Showing 24 results for Sars-Cov-2
Volume 6, Issue 4 (11-2020)
Abstract
Background: The new unknown pandemic introduced in December 2019 in China is now known as SARS-CoV-2 induced COVID-19 (Coronavirus Disease 2019) disease. Some studies have been published by World Health Organization (WHO), Environmental Protection Agency (EPA), and Food and Drug Administration (FDA); however, there is a little information about food safety and COVID-19. The world has not sufficiently addressed the effects of COVID-19 on food safety. The remarkable point is the hypothesis that this epidemic has passed through a food source eaten by an individual and subsequently turned humans into an intermediate host. In particular, the recent state of information about SARS-CoV-2 is challenging owing to its high transmission and mortality rate in people as a potential source of pathogen and infections. However, there is currently no evidence about COVID-19 spread through food. Materials & Methods: Due to the fact that food is a basic humans need and could be an indirect carrier for the virus; therefore, hygiene protocols must be carefully implemented. Also, some studies have suggested that taking supplements, fermented dairy foods, probiotic products, as well as Vitamins C and D could be helpful. Heat treatment and pasteurization could prevent SARS-CoV-2 transmission through food.
Conclusion: It is recommended that further studies be performed on the duration of COVs survival at different levels of contact with foods under certain conditions with nanoparticles, nano-packaging, nano-emulsions, and nano-encapsulation to evaluate their size effect.
Volume 7, Issue 1 (1-2021)
Abstract
Background: In late December 2019, a new coronavirus called SARS-CoV-2, as the causative agent of COVID-19 (coronavirus disease 2019) pneumonia, began to spread from Wuhan, China. The SARS-CoV-2 virus is currently threatening the world’s public health and so far, no specific and effective treatment has been found for the disease. Due to the physiological changes in the body of pregnant women during pregnancy, the occurrence of infection in pregnant women could affect the health of both mother and her fetus. The present paper aimed to study the findings related to the effects of coronavirus on pregnant women and their fetuses during pregnancy, diagnostic methods, care protocols in pregnant women, and postpartum care.
Methods: The information included in this review was extracted from articles, published protocols, and valid statistics. In this study, articles indexed in Latin databases (PubMed, Google Scholar, Science Direct, Embase, Scopus), clinical protocols, and reports of reputable health organizations from January to august 2020 were reviewed using a combination of the following keywords: COVID-19, SARS-CoV-2, pregnant woman, and pregnancy.
Conclusion: Due to the global prevalence of this virus, protocols and health care should be applied for pregnant women in accordance with other people. It is also necessary to take preventive measures at the community level. In this regard, the management of pregnant women with COVID-19 infection is of particular importance during the pandemic period of the disease. However, more extensive studies are required to validate these principles. This review summarized the precautions that should be taken before and after delivery.
Volume 7, Issue 1 (1-2021)
Abstract
Background: In Iran, the first cases of SARS-CoV-2 disease were detected with the death of 2 people in Qom city. Then other cases were reported in Markazi, Tehran, and Gilan provinces, and after that the disease spread to all 31 provinces of the country.
Materials and Methods: All data used in this study were collected from the reports of the National Committee on COVID-19 Epidemiology in the Ministry of Health and Medical Education in Iran. To investigate the effect of traveling between neighboring provinces, a spatial rate smoothing method was used, showing the impact of neighborhood on the disease prevalence. Also, to investigate the relationship between population density and disease prevalence, spatial regression was used at a significance level of 5%.
Findings: Based on the estimated spatial rates, the disease prevalence rates changed in many provinces compared to the raw prevalence rates. Population density was also found to be directly related to the disease prevalence, so that with increasing population density, the disease prevalence rate increased (p <.001).
Conclusion: It seems that case finding process should be done actively in all provinces of Iran regardless of administrative borders. Provinces should also be classified in terms of the disease transmission risk according to population density of patients, which may indicate the probability of contact between individuals.
