Evaluation of angiotensin converting enzyme 2 (ACE2), angiotensin II (Ang II), miR-141-3p, and miR-421 levels in SARS-CoV-2 patients: a case-control study.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious virus that uses angiotensin converting enzyme 2 (ACE2), a pivotal member of the renin-angiotensin system (RAS), as its cell-entry receptor. Another member of the RAS, angiotensin II (Ang II), is the major biologically active component in this system. There is growing evidence suggesting that serum miRNAs could serve as prognostic biomarkers for SARS-CoV-2 infection and regulate ACE2 expression. Therefore, the aim of this study is to evaluate the changes in the serum levels of sACE2 and Ang II, as well as the expression level of miR-141-3p and miR-421 in SARS-CoV-2 positive and negative subjects. METHODS: In the present study, the serum levels of sACE2 and Ang II were measured in 94 SARS-CoV-2 positive patients and 94 SARS-CoV-2 negative subjects with some symptoms similar to those of SARS-CoV-2 positive patients using the ELISA method. In addition, the expression level of miR-141-3p and miR-421 as ACE2 regulators and biomarkers was evaluated using quantitative real-time PCR (qRT-PCR) method. RESULTS: The mean serum sACE2 concentration in the SARS-CoV-2-positive group was 3.268 ± 0.410 ng/ml, whereas in the SARS-CoV-2 negative group, it was 3.564 ± 0.437 ng/ml. Additionally, the mean serum Ang II level in the SARS-CoV-2 positive and negative groups were 60.67 ± 6.192 ng/L and 67.97 ± 6.837 ng/L, respectively. However, there was no significant difference in the serum levels of sACE2 (P value: 0.516) and Ang II (P value: 0.134) between the SARS-CoV-2 positive and negative groups. Meanwhile, our findings indicated that the expression levels of miR-141-3p and miR-421 in SARS-CoV-2 positive group were significantly lower and higher than SARS-CoV-2 negative group, respectively (P value < 0.001). CONCLUSIONS: Taken together, the results of this study showed that the serum levels of sACE2 and Ang II in SARS-CoV-2 positive and negative subjects were not significantly different, but the expression levels of miR-141-3p and miR-421 were altered in SARS-CoV-2 positive patients which need more investigation to be used as biomarkers for COVID-19 diagnosis.

Beyond prediction: unveiling the prognostic power of µ-opioid and cannabinoid receptors, alongside immune mediators, in assessing the severity of SARS-CoV-2 infection.

BACKGROUND: This study aims to explore the potential of utilizing the expression levels of cannabinoid receptor 2 (CB2), µ-opioid receptor (MOR), MCP-1, IL-17, IFN-γ, and osteopontin as predictors for the severity of SARS-CoV-2 infection. The overarching goal is to delineate the pathogenic mechanisms associated with SARS-CoV-2. METHODS: Using quantitative Real-time PCR, we analyzed the gene expression levels of CB2 and MOR in nasopharynx specimens obtained from patients diagnosed with SARS-CoV-2 infection, with 46 individuals classified as having severe symptoms and 46 as non-severe. Additionally, we measured the circulating levels of MCP-1, IL-17, IFN-γ, and osteopontin using an ELISA assay. We examined the predictive capabilities of these variables and explored their correlations across all patient groups. RESULTS: Our results demonstrated a significant increase in MOR gene expression in the epithelium of patients with severe infection. The expression of CB2 receptor was also elevated in both male and female patients with severe symptoms. Furthermore, we observed concurrent rises in MCP-1, IL-17, IFN-γ, and osteopontin levels in patients, which were linked to disease severity. CB2, MOR, MCP-1, IL-17, IFN-γ, and osteopontin showed strong predictive abilities in distinguishing between patients with varying degrees of SARS-CoV-2 severity. Moreover, we identified a significant correlation between CB2 expression and the levels of MOR, MCP-1, osteopontin, and IFN-γ. CONCLUSIONS: These results underline the interconnected nature of molecular mediators in a sequential manner, suggesting that their overexpression may play a role in the development of SARS-CoV-2 infections.

