SARS-CoV-2 in patient with protein C deficiency: A case report.

In SARS-CoV-2 pandemic different disorders in coagulation pathways in COVID-19 patients were reported. We described a 44-year-old female with COVID-19 and protein C deficiency history. She did not show any coagulation disorder during her disease course. Complete genome sequencing of SARS-CoV-2 was performed and some mutations identified and compared with Wuhan strain. Besides hospitalized patients, in COVID-19 outpatients with low concentration of protein C, early prescription of an anticoagulant such as heparin could be helpful in prevention of venous thromboembolism or pulmonary embolism.

Genetic Characterization of the H Gene of MeV Strains (H1, B3, and D4) Recently Circulated in Iran for Improving the Molecular Measles Surveillance in the National Measles Lab.

Background: Despite decreasing the global burden of measles disease after the introduction of vaccination, measles remains one of the most devastating childhood diseases. Since genotype B3 is reported as a predominant Measles Virus (MeV) genotype recently, the current study aimed to better understand MeV genetic variation by analyzing the complete sequence of Hemagglutinin (H) gene associated with outbreaks of circulated genotypes in Iran. Methods: Nine positive measles specimens were selected from three circulated different genotypes H1, B3, and D4. Two different regions of MeV RNA were detected by RT-PCR assay. Sequence data and phylogenetic trees were analyzed and constructed by MEGA X software program. Moreover, missense and silent mutations in critical positions of the MeV-H protein were investigated. Results: The result of phylogenetic analysis from the C-terminus of the Nucleoprotein gene (NP-450) and the complete H gene revealed that the mean sequence diversity was 0.06%-0.08% and 0.04%, respectively. Genotype H1 had the highest mutation in this study; however, the substitutions in genotype B3 fundamentally occurred in critical epitopes. Moreover, genotype D4 was more stable than genotypes B3 and H1. Conclusion: Mutations were investigated in the whole sequence of H protein. Moreover, the mutations that occur in the critical sites of the protein have an important effect on the pathogenicity of the virus. In this way, we were able to illustrate why genotype B3 is more transmissible than other measles genotypes and is the most important circulating genotype around the world.

Reinfection and reactivation of SARS-CoV-2.

As the cases of SARS-CoV-2 infection escalates, the essence of in-depth knowledge around acquired immunity and emergence of reinfection and reactivation have to be captured. While being a rare phenomenon, reinfection occurs as the result of diminishing protection conferred by antibodies, especially IgG. Reactivation is more concerned with the role of various elements including shedding lingering viral RNA for a prolonged time and incomplete resolution of infection along with the insight of dormant viral exosomes' role. The concept of testing positive after two consecutive negative results requires proper discrimination of reinfection from reactivation. In this review, we summarized the current evidence for possible mechanisms leading to viral reactivation or test re-positivity. We also pointed out risk factors associated with both reinfection and reactivation.

The effect of influenza virus on the metabolism of peripheral blood mononuclear cells with a metabolomics approach.

Respiratory viruses have led to many deaths and hospitalizations per year in the world. The influenza virus is one of the most important respiratory viruses. Recently, metabolic studies in viral infections have been widely studied by scientists. Metabolomics states the metabolites present in a living organism under certain conditions. In this study, peripheral blood mononuclear cells were spinoculated using a virus produced by the Madin-Darby canine kidney cell culture system, and cells were harvested following spinoculation by the influenza virus. Isolation of peripheral blood mononuclear cells was performed by Ficoll-Paque density gradient centrifugation. Metabolites were extracted using organic and water approaches. Metabolic profiling was performed by a nontargeted  technique using liquid chromatography with tandem mass spectrometry. Multivariate analysis methods were used to determine the main variables. the metabolic pathways involved were determined using databases. Results of the present study showed changes in biosynthesis pathways such as lipids, polyamines, catecholamines, and vitamins. Findings also showed that it is possible to explain the process of inflammation caused by the influenza virus by studying the metabolism of immune cells.

SARS-Cov-2 and COVID-19, Basic and Clinical Aspects of the Human Pandemic: A Review.

