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Background: The disease process involves the occurrences happening during the disease and treatment course for the patient. Investigating this process is a significant and necessary issue for all diseases, including coronavirus disease 2019 (COVID-19). Materials and Methods: Using the information of 4372 patients with COVID-19 referring to Dr. Masih Daneshvari Hospital in Tehran during the COVID-19 epidemic, being hospitalized, cared for, and home quarantined due to having mild symptoms, the COVID-19 process and its related occurrences were investigated during the treatment course. Results: In the COVID-19 course, considering the disease severity, the likelihood of hospitalization in the general ward or the intensive care unit (ICU) ward, the likelihood of isolation or home quarantine, and the likelihood of occurrences such as recovery or death at the end of the disease course were taken into consideration. Based on the results of this study, the likelihood of hospitalization in the general ward, the ICU ward, and isolation or home quarantine was determined to be approximately 49.54%, 14.73%, and 35.73%, respectively. Also, for patients hospitalized in the general ward, the ICU ward, and isolated or home quarantined, the likelihood of recovery was estimated at approximately 64.79%, 10.82%, and 96.31%, respectively, and the likelihood of death was also estimated at about 35.21%, 89.18%, and 3.69% respectively. Conclusion: Investigating the COVID-19 process and estimating the likelihood of incidence of its related occurrences during the treatment course both create an accurate prognosis and provide the possibility of achieving an efficient treatment for these patients. [ABSTRACT FROM AUTHOR]

Background: We aimed to evaluate the accuracy of genotyping of Leishmania species by the spliced leader mini-exon gene. Methods: Suspected leishmaniasis patients, referred to Masieh Daneshvary Hospital, Tehran, Iran were included from May 2017 to September 2021. The Leishmania species were genotyped by PCRRFLP based on the SL mini-exon gene and the ITS1 region of SSU-rRNA gene and compared with the sequencing results. The expressed metabolites of metacyclic promastigotes were evaluated by Proton nuclear magnetic resonance (1H-NMR). Results: Out of 66 suspected cases, 36 (54.4%) were positive for Leishmania species based on the PCR assays. In 21 (31.8%) cases, promastigotes grew on culture tubes. Based on the RFLP of SL RNA profile, 13 (19.7%) L. tropica, 9 (13.6%) L. major, 3 (4.5%) L. infantum, and 8 (12.1%) C. fasciculata isolates, isolated from culture media, were identified; however, 3 (4.5%) cases were unidentifiable due to the low number of parasites. Seventeen metabolites were expressed by the metacyclic forms of L. major, L. tropica and C. fasciculata isolates. The top differential metabolites expressed more in C. fasciculata were FAD, p-Methoxybenzyl alcohol and S-b-G-5, 5-G-b-S (A = CH2) (P<0.005) whereas Veratryl glycerols and D-(+)-Mannose were significantly increased in L. major and Betulin, LTyrosine in L. tropica (P<0.01). Conclusion: The invaluable techniques such as sequencing and 1H-NMR confirmed the results of genotyping of Leishmania species based on the SL mini-exon gene. SL mini exon gene can be used as a diagnostic tool to differentiate various Leishmania genotypes and detect contamination of culture media with C. fasciculata. [ABSTRACT FROM AUTHOR]

Introduction: Cytokine storm and critical COVID-19 pneumonia are caused in at least 10% of patients by inborn errors of or auto-Abs to type I IFNs. The pathogenesis of life-threatening COVID-19 pneumonia in other patients remains unknown. Methods: This study was conducted at Masih Daneshvari Hospital, Tehran, Iran. In the period of study, 75 confirmed cases of COVID-19 with presentations ranging from mild upper respiratory tract infection to lower respiratory tract infection, including moderate, severe, and critical disease, were recruited. Expression of STING mRNA was measured in peripheral blood mononuclear cells (PBMCs) and compared between patients with different severity and outcome. Results: There was a significant negative correlation between age and STING expression level (p value = 0.010). Patients with "severe to critical" illness had a 20-fold lower STING expression level compared to the "mild to moderate" group (p value = 0.001). Also, the results showed lower expressions of STING in the patients admitted to the ICU (p value = 0.015). Patients who finally died had lower expression of STING at the time of sampling (p value = 0.041). Conclusion: STING mRNA expression in PBMCs was significantly lower in older COVID-19 cases, the patients with more severe illness, who needed intensive care, and who eventually died. [ABSTRACT FROM AUTHOR]

