High resolution melting curve analysis for rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants.

Since the emergence of the original Wuhan SARS-CoV-2 strain, several new variants of the virus have emerged. Alpha, Beta, Gamma, Delta and the most recent Omicron variants have been introduced during this pandemic. Several methods including, but not restricted to, allele-specific PCR, ligation with rolling circle amplification and real-time PCR with allele-specific probes are able to detect mutations as low as a single nucleotide polymorphism. High-resolution melting curve analysis is ano-ther technique to assess any mutations in a nucleic acid chain. Confirmed samples with SARS-CoV-2 infection were subjected to variant identification using a de novo-designed HRM assay. In order to select for mutations with the highest effect on Tm of the amplicon, deletion mutations of NSP6 (Del 3675-3677), and S1 (Del 144) were chosen for HRM analysis. HRM analysis for the amplicon of the primer set-1 (NSP6) resulted in Tm differences of -0.39°C, +0.4°C, and -0.6°C between Alpha, Delta, and Omicron variants, respectively, in comparison to the original Wuhan strain. Moreover, HRM analysis of the amplification performed by primer set-2 (S1) led to Tm differences of +0.32°C, -0.26°C, and +0.24°C between Alpha, Delta, and Omicron variants, respectively, in comparison to original Wuhan strain. The test was able to specify each sample to its variant group with more than 90 percent of confidence. The results obtained in this study demonstrate that using a single closed-tube strategy with a HRM-equipped machine, screening new variants of the virus is possible in a fast and reliable way. Keywords: high resolution melting; SARS coronavirus 2; mutation; variant; genotyping.

Risk Communication in Early Containment of COVID-19 Pandemic in Iran: Implementation of the World Health Organization Strategic Preparedness and Response Plan (WHO-SPRP).

Background: Health systems must have functional and efficient preparedness and response plans to manage pandemics. Moreover, it is essential to adjust to changing circumstances and the dynamic character of pandemics. The World Health Organization (WHO) introduced the Strategic Preparedness and Response Plan (SPRP), emphasizing 144 measures across 10 pillars, helping governments prepare and respond to the coronavirus disease 2019 (COVID-19) pandemic. This study aimed to determine how the Iranian health system, based on the WHO-SPRP, addresses strategic preparedness and response plan in the COVID-19 pandemic at the national level. Methods: The WHO-SPRP was adopted and translated into Persian by 2 bilingual natives. The chief of the health office requested that authorized officers complete the SPRP. Then, a meeting was held by officers of related units involved in COVID-19 management to address the SPRP at regional and national levels. Results: Our findings suggest that up to August 2020, effective risk communication and community engagement were not fully established. Our response plan lacked evidence-based information and educational messaging to consistently shape public opinion and impression of a respiratory pandemic. Conclusion: The Iranian health care system and services were almost able to address the SPRP and perform the major indicators that the WHO had proposed. However, special attention should be paid to risk communication and community engagement to empower informed decision-making by individuals and communities.

Prevalence of COVID-19 in Different Types of Collagen Vascular Diseases and its Relationship with Drugs Used in these Patients.

Objectives: The outcome of COVID-19 disease in collagen vascular disease and its comparison with other infected people in the community, are not fully understood yet.In this study, we examined whether the prevalence and severity of COVID-19 in these patients is higher than the general population or not? Methods: This cross-sectional study was performed between August and December 2020 on collagen vascular patients referred to the rheumatology clinic of Firouzgar Hospital. Patients were evaluated for a history of COVID-19. The prevalence of the and its relationship with age, sex, type of disease, medications, blood. The history of influenza vaccine was also evaluated in these patients. Results: Among the total of 748 patients, 574 (76.6%) subjects were women, and 174 (23.3%) subjects were men. The mean age of the patients was 47.46 ± 13.56 years old. The prevalence of COVID-19 was 8.0% and its highest prevalence was related to rheumatoid arthritis (36.7%) and the lowest one was for vasculitis (1.7%). Notably, 12.5% of the patients who did not suffer from COVID-19, were vaccinated against influenza (p-value = 0.54). In this regard, a significant relationship was found between COVID-19 prevalence and previous existence of interstitial lung disease (p -value = 0.017). Conclusions: The prevalence of COVID-19 in collagen vascular patients was not higher than the general population. There was also no significant relationship between the prevalence of COVID-19 and its severity and collagen vascular patient's blood group, the type of their disease and drug. More studies are required on the effect of DMARD drugs on the prevalence and severity of COVID-19 disease in collagen patients. Better results could be obtained if this study is done with a larger sample size.