Volume 7, Issue 2 (5-2021)
Abstract
Backgrounds: Coronavirus disease 2019 (COVID-19) pandemic is considered as a global health challenge, and Iran is among the top ten countries with the highest mortality rate. This study aimed to analyze epidemiological, clinical, and laboratory features of hospitalized SARS-CoV-2 infected patients and identify the risk factors of mortality among them to facilitate the prioritization of resources and vaccine allocation in the population using data available in a large university hospital in Tehran, Iran.
Materials & Methods: From February 20 to May 14, 2020, a total of 684 COVID-19 confirmed cases were admitted to Imam Hossein University hospital in Tehran and enrolled in this retrospective observational study.
Findings: The mean age of the participants was 59.48±16.65 years, and 55.8% were male. Compared to survivors, non-survivors (n=127, 18.57%) were older (69.09±14.16 vs. 57.29±16.40), had higher average number of comorbidities, and more frequently suffered from dyspnea, convulsion, loss of consciousness (LOC), tachycardia, tachypnea, and hypoxia. They also had higher levels of leukocytes, neutrophil count, C-reactive protein (CRP), creatine phosphokinase (CPK), aspartate aminotransferase (AST), lactate dehydrogenase (LDH), international normalized ratio (INR), prothrombin time (PT), partial thromboplastin time (PTT), urea, and serum creatinine (p<.05). Serum potassium (K), lymphocyte count, hemoglobin, HCO3, and serum sodium (Na) were significantly lower in non-survivors. Multivariable logistic regression analysis results revealed that nine variables were positively associated with mortality.
Conclusion: Among COVID-19 patients admitted to the hospital, having more than two or three comorbidities, loss of consciousness, SpO2 < 90%, increased CRP, CPK, urea, and serum potassium, were associated with mortality.
Volume 7, Issue 2 (5-2021)
Abstract
Backgrounds: A novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread to all countries of the world, including Iran. Although anti-SARS-CoV-2 antibodies may be identified in patients using immunological methods with sufficient sensitivity and specificity, the conclusive diagnosis of the disease is made using the molecular RT-PCR method. A population-based seroepidemiological survey was conducted to quantify the proportion of the exposed population with SARS-CoV-2 antibodies and evaluate whether the antibodies are a marker of total or partial immunity compared to the population that remains susceptible to the virus.
Material & Methods: This cross-sectional study was conducted to investigate the seroprevalence of COVID-19 in Valiasr, Sajad, and Ghaem hospitals in Tehran, the capital of Iran, from April to the end of October 2020. Clotted and heparinized blood specimens (2mL) were collected from the patients. The serum and plasma were separated and stored at −80 °C until use. Anti-SARS-CoV-2 IgG and IgM antibodies were examined in the serum samples of 1375 in-patients admitted to the hospitals using ELISA kits. The obtained data were analyzed using SPSS software Ver.22.0 by employing statistical tests such as Chi-square and Fisher’s exact tests. A p-value <.05 was considered as significant.
Findings: In total, 1375 participants were enrolled in this study, and SARS‐CoV‐2 antibodies were detected in 291 patients using IgM‐IgG antibody assay. Among the seropositive patients studied, 187 were male (64.3%), and 104 were female (35.7%) (p<.05). The mean age of the patients was 49±8.4 years; the majority of whom (27%) were in the age group of 31-40 years. Also, the lowest frequency of infected cases was related to the age group of 1-10 years (p <.05). The seroprevalence of SARS‐CoV‐2 IgM or IgG antibodies was determined to be 21.2%. Diabetes mellitus was the most common underlying disease among SARS‐CoV‐2 patients [p=.05; Odd Ratio=1.61(0.90-2.91)].
Conclusion: The use of conventional serological assays, such as the enzyme-linked immunoassay (ELISA), for detecting specific IgM and IgG antibodies in SARS‐CoV‐2 patients has a high-throughput advantage while minimizing false-negative results obtained using the RT-PCR method. In this study, the seroprevalence of SARS-CoV-2 antibodies was determined to be 21%. Control of diabetes, among other influential factors, plays an important role in the management and control of COVID-19.
