Comparative Analysis and Identification of Spike Mutations in Iranian COVID-19 Samples from the First Three Waves of Disease.

Background: The spike surface glycoprotein of SARS-CoV-2 is the essential protein in virus attachment to the target cell and cell entrance. As this protein contains immunodominant epitopes and is the main target for immune recognition, it is the critical target for vaccine and therapeutics development. In the current research, we analyzed the variability and mutations of the spike glycoprotein isolated from 72 COVID-19-positive patients from Iran's first three waves of disease. Materials and Methods: The RNA was extracted from nasopharyngeal samples of confirmed COVID-19 cases and served as a template for cDNA synthesis and reverse transcriptase polymerase chain reaction. The reverse transcriptase polymerase chain reaction products of each sample were assembled and sequenced. Results: After analysis of 72 sequences, we obtained 46 single nucleotide polymorphisms, including 23 that produce amino acid changes. Our analysis showed that the most frequent mutation was the D614G (in the samples of the second and third waves). Conclusions: Our findings suggest that developing effective vaccines requires identifying the predominant variants of SARS-CoV-2 in each community.

Isfahan COvid-19 REgistry (I-CORE): Design and methodology.

Health authorities usually exploit after-action reports to collect data on their experience in responding to public health emergencies. To develop an effective approach to manage and learning from health emergencies, we have launched Isfahan COvid-19 REgistry for data collection during routine clinical care as a first "critical incident registry" in Iran. Registries can be employed to explain the natural history of the disease, learn about a particular disease in terms of patient outcomes, the cost-effectiveness of clinical management, monitoring the quality of health-care service, and developing research hypotheses.

Colonization with hospital flora and its associated risk factors in neonates hospitalized in neonatal ward of a teaching center in Isfahan, Iran.

BACKGROUND: Due to the high incidence and prevalence of infection in neonatal ward, especially Neonatal Intensive Care Units (NICUs) reported by different studies and the important role of colonization with hospital germs in the development of nosocomial infections, we intended to evaluate the risk of colonization with hospital germs in neonates and its associated risk factors. MATERIALS AND METHODS: This cross-sectional, descriptive-analytical study was conducted in 2016 in a Teaching Center in Iran. In total, 51 neonates were selected based on the inclusion criteria, and after recording their information in a checklist, samples were taken by swab from outer ear, axilla, and groin for culture. Neonates with negative culture from mentioned regions were enrolled in the study. The swab samples again were taken and sent for culture from mentioned regions in at least 3 days after hospitalization. Culture results from first and second sampling were collected and analyzed statistically. RESULTS: This study was conducted on 51 neonates. The mean gestational age among the neonates ranged from 35.25 (Week) ± 2.98. 22 girls (43.1%) and 29 boys (56.9%), most of them were born by cesarean. Based on the results of logistic regression, a significant association was found between the occurrence of colonization of hospital flora and the place hospitalization of the newborns (odds ratio (OR): 4.750; 95% confidence interval (CI): 1.26-17.85). CONCLUSION: This study revealed that the only risk factors of colonization with hospital flora in neonates are the type of delivery and place of hospitalization. Based on findings of the study, it is recommended to focus on efforts in increasing the rate of natural birth as well as improving conditions of infection control in NICUs to reduce the number of incidences of colonization with hospital flora in neonates.

The Immune Response of Vaccination Against Hepatitis B virus in Iranian Patients Undergoing Chemotherapy.

INTRODUCTION: Hepatitis B virus (HBV) infection and its complications are major public health problems. As it is hard to treat and control the chronic state, control of disease depends on the prevention especially by vaccination. There is an impaired immune response to vaccinations including HBV in patients with some malignancies. The aim of this study is to assess the response rate of patients undergoing chemotherapy to HBV vaccination. MATERIALS AND METHODS: All patients from two hematology/oncology clinics in Isfahan, Iran with the history of at least 1 month chemotherapy who had the inclusion criteria were enrolled in a case control study. Also a sex- and age-matched control group from healthy population was selected. They were vaccinated in a schedule of 0, 1, and 6 months and were examined for antibody titers 1 month after the last dose. The titers more than 10 mIU/ml were determined as positive response to vaccination. RESULTS: In this study, 50 patients and 50 healthy subjects were enrolled. The two groups were age and sex matched (P > 0.05). Frequency of negative responses to HBV vaccination in case and control groups were 9 (18%) and 1 (2%), respectively (OR = 10.75, CI = 1.30-88.47, P = 0.027). Of 50 patients, 54%, 12%, 22%, and 12% had breast cancer, lymphoma, gastrointestinal, and genitourinary cancers, respectively, and frequency of negative responses were 3 (11%), 1 (16%), 4 (36.4%), and 1 (16%), respectively (P = 0.167). CONCLUSION: According to our results, malignancy and chemotherapy will have an important effect on the immune system and cause negative response to HBV vaccination. Our results revealed the importance of passive immunity and screening for HBV infection in patients undergoing chemotherapy. Also more studies for better vaccination schedules in this group of patients are recommended.