Background: In December 2019, in Wuhan, China, coronavirus disease 2019 (COVID-19) was emerged due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). It seems that children and neonates, similar to adult and elderly individuals, are at risk of SARS-CoV-2 infection. However, adequate data are not available about neonates infected with SARS-CoV-2.Methods: This study evaluated the presence of SARS-CoV-2 infection in neonates born to mothers or relatives with COVID-19. This cross-sectional study was performed on 25,044 consecutive Iranian participants in Tehran, Iran, from January 2020 to August 2020. Viral ribonucleic acid (RNA) was extracted from 500 µl of the oropharyngeal and nasopharyngeal specimens of the participants. The genomic RNA of SARS-CoV-2 was detected by real-time polymerase chain reaction (PCR) assay.Results: Out of all participants, 98 (0.40%) cases were neonates born to mothers or relatives with SARS-CoV-2 infection. Therefore, the current study was performed on these neonates. Out of 98 studied neonates, 6 (6.1%) cases had positive PCR results for SARS-CoV-2 infection. Moreover, among 98 studied neonates' mothers, 25 (25.5%) cases had positive PCR results for SARS-CoV-2 infection.Conclusion: The findings of this study demonstrated that the rate of COVID-19 in neonates born to mothers or relatives with SARS-CoV-2 infection in the Iranian population is about 6.1%. [ABSTRACT FROM AUTHOR]

Background: Post-vaccination BCG disease typically attests to underlying inborn errors of immunity (IEIs), with the highest rates of complications in patients with Mendelian susceptibility to mycobacterial disease (MSMD). However, therapeutic protocols for the management of BCG-osis (disseminated) and persistent BCG-itis (localized) are still controversial. Methods: Twenty-four Iranian patients with MSMD (BCG-osis or BCG-itis), followed from 2009 to 2020 in Tehran, were included in the study. Their medical records were retrospectively reviewed for demographics, clinical features, laboratory findings, and molecular diagnosis. The therapeutic protocol sheets were prepared to contain the types and duration of anti-mycobacterial agents. Results: BCG disease either as BCG-itis (33.3%) or BCG-osis (66.7%) was confirmed in all patients by positive gastric washing test (54.2%), microbial smear and culture (58.3%), or purified protein derivative (PPD) test (4.2%). The duration between BCG-osis onset and MSMD diagnosis was 21.6 months. All except three patients were initiated on second-line anti-mycobacterial agents with either a fluoroquinolone (levofloxacin: 15 mg/kg/day, ciprofloxacin: 20 mg/kg/day, ofloxacin: 15 mg/kg/day), aminoglycoside (amikacin: 10–15 mg/kg/day, streptomycin: 15 mg/kg/day), and/or macrolide (clarithromycin: 15 mg/kg/day) along with oral rifampin (10 mg/kg/day), isoniazid (15 mg/kg/day), and ethambutol (20 mg/kg/day). Three patients showed a clinical response to rifampin, despite in vitro resistance. Fourteen (58.3%) patients received also adjuvant subcutaneous IFN-γ therapy, 50 µ/m2 every other day. At the end of survey, most patients (n = 22, 91.7%) were alive and two patients died following BCG-osis and respiratory failure. Conclusions: We recommend the early instigation of second-line anti-mycobacterial agents in MSMD patients with BCG disease. [ABSTRACT FROM AUTHOR]

