Implementation of an In-House Platform for Rapid Screening of SARS-CoV-2 Genome Variations.

BACKGROUND: Global real-time monitoring of SARS-CoV-2 variants is crucial to controlling the COVID-19 outbreak. The purpose of this study was to set up a Sanger-based platform for massive SARS-CoV-2 variant tracking in laboratories in low-resource settings. METHODS: We used nested RT-PCR assay, Sanger sequencing and lineage assignment for 930-bp of the SARS-CoV-2 spike gene, which harbors specific variants of concern (VOCs) mutations. We set up our platform by comparing its results with whole genome sequencing (WGS) data on 137 SARS-CoV-2 positive samples. Then, we applied it on 1028 samples from March-September 2021. RESULTS: In total, 125 out of 137 samples showed 91.24% concordance in mutation detection. In lineage assignment, 123 out of 137 samples demonstrated 89.78% concordance, 65 of which were assigned as VOCs and showed 100% concordance. Of 1028 samples screened by our in-house method, 78 distinct mutations were detected. The most common mutations were: S:D614G (21.91%), S:P681R (12.19%), S:L452R (12.15%), S:T478K (12.15%), S:N501Y (8.91%), S:A570D (8.89%), S:P681H (8.89%), S:T716I (8.74%), S:L699I (3.50%) and S:S477N (0.28%). Of 1028 samples, 980 were attributed as VOCs, which include the Delta (B.1.617.2) and Alpha (B.1.1.7) variants. CONCLUSION: Our proposed in-house Sanger-based assay for SARS-CoV-2 lineage assignment is an accessible strategy in countries with poor infrastructure facilities. It can be applied in the rapid tracking of SARS-CoV-2 VOCs in the SARS-CoV-2 pandemic.

COVID-19 cases, hospitalizations and deaths after vaccination: a cohort event monitoring study, Islamic Republic of Iran.

Objective: To investigate the incidence of coronavirus disease 2019 (COVID-19) cases, hospitalizations and deaths in Iranians vaccinated with either AZD1222 Vaxzevria, CovIran® vaccine, SARS-CoV-2 Vaccine (Vero Cell), Inactivated (lnCoV) or Sputnik V. Methods: We enrolled individuals 18 years or older receiving their first COVID-19 vaccine dose between April 2021 and January 2022 in seven Iranian cities. Participants completed weekly follow-up surveys for 17 weeks (25 weeks for AZD1222) to report their COVID-19 status and hospitalization. We used Cox regression models to assess risk factors for contracting COVID-19, hospitalization and death. Findings: Of 89 783 participants enrolled, incidence rates per 1 000 000 person-days were: 528.2 (95% confidence interval, CI: 514.0-542.7) for contracting COVID-19; 55.8 (95% CI: 51.4-60.5) for hospitalization; and 4.1 (95% CI: 3.0-5.5) for death. Compared with SARS-CoV-2 Vaccine (Vero Cell), hazard ratios (HR) for contracting COVID-19 were: 0.70 (95% CI: 0.61-0.80) with AZD1222; 0.73 (95% CI: 0.62-0.86) with Sputnik V; and 0.73 (95% CI: 0.63-0.86) with CovIran®. For hospitalization and death, all vaccines provided similar protection 14 days after the second dose. History of COVID-19 protected against contracting COVID-19 again (HR: 0.76; 95% CI: 0.69-0.84). Diabetes and respiratory, cardiac and renal disease were associated with higher risks of contracting COVID-19 after vaccination. Conclusion: The rates of contracting COVID-19 after vaccination were relatively high. SARS-CoV-2 Vaccine (Vero Cell) provided lower protection against COVID-19 than other vaccines. People with comorbidities had higher risks of contracting COVID-19 and hospitalization and should be prioritized for preventive interventions.

Epidemiological and clinical risk factors related to severe COVID-19 in Iran: a multi-center study.

