Differential gene expression analysis of common target genes for the detection of SARS-CoV-2 using real time-PCR.

COVID-19 currently is the main cause of the severe acute respiratory disease and fatal outcomes in human beings worldwide. Several genes are used as targets for the detection of SARS-CoV-2, including the RDRP, N, and E genes. The present study aimed to determine the RDRP, N, and E genes expressions of SARS-CoV- 2 in clinical samples. For this purpose, 100 SARS-CoV-2 positive samples were collected from diagnostic laboratories of Mazandaran province, Iran. After RNA extraction, the real-time reverse transcription PCR (real-time RT-PCR) assay was performed for differential gene expressions' analysis of N, E, and RDRP. The threshold cycle (Ct) values for N, RDRP, and E targets of 100 clinical samples for identifying SARS-CoV-2 were then evaluated using quantitative real-time PCR (qRT-PCR). This result suggests N gene as a potential target for the detection of the SARS-CoV-2, since it was observed to be highly expressed in the nasopharyngeal or oropharynges of COVID-19 patients (P < 0.0001). Herein, we showed that SARS-CoV- 2 genes were differentially expressed in the host cells. Therefore, to reduce obtaining false negative results and to increase the sensitivity of the available diagnostic tests, the target genes should be carefully selected based on the most expressed genes in the cells.

Characteristics and outcome of infants born to mothers with SARS-CoV-2 infection during the first three waves of COVID-19 pandemic in northern Iran: A prospective cross-sectional study.

Background: Despite the rapid increase in knowledge about coronavirus disease 2019 (COVID-19), there is limited data on vertical transmission, viral loads in mother-neonate pairs, and health outcomes. We aimed to describe the characteristics, viral loads, and short-and mid-term outcomes of neonates born to mothers with confirmed COVID-19 infection in northern Iran. Materials and methods: In a cross-sectional study, we prospectively collected and analyzed the clinical features, reverse transcription-polymerase chain reaction (RT-PCR) results, viral loads, and outcomes of 60 neonates delivered by 58 SARS-CoV-2 infected pregnant women in maternity hospitals of Mazandaran University of Medical Sciences (northern Iran) during first three waves of the pandemic from March 1 to December 31, 2020. We assessed neonates' short and mid-term outcomes up to 24 months after the pandemic. We also described the timing of mother-to-infant transmission based on the classification presented by the World Health Organization. Results: Of the 17767 deliveries, 58 mothers had confirmed and probable COVID-19 infection. Twenty (33.3%) neonates were positive for SARS-CoV-2, two of whom had possible in utero transmission. Twenty-five (41.2%) neonates were preterm, most of whom were born during the first and second waves in which mothers were critically ill. 19 (31.7%) patients needed resuscitation in the delivery room. 34 (56.7%) neonates were isolated in the neonatal intensive care unit. We observed a significant relationship between the maternal and neonatal viral load (correlation coefficient = 0.983, P = 0.00). No neonatal death was observed and all babies had a good outcome. Conclusions: The results showed that vertical transmission of SARS-CoV-2 is possible but rare. Regional factors and severity of mother's disease may influence the clinical course of neonates. With increasing experience, proper observance of health precautions, and rapid development of evidence-based response systems for regional and global disasters, the transmission rate of SARS-CoV-2 from mother to newborn is reduced.

Differential gene expression of SARS-CoV-2 transcriptome provides insight into the design of more sensitive diagnostic tests.

The Coronavirus disease 2019 (COVID-19) pandemic is being addressed through RT-PCR, a frontline diagnostic technique. We evaluated gene expression patterns to improve the accuracy and sensitivity of current diagnostic tests. We downloaded relevant next-generation sequencing (NGS) data from the Sequence Read Archive (SRA) database, checked for quality, and mapped them onto the target reference sequence. It was determined that ORF1ab, N, S, and ORF8 genes are mainly expressed based on the results of the quantitative evaluation after normalization by HPRT and elimination of insufficient expression data. ORF8, ORF3a, and M genes were found to have higher expression values than the E gene as a routine RT-PCR detector gene (p*0.05). M gene expression values are also close to ORF8 values. Taking into account the importance of differential expression of genes in the design of diagnostic kits as well as the findings of from this study, it is likely that the M gene is worth further investigation due to its high expression and low mutation rate.

Clinical course, radiological findings and late outcome in preterm infant with suspected vertical transmission born to a mother with severe COVID-19 pneumonia: a case report.

