Real-time Reverse Transcriptase-polymerase Chain Research Articles

Study of MicroRNA-124 in Patients with Lupus Nephritis.

Lupus nephritis is associated with a six-fold increase in mortality compared with the general population. MicroRNAs studies revealed that increased MicroRNA -21 and MicroRNA -155 levels represent risk factors for active LN patients. MicroRNAs can be used as biomarkers in the diagnosis of clinical stages of LN. The present study aimed to determine the level of miR-124 in patients with lupus nephritis by reverse transcriptase real-time polymerase chain reaction compared to healthy control and correlate its levels with biochemical findings in those patients. The study was a case-control study that included fifty patients with lupus nephritis in addition to fifty healthy controls. Blood samples from the participants were subjected to the determination of serological markers of SLE. Moreover, real-time PCR was used for the determination of miR-124. The comparison of Micro-RNA124 between patients and control subjects revealed a statistically significant decrease in Micro-RNA124 in patients (1.193 ± 0.56) compared to the control (3.36 ± 0.50, p <0.001); the comparison of the level of MicroRNA 124 in the patients with different clinical and serological findings of SLE revealed a significant decrease in the level of MicroRNA 124 in patients with muscular findings (1.02 ± 0.5) compared to the patients with negative manifestations (1.47 ± 0.5, p =0.005) Conclusion: In the present study, a comparison of MicroRNA-124 in LN patients with different stages compared to normal control showed a statistically significant decrease in Micro-RNA124 in patients with lupus nephritis p <0.001 with significant correlation to the patients' different clinical and serological findings of SLE. Therefore, it may be used as a new noninvasive therapeutic approach to monitor response to therapy, predict relapses, and identify the degree of the activity of the disease or the progression to the chronic stage.

Anti-Inflammatory Efficacy of Nanobody Specific to β-Glucan on a Fungal Cell Wall in a Murine Model of Fungal Keratitis.

Purpose: to explore the anti-inflammatory effects of a nanobody (Nb) specific to β-glucan on fungal keratitis (FK). Methods: in order to verify the therapeutic and anti-inflammatory efficacy of Nb in FK, the severity of inflammation was assessed with inflammatory scores, hematoxylin-eosin (HE) staining, and myeloperoxidase (MPO) assays. In corneas of mice of FK model and human corneal epithelial cells stimulated by fungal hyphae, real-time reverse transcriptase polymerase chain reaction, Western blot, and enzyme-linked immunosorbent assay were used to detect the expression levels of inflammatory cytokines and pattern recognition receptors (PRRs). In vivo, macrophages and neutrophils infiltration in the cornea stroma was detected by immunofluorescence (IFS) staining. Results: In murine models infected with Aspergillus fumigatus (A. fumigatus), Nb treatment could reduce the inflammatory scores. HE staining and MPO results showed Nb significantly alleviated corneal edema and reduced inflammatory cell infiltration 3 days post-infection. In addition, the expression levels of LOX-1 and Dectin-1 were significantly decreased in the Nb group in vivo. The expression of chemokines CCL2 and CXCL2 also decreased in the Nb group. Compared with the PBS group, the number of macrophages and neutrophils in the Nb group was significantly decreased, which was shown in IFS results. Moreover, Nb attenuated the expression of Dectin-1, LOX-1, and inflammatory mediators, including IL-6 and IL-8 in vitro. Conclusion: our study showed that Nb could alleviate FK by downregulating the expression of PRRs and inflammatory factors as well as reducing the infiltration of macrophages and neutrophils.

Effect of Quorum Sensing Systems on Biofilm Formation and Virulence in Salmonella