In the last two decades, we have witnessed three major epidemics of the coronavirus human disease namely, severe acute respiratory syndrome (SARS), Middle Eastern respiratory syndrome, and more recently an ongoing global pandemic of coronavirus disease 2019 (COVID-19). Iran, a country of nearly 84 million, in the Middle East, severely involved with the COVID-19 disease. A documented multidimensional approach to COVID-19 disease is therefore mandatory to provide a well-balanced platform for the concerned medical community in our county and beyond. In this review, we highlight the disease status in Iran and attempt to provide a multilateral view of the fundamental and clinical aspects of the disease including the clinical features of the confirmed cases, virology, pathogenesis, epidemiology, and laboratory methods needed for diagnosis.

Molecular characterization of low pathogenic avian influenza H9N2 virus during co-circulation with newly-emerged highly pathogenic avian influenza H5N8 virus in Iran.

 Identification of molecular characteristics of low pathogenic avian influenza (LPAI) H9N2 virus provides insights into the evolution of this subtype due to the modulation of genomic characteristics in co-circulation with another subtype. The present study aimed to analyze the molecular and phylogenetic characteristics of the current LPAI H9N2 virus in characteristics of internal proteins are crucial for the adaptations of AIVs viruses to a new host. Since H9N2 is indigenous among poultry, continuous monitoring of viral genetic changes is needed for risk assessment of potential transmissibility to human population and emergence of new reassortant virus. domestic poultry during the emergence of new highly pathogenic avian influenza (HPAI) H5N8 virus in Iran. To this end, deep sequencing of LPAI H9N2 virus was performed on Illumina MiSeq sequencing platform and the complete sequences of avian influenza viruses were obtained from GISAID EpiFlu database. Phylogenetic analysis of the surface and internal gene segments showed that the H9N2 2018 virus was closely related to Pakistani H9N2 isolates. HA cleavage site motif sequence of the Iranian isolate was 317KSSR GLF323. The A/chicken/Iran/1/2018 H9N2 strain carried the amino acid substitution (Q216L), which is a mutation correlated with a shift in the affinity of the HA from avian type sialic receptors to human type. Besides surface glycoproteins, molecular. Keywords: A/H9N2; molecular characterization; A/H5N8; co-circulation; A/H5N1; Illumina MiSeq.

Impact of human rhinoviruses on gene expression in pediatric patients with severe acute respiratory infection.

Human rhinovirus (HRV) is one of the most common viruses, causing mild to severe respiratory tract infections in children and adults. Moreover, it can lead to patients' hospitalization. Nowadays, evaluation of gene expression alterations in host cells due to viral respiratory infections considered essential to understand the viral effects on cells. OBJECTIVE: In this study, we aimed to find important differentially expressed genes (DEGs) related to rhinitis and asthma exacerbation stimulated with Poly (I: C) and then to validate their expression in clinical samples of children how were less than 5 years old, hospitalized with severe acute respiratory infection (SARI) due to HRV infection in comparison with healthy cases. METHODS: Eight candidate genes involved in immunity, viral defense, inflammation, P53 pathway, and viral release processes were selected based on the analysis of a gene expression data set (GSE51392) and gene enrichment analysis. Then quantitative real-time PCR on cDNAs was performed for selected genes. The results were analyzed by Livak method and visualized by GraphPad prism software (8.4.3). RESULT: CXCL10, CMPK2, RSAD2, SERPINA3, TNFAIP6, CXCL14, IVNS1AB, and ZMAT3 were selected based on the enrichment and topological analysis of the constructed protein-protein interaction (PPI) network. Laboratory validation by real-time PCR showed CXCL10, CMPK2, RSAD2, SERPINA3, and TNFAIP6 (belonged to immunity, inflammatory responses and viral defense) were up-regulated, whereas CXCL14 (related to immunity) and IVNS1AB, ZMAT3 (associated to Influenza and P53 pathway) were down-regulated. CONCLUSION: Our results showed, that in children less than 5 years old affected by HRV and hospitalized with SARI, the inflammatory responses, antiviral defense, and type 1 interferon-signaling pathway have significantly affected by viral infection.