BACKGROUND: Iran was one of the first countries to be affected by COVID-19. Identifying factors associated with the severity of COVID-19 is effective in disease management. This study investigated the epidemiological and clinical features and factors related to the severity of COVID-19 in one of the less privileged areas in Iran. METHODS: In a multi-center study, all patients admitted to Zahedan University of Medical Sciences hospitals in southeastern Iran were investigated from February 29 to April 31, 2020. Demographic, epidemiological, and clinical data of patients were extracted from medical records. Bivariate and multivariate logistic regression models were used to explore the risk factors associated with the severity of COVID-19. RESULTS: Among the 413 patients, 55.5% were male, and 145 (35.10%) were in a severe condition at admission time. Multivariate analysis showed that the adjusted odds of the disease severity increased in patients with older age (OR 2.27; 95% CI 1.41-3.65), substance abuse (OR 2.49; 95% CI 1.14-5.43), having one underlying disease (OR 1.52; 95% CI 0.90-2.55), having two underlying disease (OR 2.31; 95% CI 1.19-4.50), and having three or more underlying disease (OR 2.60; 95% CI 1.19-5.66). CONCLUSIONS: COVID-19 was more severe in older patients, patients with a history of substance abuse, and patients with the underlying disease. Understanding the factors affecting the disease severity can help the clinical management of COVID-19, especially in less privileged areas where fewer resources are available.

Disease Waves of SARS-CoV-2 in Iran Closely Mirror Global Pandemic Trends.

BACKGROUND: Complete SARS-CoV-2 genome sequencing in the early phase of the outbreak in Iran showed two independent viral entries. Subsequently, as part of a genome surveillance project, we aimed to characterize the genetic diversity of SARS-CoV-2 in Iran over one year after emerging. METHODS: We provided 319 SARS-CoV-2 whole-genome sequences used to monitor circulating lineages in March 2020-May 2021 time interval. RESULTS: The temporal dynamics of major SARS-CoV-2 clades/lineages circulating in Iran is comparable to the global perspective and represent the 19A clade (B.4) dominating the first disease wave, followed by 20A (B.1.36), 20B (B.1.1.413), 20I (B.1.1.7), leading the second, third and fourth waves, respectively. We observed a mixture of circulating B.1.36, B.1.1.413, B.1.1.7 lineages in winter 2021, paralleled in a fading manner for B.1.36/B.1.1.413 and a growing rise for B.1.1.7, prompting the fourth outbreak. Entry of the Delta variant, leading to the fifth disease wave in summer 2021, was detected in April 2021. This study highlights three lineages as hallmarks of the SARS-CoV-2 outbreak in Iran; B4, dominating early periods of the epidemic, B.1.1.413 (B.1.1 with the combination of [D138Y-S477N-D614G] spike mutations) as a characterizing lineage in Iran, and the co-occurrence of [I100T-L699I] spike mutations in half of B.1.1.7 sequences mediating the fourth peak. It also designates the renowned combination of G and GR clades' mutations as the top recurrent mutations. CONCLUSION: In brief, we provided a real-time and comprehensive picture of the SARS-CoV-2 genetic diversity in Iran and shed light on the SARS-CoV-2 transmission and circulation on the regional scale.

SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions.

The SARS-CoV-2 virus has been rapidly spreading globally since December 2019, triggering a pandemic, soon after its emergence. While Iran was among the first countries confronted with rapid spread of virus in February 2020, no real-time SARS-CoV-2 whole-genome tracking in early phase of outbreak was performed in the country. To address this issue, we provided 50 whole-genome sequences of viral isolates ascertained from different geographical locations in Iran during March-July 2020. The corresponding analysis on origins, transmission dynamics and genetic diversity of SARS-CoV-2 virus, represented at least two introductions of the virus into the country, constructing two major clusters defined as B.4 and B.1*. The first entry of the virus might have occurred around very late 2019/early 2020, as suggested by the time to the most recent common ancestor, followed by a rapid community transmission that led to dominancy of B.4 lineage in early epidemic till the end of June. Gradually, reduction in dominancy of B.4 occurred possibly as a result of other entries of the virus, followed by surge of B.1* lineages, as of mid-May. Remarkably, variation tracking of the virus indicated the increase in frequency of D614G mutation, along with B.1* lineages, which showed continuity till October 2020. The increase in frequency of D614G mutation and B.1* lineages from mid-May onwards predicts a rapid viral transmission that may push the country into a critical health situation followed by a considerable change in composition of viral lineages circulating in the country.