Congenital cytomegalovirus infection in newborns suspected of congenital rubella syndrome in Iran: a cross-sectional study.

BACKGROUND: Following rubella virus control, the most important cause of congenital infections is human cytomegalovirus (HCMV). Congenital CMV (cCMV) may happen both in primary and non-primary maternal infections. The present study aimed to screen cCMV in symptomatic newborns suspected of congenital rubella syndrome (CRS) in Iran. METHODS: Out of 1629 collected infants' serum samples suspected of CRS but negative for rubella IgM, 524 samples were selected regarding cCMV complications. These samples were divided into two age groups: 1- one month and younger, 2- older than 1 month up to one year. Anti-HCMV IgM detection was performed on these serums. Then HCMV IgG avidity assay and HCMV DNA detection were carried out on all samples with positive and borderline results in IgM detection. RESULTS: Herein, 3.67% of symptomatic infants aged one month and younger had positive and borderline HCMV IgM, 12.5% of which had a low avidity index (AI). HCMV IgM detection rate among symptomatic infants older than one month to one year was 14.5%. Identified genotypes in this study were gB-1(63.63%), gB2 (18.18%), and gB3 (18.18%), respectively. CONCLUSIONS: This comprehensive study was performed on serum samples of symptomatic infants clinically suspected of cCMV from all over Iran. There was a good correlation between serology findings and PCR.

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.

Impact of COVID-19 on the changing pattern of human orthopneumovirus (respiratory syncytial virus) infection in Iran.

BACKGROUND: Human orthopneumovirus (HOPV) or respiratory syncytial virus (RSV) is one of the important causes of acute respiratory infections (ARIs) during the cold months of the year worldwide. Many countries have reported an absence of ARIs due to HOPV during the winter of 2020-2021 associated with preventive measures to reduce the spread of SARS-CoV2. However, with the reduction of COVID-19 public health restrictions and the absence of immunity in the community due to the lack of exposure in the previous season, many countries had a delayed HOPV outbreak. Here we reported the impact of COVID-19 on the changing pattern of HOPV infection in Iran. METHODS: Throat and nasopharyngeal swab samples were collected from patients (children and adults) with ARIs and sent to the Iran National Influenza Center. After RNA extraction, Real time RT-PCR was performed for HOPV detection. RESULTS: In 260 samples collected from patients with ARIs in three different groups, which included children in March 2021, pilgrims in July 2022, and outpatients during November and December 2022, no HOPV was detected in any group. CONCLUSIONS: The lack of HOPV activity in Iran during the winter of 2020-2021 and then the resurgence in spring 2022 and again the absence of activity in summer and autumn 2022 was extraordinary in the HOPV epidemiology, and probably due to the implementation of public health non-pharmaceutical interventions to reduce the spread of SARS-CoV2. Although it is not possible to keep such restrictions, similar methods can be taken to control outbreaks caused by respiratory viruses.

15-lipoxygenase and cyclooxygenase expression profile and their related modulators in COVID-19 infection.

BACKGROUND: The role of the lipoxygenase (LOX) and cyclooxygenase (COX) enzymes in maintaining cellular homeostasis and regulating immune responses promoted us in this study to analyze the pattern of changes in 15-lipoxygenase and cyclooxygenase isoforms and their related cytokines in SARS-CoV-2 infection. METHODS: 15-LOX-1, 15-LOX-2, COX-1 and COX-2 gene expression levels were determined using qRT-PCR in nasopharynx specimens from patients with severe [N = 40] and non-severe [N = 40] confirmed SARS-CoV-2 infections and healthy controls. Circulating levels of lL-6, lL-10, PGE2, and IFN-γ were measured in patients and healthy controls using ELISA assay. The associations between the measured variables and the patient's clinic-pathological characteristics were assessed for all groups. RESULTS: The expression level of 15-LOX-1 was elevated significantly in male patients with severe infection; although female patients showed a different expression profile. 15-LOX-2 expression level was considerably increased in male patients with severe infection; while changes in its expression remained inconclusive in female patients. The relationship between 15-LOX expression and the male gender was prominent. Both COX isoforms expression showed elevation in male and female patients that were correlated with disease severity. The simultaneous increase in lL-6, PGE2 and IFN-γ levels also decrease in lL-10 in patients with severe infection indicating the possible regulatory network related to the COX and 15-LOX enzymes in the output of the SARS-CoV-2 infection. CONCLUSION: The results of this study determined the pattern of possible changes in key enzymes of prostaglandin and eicosanoids synthesis pathway and their mediators, which can be helpful in mapping the SARS-CoV-2 pathogenicity and pharmaceutical approaches.