Antibiotic resistance pattern and evaluation of metallo-beta lactamase genes (VIM and IMP) in Pseudomonas aeruginosa strains producing MBL enzyme, isolated from patients with secondary immunodeficiency.

BACKGROUND: One of the most common causes of hospital-acquired secondary infections in hospitalized patients is Pseudomonas aeruginosa. The aim of this study is to evaluate the expression of IMP and VIM in Pseudomonas aeruginosa strains (carbapenem resistant and producer MBL enzyme) in patients with secondary immunodeficiency. MATERIALS AND METHODS: In a cross sectional study, 96 patients with secondary immunodeficiency hospitalized in the Al-Zahra hospital were selected. Carbapenem resistant strains isolated and modified Hodge test was performed in order to confirm the presence of the metallo carbapenemase enzyme. Under the standard conditions they were sent to the central laboratory for investigating nosocomial infection Multiplex PCR. RESULTS: Of 96 samples 28.1% were IMP positive, 5.2% VIM positive and 3.1% both VIM and IMP positive. The prevalence of multidrug resistance in the IMP and/or VIM negative samples was 29%, while all 5 VIM positive samples have had multidrug resistance. Also the prevalence of multi-drug resistance in IMP positive samples were 96.3% and in IMP and VIM positive samples were 100%. According to Fisher's test, the prevalence of multi-drug resistance based on gene expression has significant difference (P < 0.001). CONCLUSION: Based on the results of this study it can be concluded that, a significant percentage of patients with secondary immunodeficiency that suffer nosocomial infections with multidrug resistance, especially Pseudomonas aeruginosa, are probably MBL-producing gene positive. Therefore the cause of infection should be considered in the hospital care system to identify their features, the presence of genes involved in the development of multi-drug resistance and antibiotic therapy.

Serological evaluation of Crimean-Congo hemorrhagic fever in humans with high-risk professions living in enzootic regions of Isfahan province of Iran and genetic analysis of circulating strains.

Crimean-Congo hemorrhagic fever (CCHF) is a zoonotic viral disease that is asymptomatic in infected livestock, but causes a serious threat to humans with a mortality rate up to 50%. Although the CCHF virus (CCHFV) is often transmitted by ticks, livestock-to-human and human-to-human transmission also occurs. In the current study, we focused on CCHF in the province of Isfahan, located in the center of Iran and deemed to be the second most infected province. Human and livestock sera and resident ticks in the livestock are collected from different regions of the province and analyzed with specific IgG ELISA and RT-PCR tests. Overall, 12% and 12.7% of studied human and livestock populations were IgG positive, respectively. The genome of CCHFV was detected in 9% of ticks resident in livestock involved in this survey. The CCHFV isolates from infected ticks were genetically examined. Nucleotide sequence of the S-segment revealed that the different isolates were closely related to each other, with nucleotide sequence identities higher than 98%. Phylogenetic analysis demonstrated that a variant isolate clustered with the Iraq strain. This high proportion of IgG-positive sera and nearly high proportion of infected ticks increases the risk of CCHF outbreaks in the province and probably posits a great danger to other provinces.

First report on isolation and molecular characterization of clinical Mycobacterium setense isolates in Asia.

We herein present the third set of documented clinical Mycobacterium setense cases. Three clinically unrelated isolates were identified and characterized using various key conventional and molecular diagnostic tests. Phenotypic and molecular data analysis, particularly 16S rDNA, hsp65, and rpoB sequencing, provided evidence of M. setense involvement in clinical infections in Iranian patients. Our findings may shed light on the capability of this rare Mycobacterium sp. to cause infection in both healthy and immunocompromised patients.