Mr Noori-Daloii, N Moazami, M Izadyar, S Farhangi, F Beyrami Jamal, A Atalay, Ln Geren, L Akar, E Atalay, B Cirakoglu, E Bermek,
Volume 8, Issue 2 (8-1994)
Abstract
By application of modern recombinant DNA technology, especially the
polymerase chain reaction (PCR)/dot-blot hybridization techniques, we have
investigated the molecular basis of β-thalassemia from four different regions of Iran:
central, south-east, south and north. In this study, the DNA samples were isolated
from patients and for the identification of the mutations, the 6 oligonucleotide probes
for the mutations of IVS.1/nt. 110, .lVS.1/nt.6, IVS.1/nt.1 , nonsense codon 39,
frameshift codon 8 and IVS. 2/nt.1 were selected with respect to their relative
frequency in the neighbouring country, Turkey. Four mutations accounted for76.2%
and of these, the most frequent was the nonsense codon 39 mutation, which accounts
for 60.3% of the β-thalassemia alleles tested. The remainder, in decreasing order of
frequency, wereframeshift codon 8(9.5%), lVS. 1/nt.6 (4.8%) and IVS.1/nt.11O(1.6%).
No hybridization was observed with the probes corresponding to the mutations of
rvS.I/nt I (0/ A) and rvS.2/nt.1 (0/ A). These results also revealed that the distributions
of different types of mutations were different in the four regions. This information
and the introduction to the methodology used in this study will facilitate the prenatal
diagnosis of the disease in Iran.
M Nasrolahei, M Sharif, Hg Robson,
Volume 17, Issue 3 (11-2003)
Abstract
An amplification polymerase chain reaction (PCR) test for the direct detection
of Chlamydia trachomatis in urethral and endocervical swab specimens from
symptomatic and asymptomatic women and men were compared to standard culture
technique.
During 6 months, 300 endocervical swab specimens from 205 asymptomatic
women (64.4%) and 95 symptomatic women (31.6%), and 187 urethral swab
specimens from 79 asymptomatic men (42.3%) and 108 symptomatic men (57.7%)
attending the Gynecology Dept. and Genitourinary Clinic of Royal Victoria Hospital,
Montreal, were collected. Processed specimens were cultured in McCoy
cells and PCR was performed in a tube containing primer for C. trachomatis and
internal control (IC). PCR products were detected by colorimetric and hybridization
assay. Discrepant analysis for any specimens without unanimous results were
performed by direct fluorescent antibody (DFA) or major outer membrane gene
test (MOMP) with the 2SP medium sediment. In this study culture detected 13.1 %
of asymptomatic and 33.6% of symptomatic infected women. By PCR, 16% of
asymptomatic and 45.2% of symptomatic infected women exhibited positive results.
By culture, 36.6% of asymptomatic and 45.3% of symptomatic men were
positive, whereas 50.6% of asymptomatic and 51.8% of symptomatic men were
positive by PCR. Sensitivity and specificity of PCR for asymptomatic and symptomatic
women were 82.5% and 99.3%, and 89.5% and 97.8% respectively. Sensitivity
and specificity of PCR for asymptomatic and symptomatic men were
93% and 100%, and 93.3% and 97.9% respectively. Sensitivity and specificity of
culture for asymptomatic and symptomatic women and men were 67.5% and 100%,
66.6% and 100%,67.4% and 81.6%, and 100% and 100% respectively. The overall
sensitivity and specificity of PCR and culture were 90% and 98%, and 75.6%
and 100%. The internal control revealed that 3.9% of specimens were inhibitory,
but when an aliquot of 10 fold dilution of these specimens was retested, 73.6% of
them were non-inhibitory. In this study PCR exhibited higher sensitivity than
culture for detection of C. trachomatis in both endocervical and urethral swab
specimens and can be recommended for use in the c1inical laboratory.