Volume 7, Issue 2 (5-2021)
Abstract
Backgrounds: A potential cross-immunity between SARS-CoV-2 and MERS-CoV could lead to the development of a serodiagnostic test and/or serotherapy against SARS-CoV-2 using dromedary camel anti MERS-CoV serum.
Materials & Methods: Epidemiological and 66 literature data, of which 35 have been published during 2015-2021, and findings were analysed.
Findings: According to the statistical data reported during COVID-19 pandemic, there are less cases and deaths associated with COVID-19 in countries known for dromedary breeding and the circulation of MERS-CoV (another betacoronavirus disease transmitted by dromedary camels) among humans and dromedaries. This observation and the similarity in genome and immunopathogenicity between SARS-CoV-2 and MERS-CoV, suggest that individuals who have been in contact with MERS-CoV infected dromedaries and/or consumed their products (milk, meat, urine) might have acquired an immunity protecting them against SARS-CoV-2. In addition to neutralizing antibodies, this immunity could also be due to complement proteins, chemokines, and especially antimicrobial peptides (AMP), known for their effect on enveloped viruses.
Conclusion: Most research has focused on vaccines as a solution to stop the pandemic, while serotherapy hasn’t significantly aroused the interest of researchers. This potential cross-immunity between SARS-CoV-2 and MERS-CoV could lead to the development of a serodiagnostic test and/or serotherapy against SARS-CoV-2 using dromedary camel anti MERS-CoV serum.
Volume 8, Issue 4 (12-2022)
Abstract
Backgrounds: SARS-COV-2 infection is not always correlated with protection. Antibody seroprevalence in unvaccinated individuals, which is usually measured by N-specific antibodies, is not necessarily correlated with protection, while antibodies against S protein show a better correlation with protection due to its neutralizing epitopes. In this study, we tried to improve our conception of the hidden perspective of SARS-COV-2 in epidemiological reports and investigate anti-S antibody prevalence among anti-N antibody-positive asymptomatic and mildly symptomatic patients.
Materials & Methods: Blood samples were collected from asymptomatic or mildly symptomatic volunteer participants and symptomatic hospitalized patients with negative PCR results from May 30 to June 17, 2020. Detection of SARS-COV-2 antibodies was done using an ELISA kit targeting N or S protein.
Findings: Totally, 716 samples from volunteer participants and 81 samples from symptomatic hospitalized patients with negative PCR results were evaluated. The test performance-adjusted seroprevalence (95% CI) of SARS-COV-2 antibody was 17.3% (8.8-25.8%) for anti-N IgG in volunteers and 25.5% (12.8-39.7%) for anti-N and anti-S IgM in hospitalized patients. Among anti-N IgG positive infected individuals, 49.2% (21.4 and 78.8%) were anti-S antibody positive.
Conclusion: The results showed that SARS-COV-2 infection sometimes occurs in individuals without symptoms or with mild symptoms, but in more than half of them, the produced antibody is not protective. The findings of hospitalized patients showed that the combination of IgM assay with real-time PCR improved the disease diagnosis by more than 25% in cases with negative molecular test results.
Volume 9, Issue 1 (3-2023)
Abstract
Backgrounds: Immune-inflammatory responses appear to play a key role in severe SARS-CoV-2 infections. Interleukin-35 (IL-35) and presepsin (PSN) are inhibitory cytokine and pro-inflammatory interleukin, which play a crucial role in the immune system modulation, respectively. Therefore, the study of IL-35 and PSN interaction with other parameters may be critical for managing patients with COVID-19.
