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Background & Objective: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in a worldwide pandemic. The first case of COVID-19 was reported from Wuhan in the Hubei Province of China in December 2019; however, the disease's origin is still mysterious. Wholegenome sequence analysis is essential for monitoring the spread of infectious diseases as well as studying the pathogenesis and evolution of viruses. In this study, analysis of 198 fully sequenced genomes from Iran and West Asia was carried out to study mutations, phylogeny, amino acid changes, clades, and lineages of these genomes as well as comparison of these sequences with those of reference Wuhan genome of NC_045512.2. Methods: In total, 198 completely sequenced genome data from Iran and West Asia were collected from GenBank. Mutation detection was carried out using a trial version of CLC Genomics Workbench v.21.0 (QIAGEN, Germany). Online tools such as GISAID Mutations App and Pangolin were used for further analysis of the results. Results: In this study, several unique mutation sites were identified in the Iranian genomes (n = 8); positions 1397 G>A and 29742 G>T were the most frequent changes in more than 85% of the Iranian genomes. Mutation rate, mutation per sequence, and transition versus transversion for the Iranian genomes included 4.73, 14.14, and 1.6, respectively. Generally, C>T alteration was the most common substitution in all the sequences. Conclusion: The ORF1ab, N, and S were the genes with the most changes. The current data can help researchers predict future epidemics and establish better strategies to control viral pandemics. [ABSTRACT FROM AUTHOR]

Since the onset of the coronavirus disease 2019 (COVID‐19) pandemic, the clinical manifestations of the virus have undergone many changes. Recently, there have been many reports on gastrointestinal symptoms in COVID‐19 patients. This study is aimed to perform a detailed phylogenetic study and assessment of different SNVs in the RNA genome of viruses isolated from fecal samples of patients with COVID‐19 who have gastrointestinal symptoms, which can help better understand viral pathogenesis. In the present study, 20 fecal samples were collected by written consent from COVID‐19 patients. According to the manufacturer's protocol, virus nucleic acid was extracted from stool samples and the SARS‐CoV‐2 genome presence in stool samples was confirmed by RT–PCR assay. Three viral genes, S, nsp12, and nsp2, were amplified using the reverse transcription polymerase chain reaction (RT–PCR) method and specific primers. Multiple sequencing alignment (MSA) was performed in the CLC word bench, and a phylogenetic tree was generated by MEGA X based on the neighbor‐joining method. Of all cases, 11 (55%) were males. The mean age of the patients was 33.6 years. Diabetes (70%) and blood pressure (55%) were the most prevalent comorbidities. All 20 patients were positive for SARS‐CoV‐2 infection in respiratory samples. Molecular analysis investigation among 20 stool samples revealed that the SARS‐CoV‐2 genome was found among 10 stool samples; only three samples were used for sequencing. The polymorphism and phylogenetic analysis in SARS‐CoV‐2 showed great similarity among all of the evaluated genes with the Wuhan reference sequence and all of the current variants of concern (VOCs). The current study represents a great similarity in polymorphism and phylogenetic analysis of the SARS‐CoV‐2 isolates with the Wuhan reference sequence and all of the current VOC in the particular evaluated partial sequences of S, nsp12, and nsp2. [ABSTRACT FROM AUTHOR]

Biological attack or bioterrorism is one of the sides to cause disease or death in all living things by using biological causative agents of disease due to reasons such as political, ideological and economic. There were many biological attacks from the primitive ages when poisoned arrows were used to the use of anthrax spores in 2001 against USA. Although chemical attacks are not as deep-rooted as biological attacks, they have been used for a long time, but the period when they came to the stage of history was the 19th century with the development of the modern chemical industry. Chemical attacks caused injuries, permanent damage and death to many people especially during the period of World wars. The pandemic that can be caused by natural epidemic diseases is the spread of a factor or disease in a very wide area. With the spread of disease; panic, unrest and chaos environment occurs in the spreading area. Coronavirus (Covid-19), which causes the current pandemic, is the most recent example. Coronavirus out broke in Wuhan, China, and started to spread in China first, and then Iran, and had an impact on Italy as well as European continent and around the world with the American continent. It infected millions of people, hundreds of thousands of people died, and caused environmental, social, psychological and economic problems on a global scale. Recently, different pandemic processes related to influenza have been experienced, but states have not been able to demonstrate an effective and efficient defense against the new type of coronavirus since the necessary preparations were not made despite the death of millions of people. Since biological attack and natural epidemics have the same effects and characteristics, it is not possible to predict how the states will respond in a possible biological attack. As in the current pandemic process, the possible consequences that will arise when caught unprepared are doubtful. In this study, it is evaluated how biological agents and natural epidemics are similar to each other and how to take measures against a possible attack or a new disaster. [ABSTRACT FROM AUTHOR]