In recent years, as the paradigm of communication between cells has been clarified, the ability of bacteria to change their gene expression patterns in response to various extracellular signals has attracted great interest. In particular, intracellular and intercellular communication between bacterial populations, called quorum sensing (QS), is essential for coordinating physiological and genetic activities. QS studies are critical, particularly in elucidating the regulatory mechanisms of infectious processes in food-borne pathogens. Elucidating the QS mechanisms in Salmonella is effective in silencing the virulence factors in the fight against this bacterium. The aims of this study were; to create luxS gene mutants that play a vital role in the QS activity of Salmonella and to determine the effect of this mutation on the expression of virulence genes in the bacteria and to determine the impact of synthetic N-hexanoyl-homoserine lactone (C6HSL) on biofilm formation and AI-2 signaling pathway of Salmonella wild strain and luxS gene mutants. luxS gene mutants were constructed by recombining the gene region with the chloramphenicol gene cassette based on homologous region recombination. In the luxS mutants obtained in this way, the expression of eight different virulence genes (hilA, invA, inv, glgC, fimF, fliF, lpfA, gyrA), which have essential roles in Salmonella pathogenicity, was determined by quantitative real-time reverse transcriptase polymerase chain reaction (rRT-qPCR) method and compared with natural strains. As a result of these studies, it was determined that the expression of each gene examined was significantly reduced in luxS mutant strains. The relative AI-2 activities of Salmonella strains were analyzed depending on time. It was determined that the highest activity occurred at the fourth hour and the AI-2 activities of luxS mutants were reduced compared to the wild strain. Finally, it was determined that C6HSL increased the biofilm activity of Salmonella Typhimurium DMC4, SL1344 wild strains, and mutants, mainly at the 72nd hour. In conclusion, our results proved that C6HSL stimulated QS communication in all strains and increased biofilm of Salmonella formation and autoinducer activity. This situation determines that Salmonella responds to external signals by using QS systems. In addition, this research contributed to provide additional information on interspecies communication mechanisms to develop strategies to prevent biofilm formation of this pathogen.

Expression profile of long noncoding RNAs and comprehensive analysis of lncRNA-cisTF-DGE regulation in condyloma acuminatum

ObjectiveTo identify differentially expressed long noncoding RNAs (lncRNAs) in condyloma acuminatum (CA) and to explore their probable regulatory mechanisms by establishing coexpression networks.MethodsHigh-throughput RNA sequencing was performed to assess genome-wide lncRNA expression in CA and paired adjacent mucosal tissue. The expression of candidate lncRNAs and their target genes in larger CA specimens was validated using real-time quantitative reverse transcriptase polymerase chain reaction (RT‒qPCR). Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used for the functional enrichment analysis of these candidate lncRNAs and differential mRNAs. The coexpressed mRNAs of the candidate lncRNAs, calculated by Pearson’s correlation coefficient, were also analysed using GO and KEGG analysis. In addition, the interactions among differentially expressed lncRNAs (DElncRNAs)-cis-regulatory transcription factors (cisTFs)-differentially expressed genes (DEGs) were analysed and their network was constructed.ResultsA total of 546 lncRNAs and 2553 mRNAs were found to be differentially expressed in CA compared to the paired control. Functional enrichment analysis revealed that the DEGs coexpressed with DElncRNAs were enriched in the terms of cell adhesion and keratinocyte differentiation, and the pathways of ECM-receptor interaction, local adhesion, PI3K/AKT and TGF-ß signaling. We further constructed the network among DElncRNAs-cisTFs-DEGs and found that these 95 DEGs were mainly enriched in GO terms of epithelial development, regulation of transcription or gene expression. Furthermore, the expression of 3 pairs of DElncRNAs and cisTFs, EVX1-AS and HOXA13, HOXA11-AS and EVX1, and DLX6-AS and DLX5, was validated with a larger number of specimens using RT‒qPCR.ConclusionCA has a specific lncRNA profile, and the differentially expressed lncRNAs play regulatory roles in mRNA expression through cis-acting TFs, which provides insight into their regulatory networks. It will be useful to understand the pathogenesis of CA to provide new directions for the prevention, clinical treatment and efficacy evaluation of CA.

Construction and Bioinformatics Analysis of ceRNA Regulatory Networks in Idiopathic Pulmonary Fibrosis.

