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PubMed2002

Temperature-controlled primer limit for multiplexing of rapid, quantitative reverse transcription-PCR assays: application to intraoperative cancer diagnostics.

BACKGROUND: Rapid-cycling, real-time PCR instruments bring the opportunity for improved intraoperative detection of metastasis to sentinel lymph nodes. Rapid, standardized, and internally controlled assays need to be developed that are sensitive and accurate. METHODS: We describe rapid, multiplexed, internally controlled, quantitative reverse transcription-PCR (QRT-PCR) assays for tyrosinase and carcinoembryonic antigen mRNAs on the SmartCycler (Cepheid). We used a temperature-controlled primer-limiting approach to eliminate amplification of the endogenous control gene as soon as its signal had reached threshold. Positive-control oligonucleotide mimics were incorporated into all reactions to differentiate failed reactions from true negative samples. RESULTS: The optimized assays for rapid QRT-PCR yielded results with threshold cycle values that were only 1-2 cycles higher than slower, more conventional protocols. In rapid PCR, the temperature-controlled multiplex assay was quantitative over a dynamic range of at least 15 cycles, compared with only 6 cycles for conventional multiplexing methods. All histologically positive lymph nodes examined were also QRT-PCR positive for the appropriate marker, and the exogenous, internal positive-control mimics produced signals in all negative samples. CONCLUSION: Internally controlled, rapid QRT-PCR assays can be performed in an intraoperative time frame and with sufficient sensitivity to detect histologically identified metastases to lymph nodes.

Base Sequence↗
PubMed2002

Quantification of bcr/abl mRNA expression level in leukemia cells by FQ-RT-PCR.

OBJECTIVE: To establish a fluorogenic probe quantitative RT-PCR (FQ-RT-PCR) method for detection of bcr/abl mRNA fusion gene expression level in leukemia cells, and provide a useful tool for leukaemia diagnosis and minimal residual disease inspectation. METHOD: The conventional RT-PCR was used to amplify bcr/abl gene from cultured K562 cells, the quantitative standard template was constructed with A-T clone method. The fluo-rogenic quantitative RT-PCR method by using Applied Biosystems 7700 Sequence Detector for detecting the expression of bcr/abl fusion gene was successfully. The sensitivity, stability and repetitiveness of this method was determined. The peripheral blood samples from 14 CML patients, one of whom before and one month after bone marrow transplantation (BMT) and 4 cases of ALL in the early stages were detected. RESULTS: The sensitivity of FQ-RT-PCR for detecting bcr/abl fusion gene was about 10(-5) micro g RNA from K562 cell and 10 copies recombined plasmid. The repetition CT value (cycle threshold) and the coefficient variation (CV) among tubes and batches were 2.0% and 3.7%, respectively. The median bcr/abl fusion gene expression level of 14 CML patients was 5.15 x 10(4) copies/ micro g RNA. The products analyzed by electrophoresis showed that 11 cases were b2a2 and 3 cases b3a2. 1.2 x 10(5) copies/ micro g RNA in one CML patient before BMT was changed to 2.3 x 10(3) copies/ micro g RNA one month after BMT. B2a2 was observed in one of the four (25.0%) patients with ALL, and its level of expression was 8.2 x 10(5) copies/ micro g RNA. CONCLUSION: The established FQ-RT-PCR method is sensitive, specific, reliable, accurate and good at repetitiveness. The results expressed in copies were easy for evaluation and comparation. Two different bcr/abl fusion gene form - b2a2, b3a2 can be detected by the method. It can be widely applied to diagnosis and detection of minimal residual disease for CML and some ALL patients.

Fusion Proteins, bcr-abl↗
PubMed2004

[Reversing multidrug resistance in breast cancer cell line MCF-7/ADR by small interfering RNA].