BACKGROUND: Vertical transmission of coronavirus disease 2019 (COVID-19) from mother to newborn infant is doubtful, and very little is known about disease severity and neonatal outcome. CASE PRESENTATION: We present a preterm Iranian infant born to a Persian mother with severe COVID-19 pneumonia. The mother underwent cesarean delivery, and amniotic fluid yielded a positive result for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction (RT-PCR). The newborn infant showed early-onset infection with SARS-CoV-2 confirmed on pharyngeal swabs by RT-PCR assay within 24 hours after birth, suggesting vertical transmission. Unfortunately, the mother died 14 days after delivery. We describe the clinical course and outcome of the infant up to 7 months of age. CONCLUSION: COVID-19 infection in pregnant women may increase maternal morbidity, mortality and possibly vertical transmission in severe cases. However, it does not seem to progress to serious early or late neonatal complications.

Frequency of 16S rRNA Methylase and Aminoglycoside-Modifying Enzyme Genes among Clinical Isolates of Acinetobacter baumannii in Iran.

BACKGROUND & OBJECTIVE: Multidrug-resistant Acinetobacter baumannii (MDR-AB) is an important nosocomial pathogen which is associated with significant morbidity and mortality, particularly in high-risk populations. Aminoglycoside-modifying enzymes (AMEs) and 16S ribosomal RNA (16S rRNA) methylation are two important mechanisms of resistance to aminoglycosides. The aim of this study was to determine the prevalence of 16S rRNA methylase (armA, rmtA, rmtB, rmtC, and rmtD), and the AME genes [aac(6')-Ib, aac(3)-I, ant(3'')-I, aph(3')-I and aac(6')-Id], among clinical isolates of A. baumannii in Tehran, Iran. METHODS: Between November 2015 to July 2016, a total of 110 clinical strains of A. baumannii were isolated from patients in two teaching hospitals in Tehran, Iran. Antimicrobial susceptibility testing was performed according to Clinical and Laboratory Standards Institute guidelines. The presence of genes encoding the AMEs and 16S rRNA methylases responsible for resistance was investigated by multiplex polymerase chain reaction. RESULTS: The results showed that colistin was an effective antibiotic and could be used as a last-resort treatment of infections caused by MDR-AB. The resistance rate to aminoglycosides were 100%, 96.36% and 90.9% for tobramycin, gentamicin and amikacin, respectively. In this study, AME genes of aac(6')-Ib, aac(3)-I and ant(3'')-I were most prevalent among the isolated strains. CONCLUSION: Markedly high resistance to tobramycin, gentamicin and amikacin was noted in current study. Our results suggested that modifying enzyme genes in conjunction with methylation of 16S rRNA might contribute to aminoglycoside resistance induced in vivo in A. baumannii. Further studies are required to determine the prevalence of the aminoglycoside resistance genes in other hospitals of Iran.

A systematic review and meta-analysis of seroprevalence of varicella zoster virus: A nationwide population-based study.

Varicella zoster virus (VZV) causes chicken pox as a primary infection following which it becomes latent in neurons. It may then reactivate to cause shingles (herpes zoster). Severity of lesions and VZV pathogenicity are depended on the host's immune response and variant in VZV Dr Athina Myrto ChioniIdentification of VZV seroprevalance rate in general population may lead to develop new health strategic managements such as vaccination. Therefore, we aimed to provide a systematic review of the seroprevalence of VZV infection among Iranian population and estimate age- and gender- specific prevalence of VZV. Keywords "seroprevalence"; "varicella zoster virus" and "Iran"; were searched in international electronic databases and also in national Persian databases. Twenty two pooled studies among 262 total studies containing (240 published articles; 18 dissertations; and 4 proceedings abstracts) from 1992 to 2014 with total sample size of 7867 individuals were included in the final review. Data was analyzed using random effect method. The heterogeneity was calculated using I-square statistics The overall IgG seroprevalence rate of VZV infection in general population of Iran was 78.50% (95% CI; 77.74%-79.25%). There was significant heterogeneity among the studies (P<0.0001; I2=99.4%). Furthermore, the relative risk of VZV infection is high in females (80.47%, 95% CI; 79.40%-81.54%) and older adults (95.30%, 95% CI; 94.11% -96.48%). Our results may represent a true background and estimation of VZV infection in Iran and generate the cost-benefits immunization program. Moreover, the ensuing data suggests further attention on disease seroprevalence in order to obtain efficient data for therapeutic intervention targeted against VZV.

Prevalence of influenza A/H3N2 virus in northern Iran from 2011 to 2013.