The Seroprevalence of COVID-19 in Intravenous Drug Users in Comparison to Non-drug Users.

BACKGROUND COVID-19 infection has led to a worldwide pandemic, and new cases are on the rise. Intravenous drug users (IVDU) are presumably at a higher risk of being infected since they have poor personal hygiene, live in groups, and have risky behaviors. The current study aimed to evaluate the seroprevalence of COVID-19 in IVDU in comparison with non-drug users (N-DU). METHODS This cross-sectional study was conducted on 167 IVDU and 134 N-DU. A questionnaire gathering data on demographics, comorbidities, and use of personal protective equipment was administered to all participants. In addition, 5 cc of blood was taken from each individual to test for SARS-CoV-2 specific antibodies (Pishtaz Teb SARS-Cov-2 ELISA kits). RESULTS The mean age of N-DU and IVDU were 38.9 ± 12.9 and 40.38 ± 10.24 years, respectively. COVID-19 seroprevalence in IVDU was 9.7%, and 4.8% in N-DU, but this finding was not statistically significant (p = 0.096). CONCLUSION While the seroprevalence of COVID-19 was not significantly different among the two groups, IVDU should still be considered by policymakers as a high-risk group due to their lifestyle and risky behaviors. Providing personal protective equipment and other means of protection and treatment to this population can help mitigate the spread of and mortality from COVID-19.

The evaluation of novel oral vaccines based on self-amplifying RNA lipid nanparticles (saRNA LNPs), saRNA transfected Lactobacillus plantarum LNPs, and saRNA transfected Lactobacillus plantarum to neutralize SARS-CoV-2 variants alpha and delta.

The aim of this study was to present and evaluate novel oral vaccines, based on self-amplifying RNA lipid nanparticles (saRNA LNPs), saRNA transfected Lactobacillus plantarum LNPs, and saRNA transfected Lactobacillus plantarum, to neutralize severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants alpha and delta. After invitro evaluation of the oral vaccines on HEK293T/17 cells, we found that saRNA LNPs, saRNA transfected Lactobacillus plantarum LNPs, and saRNA transfected Lactobacillus plantarum could express S-protein at both mRNA and protein levels. In the next step, BALB/c mice were orally vaccinated with saRNA LNPs, saRNA transfected Lactobacillus plantarum LNPs, and saRNA transfected Lactobacillus plantarum at weeks 1 and 3. Importantly, a high titer of IgG and IgA was observed by all of them, sharply in week 6 (P < 0.05). In all study groups, their ratio of IgG2a/IgG1 was upper 1, indicating Th1-biased responses. Wild-type viral neutralization assay showed that the secreted antibodies in vaccinated mice and recovered COVID-19 patients could neutralize SARS-COV-2 variants alpha and delta. After oral administration of oral vaccines, biodistribution assay was done. It was found that all of them had the same biodistribution pattern. The highest concentration of S-protein was seen in the small intestine, followed by the large intestine and liver.

The relative expression of miR-31, miR-29, miR-126, and miR-17 and their mRNA targets in the serum of COVID-19 patients with different grades during hospitalization.