How to tackle single target gene positive results of SARS-CoV-2 real-time PCR: A cross-sectional study.

Background and Aims: Real-time reverse-transcriptase polymerase chain reaction (real-time RT-PCR) is the gold standard test for diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, when the test result is near the detection limit of the assay the possibility of getting false positive or negative results is high. In addition, it might result in single target gene positive (STGP) results which should be interpreted with caution. Methods: This study was performed on 29,962 nasal swabs from July 1 to August 31, 2020. Ct values less than 40 for each or both of N and RdRp genes were recommended to be selected as positive. Positive samples for one gene with the Cts more than 35 were rechecked by adding more templates. Results: The results showed that 1016 (3.39%) samples were positive just for one gene with high Ct values. The results of the second reactions showed that 325 (31.99%) samples were positive for both N and RdRp which were reported positive, 301 (29.65%) were positive only for one gene which were considered as suspicious cases and resampling was suggested for them. Finally, 390 (38.385%) samples were negative for both genes. Conclusion: In conclusion, tracking weak positive results of SARS-CoV-2 real-time RT-PCR revealed that most of the individuals who were STGP clean the infection completely in less than a week which showed they were in the convalescent phase of infection. However, some of them who were in the beginning of infection showed a decrease in Ct value during a week, so they could spread the virus in the society.

Oncolytic viruses against cancer, promising or delusion?

Cancer treatment is one of the most challenging topics in medical sciences. Different methods such as chemotherapy, tumor surgery, and immune checkpoint inhibitors therapy (ICIs) are potential approaches to treating cancer and killing tumor cells, but clinical studies have shown that they have been successful for a limited group of patients. Using viruses as a treatment can be considered as an effective treatment in the field of medicine. This is considered as a potential treatment, especially in comparison to chemotherapy, which has severe side effects related to the immune system. Most oncolytic viruses (OVs) have the potential to multiply in cancer cells, which are more than normal cells in malignant tissue and can induce immune responses. Therefore, tons of efforts and research have been started on the utilization of OVs as a treatment for cancer and have shown promising in treating cancers with less side effects. In this article, we have gathered studies about oncolytic viruses and their effectiveness in cancer treatment.Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author 1 Given name: [Omid Salahi] Last name [Ardekani], Author 2 Given name: [Mohammad Mehdi] Last name [Fazeli], Author 3 Given name: [Nillofar Asadi] Last name [Jemezghani]. Also, kindly confirm the details in the metadata are correct.Confirmed.

SARS-CoV-2 intrahost evolution in immunocompromised patients in comparison with immunocompetent populations after treatment.

Many evidence suggests that long-lasting infection can develop with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This occurrence has been widely described in immunocompromised individuals. In these patients, ineffective clearance of virus infection provides an opportunity for developing immune escape mutants. This study aimed to characterize SARS-CoV-2 intrahost evolution in five immunocompromised in comparison with five immunocompetent COVID-19 patients during treatment. We performed next-generation sequencing (NGS) on collected two oropharyngeal samples from immunocompromised and immunocompetent COVID-19 patients before and after treatment. In this study, we detected alpha and delta variants of SARS-CoV-2. The most common substitutions in structural proteins in patients with alpha variant were S-ΔY143-144, A570D, D614G and D1118H, and N-R203K and G204R, and in delta variant S-T19R, G142D, E156G, 157-158del, L452R, T478K, D614G, D950N and N-D63G, R203M and D377Y were dominant. The common variations in nonstructural and accessory proteins including nsp3-A488S, P1228L, nsp6-T77A, nsp12-P323L, G671S, nsp13-P77L, NS3-S26L, and NS7a-T120I were detected. Also some infrequent substitutions were seen in immunocompromised and immunocompetent patients. After treatment, nsp12-V166A was emerged as a remdesivir resistance and S-L452M in a patient with common variable immunodeficiency. S-E484Q was detected in a patient with acute lymphoma leukemia. This study showed the possibility of the genetic diversity and development of some new mutations in immunocompromised patients. Therefore, surveillance of these patients to characterize any new variants is necessary.