BACKGROUND: Influenza A virus is the most virulent human pathogen and causes the most serious problem. Having epidemiological knowledge about this disease is important. The aim of this study was to determine the prevalence of influenza A/H3N2 virus infection in northern Iran from 2011 to 2013 using the real-time polymerase chain reaction (RT-PCR). METHODS: In this cross-sectional study 57 samples were collected from patients with influenza-like illness (T≥ 38 °C and cough or sore throat. Influenza-RNA was extracted from the samples using PureLink(TM) Viral RNA/DNA Kit. RT-PCR was one using SuperScript III Platinum, Quantitive Real Time PCR system from invitrogen with a specific type of primers and probs. All samples were examined in the Influenza laboratory of Mazandaran University of Medical Sciences. RESULTS: The mean age of patients was 38.2±14.5 year, 278 (48.69%) were males and 293 (51.31%) females. A total number of 201 patients (35.2%) were diagnosed as influenza A1 H3 N2 infection. CONCLUSION: The results show that the prevalence of A/H3N2 in the North of Iran is considerable and needs more attention for preventive measures.

FoxP3+ regulatory T cells in peripheral blood of patients with epithelial ovarian cancer.

BACKGROUND: Ovarian cancer is the fifth leading cause of death from malignancy in women. CD4+CD25+FoxP3+ regulatory T (Treg) cells are a subset of T lymphocytes with great inhibitory impact on immune response. OBJECTIVES: To investigate the percentage of CD4+CD25+FoxP3+ regulatory T cells in the peripheral blood of the Iranian patients with epithelial ovarian cancer compared to healthy women and to evaluate the correlation of the Treg cell percentage with clinicopathological characteristics including cancer stage and CA-125 serum level. METHODS: Seventeen women with epithelial ovarian cancer and 20 healthy subjects were enrolled in the study. Peripheral blood mononuclear cells were stained at the surface, for CD4 and CD25 molecules, followed by fixation, permeabilization and intracellular staining for FoxP3 molecule. After processing and flowcytometry analysis, prevalence of Treg cells was determined as the percentages of CD25+FoxP3+ cells among CD4+ lymphocytes. RESULTS: Despite no difference in the percentage of total CD4+ lymphocytes, analysis indicated that Treg cell percentage was significantly higher in ovarian cancer patients than controls (5.7 ± 3.1% versus 2.8 ± 1.4%, p=0.002). A trend toward higher Treg cells was observed in higher stages of ovarian cancer (III+IV) in comparison to lower stages (I+II) (6.5 ± 3.2% vs. 4.44 ± 2.7%, p=0.2). Higher percentage of Treg cells was also observed in the patients with high CA125 (CA-125 >100 U/mL) in comparison to those with low CA-125 serum level (CA-125 ≤ 100 U/mL) although the difference was not significant (6.44 versus 4.18%, p=0.19). CONCLUSION: Increased frequency of Tregs in ovarian cancer might participate in immune suppression in these patients. The findings collectively suggest the likely impact of Treg cell-targeted immunotherapy in ovarian cancer.

Prevalence and type distribution of high-risk human papillomavirus in patients with cervical cancer: a population-based study.

BACKGROUND: Cervical cancer is the greater cause of cancer death in women in many developing countries. Persistent infection with human papilloma virus (HPV), primarily high risk types 16 and 18, is recognized as a causal and essential factor for the development of cervical cancer. We aimed to determine the distribution of high-risk HPV genotypes in archival biopsies with cervical carcinoma in patients from Mazandaran Province, Northern Iran. METHODS: A total of 98 paraffin-embedded cervical samples consisted of 63 Squamous Cell Carcinomas (SCC), 4 Adenocarcinomas, 19 Cervical Interaepithelial Neoplasia grade I (CIN-I), 4 CIN-II and 8 CIN-III diagnosed during 2009-2011, were selected to perform high risk HPV genotyping using AmpliSens(R) HPV HCR DNA genotyping kit. The prevalence of HPV infections was assessed in low and high grade cervical lesions by age. RESULTS: Of the 98 cervical samples analysed by DNA PCR, 78 (79.59%) were positive for HPV DNA. HPV was detected in the 52 of SCC, 4 of Adenocarcinomas, 14 of CIN-I, 4 of CIN-II, and 4 of CIN-III for HPV. From the 78 HPV positive samples, 23 (29.5%) samples were positive for HPV type 16, 32 (41%) were positive for HPV 18, 19 (24.4%) were positive for HPV 45, and 4 (5.1%) of cervical specimens were positive for HPV 39. CONCLUSIONS: This study provides valuable baseline data for future assessment of the impact of current prophylactic vaccination programs that is protective against the two most common oncogenic types of HPV found in cervical cancer, HPV-16 and HPV-18, but not against other high-risk mucosal HPVs, 39 and 45, reported in this population.