As the first outbreak of COVID-19 in Wuhan, China, the elder population and those with comorbidities were at higher risk of COVID-19 infection. The mortality rate was also higher in this population. Hence, the management and prevention of this novel disease in nursing homes was of utmost importance. The health management team in Kahrizak Charity Foundation (KCF), a nursing home in Iran with more than 1400 elder or comorbid resident, have tackled the COVID-19 outbreak with a novel approach towards this problem. This commentary aims at sharing the insights and lessons learned in the management of COVID-19 in KCF. [ABSTRACT FROM AUTHOR]

Introduction: Coronavirus disease 2019 (COVID-19) is a pulmonary involvement which was reported for the first time in December 2019 in the city of Wuhan, Hubei province, China. The aim of the study was to describe the demographic, clinical, laboratory, and radiological characteristics of 204 definitive laboratory-confirmed COVID-19 patients hospitalized in Mashhad, Khorasan Razavi province, Iran. Patients and Methods: This study was performed on 204 laboratory-confirmed COVID-19 patients. A set of laboratory tests combined with various patient information and results from lung high-resolution computed tomography (HRCT) were gathered in a checklist and analyzed to give us a better view of patients who are hospitalized due to the complications caused by this disease. Results: The average age of our patients was 58.83 ± 15.93 years. There were 122 (59.8%) male and 82 (40.2%) female patients, and almost all of our patients had at least one underlying disease. Nine (4.4%) of our patients reported having gone for a trip to COVID-19-epidemic areas in the last 2 weeks. The most common signs shared among all our patients were cough, fever, and decreased O2 saturation; the average respiratory rate was 25.50 ± 6.74/min, average axillary body temperature was 37.69°C ± 0.69°C, and average O2 saturation was 88.34% ± 7.34%. Conclusion: Based on our results, the most common signs of this disease are fever, cough, and shortness of breath, similar to seasonal influenza. Our data on disease severity showed that 33 (16.2%) patients had moderate disease, 139 (68.1%) had severe disease, and 28 (13.7%) were critical; 22 (10.8%) of our hospitalized patients died due to the complications of this disease. [ABSTRACT FROM AUTHOR]

Background: Unknown cases of pneumonia appeared in late 2019 in Wuhan, China. Following the worldwide spread of the disease, the World Health Organization declared it a pandemic on March 11, 2020. The total number of infected people worldwide as of December 16, 2020, was more than 74 million, more than one million and six hundred thousand of whom died from Coronavirus Disease 2019 (COVID-19). This study aimed to identify the risk factors for the mortality of COVID-19 in Hamadan, west of Iran. Materials and Methods: This cross-sectional study used the information of all patients with COVID-19 admitted to Shahid Beheshti and Sina hospitals in Hamadan during January 2020-November 2020. Logistic regression model, decision tree, and random forest were used to assess risk factors for death due to COVID-19. Results: This study was conducted on 1853 people with COVID-19. Blood urea nitrogen change, SPO2 at admission, the duration of hospitalization, age, neutrophil count, lymphocyte count, number of breaths, complete blood count, systolic blood pressure, hemoglobin, and sodium were effective predictors in both methods of decision tree and random forest. Conclusion: The risk factors identified in the present study may serve as surrogate indicators to identify the risk of death due to COVID-19. The proper model to predict COVID-19-related mortality is random forest based on sensitivity. [ABSTRACT FROM AUTHOR]

In the last days of 2019, a new coronavirus emerged in Wuhan, China, and less than three months its disease, now called COVID-19, was announced a global pandemic by WHO. COVID-19 usually causes respiratory symptoms and can lead to more severe conditions like ARDS. HLA has a crucial role in regulating the immune system; thus, different HLA allele types can be a protective or risk factor for some diseases, so we aimed to find such associations to determine whether some alleles can predict susceptibility or resistibility to COVID-19 and finally facilitate vaccine development. In this case-control study, 15 admitted COVID-19 cases with severe symptoms and ten individuals with mild COVID-19 symptoms were enrolled in the case and control groups, respectively. They were genotyped for HLA A/B/DR loci using a low-resolution HLA typing test. These alleles were more prevalent in case (severe COVID-19) group: A*24 (53.33% vs 10%), B*50 (20% vs 10%), B*55 (20% vs 10%), DRB1*04 (40% vs 20%) and DRB1*11 (53.33% vs 30%) but the difference was only statically significant in A*24 allele (P=0.027; odd ratio=10.286). A*24 was also more prevalent in all patients than the general population in Iran. A*24 was the only allele more prevalent in severe COVID-19 cases with statistical significance. This allele was reported to be a risk factor for such autoimmune diseases as type 1 diabetes, myasthenia gravis, and systemic lupus erythematosus, which may be related to reported immune system hyperresponsiveness in severe COVID-19 cases. [ABSTRACT FROM AUTHOR]

