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1.
Acta Virol ; 67(1): 91-98, 2023.
Article in English | MEDLINE | ID: covidwho-2266313

ABSTRACT

Since the emergence of the original Wuhan SARS-CoV-2 strain, several new variants of the virus have emerged. Alpha, Beta, Gamma, Delta and the most recent Omicron variants have been introduced during this pandemic. Several methods including, but not restricted to, allele-specific PCR, ligation with rolling circle amplification and real-time PCR with allele-specific probes are able to detect mutations as low as a single nucleotide polymorphism. High-resolution melting curve analysis is ano-ther technique to assess any mutations in a nucleic acid chain. Confirmed samples with SARS-CoV-2 infection were subjected to variant identification using a de novo-designed HRM assay. In order to select for mutations with the highest effect on Tm of the amplicon, deletion mutations of NSP6 (Del 3675-3677), and S1 (Del 144) were chosen for HRM analysis. HRM analysis for the amplicon of the primer set-1 (NSP6) resulted in Tm differences of -0.39°C, +0.4°C, and -0.6°C between Alpha, Delta, and Omicron variants, respectively, in comparison to the original Wuhan strain. Moreover, HRM analysis of the amplification performed by primer set-2 (S1) led to Tm differences of +0.32°C, -0.26°C, and +0.24°C between Alpha, Delta, and Omicron variants, respectively, in comparison to original Wuhan strain. The test was able to specify each sample to its variant group with more than 90 percent of confidence. The results obtained in this study demonstrate that using a single closed-tube strategy with a HRM-equipped machine, screening new variants of the virus is possible in a fast and reliable way. Keywords: high resolution melting; SARS coronavirus 2; mutation; variant; genotyping.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , Real-Time Polymerase Chain Reaction , Biological Assay , Mutation
2.
Intervirology ; 2023 Mar 07.
Article in English | MEDLINE | ID: covidwho-2266223

ABSTRACT

INTRODUCTION: MicroRNAs, or miRNAs, with regulatory performance in inflammatory responses and infection are the prevalent manifestations of severe Coronavirus disease (COVID-19). This study aimed to evaluate whether PBMC miRNAs are diagnostic biomarkers to screen the ICU COVID-19 and diabetic-COVID-19 subjects. METHODS: Candidate miRNAs were selected through previous studies, and then the PBMC levels of selected miRNAs (miR-28, miR-31, miR-34a, and miR-181a) were measured via quantitative reverse transcription PCR. The diagnostic value of miRNAs was determined by the receiver operating characteristic (ROC) curve. The bioinformatics analysis was utilized to predict the DEMs genes and relevant bio-functions. RESULTS: The COVID-19 patients admitted to the ICU had significantly greater levels of selected miRNAs compared to non-hospitalized COVID-19 and healthy people. Besides, the mean miR-28 and miR-34a expression levels in the diabetic-COVID-19 group were upregulated considerably when compared with the non-diabetic COVID-19 group. ROC analyses demonstrated the role of miR-28, -miR-34a, and -181a as new biomarkers to discriminate the non-hospitalized COVID-19 group from the COVID-19 patients admitted to ICU samples, and also miR-34a can probably act as a useful biomarker for screening diabetic COVID-19 patients. Using bioinformatics analyses, we found the performance of target transcripts in many bio-processes and diverse metabolic routes such as regulating multiple inflammatory parameters. DISCUSSION: The difference in miRNA expression patterns between the studied groups suggested that miR-28, miR-34a, and miR181a could be helpful as potent biomarkers for diagnosing and controlling COVID-19.

3.
Tanaffos ; 20(3): 240-245, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-2169156

ABSTRACT

Background: Ventilation system besides other prevention strategies such as surface disinfecting and personal protective equipment (PPE) decrease the risk of coronavirus disease 2019 (COVID-19) infection. This study aimed to examine the ventilation system of an intensive care unit (ICU) in a hospital in Tehran, Iran to evaluate the potency of heating, ventilation, and air conditioning system (HVAC) for COVID-19 spread. Materials and Methods: Contamination of air turnover caves was evaluated in supplier diffuser and extractor grills of negative pressure HVAC by ten samples. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the samples was evaluated by the real time reverse transcription-polymerase chain reaction (PCR). Moreover, air conditioning and sick building syndrome (SBS) was assessed according to MM040EA questioning from health care workers. Results: In the health care workers, respiratory effects were more prevalent compared to other signs. Despite suitable air conditioning, this study highlighted carrier potency of ICU workers for SARS-COV-2. Conclusion: According to our results, although the HVAC of ICU ward had an appropriate air movement, it was not safe enough for health care workers.