Coronavirus disease-19 (COVID-19) pandemic, caused by SARS-CoV-2, has gradually spread worldwide, becoming a major public health event. This situation requires designing a novel antiviral agent against the SARS-CoV-2; however, this is time-consuming and the use of repurposed medicines may be promising. One such medicine is favipiravir, primarily introduced as an anti-influenza agent in east world. The aim of this study was to evaluate the efficacy and safety of favipiravir in comparison with lopinavir-ritonavir in SARS-CoV-2 infection. In this randomized clinical trial, 62 patients were recruited. These patients had bilateral pulmonary infiltration with peripheral oxygen saturation lower than 93%. The median time from symptoms onset to intervention initiation was seven days. Favipiravir was not available in the Iranian pharmaceutical market, and it was decided to formulate it at the research laboratory of School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran. The patients received favipiravir tablet at a dose of 1600 mg orally twice a day for day one and then 600 mg orally twice a day for days 2 to 6. In the second group, the patients received lopinavir-ritonavir combination tablet at a dose of 200/50 mg twice a day for seven days. Fever, cough, and dyspnea were improved significantly in favipiravir group in comparison with lopinavir-ritonavir group on days four and five. Mortality rate and ICU stay in both groups were similar, and there was no significant difference in this regard (P = 0.463 and P = 0.286, respectively). Chest X-ray improvement also was not significantly different between the two groups. Adverse drug reactions occurred in both groups, and impaired liver enzymes were the most frequent adverse effect. In conclusion, early administration of oral favipiravir may reduce the duration of clinical signs and symptoms in patients with COVID-19 and hospitalization period. The mortality rate also should be investigated in future clinical trials. [ABSTRACT FROM AUTHOR]

Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spread widely all around the world and has infected too many healthcare workers (HCWs) as the pioneers combating coronavirus disease 2019 (COVID- 19). This study aims to evaluate the symptoms and outcome of medical staff from a tertiary hospital in Tehran, Iran. Materials and Methods: The diagnoses of 29 HCWs presenting COVID-19 symptoms were confirmed by molecular and imaging studies. Epidemiologic and disease-related data were collected via phone calls and filling a questionnaire and then analyzed descriptively. Results: Eighteen (62.1%) of the affected HCWs were males. The mean age of them was 41.86 years with a lower average (38.27) for females than males. Nurses comprised 41.4% of our population. Only 2 (6.9%) patients were admitted to the respiratory care unit (RCU) (), marked as critical patients. The most presented symptoms were fever (79.3%) and dyspnea (79.3%). Overall, 55.2% of them had a longer exposure time (more than a week), which was more frequent in men than women. Conclusion: Fever was the most prevalent symptom among the study group. Even though the clinical features of COVID-19 among HCWs cannot be copiously determined by this study, it highlights the requirement for comparative studies to illustrate differences among HCWs and the general population. There might be an association between the duration of the exposure and the risk of the infection in men. [ABSTRACT FROM AUTHOR]

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19) has infected over 112M patients and resulted in almost 2.5M deaths worldwide. The major clinical feature of severe COVID-19 patients requiring ventilation is acute respiratory distress syndrome (ARDS) possibly associated with a cytokine storm. Objectives: To elucidate serum levels of TNF-α and soluble TNF-Receptor 1 (sTNFR1) in patients with severe and mild COVID-19 disease as determinants of disease severity. Methods: We determined serum TNF-α and sTNFR1 concentrations in 46 patients with laboratory-confirmed COVID-19 (17 patients with severe disease within the intensive care unit [ICU] and 29 non-severe, non-ICU patients) and 15 healthy controls upon admission using ELISA. Subjects were recruited between March-May 2020 at the Masih Daneshvari Hospital Tehran, Iran. Results: Serum levels of sTNFRI were significantly higher in ICU patients (P<0.0001) and non-ICU patients (P=0.0342) compared with healthy subjects. Serum sTNFR1 were significantly higher in ICU patients than in non-ICU patients (P<0.0001). Serum TNF-α levels were greater in ICU and non-ICU patients than in the healthy subjects group (p<0.0001). The sTNFRI concentration in ICU (r=0.79, p=0.0002) and non-ICU (r=0.42, p=0.02) patients positively correlated with age although serum sTNFRI levels in ICU patients were significantly higher than in older healthy subjects. The sTNFRI concentration in ICU patients negatively correlated with ESR. Conclusions: The study demonstrates higher sTNFRI in ICU patients with severe COVID-19 disease and this be a biomarker of disease severity and mortality. Future studies should examine whether lower levels of systemic sTNFR1 at admission may indicate a better disease outcome. [ABSTRACT FROM AUTHOR]

