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.

Background: Homeless people are prone to sexually transmitted and blood-borne infectious diseases such as hepatitis B, hepatitis C, and HIV due to their risky behaviors and low awareness of various diseases. Objectives: Thus, the present research aimed to examine the epidemiologic patterns of HBV, HCV, HIV, and related factors among the homeless population of Zahedan in 2019. Methods: A cross-sectional study was conducted on a total of 329 homeless people. Eligible people were selected using a convenience sampling method from homeless individuals residing in care centers affiliated with the Welfare Organization and the Health Deputy of Zahedan University of Medical Sciences. Data on the demographic and behavioral characteristics of the cases were collected through a structured questionnaire completed in face-to-face interviews. A 10 cc blood sample was taken from each of the cases for serological tests of hepatitis B, hepatitis C, and HIV. The test results and collected data were entered in SPSS16 software. Logistic regression analysis and chi-square tests were used to analyze the data. Results: The majority of the cases (84%) were males, and 59% were in the age-group of 35 - 50 years. Of the subjects, 93% had a history of drug abuse, 74% reported a history of smoking, and 45% had tattoos. The prevalence of hepatitis C, hepatitis B, and HIV was 13%, 2.7%, and 0.3%, respectively (only one case of HIV was identified). In a multi-variate model, imprisonment history [OR = 2.32 (1.08 - 4.98)], history of sexual abuse [OR = 3.73 (1.36 - 10.26)], being widowed or divorced [OR = 2.83, (1.21 - 6.64)], and history of injection with shared needles and syringes [OR = 5.11 (1.97 - 13.28)] remained the predicting factors of hepatitis C. Conclusions: Based on the obtained results of the study, homeless people are more prone to infections with HCV, HBV, and HIV due to their risky behaviors. Therefore, a need is highlighted for preventive interventions and developing the level of health literacy in this group regarding behaviors contributing to the aforementioned infections.

No abstract

Background: Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne disease caused by arbovirus which can be transmitted to human by several routes. Tick bite and living in a rural area have been the most common factors for inception of CCHF in adults and children in studies reported from Iran. Objectives: This study was conducted to detect the disease acquisition routes among children with confirmed CCHF in southeastern Iran. Patients and Methods:We evaluated all the files of patients with confirmed CCHF who were younger than 19 years old and were admitted to university hospitals (Zahedan, Southeastern Iran) during January 2000-January 2014. Results: Among 41 children and adolescents with CCHF (35 males and six females with age range of 5-19 years), animal contacts (23%) and living in endemic area (19%) were the most common factors for acquisition of the disease. Conclusions: Children and adolescents can acquire CCHF through the same routes that adults can be infected; but, in children tick bite is an uncommon way.

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.