Atosa Dorudinia, Masoud Shamaei, Shirin Karimi, Alireza Javadi, Leila Mohammadi Ziazi, Mihan Pourabdollah,
Volume 28, Issue 1 (1-2014)
Abstract
Background :Polymerase chain reaction (PCR) assay has widely used for the detection of tuberculosis (TB). This study tried to compare in-house PCR with some well-known commercial PCR kits for detection of TB agent.
Methods : Clinical samples obtained from 620 TB suspected patients were analyzed for the diagnosis of Mycobacterium tuberculosis complex (MTC) by in-house PCR. All samples were obtained through pulmonary specimens consisted of 384 sputum, 148 bronchial aspirates and 88 pleural effusions.
Results :Considering culture as a golden criterion, in which its diagnostic sensitivity and specificity of PCR assay were 87.7% and 85.6%, respectively. The findings of this study also indicate 22.1% (137/620) of the specimens were detected as MTC by PCR. Both PCR and culture confirmed presence of MTC in 57 of the samples. In comparison to culture, the diagnostic sensitivity of PCR for sputum was 87.5% (42/48), bronchial aspirates 100% (12/12), and 60% (3/5) for pleural effusions. The sensitivity of in-house PCR method is comparable with the sensitivity of Amplicor and CobasTaqMan for MTC.
Conclusion :The study illustrates the in-house PCR assay for detection of MTC has high sensitivity and specificity versus approved commercial kits. This could be reliable test in the diagnosis of MTC in resource-limited countries.
Ali Karimi, Ma’soumeh Moezzi, Reza Imani,
Volume 29, Issue 1 (1-2015)
Abstract
Background: Hepatitis B Virus (HBV) causes acute and chronic liver disease worldwide. HBV has eight genotypes (A to H) which is the reflection of its genome with their characteristic geographical distribution. Each genotype could have different pathogenic and therapeutic characteristics. There have been few records on HBV genotyping in general population from our region. This study aimed to determine hepatitis B genotypes using sequencing in the general population of Shahrekord, a Southwestern region of Iran.
Methods: A total of 3000 serum samples (cluster sampling method) were enrolled from general population tested for HBsAg using ELISA. Using appropriate extraction kit, HBV DNA was extracted from HBsAg positive samples and each was subjected to nested PCR for detection of HBV DNA. Finally, using sequencing, the samples were used for HBV genotyping. Data were analyzed by SPSS 19 using descriptive statistics, chi square, and Fisher’s exact test. P-value < 0.05 was considered as the level of significance.
Results: Out of 3000 serum samples, 40 (1.3%) were positive for HBsAg. HBV DNA was detected in 10 out of 40 (25%) of the samples studied. Genotype D was the predominant HBV type found in all of these 10 HBV positive samples.
Conclusion: Genotype D is probably the predominant HBV type in our region.
Maryam Payan, Nader Tajik, Mohammad Reza Rouini, Mohammad Hossein Ghahremani ,
Volume 29, Issue 1 (1-2015)
Abstract
Background: Cytochrome P450 2C19 (CYP2C19) is important in metabolism of wide range of drugs. CYP2C19*17 is a novel variant allele which increases gene transcription and therefore results in ultra-rapid metabolizer phenotype (URM). Distribution of this variant allele has not been well studied worldwide. The aim of present study was to investigate allele and genotype frequencies of CYP2C19*17 in a healthy Iranian population and compare them with other ethnic groups.
Methods : One hundred eighty healthy unrelated Iranian volunteer took part in this study and were genotyped for CYP2C19 *2, *3, *17 (-3402) by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and CYP2C19*17 (-806) by a nested-PCR assays. The distribution of CYP2C19*17 polymorphism in Iranian population was then compared with other ethnic groups.
Results : The CYP2C19*17 allele frequency was 21.6% in Iranian population. Among studied subjects 5.5% were homozygous for CYP2C19*17 and phenotyped as ultra-rapid metabolizers 28.8% were genotyped as CYP2C19*1*17 (extensive metabolizers) and 3.3% as CYP2C19*2*17 (intermediate metabolizers).