BACKGROUND & OBJECTIVE: Multidrug resistance of tumor cells often leads to failure of chemotherapy. The over-expression of P-glycoprotein (P-gp), encoded by multidrug resistance 1 (mdr1) gene, plays an important role in multidrug resistance of breast cancer. This study was to explore the feasibility of silencing mdr1 gene by small interfering RNA (siRNA) in drug resistant breast cancer cell line MCF-7/ADR. METHODS: The siRNA oligonucleotides strand designed previously was inserted into pSilencer3.1-H1 Hygro vector, the plasmid was transformed into E.coli. After amplification, the plasmid was purified, and sequenced to determine whether the ligation between siRNA insert and the vector was correct, then transfected into MCF-7/ADR cells, and relevant sensitive MCF-7 cells. MCF-7/ADR cells were screened by hygromycin, surviving cells were cultured. The positive rate of P-gp was detected by flow cytometry, and positive rate of mdr1 gene was detected by real-time relatively quantitative polymerase chain reaction (PCR). Adriamycin (ADM) resistant experiment was performed on MCF-7/ADR cells with siRNA. RESULTS: Positive rate of P-gp in MCF-7/ADR cells was decreased from 99.8% (before siRNA transfection) to 12.3% (after siRNA transfection). Real- time PCR revealed that the threshold cycle value of MCF-7/ADR cells increased from 25.22 to 30.64 after transfected with siRNA. The IC(50) of ADM for MCF-7/ADR cells transfected with siRNA was 0.51 micromol/L, while that for MCF-7/ADR cells without transfection was 17.88 micromol/L. CONCLUSION: siRNA can silence mdr1 gene in MCF-7/ADR cells, may become a new, effective medical technique.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2004

TaqMan reverse transcription polymerase chain reaction for the detection of Japanese encephalitis virus.

One step TaqMan reverse transcription polymerase chain reaction (RT-PCR) using TaqMan probe was developed for detection of Japanese encephalitis virus (JEV). Real-time RT-PCR was optimized to quantify JEV using the detection system (Rotor Gene 2000 detector) and dual-labeled fluorogenic probes. The gene specific labeled fluorogenic probe for the 3' non-translated region (3' NTR) was used to detect JEV. When the specificity of the assay using specific JEV primers was evaluated by testing three different JEV strains, other swine viruses and bovine viral diarrhea virus, no cross-reactions were detected with non-JE reference viruses. A single tube TaqMan assay was shown to be 10-fold more sensitive than the conventional two-step RT-PCR method. Detection limits of two step and real-time RT-PCR for JEV were 112 TCID(50) /ml and 11.2 TCID(50) /ml, respectively. Quantification of JEV was accomplished by a standard curve plotting cycle threshold values (C(t)) versus infectivity titer. Real-time RT-PCR assay using single tube method could be used as a sensitive diagnostic test, and supplied the results in real time for detection and quantification of JEV. We could detect JEV RNA genome in plasma samples of pigs inoculated with KV1899 strain at 2 days post inoculation, but couldn't in 41 fetus samples. This assay was sensitive, specific, rapid and quantitative for the detection of JEV from laboratory and field samples.

Animals↗
PubMed2005

Development of a Lightcycler-based reverse transcription polymerase chain reaction for the detection of foot-and-mouth disease virus.

One step TaqMan real-time reverse transcription polymerase chain reaction (R/T RT-PCR) using a set of primers/probes was developed for the detection of foot-and-mouth disease (FMD) virus. The gene-specific probes labeled fluorogen for the internal ribosomal entry site, Leader sequence and 2B regions were used to detect FMD virus (FMDV). This assay specifically detected FMDV both in cell culture preparations and clinical samples, and was capable of distinguishing FMD from other viral diseases similar to clinical signs (swine vesicular disease, vesicular stomatitis and bovine viral diarrhea). This assay was shown to be 1000-fold more sensitive than the conventional RT-PCR method. The detection limits of this assay was 1 TCID(50)/ml of the FMDV RNA concentration. Quantification was obtained by a standard curves plotting threshold cycle values versus known infectivity titer. The assay was sensitive, specific and rapid enough to detect FMDV RNA genome in probang samples. As such, the described method is reliable and provides faster disease diagnostics than the conventional RT-PCR procedure to detect FMDV.

Animals↗
PubMed2006

[Detection of physical status of human papillomavirus 16 in cervical cancer tissue and SiHa cell line by multiplex real-time polymerase chain reaction].