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive form of pulmonary fibrosis of unknown etiology. Despite ongoing research, there is currently no cure for this disease. Recent studies have highlighted the significance of competitive endogenous RNA (ceRNA) regulatory networks in IPF development. Therefore, this study investigated the ceRNA network associated with IPF pathogenesis. We obtained gene expression datasets (GSE32538, GSE32537, GSE47460, and GSE24206) from the Gene Expression Omnibus (GEO) database and analyzed them using bioinformatics tools to identify differentially expressed messenger RNAs (DEmRNAs), microRNAs (DEmiRNAs), and long non-coding RNAs (DElncRNA). For DEmRNAs, we conducted an enrichment analysis, constructed protein-protein interaction networks, and identified hub genes. Additionally, we predicted the target genes of differentially expressed mRNAs and their interacting long non-coding RNAs using various databases. Subsequently, we screened RNA molecules with ceRNA regulatory relations in the lncACTdb database based on the screening results. Furthermore, we performed disease and functional enrichment analyses and pathway prediction for miRNAs in the ceRNA network. We also validated the expression levels of candidate DEmRNAs through quantitative real-time reverse transcriptase polymerase chain reaction and analyzed the correlation between the expression of these candidate DEmRNAs and the percent predicted pre-bronchodilator forced vital capacity [%predicted FVC (pre-bd)]. We found that three ceRNA regulatory axes, specifically KCNQ1OT1/XIST/NEAT1-miR-20a-5p-ITGB8, XIST-miR-146b-5p/miR-31-5p- MMP16, and NEAT1-miR-31-5p-MMP16, have the potential to significantly affect IPF progression. Further examination of the underlying regulatory mechanisms within this network enhances our understanding of IPF pathogenesis and may aid in the identification of diagnostic biomarkers and therapeutic targets.

The Impact of Cycle Threshold Value in Influencing the Performance of COVID-19 Antigen

COVID-19 antigen is an alternative test for detecting SARS-CoV-2 infection. Viral load represented by the Cycle Threshold (CT) in the Real-Time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCR) affects the diagnostic performance of the test. Higher CT values result in reduced sensitivity of the SARS-CoV-2 antigen. The main objective of this study was to determine the highest CT value in rRT-PCR that still yielded reactive results in the COVID-19 antigen test. This cross-sectional study was conducted at the Fever Outpatient Clinic in Dr. Cipto Mangunkusumo Hospital from July 2020 to June 2021. Two hundred and thirty-five naso-oropharyngeal swabs were taken from patients with confirmed and suspected COVID-19 diagnoses. About 24.7% of subjects were tested positive. The median highest CT value giving reactive COVID-19 antigen results was 28.22 (13.33-39.16), while the median CT value for non-reactive antigen results was 34.45 (26.08-39.65). At a CT value &lt; 40, the COVID-19 antigen test demonstrated 63.8% sensitivity, 99.4% specificity, 89.3% Negative Predictive Value (NPV), and 97.4% Positive Predictive Value (PPV). At the CT value &lt; 25, the test showed 92.3% sensitivity, 99.4% specificity, 99.4% NPV, 92.3% PPV, 163.4 LR+, and 0.1 LR-. The identified cut-off point for the CT value was 29.82, with a sensitivity of 64.9% and specificity of 81%. In conclusion, COVID-19 antigen is a valuable test for screening patients with symptoms of SARS-CoV-2 infection. Understanding the influence of cycle threshold can enhance the interpretation and reliability of the antigen test.

Gastric juice piR-015551: A promising prognostic biomarker for gastric cancer.

e16074 Background: Emerging reports demonstrated that PIWI-interacting RNAs (piRNAs) played an indispensable role in tumorigenesis. However, it still remains elusive whether piR-015551 in gastric juice specific in stomach could be employed as a biomarker for gastric cancer (GC). The present work is aiming at exploring the possibility of piR-015551 in gastric juice as a potential marker to judge for diagnosis and prognosis of gastric cancer. Methods: Gastric juice was collected from 66 GC patients and 66 healthy individuals. Quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) was employed to measure the levels of piR-015551 expression. Then, the pattern of piR-015551 expression in gastric juice was determined between GC patients and healthy individuals. A receiver operating characteristic (ROC) curve was constructed for distinguishing GC from healthy individuals. Results: Gastric juice piR-015551 levels in GC were higher than those of controls (P &lt; 0.0001). The value of area under ROC (AUC) was 0.885 (sensitivity, 90.9%; specificity, 74.2%; 95% confidence interval, 0.8286 to 0.9414). High gastric juice piR-015551 expression was signally correlated with tumor size (P = 0.013) and TNM stage (P = 0.001). GC patients with high piR-015551 expression in gastric juice exerted a poorer overall survival (OS) (P = 0.0152) and progression-free survival (PFS) (P = 0.013). COX regression analysis verified that gastric juice piR-015551 expression was an independent prognostic risk variable for OS (P &lt; 0.05). Conclusions: The current study suggested that piR-015551 in gastric juice had the potential to be a useful biomarker for GC detection and prognosis prediction.

Characteristics, risk factors, and outcomes related to Zika virus infection during pregnancy in Northeastern Thailand: A prospective pregnancy cohort study, 2018-2020.