Conclusion : The CYP2C19*17 genetic distribution in Iranian population is similar to Middle East or European countries. The high frequency of CYP2C19*17 in Iranian population highlights the importance of this new variant allele in metabolism of CYP2C19 substrates. Thus, future association studies are required to reveal clinical consequence of this genetic polymorphism in carrier individuals.
Seyed Hossein Mirlohi, Kambiz Eftekhari, Rohola Shirzadi, Abolfazl Fateh, Morteza Masoumi, Mohammadreza Modaresi,
Volume 36, Issue 1 (1-2022)
Abstract
Background: Cystic Fibrosis (CF) is a life-threatening autosomal recessive disease. The purpose of this study was to evaluate the value of Polymerase Chain Reaction (PCR) in CF patients with Nontuberculous Mycobacteria (NTM) negative sputum culture.
Methods: This is a descriptive cross-sectional study. The population included all children with CF, aged between 5 - 18 years old, with an NTM negative sputum culture. The patient's sputum samples were sent for smear and culture of NTM, RFLP PCR, and PCR sequence.
Results: In total, 57 CF patients with negative NTM sputum culture were enrolled. Nine patients (15.78%) had positive sputum PCR for NTM. Among these strains, Mycobacterium simiae was the most common one with 5 cases (8.77% of total positive cases).
Conclusion: PCR can be used as an alternative diagnostic method for NTM in CF patients with negative NTM sputum culture, always under clinical suspicion of the disease.
Parsa Mohammadi, Hesam Aldin Varpaei, Arash Seifi, Sepideh Zahak Miandoab, Saba Beiranvand, Sahar Mobaraki, Mostafa Mohammadi, Alireza Abdollahi,
Volume 36, Issue 1 (1-2022)
Abstract
Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel severe acute respiratory syndrome coronavirus. The first known receptor for this virus in the human body is angiotensin-converting enzyme 2 (ACE2), the same receptor for the SARS virus.
Methods: A total of 38 hospitalized adult (18 years) patients with laboratory or clinically confirmed coronavirus disease 2019 (COVID-19) were identified in the infectious disease ward of Tehran Imam Khomeini hospital complex in this single-center cross-sectional study. A blood sample was taken at the time of hospitalization and a second one was taken 48 hours later. Blood samples are kept frozen at -80 degrees Celsius. After the complete collection of samples, the ACE2 level of the samples was measured using a serum sACE2 detection ELISA kit. The data were analyzed using SPSS v26. P value of 0.05 was considered statistically significant. An analysis of covariance was performed to examine the mean differences in day 7 serum ACE2 concentration among the 2 groups after adjusting for the baseline serum ACE2 concentration. The 1-way multivariate analysis of variance was used to determine whether there were any differences between independent groups (mechanical ventilation yes/no) on serum ACE2 levels at 3 different times.
Results: The mean age of patients was 64.13 ± 16.49 years, 21 patients (55.3%) were men, 16 patients (42%) were polymerase chain reaction test positive, and 15 patients (39.5%) died. A total of 35 individuals (92.1%) had chest computed tomography images that indicated lung involvement. A comparison of the 2 groups of patients who died and were discharged revealed that serum ACE2 at the first (p=0.033) and third (7th day) measurements were statistically different (p=0.026). Patients had a mean of serum ACE2. The results indicated that the day 7 serum ACE2 concentration did significantly differ between the 2 groups after controlling for the baseline serum ACE2 concentration (p=0.023). The model explained about 73.61% of the variance in the 7-day serum ACE2 concentration. Specifically, after adjusting for the baseline concentration, survived patients had the lowest level of serum ACE2 concentration (1 ± 0.65) on the 7th day compared with the deceased patient group (2.83 ± 1.12).
Conclusion: Soluble ACE2 in the serum of COVID-19 patients who died, later on, was significantly higher than the discharged patients when the samples were taken seven days after admission. It is suggested that serum soluble ACE2 level could be used as a prognostic factor for COVID-19 patients’ outcomes and also their need for mechanical ventilation.