The presence of SARS-CoV-2 in raw and treated wastewater in 3 cities of Iran: Tehran, Qom and Anzali during coronavirus disease 2019 (COVID-19) outbreak.

This study aimed to identifying the presence of SARS-CoV-2 RNA in raw and treated wastewater during the COVID-19 outbreak in Tehran, Qom and Anzali cities (Iran). From three wastewater treatment plants (WWTPs), 28 treated and untreated wastewater composite samples were collected from April 4 to May 2, 2020. In this study, polyethylene glycol 6000 (PEG 6000) was used through one-step real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) for identification of RNA viruses. SARS-CoV-2 RNA was elicited from wastewater composite samples in all inlet samples taken from the three above mentioned cities. The results of outlet samples were as follows: 1) Results from Qom and East Anzali outlets showed no trace of SARS-CoV-2 RNA despite the difference in treatment disinfection method used (chlorine vs. ultraviolet (UV) disinfection). 2. In Tehran, SARS-CoV-2 RNA was not detected in any of the outlet samples taken from the modules disinfected by UV. Out of the four samples taken from the modules disinfected by chlorine, two were positive for the SARS-CoV-2 RNA which could have been caused by deficiencies in operation and maintenance. It can be concluded that meeting the standards of operation and maintenance (O&M) in WWTPs can considerably ensure that wastewater does not act as one of the roots of transmission for the disease.

COVID-19, An early investigation from exposure to treatment outcomes in Tehran, Iran.

BACKGROUND: There is a growing need for information regarding the recent coronavirus disease of 2019 (COVID-19). We present a comprehensive report of COVID-19 patients in Iran. MATERIALS AND METHODS: One hundred hospitalized patients with COVID-19 were studied. Data on potential source of exposure, demographic, clinical, and paraclinical features, therapy outcome, and postdischarge follow-up were analyzed. RESULTS: The median age of the patients was 58 years, and the majority of the patients (72.7%) were above 50 years of age. Fever was present in 45.2% of the patients on admission. The most common clinical symptoms were shortness of breath (74%) and cough (68%). Most patients had elevated C-reactive protein (92.3%), elevated erythrocyte sedimentation rate (82.9%), and lymphocytopenia (74.2%) on admission. Lower lobes of the lung were most commonly involved, and ground-glass opacity (81.8%) was the most frequent finding in computed tomography scans. The administration of hydroxychloroquine improved the clinical outcome of the patients. Lopinavir/ritonavir was efficacious at younger ages. Of the 70 discharged patients, 40% had symptom aggravation, 8.6% were readmitted to the hospital, and three patients (4.3%) died. CONCLUSION: This report demonstrates a heterogeneous nature of clinical manifestations in patients affected with COVID19. The most common presenting symptoms are nonspecific, so attention should be made on broader testing, especially in age groups with the greatest risk and younger individuals who can serve as carriers of the disease. Hydroxychloroquine and lopinavir/ritonavir (in younger age group) can be potential treatment options. Finally, patients discharged from the hospital should be followed up because of potential symptom aggravation.

Potential of H1N1 influenza A virus as an air borne pathogen to induce infectivity in pancreas: a mouse model study.

INTRODUCTION: H1N1 influenza virus, as an indoor/outdoor pathogen in air, can cause the flu-like illness and respiratory complication. The aim of this study was to evaluate the H1N1 influenza virus replication in pancreas and investigate the immune response against infected pancreas. MATERIAL AND METHODS: First, mouse pancreas cell line was infected by H1N1 influenza A virus using intranasally and intravenously infection methods, and then the pancreas tissue was collected and pathology experiment was carried out. Next, the protein and genome of influenza virus were detected using immunocytochemistry and real-time PCR, respectively. In addition, serum cytokines and serum lipase were investigated using ELISA. RESULT: The in-vitro results proved that the mouse pancreatic cell line can support influenza virus replication. The result also proved that influenza virus is capable to infect pancreas and induce pancreas damage. Further, the immune response in mice with infected pancreas exhibited a completely different pattern with that of mice infected through intranasal method. CONCLUSION: It can be concluded that influenza virus can infect pancreas and change the influenza disease pathway, which might result in a pancreatic injury.