In response to the 2015-2016 Zika virus (ZIKV) outbreak and the causal relationship established between maternal ZIKV infection and adverse infant outcomes, we conducted a cohort study to estimate the incidence of ZIKV infection in pregnancy and assess its impacts in women and infants. From May 2018-January 2020, we prospectively followed pregnant women recruited from 134 participating hospitals in two non-adjacent provinces in northeastern Thailand. We collected demographic, clinical, and epidemiologic data and blood and urine at routine antenatal care visits until delivery. ZIKV infections were confirmed by real-time reverse transcriptase polymerase chain reaction (rRT-PCR). Specimens with confirmed ZIKV underwent whole genome sequencing. Among 3,312 women enrolled, 12 (0.36%) had ZIKV infections, of which two (17%) were detected at enrollment. Ten (83%, 3 in 2nd and 7 in 3rd trimester) ZIKV infections were detected during study follow-up, resulting in an infection rate of 0.15 per 1,000 person-weeks (95% CI: 0.07-0.28). The majority (11/12, 91.7%) of infections occurred in one province. Persistent ZIKV viremia (42 days) was found in only one woman. Six women with confirmed ZIKV infections were asymptomatic until delivery. Sequencing of 8 ZIKV isolates revealed all were of Asian lineage. All 12 ZIKV infected women gave birth to live, full-term infants; the only observed adverse birth outcome was low birth weight in one (8%) infant. Pregnancies in 3,300 ZIKV-rRT-PCR-negative women were complicated by 101 (3%) fetal deaths, of which 67 (66%) had miscarriages and 34 (34%) had stillbirths. There were no differences between adverse fetal or birth outcomes of live infants born to ZIKV-rRT-PCR-positive mothers compared to live infants born to ZIKV-rRT-PCR-negative mothers. Confirmed ZIKV infections occurred infrequently in this large pregnancy cohort and observed adverse maternal and birth outcomes did not differ between mothers with and without confirmed infections.

The Emergence of Linezolid-Resistant Staphylococcus Epidermidis in the COVID-19 Hospitalized Intubated Patients in North Khorasan, Iran.

The present study aimed to investigate secondary bacterial infections among patients infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Coagulase-negative Staphylococci can infect immunocompromised patients. Linezolid resistance among Staphylococcus epidermidis is one of the most critical issues. In 2019, 185 SARS-CoV-2-positive patients who were admitted to North Khorasan Province Hospital (Bojnurd, Iran), were investigated. Patients having positive SARS-CoV-2 reverse transcriptase real-time polymerase chain reaction (RT-PCR) test results, who had a history of intubation, mechanical ventilation, and were hospitalized for more than 48 hours were included. After microbiological evaluation of pulmonary samples, taken from intubated patients with clinical manifestation of pneumonia, co-infections were found in 11/185 patients (5.94%) with S. epidermidis, Staphylococcus aureus, and Acinetobacter baumani, respectively. Remarkably, seven out of nine S. epidermidis isolates were linezolid resistant. Selected isolates were characterized using antimicrobial resistance patterns and molecular methods, such as Staphylococcal cassette chromosome mec (SCCmec) typing, and gene detection for ica, methicillin resistance (mecA), vancomycin resistance (vanA), and chloramphenicol-florfenicol resistance (cfr) genes. All of the isolates were resistant to methicillin, and seven isolates were resistant to linezolid. Nine out of 11 isolated belonged to the SCCmec I, while two belonged to the SCCmec IV. It should be noted that all patients had the underlying disease, and six patients had already passed away. The increasing linezolid resistance in bacterial strains becomes a real threat to patients, and monitoring such infections, in conjunction with surveillance and infection prevention programs, is very critical for reducing the number of linezolid-resistant Staphylococcal strains. A preprint of this study was published at https://europepmc.org/article/ppr/ppr417742.

Genetic Sequence and Pathogenicity of Infectious Bursal Disease Virus in Chickens in Egypt During 2017-2021.