Materials & Methods: A total of 125 severe/critical COVID-19 patients and 60 healthy persons as a control group were enrolled in this work. These patients were admitted to Marjan medical city and Al-Sadeq hospital in Iraq during February to August 2022 and diagnosed as severe cases depending on the SpO2 percentage according to the guidelines released by the National Health World. Anti- and pro-inflammatory cytokines (IL-35 and PSN) were detected by ELISA technique.
Findings: Presepsin showed a positive correlation with admission to the respiratory care unit (RCU) (r= .022, p= .011). A negative correlation was found between presepsin and C- reactive protein (CRP) (r= .21, p= .018). Both PSN and IL-35 in biochemical tests showed a positive strong effect on glucose levels in COVID-19 patients (r= .234, p= .008 and r= .241, p= .007, respectively). IL-35 had a positive impact on alkaline phosphatase (ALP) (r= .28, p= .002). Hemoglobin (Hb) level showed a positive correlation with presepsin (r= .2, p= .02).
Conclusion: This study confirms the growing evidence showing the direct role of regulatory pro-inflammatory cytokines in the development and control of COVID-19 through the interaction with other parameters.
Volume 9, Issue 2 (8-2023)
Abstract
Backgrounds: The primary goal of this study was to identify the potential association between COVID-19 prognosis and demographic and clinical features, underlying diseases, and drug and supplement use in patients admitted to Amir al-Momenin hospital in Zabol.
Materials & Methods: This retrospective study surveyed the electronic health records of 848 COVID-19 patients hospitalized in a tertiary referral hospital in southeastern Iran from the beginning of the COVID-19 outbreak until the end of February 2021. Univariate and multiple analytical tests including unconditional and penalized logistic regressions were used for statistical analysis.
Findings: Out of a total of 848 patients, 371 (43.75%) patients were female, and 477 (56.25%) patients were male. Age, underlying pulmonary and cardiovascular diseases, and loss of consciousness predicted a higher mortality rate. On the contrary, a negative chest X-ray was associated with a lower risk of death.
Conclusion: Identifying predisposing factors of mortality in COVID-19 patients will help physicians provide more intensive care to those at higher risk of death by classifying patients based on risk factors and underlying diseases.
Volume 9, Issue 3 (10-2023)
Abstract
Background: The ongoing global health crisis caused by the infectious coronavirus disease, known as COVID-19, is attributed to the SARS-CoV-2 virus. The pandemic has significantly impacted people of all ages and nationalities and has spread across all continents, with an initial focus on Asia and subsequently reaching Europe. The objective of this study was to analyze the progression of COVID-19 in Europe in contrast to other continents around the world by examining the pandemic's trajectory across different geographic areas, allowing us to gain insights into the effectiveness of containment measures, and identifying potential patterns of virus spread.
Materials & Methods: The data source was a curated dataset provided by Our World in Data (OWD), regularly updated during the COVID-19 pandemic. The dataset consisted of 207,316 records with 67 attributes, covering 244 locations, including countries from six continents. These attributes encompassed a wide range of COVID-19-related metrics, such as cases, deaths, testing, vaccinations, and demographic indicators. This comprehensive comparative study specifically focused on the European continent data from January 01, 2020, to August 08, 2022.
Findings: The analysis revealed distinct groups of European countries with different experiences with the virus. First, some countries were found to be severely affected by the virus, grappling with higher case numbers and mortality rates. On the other hand, some countries were able to successfully manage the virus spread. Additionally, there was a group with significant case numbers but relatively lower mortality rates. Finally, certain countries effectively limited the virus transmission while maintaining low mortality rates.
Conclusion: As the pandemic continues, it is essential to emphasize the significance of international data to develop comprehensive strategies against severe health crises. Evaluating different outcomes across continents and within specific regions could provide crucial insights to guide future control measures. However, the fight against COVID-19 is far from over, necessitating ongoing research and cooperation on a global scale.
Volume 9, Issue 3 (10-2023)
Abstract
Background: The present study aimed to compare the clinical outcome as well as laboratory and clinical profiles of Coronavirus disease 2019 (COVID-19) patients with and without diabetes.
