiarize itself with the wearable technologies on the market and their wide range of clinical applications. In this Review, we highlight the basic engineering principles of common wearable sensors and where they can be error-prone. We also examine the role of these devices in the remote screening and diagnosis of common cardiovascular diseases, such as arrhythmias, and in the management of patients with established cardiovascular conditions, for example, heart failure. To date, challenges such as device accuracy, clinical validity, a lack of standardized regulatory policies and concerns for patient privacy are still hindering the widespread adoption of smart wearable technologies in clinical practice. We present several recommendations to navigate these challenges and propose a simple and practical 'ABCD' guide for clinicians, personalized to their specific practice needs, to accelerate the integration of these devices into the clinical workflow for optimal patient care.

The Interplay Between the Immune System, the Renin-Angiotensin-Aldosterone System (RAAS), and RAAS Inhibitors May Modulate the Outcome of COVID-19: A Systematic Review.

Since the discovery of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), numerous research has been undertaken to delineate the various effects of the virus which manifests in many ways all over the body. The association between the SARS-CoV-2 invasion mechanism and the renin-angiotensin-aldosterone system (RAAS) receptors, created many debates about the possible consequences of using RAAS-modulating drugs including angiotensin-converting enzyme inhibitors (ACEi) and angiotensin II receptor blockers (ARBs) during the pandemic. Many clinical studies were conducted to assess the outcomes of coronavirus disease 2019 (COVID-19) in patients who use ACEi/ARBs following the arguments claiming to discontinue these drugs as a precautionary measure. Although several studies mainly analyzed the outcomes of the disease, this review aimed to compare specific blood markers in both groups of COVID-19 patients to gain better insight into the interaction of ACEi/ARBs with different body functions during the infection. Several databases were searched using a combination of keywords followed by screening and data extraction. Only 28 studies met our inclusion criteria, the majority of which showed no significant difference between the inflammation markers of COVID-19 patients who used or did not use ACEi/ARBs. Interestingly, 6 studies reported lower inflammatory markers in COVID-19 patients who used ACEi/ARBs, and 6 studies reported better outcomes among the same group. We therefore concluded that the use of ACEi/ARBs may not lead to worse prognosis of COVID-19 and may even play a protective role against the hyperinflammatory response associated with COVID-19.

Towards potential inhibitors of COVID-19 main protease M-pro by virtual screening and molecular docking study

The COVID-19 pandemic caused by SARS-CoV-2 has started in December 2019 in Wuhan, China, and become a global health problem. The SARS-COV-2 main protease (M-pro) play a crucial role in the multiplication and control of virus activity. Therefore, we assume that the inhibition of these enzymes inhibits viral replication. To determine potential inhibitors of this protease among existing chemical libraries, we have carried out a virtual screening of 300 antiviral molecules obtained by the ASINEX database. Nine molecules were chosen based on their stability with the target (M-pro), and the molecular docking study was carried out against the same target. These molecules showed higher binding affinities than the positive control to the active site of the same target (M-pro) and exhibit interactions with the amino acids responsible for the inhibitory activity of this enzyme (Cys145 and His 41). Then, these molecules were selected and chosen as potential inhibitors of SARS-Cov-2. [GRAPHICS] Highlights Three hundred antiviral compounds obtained from the ASINEX database were subjected to a virtual screening against SARS-COV-2 main protease M-pro. Nine molecules were selected and were subjected to molecular docking against the same target to evaluate their stability and the mode of binding inside the active site. The nine molecules show favourable interactions with the two amino acids Cys145 and His41, which suggests that these molecules could have competitive inhibitory activity. against the Mpro target main protease The graphical abstract was created using BioRender.com

Genomic Sequencing and Analysis of Eight Camel-Derived Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Isolates in Saudi Arabia.

Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe respiratory illness in humans; the second-largest and most deadly outbreak to date occurred in Saudi Arabia. The dromedary camel is considered a possible host of the virus and also to act as a reservoir, transmitting the virus to humans. Here, we studied evolutionary relationships for 31 complete genomes of betacoronaviruses, including eight newly sequenced MERS-CoV genomes isolated from dromedary camels in Saudi Arabia. Through bioinformatics tools, we also used available sequences and 3D structure of MERS-CoV spike glycoprotein to predict MERS-CoV epitopes and assess antibody binding affinity. Phylogenetic analysis showed the eight new sequences have close relationships with existing strains detected in camels and humans in Arabian Gulf countries. The 2019-nCov strain appears to have higher homology to both bat coronavirus and SARS-CoV than to MERS-CoV strains. The spike protein tree exhibited clustering of MERS-CoV sequences similar to the complete genome tree, except for one sequence from Qatar (KF961222). B cell epitope analysis determined that the MERS-CoV spike protein has 24 total discontinuous regions from which just six epitopes were selected with score values of >80%. Our results suggest that the virus circulates by way of camels crossing the borders of Arabian Gulf countries. This study contributes to finding more effective vaccines in order to provide long-term protection against MERS-CoV and identifying neutralizing antibodies.