The continued circulation of infectious bursal disease virus (IBDV) in Egypt, despite the use of various vaccines, is a serious problem that requires continuous detection of IBDV. In the current study, real-time reverse transcriptase polymerase chain reaction testing of 100 diseased chicken flocks during 2017-2021 revealed the presence of very virulent IBDV (vvIBDV) in 67% of the flocks, non-vvIBDV in 11%, and a mixture of both vvIBDV and non-vvIBDV in 4%. Twenty-nine IBDV isolates were submitted for partial sequencing of the viral protein 2 hypervariable region (VP2-HVR), and 27 isolates were confirmed to be genogroup A3 (vvIBDV) with 96.3%-98.5% similarity to the global A3 (vvIBDV) and 88.9%-97% similarity to genogroup A1 vaccine strains. The remaining two isolates were non-vvIBDV and showed 91.1% and 100% identity with classical genogroup A1 strains, respectively. Furthermore, the sequence and phylogenetic analysis of VP1 (amino acids 33-254) of two selected isolates of A3, 5/2017 and 98/2021, clustered them as B2, vvIBDV-like, strains with high similarity (99.5%) to four Egyptian, 99% to Chinese and European, and 97.7% to Chinese and Polish vvIBDV isolates. Experimental infection of commercial broiler chickens with two vvIBDV-A3B2 isolates (5/2017 and 98/2021) showed no mortality despite typical tissue lesions, clear histopathological changes, and strong ELISA antibody response. Isolate 98/2021 was more pathogenic, as confirmed by histopathology, whereas isolate 5/2017 induced a stronger serological response. In conclusion, vvIBDV (A3B2) strains with two amino acid (aa) substitutions in VP1 as V141I and V234I as well as VP2 as Y220F and G254S are still circulating in Egypt.

Detection of SARS-CoV-2 variants distributed from March 2020 to May 2022 and their effect on the infection severity in Iraqi population

New SARS-CoV-2 variants appeared in late December 2020 as Mutations accumulated in the original virus. This study aimed to provide a local database about variants of COVID-19 circulating in the Iraqi population from 2020 to 2022 and the time of emergence of new strains each month since very few local studies have documented its existence in the country. Real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assays were employed to 319 collected and analyzed nasal swabs to determine whether an infection had occurred. A sophisticated diagnostic kit that sorted the distinctive mutations was implemented to evaluate the variants. Results showed Younger patients were more likely to be infected with the Alpha variant (66 patients) than older people (43 patients). Additionally, patients with wild-type infestations had more robust viral load and lower Ct threshold values, culminating in an increase in severity during infection with wild-type virus 26/32 (81.250). Meanwhile, 65/109(59.63%) of patients infected with the Alpha variant developed severe and critical illness and 51/84(60.71%)were infected with Delta or Delta plus variants. In conclusion, the Alpha variant had the highest infection percentage of 109(46.6%), followed by Delta or Delta plus variant 84(26.33%), Beta or Gamma variants 47(20.1%), Omicron variant 46(19.6%), and finally wild-type virus of 32(13.7%). February 2020 witnessed a preliminary finding of the wild-type, while the Alpha variant emerged in December 2020, Beta/Gamma variances were recognized in December 2020, Delta/Delta plus variances began in April 2021, and the Omicron variant debuted in March 2022. Keywords: SARS-CoV-2, Mutation, rRT-PCR, Coronavirus disease 2019, TaqPath, cycle threshold (Ct) value

Detection of SARS-CoV-2 variants distributed from March 2020 to May 2022 and their effect on the infection severity in Iraqi population

New SARS-CoV-2 variants appeared in late December 2020 as Mutations accumulated in the original virus. This study aimed to provide a local database about variants of COVID-19 circulating in the Iraqi population from 2020 to 2022 and the time of emergence of new strains each month since very few local studies have documented its existence in the country. Real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assays were employed to 319 collected and analyzed nasal swabs to determine whether an infection had occurred. A sophisticated diagnostic kit that sorted the distinctive mutations was implemented to evaluate the variants. Results showed Younger patients were more likely to be infected with the Alpha variant (66 patients) than older people (43 patients). Additionally, patients with wild-type infestations had more robust viral load and lower Ct threshold values, culminating in an increase in severity during infection with wild-type virus 26/32 (81.250). Meanwhile, 65/109(59.63%) of patients infected with the Alpha variant developed severe and critical illness and 51/84(60.71%)were infected with Delta or Delta plus variants. In conclusion, the Alpha variant had the highest infection percentage of 109(46.6%), followed by Delta or Delta plus variant 84(26.33%), Beta or Gamma variants 47(20.1%), Omicron variant 46(19.6%), and finally wild-type virus of 32(13.7%). February 2020 witnessed a preliminary finding of the wild-type, while the Alpha variant emerged in December 2020, Beta/Gamma variances were recognized in December 2020, Delta/Delta plus variances began in April 2021, and the Omicron variant debuted in March 2022. Keywords: SARS-CoV-2, Mutation, rRT-PCR, Coronavirus disease 2019, TaqPath, cycle threshold (Ct) value