Materials & Methods: The present study is a retrospective study that included 266 non-diabetic and 259 diabetic patients who were admitted to a tertiary healthcare center in South India between March 2021 to April 2021.The objective of the study was to compare the clinical outcome and laboratory profiles of COVID-19 patients with and without diabetes. Patients aged 18 years or above, diagnosed with COVID-19 by either RT-PCR and/or HRCT chest as well as diagnosed to be diabetic or non-diabetic were included in the study. After observing inclusion and exclusion criteria, the study included patients whose medical records were scrutinized, and data was analyzed using SPSS v 28.0 and the continuous variables were expressed in mean, standard deviation, minimum and maximum value. The categorical variables are expressed in frequency and percentage. Comparison was done using binomial test and Mann-Whitney U test while association was tested using Fischer exact test.
Findings: Primary outcomes show that higher number of patients with diabetes (84.94%) presented with abnormal Interleukin-6 (IL-6) levels and this difference was found to a statistically significant (p<0.001). Hypertension was the most common comorbidity among both diabetic (46.72%) and non-diabetic (33.52%) patients and it was shown to be associated with clinical outcome and oxygen requirement (p<0.001). A significant difference was observed in the mean score of age, total count, IL-6 and number of days admitted between COVID-19 subjects of both groups with the mean being higher in the group of patients with diabetes (p<0.001).
Conclusion: The results of the present study reinforce available evidence that IL-6 levels can be used to ascertain progression, morbidity, and mortality to ensure proper management of COVID-19 patients and that diabetes state results in higher total count, IL-6 and number of days admitted.
Volume 9, Issue 4 (12-2023)
Abstract
Aims: SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has caused a worldwide health crisis, impacting millions of individuals across the globe. The focus of In this study, is to conduct an epidemiological investigation was carried out on the progression of COVID-19 in the North African region, encompassing Morocco, Algeria, Tunisia, Libya, and Egypt, from January 2020 to May 2023. The aim of this study was to conduct an epidemiological investigation into the progression of COVID-19 in the North African region, encompassing Morocco, Algeria, Tunisia, Libya, and Egypt, from January 2020 to May 2023, with a primary focus on analyzing and understanding the COVID-19 data in these five North African countries.
Materials & Methods: This research aimed toinvolved the observeation and analyzesis of an international database from our World in Data, using SPSS and Excel,. A comparative analysis was carried out, considering the number of COVID-19 cases, fatalities, and vaccination rates in the five specified North African countries.
Findings: Over the course of three years, a total of 3,722,56017,862 new COVID-19 cases and 83,860757 deaths were documented in North African countries, and the year 2021 emerged as the most devastating period, with the highest number of COVID-19 cases (1,767,410) and fatalities (50,341) across the region. Among the countries studied, Morocco (1,274,180 cases, 34.23% ) and Tunisia (1,153,261 cases, 31%) of cases, reportedwere the mosthighest infection ratesaffected, with Morocco reporting 1,272,490 cases (34%) and Tunisia 150,962 cases (31%). Similarly, the highest death tolls were recorded in Tunisia , accounting for (29,415331 deaths, (35%), and Egypt, with (24,83012 deaths, (30%). Additionally, Morocco led the region in vaccination efforts in the region, administering 47% of the total of 384,851,069 vaccine doses.
Conclusion: The COVID-19 pandemic has posed a significant global health challenge, affecting each North African country differently, depending on various factors such as their population, control measures, and vaccination campaigns. This study emphasizes the importance of continued efforts and tailored strategies for each country in the region to combat the pandemic in the region and underscores the significance of tailored strategies for each country to effectively address the ongoing crisis.
Volume 10, Issue 1 (2-2024)
Abstract
Background: Despite the passage of more than two years since the coronavirus disease 2019 (COVID-19) pandemic, the persistence of the coronavirus and its circulation at varying levels globally necessitates a deeper understanding of the factors influencing its transmission and impact. This study aimed to investigate the relationship between environmental factors, population density, and genetic variations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with a specific focus on elucidating their implications for public health measures and vaccine development.