Background: Following the recent epidemic of coronavirus disease 2019 (COVID-19) in Wuhan, China, a novel betacoronavirus was isolated from two patients in Iran on February 19, 2020. In this study, we aimed to determine the clinical manifestations and outcomes of the first confirmed cases of COVID-19 infection (n=127). Materials and Methods: This prospective study was conducted on all COVID- 19-suspected cases, admitted to Masih Daneshvari Hospital (a designated hospital for COVID-19), Tehran, Iran, since February 19, 2020. All patients were tested for COVID-19, using reverse transcription-polymerase chain reaction (RT-PCR) assay. Data of confirmed cases, including demographic characteristics, clinical features, and outcomes, were collected and compared between three groups of patients, requiring different types of admission (requiring ICU admission, admission to the general ward, and transfer to ICU). Results: Of 412 suspected cases, with the mean age of 54.1 years (SD=13.4), 127 (31%) were positive for COVID-19. Following the patients' first visit to the clinic, 115 cases were admitted to the general ward, while ten patients required ICU admission. Due to clinical deterioration in the condition of 25 patients (out of 115 patients), ICU admission was essential. Based on the results, the baseline characteristics of the groups were similar. Patients requiring ICU admission were more likely to have multiorgan involvement (liver involvement, P<0.001; renal involvement, P<0.001; and cardiac involvement, P=0.02), low O2 saturation (P<0.001), and lymphopenia (P=0.05). During hospital admission, 21 (16.5%) patients died, while the rest (83.5%) were discharged and followed-up until March 26, 2020. Also, the survival rate of patients, who received immunoglobulin, was higher than other patients (60.87% vs. 39.13%). Conclusion: The mortality rate of COVID-19 patients was considerable in our study. Based on the present results, this infection can cause multiorgan damage. Therefore, intensive monitoring of these patients needs to be considered. [ABSTRACT FROM AUTHOR]

Background: Infection with Human Immune deficiency Virus (HIV) is a growing problem in developing countries. Among HIV infected cases, respiratory complications are common, dissimilar in different setting and their diagnosis is challenging. The aim of this study was to determine the spectrum of infectious and non-infectious pulmonary complications among HIV infected patients. Materials and Methods: The retrospective study was done among 710 HIV infected patients admitted in Masih Daneshvari Hospital, National Research Institute of Tuberculosis and Lung Diseases, Tehran, Iran from January 2003 to March 2017. Demographic, clinical, radiologic and laboratory data of 836 episodes of pulmonary complications were reviewed and final diagnosis were extracted. Results: Mean of CD4 cell count was 90±131 x106 cells/L. Definite etiology was found for 653 episodes (78.1%) of pulmonary complications. Infectious respiratory diseases were clearly more common than non-infectious etiologies, 86.1 and 7.6%, respectively. Pulmonary tuberculosis, as the leading cause, involved 542 cases (64.8%) and Pneumocystis jiroveci (P. jiroveci) was the second infectious agent that was found in 111 cases (13.2%). Among non- infectious causes, bronchiectasis and Chronic Obstructive Pulmonary Disease (COPD) exacerbation were on the top of the list, 21 of 64 (32.8%) and 18 0f 64 (28.1%), respectively. Many patients had more than one etiology. P. jiroveci had the highest tendency for dual infections (43 episodes). Conclusion: Pulmonary complications, especially infections are common among HIV cases in Iran, among them tuberculosis is the most common. Respiratory problems may be the first presentation of HIV infection. Clinicians should be aware about the risk of dual infections. Screening for HIV among all tuberculosis cases and vice versa is recommend. [ABSTRACT FROM AUTHOR]