Serum and tissue miRNAs: potential biomarkers for the diagnosis of cervical cancer.

BACKGROUND: Finding new biomarkers for the early detection of cervical cancer is an essential requirement in this field. In this study, we aimed to evaluate the expression level of potential biomarkers in progression of cervical cancer in patients with cervical cancer compared to normal subjects. METHODS: The expression levels of tissue and serum miRNAs, including miR-9, miR-192 and miR-205, were investigated in 36 normal, 18 precancer, and 18 cervical cancer samples using real-time polymerase chain reaction. RESULTS: The results showed the higher significant expressions of miR-9, miR-192 and miR-205 in the tissue of cancer samples than those in the normal samples. Moreover, the miR-192 and miR-205 expression were significantly increased in the cancer group in comparison with the precancer group. Examination of serum samples revealed the increase in the expression level in the cancer groups than in the normal samples, for miR-9, miR-192 and miR-205 and the expressions of miR-9, miR-192 and miR-205 were significantly up-regulated in the precancer group in comparison with the normal group. Also the expression of miR-205 was remarkably increased in the cancer group in comparison with the precancer group. The receiver operating characteristic (ROC) analyses showed the highest area under the curve value for miR-192. CONCLUSIONS: Given the increased expression level of miR-192 in cancer and in precancerous tissue and serum compared with the normal tissue and serum validated by analysing the ROC curve, miR-192 can be used as potential biomarker for the early detection of cervical cancer.

Prevalence of adeno-associated virus and human papillomavirus DNA in Iranian women with and without cervical cancer.

There is plenty of substantial evidence to support anti-tumor activity of viruses. Adeno-associated virus (AAV) may interact with human papillomavirus (HPV) to modify the risk of cervical neoplasia. The seroprevalence of AAV among women with cervical cancer has been reported to be lower than healthy ones. In spite of this finding, detection of AAV DNA in cervical biopsies does not entirely support the inverse association between AAV seropositivity and cervical cancer. This association is still controversial and requires more thorough evaluation in different countries. The aim of this case-control study was to find the prevalence of AAV and HPV DNA sequences in Iranian women with and without cervical cancer to assess the probable association of AAV infection and cervical cancer. In this study, paraffin-embedded tissue samples of 61 cervical cancer cases and 50 healthy controls (HCs) were investigated for AAV and HPV DNA by semi-nested and nested PCRs respectively. AAV DNA was detected in 7 cases (14%) of HCs and 9 specimens (14.8%) of case group. According to the branching in the phylogenetic tree, AAV2 was the only type detected in this study. Moreover, HPV DNA was detected in 8 cases (16%) of HCs and 44 specimens (72.13%) of case group. In conclusion, a low proportion of cervical biopsies from Iranian women contained AAV-2 genome. No significant difference in correlation between HPV and cervical cancer in presence or absence of AAV genome in cervix was found.

Research agenda on persistent and unpredictable threat of influenza and emerging respiratory infections: a public health necessity in the Eastern Mediterranean Region (Guest Editorial).

Infectious diseases continue to represent a significant threat to global health security, particularly in the context of increasing globalization, interconnectedness and interdependence. Chief among such threats are influenza viruses and other respiratory pathogens, such as Middle East Respiratory Syndrome coronavirus (MERS-CoV), because of their risk of high transmissibility and acuity of illness. Annual epidemics of seasonal influenza cause an estimated 3-5 million cases of severe illness and more than 500 000 deaths, with the prospect of pandemic influenza viruses causing far greater impact. In addition, the appearance of severe acute respiratory syndrome (SARS) in 2003, widespread and continued outbreaks of avian influenza A (H5N1) since 2004, the H1N1 pandemic in 2009 and emergence of MERS CoV in 2012 reflect the seriousness of public health challenges posed by influenza and emerging respiratory infections.

Cluster of Middle East respiratory syndrome coronavirus infections in Iran, 2014.