Materials & Methods: This observational analysis was conducted utilizing daily reported SARS-CoV-2 cases in various countries. Additionally, monthly changes in ultraviolet (UV) radiation index, population density per km2, and viral genetic variations were assessed. Comparative analysis was performed to examine correlations between these variables. Data analysis was conducted using SAS 9.3 software with a generalized linear model (GLM) approach.
Findings: This study revealed significant correlations between UV index and key epidemiological parameters, including mortality rate, average case number, and transmission rate. Population density per square kilometer did not exhibit any substantial relationship with these variables. Analysis of viral clades suggests potential immunological insights, indicating varying degrees of immunity conferred by certain genetic variants.
Conclusion: These findings underscore the importance of environmental and genetic factors in shaping the trajectory of the COVID-19 pandemic. By elucidating the role of UV radiation and viral genetic diversity, this study informs public health strategies and underscores the necessity of ongoing surveillance and vaccine development efforts tailored to the evolving SARS-CoV-2 landscape.
Volume 10, Issue 3 (7-2022)
Abstract
Aims: This research aimed to investigate the spread of COVID-19 infection among suspected adults and assess the relationship between tobacco smoking, diabetes, and high blood pressure comorbidities, and their association with susceptibility to acquiring the infection with COVID-19.
Material & Methods: This study was carried put on 214 suspected cases of CoV-2, among male and female adults (age ≥ 20 years) in 2021, and tested for CoV-2 infection by RT-PCR. Plus the IgG/IgM Rapid Test Cassette, along with CoV-2-related symptoms. Information on whether the subjects smoke or suffer from diabetes and high blood pressure has also been supplemented.
Findings: According to the results, the age group of 61-80 was the most affected group among the COVID-19 patients by 45%. In addition, the proportion of males infected with COVID-19 was higher across all age groups (64%) than females (36%). A significant difference was observed between the patients concerning age and gender (p<0.05). The percentage of smoker patients versus non-smokers was 47% vs 53%. The proportion of diabetics to nondiabetics was 43 % vs 57 %. As well as the ratio of hypertensive to normotensive COVID-19 patients was 62 % vs 38 %. There was a significant difference between smoker and non-smoker, diabetic and non-diabetic, and hypertensive and non-hypertensive patients in terms of affected by COVID-19 (p<0.05).
Conclusion: Age, gender, smoking, diabetes, and hypertension are some risk factors for Coronavirus infection. Gender and age are associated with infection rates and their consequences. Also, the likelihood of COVID-19 infection is likely to be lowered in half for active smokers. Patients with diabetes and hypertension especially those who use ACE2-increasing medications are at a higher risk of developing a severe COVID-19 infection.
Volume 10, Issue 4 (12-2024)
Abstract
Background: This study aimed to assess the relationship between cycle threshold (Ct) values and disease severity, symptoms, and comorbidities in COVID-19-positive individuals.
Materials & Methods: This cross-sectional study was conducted on COVID-19 patients who were admitted to General Ghadamis hospital and diagnosed with COVID-19 from August 2020 to 2021. The association between Ct values and symptoms, demographic characteristics, and clinical characteristics was analyzed by SPSS analysis.
Findings: A total of 286 patients were included in this study, of whom 53.5% were female, and 46.5% were male, with a median age of 53 years (range: 1–90 years). Among symptomatic individuals, 51.4% had severe COVID-19 symptoms, and 26.6% had mild symptoms. Severe systemic symptoms were significantly associated with older age groups. The majority of elderly patients (66%) exhibited low Ct values (Ct ≤ 24), indicating a high viral load. Additionally, 64.6 and 40.8% of patients with severe and mild symptoms had low Ct values. Symptoms varied significantly across patients with low, medium, and high Ct values. There was a strong correlation between lower Ct values and the presence of comorbidities such as hypertension, diabetes mellitus, ischemic heart disease (IHD), cerebrovascular accident, and cancer.