Background: The novel coronavirus disease 2019 (COVID-19) was emergency turned into global public health after the first patients were detected in Wuhan, China, in December 2019. The disease rapidly expanded and led to an epidemic throughout China, followed by the rising number of cases worldwide. Given the high prevalence of COVID-19, rapid and accurate diagnostic methods are immediately needed to identify, isolate and treat the patients as soon as possible, decreasing mortality rates and the risk of public contamination by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).Methods: This case-control study was conducted in two hospitals in Alborz Province in Iran. All recruited cases in this study were symptomatic adults hospitalized as COVID-19 patients with compatible Computed tomographic (CT) scan findings and available rRT-PCR results. The patients were recruited in this study. The patients were categorized into positive and negative rRT-PCR groups and evaluated for symptoms, initial vital signs, comorbidity, clinical and laboratory findings. Finally, the results were assessed by SPSS software.Results: Between March 5 to April 5, 2020, 164 symptomatic COVID-19 patients were studied. In total, there were 111 rRT-PCR positive (67.6%) and 53 rRT-PCR negative patients (32.4%). In terms of statistics, the frequency of symptoms revealed no difference, except for cough (P.V:0.008), dizziness (PV: 0.048), and weakness (P.V:0.022). Among initial vital signs, PR (P.V:0.041) and O2 Saturation (PV: 0.014) were statistically different between the two groups. Evaluation of comorbidities revealed no difference except for hyperlipidemia (P.V:0.024). In the comparison of laboratory findings, only WBC count (PV: 0.001), lymphocyte count (PV: 0.001), and Hb (P.V:0.008) were statistically different between the two groups.Conclusion: In case of the negative rRT-PCR result, it is necessary to take a logical approach, and we recommended that the physician decides according to clinical manifestations, laboratory findings, and positive CT results. [ABSTRACT FROM AUTHOR]

• We found 258 missense mutations in spike glycoprotein of Iranian SARS-CoV-2. • Most of these mutations could potentially result in escape from neutralizing antibodies. • We found circulation of four current VOCs – Alpha, Beta, Gamma and Delta - indifferent regions in Iran. Since late 2019, when SARS-CoV-2 was reported at Wuhan, several sequence analyses have been performed and SARS-CoV-2 genome sequences have been submitted in various databases. Moreover, the impact of these variants on infectivity and response to neutralizing antibodies has been assessed. In the present study, we retrieved a total number of 176 complete and high-quality S glycoprotein sequences of Iranian SARS-COV-2 in public database of the GISAID and GenBank from April 2020 up to May 2021. Then, we identified the number of variables, singleton and parsimony informative sites at both gene and protein levels and discussed the possible functional consequences of important mutations on the infectivity and response to neutralizing antibodies. Phylogenetic tree was constructed to represent the relationship between Iranian SARS-COV2 and variants of concern (VOC), variants of interest (VOI) and reference sequence. We found that the four current VOCs – Alpha, Beta, Gamma and Delta – are circulated in different regions in Iran. The Delta variant is notably more transmissible than other variants, and is expected to become a dominant variant. However, some of the Delta variants in Iran carry an additional mutation, namely E1202Q in the HR2 subdomain that might confer an advantage to viral/cell membrane fusion process. We also observed some more common mutations such as an N-terminal domain (NTD) deletion at position I210 and P863H in fusion peptide-heptad repeat 1 span region in Iranian SARS-COV-2. The reported mutations in the current project have practical significance in prediction of disease spread as well as design of vaccines and drugs. [ABSTRACT FROM AUTHOR]

Background: Since December 2019, when a cluster of pneumonia cases due to SARS-CoV-2 initially emerged in Wuhan city and then rapidly spread throughout the world, the necessity for data concerning the clinical and para-clinical features of Iranian patients with COVID-19 was highlighted. Therefore, we aimed to compare the clinical, para-clinical and laboratory evidences of deceased patients with survival group.Methods: We extracted data regarding 233 patients with laboratory-confirmed COVID-19 from Buali Hospital in Iran; clinical/para-clinical and inflammatory indexes data were collected and analyzed. The data of laboratory examinations and chest CT findings were compared between deceased and survived patients.Results: The mean age of the patients was 49.8 years and 64% of our patients were male. The acute respiratory distress syndrome occurred in 64 patients, 52 who were admitted to the ICU, which all of them underwent invasive mechanical ventilation, and 28 who died. Lymphopenia (79%), neutrophilia (79%), and thrombocytopenia (21%) were the most frequently observed laboratory findings of the deceased group on admission. Most patients (68%) had a high systematic immune-inflammation (SII) index of > 500 and increased C-reactive protein level (88%). Levels of inflammatory indexes such as neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR) and SII were documented to be significantly elevated in the deceased group when compared with the patients who survived (P < 0.0001, P < 0.001, P < 0.0001, respectively). The most commonly presented symptoms were fever (70%) and cough (63%) on admission. Headache was uncommon (11%). Ground-glass opacity with consolidation (mixed) was the most common radiologic finding on chest CT (51%). No radiographic or CT abnormality was found in 15 of 204 patients (7%).Conclusion: Small fraction of patients with COVID-19 may present without fever and abnormal radiologic findings. Elevated NLR, PLR and SII can be considered as prognostic and risk stratifying factor of severe form of disease. [ABSTRACT FROM AUTHOR]