The nature of tuberculosis (TB), being one of the most common opportunistic infections, is different among HIV-infected patients than HIV-negative patients. A retrospective study was conducted on HIV-positive and HIV-negative patients with new TB pleural effusion who were admitted to the National Research Institute of Tuberculosis and Lung Diseases in Tehran, Iran from 2005 to 2012. The two groups were compared with respect to clinical, imaging, mycobacteriologic and histopathologic characteristics of TB pleural effusion. In all, 42 HIV-positive and 132 HIV-negative cases of TB pleural effusion were included. Bilateral pleural effusion was statistically more common in the HIV-positive group (p = 0.004, OR = 3.81, 95% CI: 1.46-9.94) without any correlation with CD4 cell count. Pulmonary infiltration was found in 81% of HIV-positive and 49.2% of HIV-negative patients (p = 0.001, OR = 4.38, 95% CI: 1.88-10.1). Mycobacteriologic studies led to the diagnosis of TB in 66.6% of HIV-infected and 49.2% of HIV-negative patients. In 23.8% of HIV-positive and 50.7% of HIV-negative patients TB was ultimately diagnosed by pleural biopsy. HIV remained significantly associated with positive culture of pleural fluid in multivariate analysis. The diagnostic approach to TB pleural effusion in HIV-infected patients may be different. The diagnostic yield of mycobacteriologic studies was higher among HIV-positive patients, which may help in reducing the need for invasive procedures like pleural biopsy. [ABSTRACT FROM AUTHOR]

In healthcare settings, contamination of environment with toxigenic and hypervirulent Clostridioides difficile strains is a serious concern. Here, we assessed whether patients with C. difficile have a role to play in the dissemination of C. difficile in our settings or other sources are implicated in its circulation. A total of 700 fecal specimens and 1435 environmental samples from surfaces, equipment and air of rooms occupied by patients suspected of C. difficile infection were taken from 4 tertiary hospitals in Tehran, Iran between April 2016 and August 2017. Antibiotic susceptibility testing and detection of resistance genes were performed for the environmental isolates. The clinical and environmental isolates of C. difficile were subjected to Pulsed Field Gel Electrophoresis (PFGE) analysis. Forty three (6.14%) and 2 (0.13%) isolates of C. difficile were recovered from the clinical and environmental samples, respectively. In the clinical settings, 2 patients were suspected of recurrent C. difficile infection. Thirty distinct pulsotypes were found among the C. difficile isolates including 28 singletons and 2 common types. One of the two environmental isolates was isolated from floor in the Medical ward, of pulsotype/ribotype/toxinotype PT10/New ribotype/toxinotype V, harbored cdtA / B and tcdC-A , and resistant to ciprofloxacin. The other one was isolated from air of a room in ICU, assigned to PT11/RT001/toxinotype 0, belonged to tcdC-sc3 genotypes and resistant to metronidazole. The environmental isolates did not generate amplicons in PCR assays targeting vanA and nim genes. This study provided evidence for dissemination of genetically diverse strains of C. difficile in hospitalized patients, presence of C. difficile in hospital air, existence of binary toxin positive/antibiotic-resistant isolate on the floor and intra-hospital dissemination of this pathogen. • Dissemination of genetically diverse strains of C. difficile in hospitalized patients. • Presence of C. difficile in hospital air. • Existence of an antibiotic-resistant isolate of C. difficile on the floor. • Intra-hospital dissemination of C. difficile. [ABSTRACT FROM AUTHOR]

Since the outbreak of the novel coronavirus disease-2019 (COVID-19) in December 2019, limited studies have investigated the histopathologic findings of patients infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This study was conducted on 31 deceased patients who were hospitalized for COVID-19 in a tertiary hospital in Tehran, Iran. A total of 52 postmortem tissue biopsy samples were obtained from the lungs and liver of decedents. Clinical characteristics, laboratory data, and microscopic features were evaluated. Reverse transcription polymerase chain reaction (RT-PCR) assay for SARS-CoV-2 was performed on specimens obtained from nasopharyngeal swabs and tissue biopsies. The median age of deceased patients was 66 years (range, 30–87 years) and 25 decedents (81 %) were male. The average interval from symptom onset to death was 13 days (range, 6–34 days). On histopathologic examination of the lung specimens, diffuse alveolar damage and thrombotic microangiopathy were the most common findings (80 % and 60 %, respectively). Liver specimens mainly showed macrovesicular steatosis, portal lymphoplasmacytic inflammation and passive congestion. No definitive viral inclusions were observed in any of the specimens. In addition, 92 % of lung tissue samples tested positive for SARS-CoV-2 by RT-PCR. Further studies are needed to investigate whether SARS-CoV-2 causes direct cytopathic changes in various organs of the human body. [ABSTRACT FROM AUTHOR]