BACKGROUND & OBJECTIVE: The integration of high-risk human papillomavirus (HPV) into host cell genome is one of the major contributing factors to cervical malignant transformation. The detection of HPV integration is helpful for understanding its role in cervical carcinogenesis and tumor progression. However, there is no ideal detection method of HPV physical status for clinical use. The study was to explore an ideal method of detecting the physical status of HPV-16. METHODS: Setting HPV-16 plasmid as standard, multiplex real-time polymerase chain reaction (PCR) using 2 different fluorescent report radicals was used to quantify the copy numbers of E2 and E6 genes for analysis of the physical status of HPV-16 according to E2/E6. Multiplex real-time PCR test and Southern blot results of cervical cancer cell line SiHa and 27 specimens of HPV-16-positive cervical squamous cell carcinoma were compared. RESULTS: There was a linear relationship between the threshold cycle values and the copy numbers of E2 and E6 in both standard curves, with the correlation coefficients of 1.00 and the amplification efficiencies of above 95%. The 95% reference range of plasmid E2/E6 ratio, in which the amount of E2 DNA was equal to that of E6 DNA, was 0.81-1.29. The cut-off value of E2/E6, which was used to distinguish the pure episomal form from a mixed form of episomal and integrated HPV-16, was 0.81 in the multiplex real-time PCR test. HPV-16 was observed to be integrated into the host genome of SiHa cells by multiplex real-time PCR and Southern blot. The coincidence rate of multiplex real-time PCR and Southern blot was 81.5% (22/27) in the cervical squamous cell cancer tissues (kappa=0.844, P<0.001). CONCLUSION: Multiplex real-time PCR test is a rapid, sensitive and reliable method for detecting the physical status of HPV-16 DNA, and is convenient to be applied in paraffin-embedded tissue and small preneoplastic or early neoplastic cervical lesions, even in cervical scrapes which contain a small amount of DNA.

Adult↗
PubMed2006

[Detection of mdr1 gene by real-time fluorescence quantitative polymerase chain reaction using Taq Man-MGB probe].

OBJECTIVE: Primer Express 2.0 software was used to design the primers and the MGB probe. With the plasmid pHaMDR1/A containing mdr1 cDNA as the template, we established a real-time fluorescent quantitative polymerase chain reaction system, which, at the template concentration of 3.061 x 10(3) to 3.061 x 10(9) cps/ml, had a correlation coefficient of 0.988243 between template concentration and threshold cycle value. This PCR method allows sensitive, specific and quantitative detection of human mdr1 gene.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2026

Evaluation of amplicon-based nanopore sequencing for foot-and-mouth disease viruses in clinical and environmental samples.

Foot-and-mouth disease (FMD) causes severe global economic loss, necessitating rapid viral characterization. Nanopore sequencing provides a simple, real-time workflow suitable for on-site outbreak response, addressing the limitations of conventional methods. In this study, we optimized a previously published amplicon-based protocol and used this method to characterize a diverse range of samples (vesicular fluid, epithelium, serum, nasal/oral swabs, and environmental samples) collected during FMD outbreaks in 2025 in the Republic of Korea. Of the 129 samples collected, we successfully recovered complete genomes from 37 samples and VP1 sequences from 85 samples. Amplifying the S-fragment in isolation and separately barcoding each pool of PCR amplicons markedly improved sequence recovery. Furthermore, sequencing success depended on viral load and sample type. Based on comparisons with real-time RT-PCR results, whole-genome sequence (WGS) recovery exceeded 77.3% at cycle threshold (Ct) values &#x2264;25 across all clinical samples. In the Ct > 30 category, serum samples yielded the highest WGS recovery rates (44.4%). This rate was markedly higher than the success rates observed for epithelium (20.0%) and nasal swabs (9.1%), whereas oral swabs and environmental samples failed to yield any sequences (0%). However, VP1 recovery from environmental samples reached 80% at Ct &#x2264; 30 (8/10), providing an approach to enable non-invasive monitoring. These findings demonstrate that amplicon-based nanopore sequencing is a practical method for the rapid generation of genomic data during FMD outbreaks.IMPORTANCEAlthough rapid detection and genomic data analysis are crucial for effective foot-and-mouth disease (FMD) control, the collection of these data can be challenging for certain sample types and impacted by reduced viral loads that result from nationwide FMD vaccination. This study provides a practical solution through large-scale evaluation of an optimized amplicon-based nanopore sequencing protocol to enhance the sequencing success rates for both clinical and environmental samples. Using a modified protocol to enhance genome recovery, we demonstrated that sequence data could be retrieved from diverse sample types (even with high real-time RT-PCR cycle threshold values). We identified serum as the most suitable sample, with environmental sample sequencing allowing for non-invasive monitoring during outbreaks. These results support the use of nanopore sequencing for rapid genomic analysis, particularly in outbreak responses, such as rapid surveillance, emergency vaccine selection, and epidemiological monitoring.

Foot-and-Mouth Disease↗
PubMed1990

Prevention of cisplatin neurotoxicity with an ACTH(4-9) analogue in patients with ovarian cancer.