Validation of improved automated nucleic acid extraction methods for direct detection of polioviruses for global polio eradication

Polioviruses (PV), the main causative agent of acute flaccid paralysis (AFP), are positive-sense single-stranded RNA viruses of the family Picornaviridae. As we approach polio eradication, accurate and timely detection of poliovirus in stool from AFP cases becomes vital to success for the eradication efforts. Direct detection of PV from clinical diagnostic samples using nucleic acid (NA) extraction and real-time reverse transcriptase polymerase chain reaction (rRT-PCR) instead of the current standard method of virus isolation in culture, eliminates the long turn-around time to diagnosis and the need for high viral titer amplification in laboratories. An essential component of direct detection of PV from AFP surveillance samples is the efficient extraction of NA. Potential supply chain issues and lack of vendor presence in certain areas of the world necessitates the validation of multiple NA extraction methods. Using retrospective PV-positive surveillance samples (n=104), two extraction kits were compared to the previously validated Zymo Research Quick-RNA™ Viral Kit. The Roche High Pure Viral RNA Kit, a column-based manual extraction method, and the MagMaX™ Pathogen RNA/DNA kit used in the automated Kingfisher Flex system were both non-inferior to the Zymo kit, with similar rates of PV detection in pivotal rRT-PCR assays, such as pan-poliovirus (PanPV), poliovirus serotype 2 (PV2), and wild poliovirus serotype 1 (WPV1). These important assays allow the identification and differentiation of PV genotypes and serotypes and are fundamental to the GPLN program. Validation of two additional kits provides feasible alternatives to the current piloted method of NA extraction for poliovirus rRT-PCR assays.

Surveillance of Nipah virus in Pteropus medius of Kerala state, India, 2023.

Since 2018, the Indian state of Kerala has reported four Nipah virus (NiV) disease outbreaks, raising concerns about NiV spillover from bats to the human population. Considering this, a cross-sectional study was undertaken in the Pteropus medius bat population around the Nipah virus-affected regions of Kozhikode, Kerala, India, during February, July, and September 2023. Throat swabs, rectal swabs, and organ samples were collected from bats to test for NiV using the real-time reverse transcriptase polymerase chain reaction (RT-PCR), while serum samples were screened for anti-Nipah IgG antibodies through ELISA. An overall seroprevalence of 20.9% was observed in 272 P. medius bats tested. The throat and rectal swab samples of 321 bats were negative for NiV RNA. However, 4 of 44 P. medius bats tested positive for NiV in their liver/spleen samples. The partial N gene retrieved showed more than 99% similarity with the earlier reported NiV genome from Kerala state, India. The findings of the study caution that there is a spillover risk in the region and necessary precautions should be taken.

Advances and Challenges in SARS-CoV-2 Detection: A Review of Molecular and Serological Technologies.

The urgent need for accurate COVID-19 diagnostics has led to the development of various SARS-CoV-2 detection technologies. Real-time reverse transcriptase polymerase chain reaction (RT-qPCR) remains a reliable viral gene detection technique, while other molecular methods, including nucleic acid amplification techniques (NAATs) and isothermal amplification techniques, provide diverse and effective approaches. Serological assays, detecting antibodies in response to viral infection, are crucial for disease surveillance. Saliva-based immunoassays show promise for surveillance purposes. The efficiency of SARS-CoV-2 antibody detection varies, with IgM indicating recent exposure and IgG offering prolonged detectability. Various rapid tests, including lateral-flow immunoassays, present opportunities for quick diagnosis, but their clinical significance requires validation through further studies. Challenges include variations in specificity and sensitivity among testing platforms and evolving assay sensitivities over time. SARS-CoV-2 antigens, particularly the N and S proteins, play a crucial role in diagnostic methods. Innovative approaches, such as nanozyme-based assays and specific nucleotide aptamers, offer enhanced sensitivity and flexibility. In conclusion, ongoing advancements in SARS-CoV-2 detection methods contribute to the global effort in combating the COVID-19 pandemic.