Vaccine hesitancy from the parent perspectives: protocol for a qualitative study in Iran.

INTRODUCTION: WHO declared vaccine hesitancy as a global public health threat in 2019. Since even a slight reduction in vaccine coverage rates can lead to a decrease in herd immunity, it is imperative to explore the underlying factors affecting vaccine hesitancy. This qualitative study protocol aims to explore determinant factors that influence vaccine hesitancy in Iran from the parent's perspective. METHODS AND ANALYSIS: Descriptive-Interpretive Qualitative research will be conducted to gain an insight into vaccine hesitancy in the west of Tehran province in Iran. Participants in the study will be recruited from vaccine-hesitant parents of children under 5 years' old who will be recognised as being hesitant to extract from the national health information system. The semistructured interviews and in-depth questions will be performed both face-to-face in an open space such as a park near their homes and via video call because of the COVID-19 pandemic and social distancing. Interviews will be conducted by a trained qualitative person. Transcribed data will be analysed through thematic analysis. ETHICS AND DISSEMINATION: Ethics approval was obtained from the research ethics committee at the Iran University of Medical Sciences (Approval ID #IR.IUMS.REC.1399.273). The results of the study are expected to be presented by the end of 2022 year. A variety of dissemination methods will be employed to communicate research findings, including presentations at conferences and peer-reviewed publications.

Adverse effects following COVID-19 vaccination in Iran.

BACKGROUND: Vaccination is a key intervention to prevent COVID-19. Many vaccines are administered globally, yet there is not much evidence regarding their safety and adverse effects. Iran also faces this challenge, especially as data regarding the Sputnik V vaccine is sparse. Therefore, the aim of this study is to determine the adverse effects of the most commonly used vaccines in Iran. METHODS: Using a retrospective cohort study design, 6600 subjects aged 18 years or older who had received two doses of any of the three COVID-19 vaccines (Sinopharm, AstraZeneca, and Sputnik V) were selected using a random sampling method between March and August 2021. Subjects were asked about any adverse effects of the vaccines by trained interviewers via telephone interview. Vaccine-related adverse effects in individuals during the first 72 h and subsequently following both doses of the vaccines were determined. The demographic variables, type of administered vaccine, adverse effects, and history of the previous infection with COVID-19 were collected. Descriptive statistics (mean, standard deviation) and analytical statistics (Chi-squared and Wilcoxon tests) were performed at a 95% significance level using STATA software version 15 (STATA Corp, College Station, TX, USA). RESULTS: From 6600 participants, 4775 responded (response rate = 72.3%). Of the participants, 1460 (30.6%) received the AstraZeneca vaccine, 1564 (32.8%) received the Sinopharm vaccine and 1751 (36.7%) received the Sputnik V vaccine. 2653 participants (55.56%) reported adverse effects after the first dose and 1704 (35.7%) after the second dose. Sputnik V caused the most adverse effects with 1449 (82.7%) vaccine recipients reporting symptoms after the first or second dose, compared with 1030 (70.5%) for AstraZeneca and only 585 (37.4%) for the Sinopharm vaccine. The most common adverse effects after the first dose were fatigue (28.37%), chill/fever (26.86%), and skeletal pain (22.38%). These three adverse effects were the same for the second dose, although their prevalence was lower. CONCLUSIONS: In this study, we demonstrate that the Sputnik V vaccine has the highest rate of adverse effects, followed by the AstraZeneca and Sinopharm vaccines. COVID-19 vaccines used in Iran are safe and there were no reports of serious adverse effects.

The effect of COVID-19 mRNA vaccines against postvaccination laboratory-confirmed SARS-CoV-2 infection, symptomatic COVID-19 infection, hospitalization, and mortality rate: a systematic review and meta-analysis.

OBJECTIVES: We systematically reviewed the literature to investigate the pooled effect of COVID-19 mRNA vaccination against SARS-CoV-2 infection and its clinical outcomes. METHODS: Scopus, Web of Science, PubMed (Medline), and Embase were searched on 9 September 2021. The odds ratio (OR) of COVID-19 infection and its clinical outcomes in fully/ partially vaccinated versus unvaccinated participants were calculated and pooled by using a random-effects model. RESULTS: The pooled analysis showed that among health care workers and general population, vaccinated participants with one or two doses were less likely to infect with SARS-CoV-2 (OR = 0.16; 95%CI: 0.08-0.32; I2 = 79.86%; 95%CI I2: 68.99-87.21%), to develop symptomatic COVID-19 infection (OR = 0.09; 95%CI: 0.03-0.32; I2 = 80.43%; 95%CI I2: 70.83-89.33%), to admit to the hospital because of COVID-19 (OR = 0.13; 95%CI: 0.06-0.28; I2 = 86.19%; 95%CI I2: 67.80-93.88%), and to die from COVID-19 (OR = 0.14; 95%CI: 0.06-0.35; I2 = 66.76%; 95%CI I2: 54.00-76.99%) than unvaccinated participants. CONCLUSIONS: COVID-19 mRNA vaccines, especially following administration of two doses, are extremely effective. It would be suggested further studies with large sample size and different ethnicities to be conducted among the general population to warrant these results.