Conclusion: Compared to asymptomatic individuals, most symptomatic patients with severe and mild symptoms had significantly lower Ct values. These findings highlight the critical role of viral load in SARS-CoV-2 progression and suggest that Ct values could be used to predict the spread of infection in the community.
Volume 10, Issue 4 (12-2024)
Abstract
Background: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an infectious disease with an unprecedented transmission rate. Considering that there is limited information about the prevalence of influenza co-infection among SARS-CoV-2 positive Iranian patients, and that SARS-CoV-2 co-infection with other respiratory pathogens complicates its diagnosis, prevention, and treatment, this systematic review aimed to evaluate the prevalence of influenza co-infection among SARS-CoV-2 positive Iranian population to facilitate rapid disease management.
Materials & Methods: A comprehensive search was conducted in Web of Science, PubMed, Scopus, and Google Scholar databases using relevant keywords to find all relevant articles published in English from December 2019 to July 2024. Patients of various ages with influenza-SARS-CoV-2 co-infection were evaluated. This study was conducted according to PRISMA (preferred reporting items for systematic reviews and meta-analyses) guidelines.
Findings: Totally, 631 articles were recognized in electronic databases, among them nine articles meeting the inclusion criteria were reviewed in this research. The prevalence of influenza co-infection among SARS-CoV-2 positive patients was 4.38%. The majority of SARS-CoV-2 positive patients were male, while the frequency distribution of influenza-SARS-CoV-2 co-infection was almost the same in both sexes. The viral load was the highest in patients aged 18-60 years.
Conclusion: The findings suggest that the prevalence of influenza co-infection among SARS-CoV-2 positive patients is low. However, the significance of this issue should not be ignored, and influenza vaccination in high-risk groups including hospitalized patients and the elderly is highly recommended due to the probability of serious complications.
Volume 11, Issue 2 (4-2025)
Abstract
Background: Several SARS-CoV-2 variants with distinct characteristics have emerged, with Omicron sub-variants such as BA.1 to BA.5 being predominant since late 2021. Distinguishing sub-variants using phylogenetic and molecular analyzes provides a valuable approach in the context of epidemiological research.
Materials & Methods: Molecular epidemiology and sub-variants of SARS-CoV-2 omicron were investigated using 150 nasopharyngeal samples from COVID-19 patients in Tehran (Iran) from May 2022 to August 2023. Omicron lineages were differentiated using RT-PCR targeting Q493R, L452R, and ∆69-70 spike mutations. SARS-CoV-2 omicron sub-variants were determined by amplicon sequencing.
Findings: The mean age of the study participants was 44±7 years, comprising 38.6% males and 61.4% females , which may have an effect on transmission and susceptibility of different ages. Also, 117 (78%) samples were positive for one of the three lineages, while 33 (22%) was none of the lineages, which were referred to as conclusive and inconclusive results, respectively. 60.7% of the samples was the omicron lineage BA.4 or BA.5.
Conclusion: Considering the prevalence of BA.4 and BA.5 in the study population and their differences with the parental SARS-CoV-2 variant, the primary vaccine seems to be not effective against the current omicron sub-variants. These results underscore the importance of vaccination as a critical strategy to prevent the spread of these variants. The suggested primer sets could be an easy way to screen sample variants and lineages and are useful for screening and sequencing samples in countries with limited resources. Continuous monitoring of omicron sub-variants is recommended for preventing the resurgence of COVID-19.
Volume 11, Issue 2 (4-2025)
Abstract
Background: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a significant global health threat. The host immune response determines the disease severity, with factors like human leukocyte antigen (HLA) genes, age, sex, and nutritional status influencing outcomes. HLA genes, known for their genetic diversity, are implicated in determining susceptibility and severity of infectious diseases. This study investigated the association between HLA class I genotypes and COVID-19 severity in the Isfahan population, Iran.