4.
Biologicals ; 80: 27-34, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-2031158

ABSTRACT

The present study aimed to scrutinize the expression profile of inflammatory-related genes (IFI-16, NOTCH2, CXCL8, and THBS1) from acute to post-acute stage of this infectious epidemic. The current cross-sectional study consisted of 53 acute-phase COVID-19 patients and 53 healthy individuals between February and March 2021. The extraction of total RNA was performed from PBMC specimens and also expression level of selected genes (IFI-16, NOTCH2, CXCL8, and THBS1) was evaluated by real-time PCR. Subsequently, levels of these factors were re-measured six weeks after the acute phase to determine if the levels of chosen genes returned to normal after the acute phase of COVID-19. Receiver operating characteristic (ROC) curve was plotted to test potential of genes as a diagnostic biomarker. The expression levels of inflammatory-related genes were significantly different between healthy and COVID-19 subjects. Besides, a significant higher CXCL8 level was found in the acute-phase COVID-19 compared to post-acute-phase infection which may be able to be considered as a potential biomarker for distinguishing between the acute phases from the post-acute-phase status. Deregulation of the inflammatory-related genes in COVID-19 patients, especially CXCL-8, can be serving as potent biomarkers to manage the COVID-19 infection.


Subject(s)
COVID-19 , Humans , COVID-19/genetics , SARS-CoV-2/genetics , Cross-Sectional Studies , Leukocytes, Mononuclear , Inflammation/genetics , Biomarkers , Receptor, Notch2
5.
BMC Infect Dis ; 22(1): 730, 2022 Sep 08.
Article in English | MEDLINE | ID: covidwho-2021251

ABSTRACT

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%.


Subject(s)
COVID-19 , Pregnancy Complications, Infectious , Adult , Aged , COVID-19/epidemiology , Child , Cross-Sectional Studies , Female , Humans , Infant, Newborn , Infectious Disease Transmission, Vertical , Iran/epidemiology , Mothers , Pregnancy , Pregnancy Complications, Infectious/epidemiology , Prevalence , RNA , SARS-CoV-2/genetics
6.
Int J Immunogenet ; 49(4): 243-253, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1937936

ABSTRACT

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but the pathogenesis is unclear. Host genetic background is one of the main factors influencing the patients' susceptibility to several viral infectious diseases. This study aimed to investigate the association between host genetic polymorphisms of two genes, including vitamin D receptor (VDR) and vitamin D binding protein (DBP), and susceptibility to COVID-19 in a sample of the Iranian population. This case-control study enrolled 188 hospitalized COVID-19 patients as the case group and 218 suspected COVID-19 patients with mild signs as the control group. The VDR (rs7975232, rs731236 and rs2228570) and DBP (rs7041) gene single nucleotide polymorphisms (SNPs) were genotyped by Polymerase Chain Reaction Restriction - Fragment Length Polymorphism (PCR-RFLP) method. A significant association between rs2228570 SNP in the VDR gene and the susceptibility of COVID-19 was found between case and control groups. The CT genotype (Heterozygous) of rs2228570 C > T polymorphism showed significant association with a 3.088 fold increased odds of COVID-19 (p < .0001; adjusted OR: 3.088; 95% CI: 1.902-5.012). In addition, a significant association between CC genotype of rs2228570 CT polymorphism and increased odds of COVID-19 in male and female groups (p = .001; adjusted OR: 3.125; 95% CI: 1.630-5.991 and p = .002; adjusted OR: 3.071; 95% CI: 1.485-6.354 respectively) were determined. Our results revealed no significant differences in the frequency of genotype and allele of VDR (rs7975232 and rs731236) and DBP (rs7041) between SARS-CoV-2-infected patients and controls (p > .05). Our results showed that polymorphism of VDR (rs2228570) probably could influence individual susceptibility to COVID-19. The polymorphisms of VDR (rs7975232 and rs731236) and DBP (rs7041) were not associated with SARS-CoV-2 infection susceptibility.