During January 2013-August 2014, a total of 1,800 patients in Iran who had respiratory illness were tested for Middle East respiratory syndrome coronavirus. A cluster of 5 cases occurred in Kerman Province during May-July 2014, but virus transmission routes for some infections were unclear.

Genotype circulation pattern of human respiratory syncytial virus in Iran.

In order to have information on the molecular epidemiology and genetic circulation pattern of human respiratory syncytial virus (HRSV) in Iran, we studied the genetic variability of both group A and B HRSV strains during seven consecutive years by sequencing the hypervariable C-terminal domain of G protein. A total of 485 children <2years of age who were negative for influenza viruses, screened for the presence of HRSV in this research. HRSV was detected in 94 (19.38%) of the samples using nested RT-PCR. Group A viruses were isolated during each year, while group B viruses were isolated during 2009 and 2013. Phylogenetic analysis showed that all HRSV group A viruses belonged to three genotypes: GA1, GA2, GA5 and the group B viruses were in BA genotype.

Drug-related mutational patterns in hepatitis B virus (HBV) reverse transcriptase proteins from Iranian treatment-naïve chronic HBV patients.

BACKGROUND: Immunomodulators and Nucleotide analogues have been used globally for the dealing of chronic hepatitis B virus (HBV) infection. However, the development of drug resistance is a major limitation to their long-term effectiveness. OBJECTIVES: The aim of this study was to characterize the hepatitis B virus reverse transcriptase (RT) protein variations among Iranian chronic HBV carriers who did not receive any antiviral treatments. MATERIALS AND METHODS: Hepatitis B virus partial RT genes from 325 chronic in active carrier patients were amplified and directly sequenced. Nucleotide/amino acid substitutions were identified compared to the sequences obtained from the database. RESULTS: All strains belonging to genotype D.365 amino-acid substitutions were found. Mutations related to lamivudine, adefovir, telbivudine, and entecavir occurred in (YMDD) 4% (n = 13), (SVQ) 17.23% (n = 56), (M204I/V + L180M) 2.45% (n = 8) and (M204I) 2.76% (n = 9) of patients, respectively. CONCLUSIONS: RT mutants do occur naturally and could be found in HBV carriers who have never received antiviral therapy. However, mutations related to drug resistance in Iranian treatment-naïve chronic HBV patients were found to be higher than other studies published formerly. Chronic HBV patients should be monitored closely prior the commencement of therapy to achieve the best regimen option.

Successful control and impending elimination of measles in the Islamic Republic of Iran.

Measles is still one of the most common infectious killers of children in the world, especially in developing countries. In Iran, during the prevaccine era, 150,000-500,000 cases of measles were reported annually, with a death rate of 10%-15%. After the establishment of Expanded Program on Immunization program in 1984, vaccination rates for the first and second doses of measles vaccine increased to >90% by the mid-1990s, and the number of measles cases decreased to 2652 in 1996. In response to increased numbers of cases in older age groups during 1996-2002, a nationwide measles-rubella vaccination campaign was conducted in 2003, and 33,100,000 persons (99%) aged 5-25 years were vaccinated. During 2004-2009, 221 laboratory-confirmed measles cases (<1 case per million population) were detected, primarily in rural areas and among migrant groups who traveled to or came from high-incidence countries. High routine immunization coverage, low disease incidence, and surveillance system data suggest that interruption of endemic virus transmission might have already been achieved in Iran, but challenges remain and continued efforts are needed to sustain this accomplishment.

Amantadine resistance in relation to the evolution of influenza A(H3N2) viruses in Iran.

The aminoadamantanes, amantadine and rimantadine, have been used to prevent and treat influenza A virus infections for many years. Several reports have shown an increased level of resistance to these drugs, particularly among influenza A(H3N2) subtype viruses, during recent years. We observed an increase in amantadine resistance, due to a Ser31Asn mutation in the M2 channel protein, among A(H3N2) viruses circulating in Iran during 2005-2007. Sequence analyses of the haemagglutinin and neuraminidase genes as well as the M gene of these viruses revealed that the emergence of resistance was in general consistent with the progressive worldwide evolution of H3N2 viruses.