COVID-19 Infection and Mortality Rates within Medical Specialists and General Practitioners and Its Comparison with the General Population: A Longitudinal Nationwide Study.

BACKGROUND: We aimed to provide data regarding COVID-19 infection and mortality rates within different specialties of physicians and general medical practitioners in a longitudinal nationwide study and to compare the results with general population. METHODS: Data on COVID-19 infection and mortality of medical physicians in Iran was actively gathered through the Iranian Medical Council (IRIMC). Population COVID-19 cumulative incidence and mortality data were extracted from WHO situation analysis reports and data on Iranian population were obtained from the Statistical Center of Iran. RESULTS: As of Jul 27th 2020, COVID-19 infection and mortality rates were 0.680% and 0.0396% among 131223 physicians. The highest cumulative infection rates as of 27th July 2020, were observed in specialists of infectious diseases (3.14%) followed by neurology (2.18%), and internal medicine (2.13%). The highest cumulative mortality rates as of Nov 3rd 2020 were observed in specialties of forensic medicine (0.314%), anesthesiology (0.277%), urology (0.237%), and infectious diseases (0.20%). Male physicians comprised 95% of cumulative mortality as of Nov 3rd. The physicians' COVID-19 mortality in July and November were 49% and 23% higher than the general population respectively. CONCLUSION: Infection and mortality rates in Iranian physicians were higher than the general population, however the magnitude of difference was narrowing in longitudinal investigation. Provision of personnel protective equipment should be prioritized to specialists of infectious diseases, forensic medicine, anesthesiology, internal and emergency medicine, and urology.

Evaluation of Reinfection in COVID-19 Patients in the World: A Narrative Review.

Background: The evaluation of reinfection and the genetic structure of all human and virus genomes could help to develop programs and protocols for providing services and ultimately to prevent the disease by producing more effective vaccines. Therefore, the aim of this study was to investigate the presence and occurrence of COVID-19 reinfection through a narrative review study. Methods: We searched the Medline (PubMed), Embase, Scopus, Web of Science, Cochrane library, Ovid, and CINHAL databases. Inclusion criteria included all studies whose main purpose was to provide information about the occurrence or presence of reinfection in patients with COVID-19. An independent samples t test was used to compare the continuous outcomes between the 2 groups. Results: The mean duration of the first episode in the group with mild or moderate COVID-19 was 24.42±1.67 days, and it was 21.80±3.79 days in the group with severe COVID-19. The mean duration of the second episode (reinfection) in patients with mild or moderate form was 15.38 ± 5.57 days, and it was 19.20±2.98 days in patients with severe form. In both episodes, the duration of the disease did not significantly differ between the 2 groups (p=0.484 in the first episode; p=0.675 in the second episode), but the interval to the occurrence of reinfection in patients with the mild or moderate form was significantly longer than those with the severe form (p<0.001). In this instance, the time interval in patients with the mild or moderate form was 36.63±5.71 days while in those with the severe form of the disease it was 29.70±5.65 days. Besides, the genomes of the viruses isolated from the first and second episode were different. Conclusion: According to the results, all patients should be very careful about the severity of the second episode because of the more need for medical interventions for saving the patients. The interval between the first end and the second episode as well as the duration of each episode is highly important for better management of the disease.

Interdisciplinary Approaches to COVID-19.

The coronavirus disease 2019 (COVID-19) pandemic has been a significant concern worldwide. The pandemic has demonstrated that public health issues are not merely a health concern but also affect society as a whole. In this chapter, we address the importance of bringing together the world's scientists to find appropriate solutions for controlling and managing the COVID-19 pandemic. Interdisciplinary cooperation, through modern scientific methods, could help to handle the consequences of the pandemic and to avoid the recurrence of future pandemics.

Iran COVID-19 Epidemiology Committee: A Review of Missions, Structures, Achievements, and Challenges.