BACKGROUND: The aim of this study was to evaluate the expression of four up/down-regulated inflammatory miRNAs and their mRNA targets in the serum samples of COVID-19 patients with different grades. Also, we investigated the relative expression of these miRNAs and mRNAs during hospitalization. METHODS: In this cross-sectional study, 5 mL of blood sample were taken from COVID-19 patients with different grades and during hospitalization from several health centers of Yazd, Tehran, and Zahedan province of Iran from December 20, 2020 to March 2, 2021. The relative expression of miRNAs and mRNAs was evaluated by q-PCR. RESULTS: We found that the relative expression of hsa-miR-31-3p, hsa-miR-29a-3p, and hsa-miR-126-3p was significantly decreased and the relative expression of their mRNA targets (ZMYM5, COL5A3, and CAMSAP1) was significantly increased with the increase of disease grade. Conversely, the relative expression of hsa-miR-17-3p was significantly increased and its mRNA target (DICER1) was significantly decreased with the increase of disease grade. This pattern was exactly seen during hospitalization of COVID-19 patients who did not respond to treatment. In COVID-19 patients who responded to treatment, the expression of selected miRNAs and their mRNA targets returned to the normal level. A negative significant correlation was seen between (1) the expression of hsa-miR-31-3p and ZMYM5, (2) hsa-miR-29a-3p and COL5A3, (3) hsa-miR-126-3p and CAMSAP1, and (4) hsa-miR-17-3p and DICER1 in COVID-19 patients with any grade (P < 0.05) and during hospitalization. CONCLUSIONS: In this study, we gained a more accurate understanding of the expression of up/down-regulated inflammatory miRNAs in the blood of COVID-19 patients. The obtained data may help us in the diagnosis and prognosis of COVID-19. TRIAL REGISTRATION: The ethics committee of Zahedan University of Medical Sciences, Zahedan, Iran. (Ethical Code: IR.ZAUMS.REC.1399.316) was registered for this project.

Sources of news as a necessity for improving community health literacy about COVID-19.

Background: In the 21st century, the world has become a global village and a disease outbreak in one part of the world can spread rapidly to other countries far away. Methods: The emergence of the new Coronavirus (COVID-19) in China in January 2020 and its growing level of spread and severity between and within other countries as well as different continents has become a global emergency. Moreover, low health literacy results in more problems and continuation of the outbreak. Consequently, COVID-19 pandemic may produce new debates, discussions, and disturbing developments every day. In the meantime, cyberspace plays an important role in this case. Results: Improving people's health literacy can lead to increased potential of patients to make informed decisions, reduce health risks, increase disease prevention, and improve quality of life. Conclusion: The experience during COVID-19 pandemic has shown that health literacy plays an important role in preventing and controlling diseases and pandemic.

Socioeconomic - related inequalities in overweight and obesity: findings from the PERSIAN cohort study.

BACKGROUND: Overweight and obesity are major health concerns worldwide, with adverse health consequences during the life span. This study measured socioeconomic inequality in overweight and obesity among Iranian adults. METHODS: Data were extracted from 129,257 Iranian adults (aged 35 years and older) participated in the Prospective Epidemiologic Research Studies in IrAN (PERSIAN) in 14 provinces of Iran in 2014. Socioeconomic-related inequality in overweight and obesity was estimated using the Concentration Index (Cn). The Cn further decomposed to find factors explaining the variability within the Socioeconomic related inequality in overweight and obesity. RESULTS: Of the total number of participants, 1.98, 26.82, 40.76 and 30.43% had underweight, normal weight, overweight and obesity respectively. The age-and sex standardized prevalence of obesity was higher in females than males (39.85% vs 18.79%). People with high socioeconomic status (SES) had a 39 and 15% higher chance of being overweight and obese than low SES people, respectively. The positive value of Cn suggested a higher concentration of overweight (0.081, 95% confidence interval [CI]; 0.074-0.087) and obesity (0.027, 95% CI; 0.021-0.034) among groups with high SES. There was a wide variation in socioeconomic-related inequality in overweight and obesity rate across 14 provinces. The decomposition results suggested that SES factor itself explained 66.77 and 89.07% of the observed socioeconomic inequalities in overweight and obesity among Iranian adults respectively. Following SES, province of residence, physical activity, using hookah and smoking were the major contributors to the concentration of overweight and obesity among the rich. CONCLUSIONS: Overall, we found that overweight and obesity is concentrated among high SES people in the study population. . Accordingly, it seems that intersectional actions should be taken to control and prevent overweight and obesity among higher socioeconomic groups.