Prospective role of lusianthridin in attenuating cadmium-induced functional and cellular damage in rat thyroid

The thyroid represents the most prevalent form of head and neck and endocrine cancer. The present investigation demonstrates the anticancer effects of Lusianthridin against cadmium (Cd)-induced thyroid cancer in rats. Swiss Wistar rats were utilized in this experimental study. Cd was employed to induce thyroid cancer, and the rats were divided into different groups, receiving oral administration of Lusianthridin (20 mg/kg) for 14 days. Thyroid parameters, deiodinase levels, hepatic parameters, lipid parameters, and antioxidant parameters were respectively estimated. The mRNA expression was assessed using real-time reverse transcriptase polymerase chain reaction (RT-PCR). Lusianthridin significantly (P < 0.001) improved protein levels, T4, T3, free iodine in urine, and suppressed the level of TSH. Lusianthridin significantly (P < 0.001) enhanced the levels of FT3, FT4, and decreased the level of rT3. Lusianthridin significantly (P < 0.001) reduced the levels of D1, D2, D3, and enhanced the levels of hepatic parameters like AST, ALT. Lusianthridin remarkably (P < 0.001) altered the levels of lipid parameters such as LDL, total cholesterol, HDL, and triglycerides; antioxidant parameters viz., MDA, GSH, CAT, and SOD. Lusianthridin significantly altered the mRNA expression of Bcl-2, Bax, MEK1, ERK1, ERK2, p-eIf2α, GRP78, eIf2α, and GRP94. The results clearly state that Lusianthridin exhibits protective effects against thyroid cancer.

COVID-19 in Patients with Different Hematological Malignancies: Treatment Strategy and Outcome: An Iraqi Experience

Background: Patients with hematological malignancies may have higher rates of morbidity and mortality due to SARS-COVID-19 than those in the general population. Objectives: To evaluate the outcome of SARS-COVID-19 in patients with different hematological malignancies undergoing active or modified therapy. Settings: This was a retrospective cohort, multicenter study conducted on 167 patients diagnosed with SARS-COVID-19. The selected patients had been diagnosed with different hematological malignancies and had received treatment (chemotherapy or immunosuppressive). The study was carried out in different centers across Iraq between 1 December 2020 and 1 December 2021. Patients and Methods: This study was conducted in seven hematology centers across Iraq with 167 patients; of these, this study showed that 88 (52.7%) were males and 79 (47.3%) were females (mean age 51.9 ± 18.3 years). All patients had had a COVID-19 infection confirmed through RNA-specific fragments by real-time reverse transcriptase polymerase chain reaction (RT-PCR) of the nasopharyngeal swab specimens, and by computed tomography (CT) of the chest. Demographic data were obtained from patient files, which included the type of hematological malignancy, treatment (chemotherapy, immunotherapy, supportive), severity of COVID-19, modification of treatment and disease outcome for patients, whether alive or not. Patients identified as having benign or non-hematological malignancies were excluded. Results: The treatment protocol was modified in 124 patients (74.3%), while 43 patients (25.7%) continued on the same protocol. Regarding treatment outcomes, 77.2% of patients were alive at the end of the study and 22.8% had died. The survival of COVID-19 patients did not change significantly when the treatment protocol was modified compared to those who continued on treatment as per protocol. The death rate was significantly higher among patients with severe disease compared to those with mild and moderate disease (61.4% v. 0% and 5.0%, respectively) (p&lt;0.001). Conclusions: The management of patients with hematological malignancies during the COVID-19 pandemic may be challenging, with higher mortality in patients with concurrent hematological malignancies and COVID-19. The survival of COVID-19 patients did not change significantly when treatment was modified. Age groups, sex, type of hematological malignancy, and disease status did not affect the survival of these patients. The death rate was significantly higher among patients with hematological malignancies and severe COVID-19 compared with mild or moderate disease.

Optimization of an allelic discrimination real-time RT-PCR assay for detection of H275Y oseltamivir resistance gene mutation among influenza A(H1N1)pdm09 patients from 2020 to 2022.