Subject(s)
COVID-19 , COVID-19/genetics , Case-Control Studies , Female , Gene Frequency , Genetic Predisposition to Disease , Genotype , Humans , Iran/epidemiology , Male , Polymorphism, Single Nucleotide , Receptors, Calcitriol/genetics , SARS-CoV-2
7.
Braz J Infect Dis ; 26(3): 102354, 2022.
Article in English | MEDLINE | ID: covidwho-1803609

ABSTRACT

INTRODUCTION: One of the hallmarks of COVID-19 is overwhelming inflammation, which plays a very important role in the pathogenesis of COVID-19. Thus, identification of inflammatory factors that interact with the SARS-CoV-2 can be very important to control and diagnose the severity of COVID-19. The aim of this study was to investigate the expression patterns of inflammation-related non-coding RNAs (ncRNAs) including MALAT-1, NEAT-1, THRIL, and miR-155-5p from the acute phase to the recovery phase of COVID-19. METHODS: Total RNA was extracted from Peripheral Blood Mononuclear Cell (PBMC) samples of 20 patients with acute COVID-19 infection and 20 healthy individuals and the expression levels of MALAT-1, NEAT-1, THRIL, and miR-155-5p were evaluated by real-time PCR assay. Besides, in order to monitor the expression pattern of selected ncRNAs from the acute phase to the recovery phase of COVID-19 disease, the levels of ncRNAs were re-measured 6‒7 weeks after the acute phase. RESULT: The mean expression levels of MALAT-1, THRIL, and miR-155-5p were significantly increased in the acute phase of COVID-19 compared with a healthy control group. In addition, the expression levels of MALAT-1 and THRIL in the post-acute phase of COVID-19 were significantly lower than in the acute phase of COVID-19. According to the ROC curve analysis, these ncRNAs could be considered useful biomarkers for COVID-19 diagnosis and for discriminating between acute and post-acute phase of COVID-19. DISCUSSION: Inflammation-related ncRNAs (MALAT-1, THRIL, and miR-150-5p) can act as hopeful biomarkers for the monitoring and diagnosis of COVID-19 disease.


Subject(s)
COVID-19 , MicroRNAs , RNA, Long Noncoding , Biomarkers , COVID-19/complications , COVID-19/diagnosis , COVID-19 Testing , Humans , Inflammation/genetics , Leukocytes, Mononuclear , MicroRNAs/genetics , RNA, Long Noncoding/genetics , SARS-CoV-2 , Post-Acute COVID-19 Syndrome
8.
Med J Islam Repub Iran ; 35: 114, 2021.
Article in English | MEDLINE | ID: covidwho-1594586

ABSTRACT

Background: The COVID-19 infection is a novel virus that mainly targets the respiratory system via specific receptors without any coronavirus-targeted therapies. Many efforts have been made to prepare specific vaccines for COVID-19 or use of prefabricated vaccines of other similar viruses, especially severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and influenza (flu). We aimed to evaluate the effects of previous flu vaccine injection on severity of incoming COVID-19 infection. Methods: We conducted a large cross-sectional study of 529 hospitalized Iranian COVID patients to evaluate the severity of disease courses in patients with or without previous flu vaccination history using some main factors like length of hospitalization, need for the intensive care unit (ICU) admission and length of stay in the ICU for comparison between COVID-19 infected patients with or without flu vaccination history. For the quantitative data, we used independent-samples t and Mann-Whitney tests. The qualitative data were calculated using the Fisher exact and chi-square tests in IBM SPSS Statistics version 22 (SPSS Inc) and P value <0.05 was considered statistically significant. Results: There were no significant differences in the demographic data of patients, disease, and severity-related parameters between the 2 groups. It means that there were not any significant differences between patients with and without history of flu vaccination regarding mean days of hospitalization, percentage of needing to be admitted to the ICU, days being admitted to the ICU (8.44±6.36 vs 7.94±8.57; 17% vs 11.5%; and 1.17±3.09 vs 0.92±3.04, retrospectively) (p=0.883, 0.235, and 0.809, respectively). In the laboratory tests, in comparison between patients with and without history of previous flu vaccination, only lymphocytes count in the vaccine positive group was higher than the vaccine negative group (20.82±11.23 vs 18.04±9.71) (p=0.067) and creatine phosphokinase (CPK) levels were higher in the vaccine negative group (146.57±109.72 vs 214.15±332.06) (p=0.006). Conclusion: We did not find any association between flu vaccination and decrease in disease severity in our patients. It seems that patients with previous history of flu vaccination may experience less laboratory abnormalities in some parameters that could be interpreted in favor of lower overall inflammation; however, this study cannot answer this definitely because of its design. As we collected retrospective data from only alive discharged patients and had no healthy control group, we could not discuss the probable effect of the vaccine on the mortality rate or its probable protective role against the infection. We need more well-designed controlled studies with different populations in different geographic areas to address the controversies.