Diagnosis of acute toxoplasmosis by IgG avidity method in pregnant women referred to health centers in south-eastern Iran.

Toxoplasmosis, one of the most common parasitic infections, can cause abortions in human. The purpose of this study was to determine seroprevalence of toxoplasmosis and acute form of toxoplasmosis in pregnant women. 208 pregnant women who referred to health centers in south-eastern Iran were taken under study after signing the informed consent forms and filling out the checklists. For those with high levels of IgG or IgM antibody titers, IgG Avidity test was performed to determine the acute infection. High level of IgG anti-body were found in sera of 81 pregnant women and 7 persons had borderline titer. IgM antibody results were positive in 33 and borderline in 4 cases. Then, the samples with positive and borderline results for IgM and IgG were evaluated by IgG avidity test. In this study, approximately 60% of pregnant women were not immune to risks posed by Toxoplasma gondii. Therefore, this group are at risk of acquiring primary infection of toxoplasmosis during gestation.

Sexually Transmitted Infections Among Hospitalized Patients With Human Immunodeficiency Virus Infection and Acquired Immune Deficiency Syndrome (HIV/AIDS) in Zahedan, Southeastern Iran.

BACKGROUND: Studies show that nearly 40 million people are living with human immunodeficiency virus infection and acquired immune deficiency syndrome (HIV/AIDS) around the world and since the beginning of the epidemic, about 35 million have died from AIDS. Heterosexual intercourse is the most common route for transmission of HIV infection (85%). People with a sexually transmitted infection (STI), such as syphilis, genital herpes, chancroid, or bacterial vaginosis, are more likely to obtain HIV infection during sex. On the other hand, a patient with HIV can acquire other infections such as hepatitis C virus (HCV) and hepatitis B virus (HBV) and also STIs. Co-infections and co-morbidities can affect the treatment route of patients with HIV/AIDs. Sometimes, physicians should treat these infections before treating the HIV infection. Therefore, it is important to identify co-infection or comorbidity in patients with HIV/AIDS. OBJECTIVES: This study was conducted in order to understand the prevalence of HIV/AIDS/STI co-infection. PATIENTS AND METHODS: In this cross-sectional study, we evaluated all HIV/AIDS patients who were admitted to the infectious wards of Boo-Ali hospital (Southeastern Iran) between March 2000 and January 2015. All HIV/AIDS patients were studied for sexually transmitted infections (STI) such as syphilis, gonorrhea, hepatitis B virus (HBV) and genital herpes. A questionnaire including data on age, sex, job, history of vaccination against HBV, hepatitis B surface antigen (HBsAg), hepatitis B core antibody (anti-HBc), hepatitis B surface antigen (anti-HBs), HCV-Ab, venereal disease research laboratory (VDRL) test, fluorescent treponemal antibody absorption (FTA-Abs) test, and urine culture was designed. Data was analyzed by the Chi square test and P values of < 0.05 were considered significant. RESULTS: Among the 41 patients with HIV/AIDS (11 females and 30 males; with age range of 18 to 69 years) five cases (12.1%) had a positive test (1:8 or more) for VDRL. The FTA-Abs was positive for all patients who were positive for VDRL. Gonorrhea was found in seven patients (17%) and three cases had genital herpes in clinical examinations. All patients who had positive test results for these STIs were male. Eleven patients (26.8%) had HBV infection (three females and eight males). hepatitis C virus (HCV) was found in 13 cases (31%). Eighty percent of patients were unemployed. Seventy-eight percent of patients with HIV/STI were aged between 18 and 38 years. There was a significant difference between sex and becoming infected with HIV and also STI (P < 0.05). CONCLUSIONS: Patients with HIV/AIDS are more likely to acquire other STIs, because the same behaviors that increase the risk of becoming HIV infected can also increase the risk of acquiring STIs. Having a sore on the skin due to an STI can make the transmission of HIV to the sex partner more likely than people who don't have such sore in their genital area.