Influenza virus is known to cause mild to severe respiratory infections and is also prone to genetic mutations. Of all the mutations, neuraminidase (NA) gene mutations are a matter of concern, as most approved antivirals target this protein. During the 2020 influenza season, an emergence of mutation in the NA gene, affecting the binding of the World Health Organization (WHO)-recommended probes to the specific site of the NA gene, was reported by our group. As a result of this mutation, the WHO-recommended allelic discrimination real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was unable to detect wild-type (H275) or mutant oseltamivir-resistant (Y275) strains of influenza A(H1N1)pmd09 viruses. In the current study, the WHO-recommended probes were redesigned according to the mutation in the probe binding site. Fifty undetermined samples (2020-2021) from the previous study were retested with the newly designed probes and found to be positive for H275 and/or Y275. The results obtained were similar to the Sanger sequencing results from the previous study, suggesting that the redesigned probes were efficient in discriminating between wild-type and mutant-type viruses. Furthermore, 133 samples from 2022, making a total of 183 samples (2020-2022), were tested using improved allelic discrimination real-time RT-PCR, and the overall prevalence rate of oseltamivir resistance in 2020-2022 was found to be 0.54%.

Prevalence and Characteristics of Influenza Cases From 2017 to 2019 at a Tertiary Care Teaching Hospital in Karnataka.

Introduction Influenza virus is a significant human pathogen causing severe acute respiratory illness (SARI) associated with significant mortality worldwide. The H1N1 Influenza virus that caused a pandemic in 2009 continued to cause periodic epidemics worldwide, with new variants posing significant public health problems. The present study was carried out to determine the prevalence and characteristics of influenza at a tertiary care teaching hospital. Methods From 2017 to 2019, respiratory samples from suspected cases of influenza belonging to category C received at the microbiology laboratory were transported to Manipal Centre for Virus Research, Manipal,in the cold chain for testing of influenza virus by real-time reverse transcriptase polymerase chain reaction (rRT-PCR) as per CDC guidelines. The microbiological reports were collected and evaluated. The details of patients positive for influenza were analyzed for demographic and clinical characteristics. Results During the study period, 172 samples from SARI patients were tested, out of which 44 patients were positive for the influenza virus, accounting for a prevalence of 25.58%; 84% (n=37) of the cases were infected with H1N1 influenza virus, and the other 11.36% (n=5) and 4.54% (n=2) cases yielded H1N2 and H1N3 influenza virus, respectively. Among 44 patients, 56.81% (n=25) were females and 43.18% (n=19) were males. Most of the patients, 65.9% (n=29), were between 40 and 60 years old. The predominant presenting symptoms were fever in 81.81% (n=36) patients, breathlessness in 56.8% (n=25) patients, and cough in 54.54% (n=24) patients. Twelve (27.27%) patients had acute severe respiratory distress syndrome (ARDS). A significant mortality rate of 22.72% (n=10) was noted in the study. Conclusion A significant prevalence of influenza was noted in the study at 25.58%. Along with the H1N1 Influenza virus, the new strains detected in our region were H1N2 and H1N3 influenza viruses. Regular surveillance is important in the early detection of cases, for timely management, to reduce mortality, and to take measures to prevent the spread of this important infectious disease.

Effects of Coronavirus Disease 2019 on Prevalence of Acute Respiratory Viruses: Changes during the Pandemic.

The coronavirus disease 2019 (COVID-19) pandemic may have influenced the prevalence and seasonality of acute respiratory viral infections. The aim of the study was to investigate the prevalence of all viruses causing acute viral respiratory infections before and after social distancing measures were lifted. Cross-sectional study where outpatients and inpatients at Kyunghee University Hospital were examined. From January 2021 to December 2022, respiratory samples were analyzed using multiplex reverse transcriptase real-time polymerase chain reaction. Of 3953 samples obtained, 412 (10.42%) were positive for acute respiratory viral infection, and 502 viruses were detected. The number of viral infections increased from 184 in 2021 to 318 in 2022. Human metapneumovirus was detected from August to November 2022. Human bocavirus (HBoV) was frequently detected from April to June 2021; however, in 2022, HBoV was frequently detected from July to October. Human parainfluenza virus 3 was rarely detected after its initial frequent detection from October to December 2021 but was continuously observed after frequent detection in September 2022. Co-infection occurred in 78 (18.9%) cases. The most common combination of simultaneous infections was human rhinovirus-HBoV (n = 30, 38.5%). During the COVID-19 pandemic, the incidence of acute respiratory viral infection decreased significantly but increased in 2022 when measures were lifted. The prevalence and seasonality of respiratory viral infections have changed since the pandemic. Our findings contribute to the prediction of an effective response to changes in the prevalence of respiratory viruses.