Materials & Methods: Blood samples were collected from 34 COVID-19 patients with varying levels of disease severity (severe, moderate, and mild). HLA genotyping was performed using polymerase chain reaction-sequence specific primers (PCR-SSP), and in silico analysis assessed the affinity of viral peptides to HLA alleles.
Findings: Statistical analyses revealed that HLA-C07 was more prevalent in patients with severe COVID-19, suggesting a potential association between this allele and the disease severity. Furthermore, HLA-A01 was more prevalent among severe cases, while HLA-A02 and HLA-A03 were less frequent, indicating a possible predisposing role for HLA-A01 and protective roles for HLA-A02 and HLA-A*03.
Conclusion: These findings highlight the role of HLA molecules in COVID-19 severity and offer insights into genetic factors influencing outcomes. Understanding the association of specific HLA alleles, such as HLA-C07, HLA-A01, HLA-A02, and HLA-A03, with the disease progression lays a foundation for advancing personalized preventive and therapeutic approaches. These results contribute to knowledge on host genetics in infectious diseases, paving the way for further research and therapeutic strategies.
Hamid Asghari, Sedigheh Asad,
Volume 14, Issue 3 (2-2024)
Abstract
In the last month of 2019, an unknown virus appeared in Wuhan, China. Sequencing studies have shown that the virus is a new member of the coronavirus family, which mostly causes a respiratory disease with pneumonia-like symptoms. The new coronavirus consists of 25 proteins, including 4 important structural proteins and 15 non-structural proteins. Spike protein is one of the most important structural proteins on the surface of the virus; It is highly glycosylated and plays a key role in the virus binding to the host cells. The binding of glycans to proteins affects their structure and function in two ways; They lead to proper protein folding, and can play an important role in protein interactions, and also, by covering the surface of the protein, it causes the virus to escape from the immune system. So it is obvious that the study of glycan structures becomes more important when either a vaccine is going to be designed or glycan structures have important roles in the folding, activity, and interaction of a protein. Therefore, since the spike protein is a non-functional structural protein, the study of glycan structures is important for two goals of vaccine design and investigating the role of glycans in protein interactions. In this article, we are going to review the most important findings on spike protein glycosylation and compare the amount of glycosylation in different viruses, indicating the importance of glycan structures in designing an effective vaccine.
Hamed Shahriarpour, Hossein Naderi-Manesh, Shahriar Arab, Najmeh Dehghanbanadaki,
Volume 15, Issue 1 (12-2023)
Abstract
The COVID-19 pandemic has created a global health crisis, and developing effective treatments is essential to prevent the spread of the disease and save millions of lives. One of the key proteins involved in the replication cycle of SARS-CoV-2, the virus that causes COVID-19, is the main protease enzyme, 3CLpro. Due to its high importance, this enzyme is the subject of molecular, structural, and clinical investigations, and efforts have been made to develop drugs that can inhibit its activity. One such drug is the chemical compound N3, which has been found to have a high inhibitory effect against 3CLpro. However, traditional medicine perspectives on this issue have been less explored. In this research, molecular docking interaction simulation and all-atom molecular dynamics (MD) simulation were conducted to study the potential inhibitory capability of generally available 21 plant-extracted compounds against the 3CLpro enzyme. Three compounds with the highest inhibition probability were selected from the molecular docking results and subjected to 100 ns of MD simulation to investigate their stability and structural-dynamic-energetic features. Beside the complexes stability, the results from the simulation demonstrated that, all our selected three compounds induce N3 comparable structural-dynamics characteristics to 3CLpro and, therefore, are expected to have a similar inhibitory ability against this enzyme. Compound number 5 was found to have the most favorable binding energy and was proposed as the best plant substitute for N3. The results from this research can be directly used to design experimental research for 3CLpro enzyme inhibition, saving the time-financial cost.