Genomic surveillance of SARS-CoV-2 strains circulating in Iran during six waves of the pandemic.

Background: SARS-CoV-2 genomic surveillance is necessary for the detection, monitoring, and evaluation of virus variants, which can have increased transmissibility, disease severity, or other adverse effects. We sequenced 330 SARS-CoV-2 genomes during the sixth wave of the COVID pandemic in Iran and compared them with five previous waves, for identifying SARS-CoV-2 variants, the genomic behavior of the virus, and understanding its characteristics. Methods: After viral RNA extraction from clinical samples collected during the COVID-19 pandemic, next generation sequencing was performed using the Nextseq and Nanopore platforms. The sequencing data were analyzed and compared with reference sequences. Results: In Iran during the first wave, V and L clades were detected. The second wave was recognized by G, GH, and GR clades. Circulating clades during the third wave were GH and GR. In the fourth wave, GRY (alpha variant), GK (delta variant), and one GH clade (beta variant) were detected. All viruses in the fifth wave were in GK clade (delta variant). In the sixth wave, Omicron variant (GRA clade) was circulating. Conclusions: Genome sequencing, a key strategy in genomic surveillance systems, helps to detect and monitor the prevalence of SARS-CoV-2 variants, monitor the viral evolution of SARS-CoV-2, identify new variants for disease prevention, control, and treatment, and also provide information for and conduct public health measures in this area. With this system, Iran could be ready for surveillance of other respiratory virus diseases besides influenza and SARS-CoV-2.

Phylogenetic characterization of rhinovirus and adenovirus in hospitalized children aged ≤ 18 years with severe acute respiratory infection in Iran.

Background and Objectives: Human rhinoviruses (HRVs) and human adenoviruses (HAdVs) are among the most prevalent viruses in hospitalized patients with severe acute respiratory infection (SARI). This study aimed to evaluate the molecular characterization of HRV and HAdV in hospitalized patients with SARI, who aged ≤ 18 years in Tehran, Iran. Materials and Methods: To detect these two viruses, a conventional nested RT-PCR (Reverse transcription-polymerase chain reaction) assay was performed on 264 throat swabs collected from December 2018 to March 2019. The epidemiological data were analyzed and phylogenetic trees were constructed. Results: Of 264 cases with SARI, 36 (13.6%) and 28 (10.6%) were positive for HAdV and HRV respectively. Of 21 HRV sequenced samples, HRV-A (42.9%), HRV-B (9.5%) and HRV-C (47.6%) and of 36 HAdV sequenced samples, HAdV-C6 (38.9%), HAdV-B7 (22.2%), HAdV-B3 (11.1%), HAdV-B16 (5.6%), HAdV-C5 (13.9%), HAdV-C57 (5.6%), HAdV-E4 (2.8%); were detected in children with SARI. Some viral genotypes appeared to cause more severe disease, which may lead to hospitalization. Conclusion: Large-scale studies are recommended to investigate the epidemiology and molecular characterizations through surveillance networks to provide useful information on etiology, seasonality, and demographic associations in patients with SARI.

Surveillance of endemic coronaviruses during the COVID-19 pandemic in Iran, 2021-2022.