9.
Int Immunopharmacol ; 101(Pt A): 108232, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1525825

ABSTRACT

More than a year after the SARS-CoV-2 pandemic, the Coronavirus disease 19 (COVID-19) is still a major global challenge for scientists to understand the different dimensions of infection and find ways to prevent, treat, and develop a vaccine. On January 30, 2020, the world health organization (WHO) officially announced this new virus as an international health emergency. While many biological and mechanisms of pathogenicity of this virus are still unclear, it seems that cytokine storm resulting from an immune response against the virus is considered the main culprit of the severity of the disease. Despite many global efforts to control the SARS-CoV-2, several problems and challenges have been posed in controlling the COVID-19 infection. These problems include the various mutations, the emergence of variants with high transmissibility, the short period of immunity against the virus, the possibility of reinfection in people improved, lack of specific drugs, and problems in the development of highly sensitive and specific vaccines. In this review, we summarized the results of the current trend and the latest research studies on the characteristics of the structure and genome of the SARS-CoV- 2, new mutations and variants of SARS-CoV-2, pathogenicity, immune response, virus diagnostic tests, potential treatment, and vaccine candidate.


Subject(s)
COVID-19/immunology , COVID-19/prevention & control , SARS-CoV-2/immunology , Animals , COVID-19/virology , COVID-19 Testing/methods , COVID-19 Vaccines/therapeutic use , Drug Design , Humans , SARS-CoV-2/chemistry , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , COVID-19 Drug Treatment
10.
Int Immunopharmacol ; 97: 107641, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1198829

ABSTRACT

BACKGROUND: When a new pathogen, such as severe acute respiratory syndrome coronavirus 2, appears all novel information can aid in the process of monitoring and in the diagnosis of the coronavirus disease (COVID-19). The aim of the current study is to elucidate the specific miRNA profile which can act as new biomarkers for distinguishing acute COVID-19 disease from the healthy group and those in the post-acute phase of the COVID-19 disease. METHODS: The expression level of selected miRNAs including let-7b-3p, miR-29a-3p, miR-146a-3p and miR-155-5p were evaluated in peripheral blood mononuclear cells (PBMCs) of COVID-19 patients, in both the acute and post-acute COVID-19 phase of the disease and healthy groups, by real-time PCR assays. Specificity and sensitivity of miRNAs was tested by receiver operating characteristic (ROC) analysis in COVID-19 patients. RESULTS: The expression level of all miRNAs in COVID-19 patients was significantly higher than in the healthy group. Therefore, the expression pattern of miR-29a-3p, miR-146a-3p and let-7b-3p in the post-acute COVID-19 phase was significantly different from the acute COVID-19 phase. ROC analyses demonstrated that miR-29a-3p, -155-5p and -146a-3p may serve as the novel biomarker for COVID-19 diagnosis with high specificity and sensitivity. In addition, miR-29a-3p, and -146a-3p can maybe act as novel biomarkers for distinguishing acute from post-acute phase of COVID-19 disease. DISCUSSION: The difference in miRNA expression pattern between COVID-19 patients and those in the healthy group, and between acute COVID-19 with post-acute COVID-19, suggested that cellular miRNAs could be used as promising biomarkers for diagnosis and monitoring of COVID-19.


Subject(s)
COVID-19/blood , COVID-19/diagnosis , Leukocytes, Mononuclear/metabolism , MicroRNAs/biosynthesis , Acute Disease , Adult , Aged , Biomarkers/blood , Female , Gene Expression Profiling , Healthy Volunteers , Humans , Male , Middle Aged , ROC Curve , Real-Time Polymerase Chain Reaction
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