Shoboo Rahmati, Abbas Bahrampour, Mahshid Nasehi, Ali Mirzazadeh, Hosna Ghaderi, Armita Shahesmaeili,
Volume 36, Issue 1 (1-2022)
Abstract
Background: Tuberculosis is one of the oldest known diseases in humans, and early detection of tuberculosis is one of the main measures to decrease the spread of tuberculosis. In many parts of the world, including Iran, the diagnosis of tuberculosis is based on the detection of acid-fast bacillus in sputum smear microscopy and PCR. this study aimed to synthesize evidence on the diagnostic accuracy of sputum smear and PCR compared to sputum culture for the diagnosis of PT in Iranian patients.
Methods: This systematic review and meta-analysis was conducted based on PRISMA guideline for systematic review and meta-analysis. Eligible studies were cross-sectional original diagnostic studies published in English and Persian in Iran which examined the sensitivity or specificity(study outcome) of sputum smear microscopy or PCR( as the test) relative to sputum culture (as the gold standard/comparator) among Iranian patients suspected of having tuberculosis( study population). Studies whose data were not complete or extractable were excluded.
Results: A total of 3518 subjects were evaluated from 15 eligible studies. The pooled sensitivity of sputum smear and PCR was 75.12 (95% CI: 66.68-83.56) and 88.02 (95% CI: 82.87-93.27), respectively. The specificity for sputum smear and PCR was 93.94 (95% CI: 91.26-96.63) and 91.82 (95% CI: 87.29-96.35) respectively. The sensitivity of both sputum smears was higher in studies published after 2010, and had higher quality. The specificity of sputum smear was a bit lower in studies published after2010 but higher in studies with higher quality. The specificity of PCR was higher in studies published after 2010 but higher in studies with higher quality.
Conclusion: The increased sensitivity of sputum smear and PCR during recent years suggests the improvement of preparation and laboratory methods in recent years. However, the imperfect sensitivity of these tests highlights the need for a more accurate diagnostic method for the detection of pulmonary tuberculosis in Iran.
Sayed Abd Elsabour Kinawy, Abdulhakim Ahmed Assalahi, Ghofran Elnour Elshikh Ahmed, Ahmed Taha, Kamel Abd Elgafar Hassan, Atef Wahdan Alrifai, Mahmoud Helmy Elsaied,
Volume 37, Issue 1 (2-2023)
Abstract
Background: Swine flu (H1N1) and Coronavirus diseases (COVID-19) have been compared in the past few months. Both pandemics sparked a worldwide major panic. Although both have some common symptoms and diagnoses, they are quite different in many aspects. The current study aimed to investigate the differences in clinical and viral behaviors between H1N1 Influenza and COVID-19 pneumonia.
Methods: This was a retrospective study of adult patients hospitalized with H1N1 influenza pneumonia between January 2019 and February 2020, and patients hospitalized with COVID-19 during the outbreak. A demographic and clinical characteristic of H1N1 influenza and COVID-19 patients were recorded. Both groups were compared—using an independent samples student t test for continuous variables and a chi-square test for categorical data—to identify significantly different parameters between the 2 diseases.
Results: A total of 78 patients were included and divided into 2 groups: 33 patients (42.3%) with H1N1 and 45 patients (57.7%) with COVID-19. The mean age of the patients was 43.3 ± 10.6 years. Bronchial asthma was significantly higher among patients with H1N1, while diabetes mellitus was significantly higher among patients with COVID-19. Right lower lobe affection was significantly present among those with H1N1 than those with COVID (100% vs 0%). The monocytic count was significantly higher among those with H1N1 than COVID-19 (11.63 ± 1.50 vs 7.76 ± 1.68; P < 0.001). Respiratory rates of more than 22 c/min significantly increased in patients with HINI than in those with COVID-19 (18.2% vs 4.4%; P = 0.05). Mortality increased in patients with HINI than in those with COVID-19 (18.2% vs 6.7%). However, the difference did not reach statistical significance (P = 0.15).
Conclusion: Clinically, it is difficult to distinguish between H1N1 and COVID-19. Thus, a polymerase chain reaction is recommended for all patients suffering from influenza-like symptoms to rule out influenza A subtype H1N1 and/or SARS-CoV2.