Background: Human coronaviruses (HCoVs) 229E, OC43, HKU1, and NL63 are common viruses that continuously circulate in the human population. Previous studies showed the circulation of HCoVs during the cold months in Iran. We studied the circulation of HCoVs during coronavirus disease 2019 (COVID-19) pandemic to find the impact of pandemic on the circulation of these viruses. Methods: As a cross-sectional survey conducted during 2021 to 2022, of all throat swabs sent to Iran National Influenza Center from patients with severe acute respiratory infection, 590 samples were selected to test for HCoVs using one-step real-time RT-PCR. Results: Overall, 28 out of 590 (4.7%) tested samples were found to be positive for at least one HCoVs. HCoV-OC43 was the most common (14/590 or 2.4%), followed by HCoV-HKU1 (12/590 or 2%) and HCoV-229E (4/590 or 0.6%), while HCoV-NL63 was not detected. HCoVs were detected in patients of all ages and throughout the study period with peaks in the cold months of the year. Conclusions: Our multicenter survey provides insight into the low circulation of HCoVs during the COVID-19 pandemic in Iran in 2021/2022. Hygiene habits and social distancing measures might have important role in decreasing of HCoVs transmission. We believe that surveillance studies are needed to track the pattern of HCoVs distributions and detect changes in the epidemiology of such viruses to set out strategies in order to timely control the future outbreaks of HCoVs throughout the nation.

Comparison of Circulating Variants during the Beginning, Middle and the End of the 4th Wave of COVID-19 in Tehran Province, Iran in 2021.

Background: Whole viral genome sequencing with next generation sequencing (NGS) technique is useful tool for determining the diversity of variants and mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study we have attempted to characterize the mutations and circulating variants of the SARSCoV-2 genome during the 4th wave of COVID-19 pandemic in Tehran, Iran in 2021. Methods: We performed complete genome sequencing of 15 SARS-CoV-2 detected from 15 COVID-19 patients during the 4th wave of COVID-19 pandemic with NGS. Three groups of the patients at the beginning, middle and the end of the 4th wave were compared together. Results: We detected alpha and delta variants during the 4th wave of the pandemic. The results illustrated a dominance of amino acid substitution D614G in spike, and the most frequent mutants were N-R203K, G204R, S235F, nsp12-P323L, nsp6-G106del, G107del and F108del. Conclusion: The detection of the virus mutations is a useful procedure for identifying the virus behavior and its genetic evolution in order to improve the efficacy of the monitoring strategies and therapeutic measures.

Molecular epidemiology of human adenoviruses in children with and without respiratory symptoms: Preliminary findings from a case-control study.

BACKGROUND: Human adenovirus (HAdV) is an important viral agent in children which can lead to severe acute respiratory infection (SARI). Reports on molecular epidemiology of HAdVs in Iran are limited. This case-control study is conducted to compare the HAdV infection rate and molecular epidemiology among two groups of children with and without respiratory symptoms in Tehran, Iran during 2018-2019. METHODS: Nested PCR was performed on 120 oropharyngeal swabs taken from children aged five and younger with SARI who were hospitalized as the case group, and 120 oropharyngeal swabs were collected from children of the same age without respiratory symptoms as the control group. For positive samples Sanger sequencing was done and a phylogenetic tree was drawn afterward. RESULTS: Out of 120 cases, 8 (6.6%) tested positive for eachHAdV types including 6 (75%) HAdV-B7, 1 (12.5%) HAdV-C2, and 1 (12.5%) HAdV-C6. Among the control group, out of 120 samples, 8 (6.6%) were positive comprising 5 (62.5%) HAdV-C5, 2 (25%) HAdV-F41, and 1 (12.5%) HAdV-C6. CONCLUSION: The present study indicated a different viewpoint of HAdV molecular epidemiology in which the genotypes were compared in children with and without respiratory symptoms. HAdV prevalence was equally common in cases and controls but different genotypes were detected in these two groups. HAdV-B7 was the main type among children with SARI, dissimilar to children with no respiratory symptoms where HAdV-C5 was the predominant type. Detecting HAdV-F in oropharyngeal swabs was a rare finding, which requires further investigation.

A delayed resurgence of respiratory syncytial virus (RSV) during the COVID-19 pandemic: An unpredictable outbreak in a small proportion of children in the Southwest of Iran, April 2022.

