Sharif Digital Repository

Purpose Whole genome sequencing of SARS-CoV2 is important to find useful information about the viral lineages, variants of interests and variants of concern. As there are not enough data about the circulating SARS-CoV2 variants in Iran, we sequenced 54 SARS-CoV2 genomes during the 5 waves of pandemic in Iran. Methods After viral RNA extraction from clinical samples collected during the COVID-19 pandemic, next generation sequencing was performed using the Nextseq platform. The sequencing data were analyzed and compared with reference sequences. Results During the 1st wave, V and L clades were detected. The second wave was recognized by G, GH and GR clades. Circulating clades during the 3rd... 

The global COVID-19 pandemic has affected the world’s population by causing changes in behavior, such as social distancing, masking, restricting people’s movement, and evaluating existing medication as potential therapies. Many pre-existing medications such as tocilizumab, ivermectin, colchicine, interferon, and steroids have been evaluated for being repurposed to use for the treatment of COVID-19. None of these agents have been effective except for steroids and, to a lesser degree, tocilizumab. Ivermectin has been one of the suggested repurposed medications which exhibit an in vitro inhibitory activity on SARS-CoV-2 replication. The most recommended dose of ivermectin for the treatment of... 

Coronaviruses are a group of envelop viruses which lead to diseases in birds and mammals as well as human. Seven coronaviruses have been discovered in humans that can cause mild to lethal respiratory tract infections. HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1 are the low-risk members of this family and the reason for some common colds. Besides, SARS-CoV, MERS-CoV, and newly identified SARS-CoV-2, which is also known as 2019-nCoV, are the more dangerous viruses. Due to the rapid spread of this novel coronavirus and its related disease, COVID-19, a reliable, simple, fast, and low-cost detection method is necessary for patient diagnosis and tracking worldwide. Human coronaviruses detection... 

The safe, highly effective measles vaccine has been recommended globally since 1974, yet in 2017 there were more than 17 million cases of measles and 83,400 deaths in children under 5 years old, and more than 99% of both occurred in low- and middle-income countries (LMICs)1–4. Globally comparable, annual, local estimates of routine first-dose measles-containing vaccine (MCV1) coverage are critical for understanding geographically precise immunity patterns, progress towards the targets of the Global Vaccine Action Plan (GVAP), and high-risk areas amid disruptions to vaccination programmes caused by coronavirus disease 2019 (COVID-19)5–8. Here we generated annual estimates of routine childhood... 

In this paper, we have trained several deep convolutional networks with introduced training techniques for classifying X-ray images into three classes: normal, pneumonia, and COVID-19, based on two open-source datasets. Our data contains 180 X-ray images that belong to persons infected with COVID-19, and we attempted to apply methods to achieve the best possible results. In this research, we introduce some training techniques that help the network learn better when we have an unbalanced dataset (fewer cases of COVID-19 along with more cases from other classes). We also propose a neural network that is a concatenation of the Xception and ResNet50V2 networks. This network achieved the best... 

This paper aims to propose a high-speed and accurate fully-automated method to detect COVID-19 from the patient's chest CT scan images. We introduce a new dataset that contains 48,260 CT scan images from 282 normal persons and 15,589 images from 95 patients with COVID-19 infections. At the first stage, this system runs our proposed image processing algorithm that analyzes the view of the lung to discard those CT images that inside the lung is not properly visible in them. This action helps to reduce the processing time and false detections. At the next stage, we introduce a novel architecture for improving the classification accuracy of convolutional networks on images containing small... 

Humanity's challenges are becoming increasingly difficult, and as these challenges become more advanced, the need for effective and intelligent action becomes more apparent. Meanwhile, the novel coronavirus disease (COVID-19) pandemic, which has plagued the world, could be considered as an opportunity to take a step toward the need for atomic engineering, compared to molecular engineering, as well as to accelerate this type of research. This approach, which can be expressed in terms of picotechnology, makes it possible to identify living cell types or in general, chemical and biological surfaces using their atomic arrays, and applied for early diagnosis even treatment of the disease. © 2020... 

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 pandemic that has been spreading around the world since December 2019. More than 10 million affected cases and more than half a million deaths have been reported so far, while no vaccine is yet available as a treatment. Considering the global healthcare urgency, several techniques, including whole genome sequencing and computed tomography imaging have been employed for diagnosing infected people. Considerable efforts are also directed at detecting and preventing different modes of community transmission. Among them is the rapid detection of virus presence on different surfaces with which people may come in... 

The application of quantum dots (QDs) for detecting and treating various types of coronaviruses is very promising, as their low toxicity and high surface performance make them superior among other nanomaterials; in conjugation with fluorescent probes they are promising semiconductor nanomaterials for the detection of various cellular processes and viral infections. In view of the successful results for inhibiting SARS-CoV-2, functional QDs could serve eminent role in the growth of safe nanotherapy for the cure of viral infections in the near future; their large surface areas help bind numerous molecules post-synthetically. Functionalized QDs with high functionality, targeted selectivity,... 