BACKGROUND: Since the beginning of the coronavirus disease 2019 (COVID-19) epidemic in Iran, the control and management of the epidemic were headed by the National Headquarter for the Control of COVID-19 Epidemic through setting up different scientific committees, including the COVID-19 National Epidemiology Committee. The present study reviews the missions, structures, achievements, and challenges of the Epidemiology Committee. STUDY DESIGN: A rapid review . METHODS: All relevant reports, documents, guidelines, published literature, and surveillance data related to the establishment, visions, missions, roles, activities, and outputs of the COVID-19 Epidemiology Committee were critically reviewed in this study. RESULTS: The efforts of the committee's working groups may have impacted improvements in data registration/usage, provincial data quality at provincial levels, and perception of the epidemic situation in the provinces. The committees have also played role in informing the policies in different stages of the epidemic through routine or problem-based data/evidence analyses, epidemic investigations, and mathematical modeling. CONCLUSION: The structure and experience gained by the committee can be used in similar situations within and outside the country. To further improve the impacts of our activities, it is essential to have effective interaction, collaboration, and data flow between the committee and a broad range of organizations within and outside the Ministry of Health and Medical Education.

Investigating the factors affecting the survival rate in patients with COVID-19: A retrospective cohort study.

Background: As hospitalized patients with COVID-19, especially those who are admitted to ICU or die afterwards, generally have comorbidities, the aim of this study was to determine the factors affecting the survival rate of COVID-19 patients in Iran using a retrospective cohort. Methods: This retrospective cohort study was conducted on patients with COVID-19 who referred to medical centers under the supervision of Iran University of Medical Sciences, Tehran, Iran, from February 22 to March 25, 2020. The final date of follow-up was April 19, 2020. All consecutive inpatients with laboratory-confirmed COVID-19 were included in this study. Clinical laboratory, radiological, treatment, and demographic data were collected and analyzed. The associations among gender, immune disease, diabetes, liver disease, cardiovascular disease, kidney disease, chronic pulmonary disease, cancer, chronic nervous disease, type of treatment, and risk of death were analyzed. The Kaplan-Meier and Log-rank tests were used to estimate survival rate and compare survival rates, respectively. Results: The total number of deaths or desired event in the study was 329 (10.3%).The risk of death in the age groups of 50-60 years, 60-70 years, and >70 years compared to the 30-40 age group was 2.17 (95% CI: 1.03, 4.55; p: 0.040); 3.72 (95 % CI: 1.80, 7.68; p: 0.001) and 5.09 (95 % CI: 2.49, 10.40; p: 0.001), respectively. The results showed men had 11.5% more risk of deaths than women (HR: 1.11; 95 % CI: 0.89, 1.39; p: 0.341). Kidney disease increased the risk of death by 52.3% in these patients, which was not statistically significant (HR: 1.78; 95 % CI: 1.04, 3.04; p: 0.035). Also, chronic pulmonary diseases and diabetes increased the risk of death in COVID-19 patients by 89.5% and 41.3% compared to COVID-19 patients without chronic pulmonary diseases and diabetes [(HR: 1.89; 95 % CI: 1.17, 3.04; p: 0.008), (HR: 1.41; 95 % CI: 1.01, 1.96; p: 0.038)]. Conclusion: Based on the results of this study, more attention and care should be paid to COVID-19 patients with underlying diseases, such as chronic obstructive pulmonary disease, diabetes, and kidney disease to reduce the number of deaths.

Estimation of the net reproductive number of COVID-19 in Iran.

Background: Estimating the net reproductive number of COVID-19 virus can reveal the rate and severity of the disease transmission in the Iranian society to health researchers and practitioners. Also, it signifies the importance of the disease to the community. Thus, the aim of this study was to determine the net reproductive number of COVID-19 in Iran and its different provinces. Methods: This study was conducted on the data of COVID-19 patients in Iran from February 21 to March 8, 2020. To determine the net reproductive number of COVID-19 in Iran, the serial interval and ß value were first determined using linear regression analysis. Then, the net reproductive number values were calculated for Iran and its different provinces. Results: The results of this study showed that the net reproductive number of COVID-19 in Iran was 1.31. Using the available data up to March 15, 2020, the highest net reproductive number was in Mazandaran, Yazd, Isfahan, Qazvin, and Zanjan provinces, with values of 2.07, 1.86, 1.84, and 1.76, respectively. The net reproductive number also showed an increasing trend in Kohgiluyeh and BoyerAhmad province. Conclusion: It seems that although the net reproductive number of the virus had a decreasing trend in the provinces, it is still high. Therefore, sanitary measures in these provinces should be pursued more seriously. On the other hand, social distancing is a topic that should be taken into consideration, that is, social gatherings and contacts should be avoided as much as possible and strategies and facilities for this action should be developed by the government and health policymakers.