The global outbreak of coronavirus disease 2019 (COVID-19), an emerging disease caused by severe acute respiratory syndrome virus-2 (SARS-CoV-2), and strict restrictions implemented to control the infection have impacted the circulation and transmission of common seasonal viruses worldwide and subsequently the rate of hospitalizations in children at young ages. Respiratory syncytial virus (RSV) surprisingly disappeared in 2020-2021 in many countries due to lockdown and precautions were taken because of the COVID-19 pandemic. Herein, we showed a notable change in the rate of hospitalization and reported an unpredictable outbreak of RSV in a small proportion of children admitted to a children's hospital in Dezful (a city in Southwest Iran) in the early spring of 2022. We performed a descriptive study of hospitalized young children (aged ≤ 5 years) with acute respiratory infections. Together with clinical information, 30 nasopharyngeal swabs were prospectively collected and 3 important respiratory viruses (RSV, influenza viruses, and SARS-CoV-2) were tested through the real-time polymerase chain reaction (real-time PCR) method. The age distribution of 30 hospital-admitted children was 1 month to 5 years old and males were the most included subjects 18/30 (60%) in this study. Although the viral genome of SARS-CoV-2 and influenza viruses was not detected, the presence of RSV was confirmed in 16/30 (53.33%) patients. Results showed that the majority of RSV-infected cases were males 10/16 (62.5%), within 12 months of life, and had changes in parameters of the complete blood count. Almost all patients with RSV infection had a cough as the most common clinical manifestation and had no history of past medical conditions as a risk factor. The presented study is the first investigation that documented an outbreak of RSV infection in young children reported since the onset of the COVID-19 outbreak in Iran. Our cases highlight the potential threats of important but neglected pathogens during the ongoing pandemic as described here for RSV, which would be challenging by easing the preimposed restrictions.

Molecular detection and genotyping of Human Cytomegalovirus in kidney transplant recipients under ganciclovir prophylaxis in Iran.

INTRODUCTION: Human Cytomegalovirus (HCMV) infection is one of the most common viral complications in kidney transplant recipients. Although there are effective treatments strategies for the HCMV infection, this infection is still one of the causes of kidney transplant rejection. METHODS: A total of 246 kidney transplant recipients participated in this cross-sectional study. Viral DNA was extracted from these plasma samples and the presence of HCMV genome was determined by Semi-nested PCR with specific primers for HCMV B glycoprotein gene. Sanger sequencing analyses were carried out to determine HCMV genotypes and Mega x software was used for nucleotide alignment and construction of a phylogenetic tree. RESULTS: Human cytomegalovirus DNA was detected in 11 (4.47%) recipients. According to the phylogenetic analysis, HCMV gB3 was 50% among kidney transplant recipients, followed by gB4 30% and gB1 20% however, the gB2 genotype was not detected. CONCLUSIONS: This study demonstrated that the HCMV infection in our patients is relatively low because all transplant recipients received appropriate prophylaxis, thereby antiviral prophylaxis is recommended for all patients at risk of HCMV infection after kidney transplantation. Also, gB3 was the most predominant genotype among our kidney transplant recipients that was related to the higher rate of prevalence of severe HCMV infections. Moreover, elevated serum creatinine level was detected in patients at the time of detection of HCMV infection.

Whole genome sequencing of SARS-CoV2 strains circulating in Iran during five waves of pandemic.

PURPOSE: Whole genome sequencing of SARS-CoV2 is important to find useful information about the viral lineages, variants of interests and variants of concern. As there are not enough data about the circulating SARS-CoV2 variants in Iran, we sequenced 54 SARS-CoV2 genomes during the 5 waves of pandemic in Iran. METHODS: After viral RNA extraction from clinical samples collected during the COVID-19 pandemic, next generation sequencing was performed using the Nextseq platform. The sequencing data were analyzed and compared with reference sequences. RESULTS: During the 1st wave, V and L clades were detected. The second wave was recognized by G, GH and GR clades. Circulating clades during the 3rd wave were GH and GR. In the fourth wave GRY (alpha variant), GK (delta variant) and one GH clade (beta variant) were detected. All viruses in the fifth wave were in clade GK (delta variant). There were different mutations in all parts of the genomes but Spike-D614G, NSP12-P323L, N-R203K and N-G204R were the most frequent mutants in these studied viruses. CONCLUSIONS: These findings display the significance of SARS-CoV2 monitoring to help on time detection of possible variants for pandemic control and vaccination plans.