Fast, efficient, and accurate detection of SARS-CoV-2 spike antigen is pivotal to control the spread and reduce the mortality of COVID-19. Nevertheless, the sensitivity of available nanobiosensors to detect recombinant SARS-CoV-2 spike antigen seems insufficient. As a proof-of-concept, MOF-5/CoNi2S4 is developed as a low-cost, safe, and bioactive hybrid nanostructure via the one-pot high-gravity protocol. Then, the porphyrin, H2TMP, was attached to the surface of the synthesized nanomaterial to increase the porosity for efficient detection of recombinant SARS-CoV-2 spike antigen. AFM results approved roughness in different ranges, including 0.54 to 0.74 μm and 0.78 to ≈0.80 μm, showing good... 

COVID-19, as the most significant epidemic of the century, infected 467 million people and took the lives of more than 6 million individuals as of March 19, 2022. Due to the rapid transmission of the disease and the lack of definitive treatment, countries have employed non-pharmaceutical interventions. This study aimed to investigate the effectiveness of the smart travel ban policy, which has been implemented for non-commercial vehicles in the intercity highways of Iran since November 21, 2020. The other goal was to suggest efficient COVID-19 forecasting tools and to examine the association of intercity travel patterns and COVID-19 trends in Iran. To this end, weekly confirmed cases and... 

Respiratory virus infections are among the most prevalent diseases in humans and contribute to morbidity and mortality in all age groups. Moreover, since they can evolve fast and cross the species barrier, some of these viruses, such as influenza A and coronaviruses, have sometimes caused epidemics or pandemics and were associated with more serious clinical diseases and even mortality. The recently identified Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a Public Health Emergency of International concern and has been associated with rapidly progressive pneumonia. To ensure protection against emerging respiratory tract... 

Application of materials capable of energy harvesting to increase the efficiency and environmental adaptability is sometimes reflected in the ability of discovery of some traces in an environment―either experimentally or computationally―to enlarge practical application window. The emergence of computational methods, particularly computer-aided drug discovery (CADD), provides ample opportunities for the rapid discovery and development of unprecedented drugs. The expensive and time-consuming process of traditional drug discovery is no longer feasible, for nowadays the identification of potential drug candidates is much easier for therapeutic targets through elaborate in silico approaches,... 

Acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also called COVID-19, is one of the most contagious viruses resulting in a progressive pandemic. Since specific antiviral treatments have not been developed yet and its fatal rate is almost high, early and fast detection is critical for controlling the outbreak. In this study, a piezoelectric microcantilever biosensor has been designed for detecting COVID-19 samples directly without requiring preparation steps. The biosensor acts as a transducer and is coated with the related antibody. When the SARS-CoV-2 antigens adsorbed on the microcantilever top surface through their spike proteins, a surface stress due to the mass change would be... 

Coronavirus disease 2019 (COVID-19) is now of global concern due to its rapid dissemination across the globe. The rapid spread of this viral infection, along with many of its unknown aspects, has posed new challenges to the health care systems. The main challenging effects of COVID-19 are rapid dissemination through close contact and varying clinical severity among different individuals. Furthermore, the medical staff in endemic areas are becoming exhausted and deal with a considerable level of job burnout, which can negatively affect their medical decision making. Also, due to the variable pulmonary manifestations of COVID-19, some physicians may misdiagnose patients. To overcome these... 

A self-report questionnaire survey was conducted online to collect big data from over 16000 Iranian families (who were the residents of 1000 urban and rural areas of Iran). The resulting data storage contained over 1 M records of data and over 1G records of automatically inferred information. Based on this data storage, a series of machine learning experiments was conducted to investigate the relationship between nutrition and the risk of contracting COVID-19. With highly accurate scores, the findings strongly suggest that foods and water sources containing certain natural bioactive and phytochemical agents may help to reduce the risk of apparent COVID-19 infection. © 2022 The Author(s)  

Municipal solid waste (MSW) directly impacts community health and environmental degradation; therefore, the management of MSW is crucial. Medical waste is a specific type of MSW which is generally divided into two categories: infectious and non-infectious. Wastes generated by coronavirus disease 2019 (COVID-19) are classified among infectious medical wastes; moreover, these wastes are hazardous because they threaten the environment and living organisms if they are not appropriately managed. This paper develops a bi-objective mixed-integer linear programming model for medical waste management during the COVID-19 outbreak. The proposed model minimizes the total costs and risks, simultaneously,... 

Viral diseases have long been among the biggest challenges for healthcare systems around the world. The recent Coronavirus Disease 2019 (COVID-19) pandemic is an example of how complicated the situation can get if we are not prepared to combat a viral outbreak in time, which brings up the need for quick and affordable biosensing platforms and vast knowledge of potential antiviral effects and drug/gene delivery opportunities. The same challenges have also existed for nonviral immunogenic disorders. Nanomedicine is considered a novel candidate for effectively overcoming these worldwide challenges. Among the versatile nanomaterials commonly used in biomedical applications, graphene has recently... 

Objective: This study analyzes the effects of lifestyle, nutrition, and diets on the status and risks of apparent (symptomatic) COVID-19 infection in Iranian families. Materials and Methods: A relatively extensive questionnaire survey was conducted on more than 20,000 Iranian families (residing in more than 1000 different urban and rural areas in the Islamic Republic of Iran) to collect the big data of COVID-19 and develop a lifestyle dataset. The collected big data included the records of lifestyle effects (e.g. nutrition, water consumption resources, physical exercise, smoking, age, gender, health and disease factors, etc.) on the status of COVID-19 infection in families (i.e. residents of...