Evaluation of SARS-CoV-2 genome detection by real-time PCR assay using pooled specimens.

Objective: To evaluate SARS-CoV-2 genome detection using pooled samples by RT-qPCR assay, compared to individual samples. Method: At first all samples were tested individually using two commercial methods targeting ORF1ab, NP and E genes. Then, four experimental groups of samples were pooled and evaluated using the same detection methods. Findings: Compared to the individual sample testing, the sample pooling conserved the sensitivity of the detection in all groups of pooled samples when the Ct value in single test was lower than 33. Conclusion: Specimen pooling may fail to detect positive samples with high Ct values. However, in scarcity of reagents or in population surveys, it could be considered as an alternative method in low prevalence settings.

No human respiratory syncytial virus but SARS-CoV-2 found in children under 5 years old referred to Children Medical Center in 2021, Tehran, Iran.

Acute respiratory infections (ARIs) are one of the leading causes of illness and death among community members worldwide. Viral infections are the most common agents estimated to be involved in these patients. This study aimed to investigate the prevalence of human respiratory syncytial virus (hRSV) and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) among children with ARIs. This study evaluated the presence of SARS-CoV-2 and hRSV in 168 throat and nasopharyngeal swab samples using real-time RT-PCR. All samples were collected from children under 5 years old with ARIs who attended Children's Medical Center, Tehran, Iran, and sent to the Iranian National Influenza Center with appropriate conditions in 2021. Chi-square and Fisher's exact tests were used for comparison of the data of the prevalence of hRSV and SARS-CoV-2 infections among children. Of 168 patients examined, 95 (57%) were male and 73 (43%) female. Out of them, 47 (28%) cases were younger than 1 year old and 121 cases (72%) were 1-5 years old. The most common clinical manifestations of patients were cough (78%), nausea (31%), diarrhea (27%), and fever (18%). Among 168 patients, no hRSV was detected, while the SARS-CoV-2 genome was identified in 16 (9.5%) patients. Among 16 positive cases of SARS-CoV-2, 8 (50%) were under 1 year old and 8 positive cases were 1-5 years old. This study was performed at cold months of the year but due to the coronavirus disease 2019 pandemic and adherence to health protocols, school closures, and virtual classes, no cases of hRSV infections were identified.

The Persistence Time of SARS-CoV-2 RNA in Hospitalized COVID-19 Patients: A Prospective Study.

BACKGROUND: In late December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the causative agent of coronavirus disease 2019 (COVID-19), spread to almost all countries worldwide. The outbreak of this virus has been confirmed on 19th February, 2020, in Iran. OBJECTIVE: The aim of this study was to investigate the time of viral RNA clearance in swab and serum samples of COVID-19 patients having received different medications. We also evaluated different factors that may affect viral RNA persistence in patients infected by SARS-CoV-2. METHODS: In March 2020, twenty-one hospitalized COVID-19 patients participated in this prospective study. All patients received antiviral agents in their routine care. Throat swabs and blood samples were obtained from all patients in different intervals, including day 3 or 5, day 7, day 10, and finally, 14 days after the first positive real-time RT-PCR (rRT-PCT) test. RESULTS: The median time from the symptom onset (SO) to the first negative rRT-PCR results for throat swabs and serum samples of COVID-19 patients was 18 and 14 days, respectively. These times were more significant in patients with lymphopenia, oxygen saturation ≤ 90%, and comorbidity. CONCLUSION: This preliminary study highlights that SASR-CoV-2 RNA was not detectable in the upper respiratory tract for longer than three weeks. In addition, SARS-CoV-2 may persist for a long period of time in the respiratory than in the serum samples. This study supports the idea that in limited resource settings, the patients should be tested earlier than three weeks for discharge management.