In a randomized, double-blind, placebo-controlled study, we assessed the efficacy of an ACTH(4-9) analogue, Org 2766, in the prevention of cisplatin neuropathy in 55 women with ovarian cancer. The analogue was given subcutaneously in a dose of 0.25 mg (low dose) or 1 mg (high dose) per square meter of body-surface area before and after treatment with cisplatin and cyclophosphamide (75 and 750 mg per square meter every three weeks). The threshold of vibration perception was used as the principal measure of neurotoxicity. After four cycles of chemotherapy, the mean (+/- SEM) threshold value for vibration perception in the placebo group increased from 0.67 +/- 0.12 to 1.61 +/- 0.43 microns of skin displacement (P less than 0.0001). In the high-dose treatment group, there was no increase in the threshold value after four cycles (from 0.54 +/- 0.12 to 0.50 +/- 0.06 micron). After six cycles of chemotherapy, the threshold value was 5.87 +/- 1.97 microns in the placebo group (more than an eight-fold increase from base line), as compared with 0.88 +/- 0.17 micron (less than a twofold increase) in the high-dose treatment group (P less than 0.005). In the high-dose group, fewer neurologic signs and symptoms were recorded than in the placebo group. With the lower dose of the analogue, these protective effects were less prominent. No side effects were seen after treatment with Org 2766. The rates of clinical response to chemotherapy were similar in all groups. These results suggest that Org 2766 can prevent or attenuate cisplatin neuropathy without adversely affecting the cytotoxic effect of the drug.

Adrenocorticotropic Hormone↗
PubMed2006

Detection and quantification of the abelson tyrosine kinase domains of the BCR-ABL gene translocation in chronic myeloid leukaemia using genomic quantitative real-time polymerase chain reaction.

INTRODUCTION: Since undetectable BCR-ABL mRNA transcription does not always indicate eradication of the Ph+ CML clone and since transcriptionally silent Ph+ CML cells exist, quantitation by genomic PCR of bcr-abl genes can be clinically useful. Furthermore, hotspot mutations in the Abelson tyrosine kinase (ABLK) domain of the bcr-abl gene translocation in Philadelphia chromosome-positive (Ph+) chronic myeloid leukaemia (CML) cells confer resistance on the specific kinase blocking agent, STI571. MATERIALS AND METHODS: Genomic DNA from K562, CESS and patient CML cells were amplified using rapid cycle quantitative real-time polymerase chain reaction for the gene regions spanning the mutation hotspots. In assays for ABLK exons 4 or 6, exonic or intronic PCR primers were used. RESULTS: We show that separation of cycle threshold (CT) values for log-fold amplicon quantification was 2.9 cycles for ABLK exon 4, and 3.8 cycles for exon 6 with rapid amplification times. K562 CML cells were found to have a approximately 2 log-fold ABLK gene amplification. In contrast, patient CML cells had CT differences of 2.2 for both exon, suggesting that there was no significant ABLK gene amplification. DNA sequencing confirmed that neither K562 nor patient CML cells contained ABLK hotspot mutations. Messenger RNA transcription analysis permitted the assessment of BCR-ABL transcription, which was qualitatively correlated to genomic amplification. CONCLUSIONS: This novel Q-PCR assay was found to have high fidelity and legitimacy, and potentially useful for monitoring minimal residual disease, transcriptionally silent Ph+ CML cells, and bcr-abl gene amplification.

Chronic Disease↗
PubMed2004

Use of an internal positive control in a multiplex reverse transcription-PCR to detect West Nile virus RNA in mosquito pools.

We report on the use of West Nile virus Armored RNA as an internal positive control (IPC) for the extraction and reverse transcription-PCR (RT-PCR) of RNA extracted from field-collected mosquitoes and on a multiplex real-time Taqman RT-PCR to simultaneously detect the 3' noncoding region of West Nile virus and the West Nile virus NS5-2 region comprising the IPC. Mosquito pools from the province of British Columbia, Canada (n = 635), were tested in duplicate and found to be negative for West Nile virus and positive for the IPC. Known West Nile virus-positive supernatants from mosquito pools from the provinces of Alberta and Manitoba were tested in duplicate and found to be positive for both regions of the West Nile virus genome. The mean cycle threshold (Ct) value for the IPC in batch extraction controls +/- 2 standard deviations was found to be 36.43 +/- 1.78 cycles. IPCs of 98.4% (624) of West Nile virus-negative pools fell within this range, indicating the reproducibility of RNA extraction and RT-PCR for pools varying in mosquito genus and number. A comparison of mosquito pool genera revealed no significant genus effect on the Ct value of the IPC. The incorporation of West Nile virus Armored RNA as an IPC allows monitoring of RNA extraction and RT-PCR and detection of false-negative results due to failures in these processes or to PCR inhibition, respectively.

Animals↗
PubMed1983

Cycle detection: a technique for estimating the frequency and amplitude of episodic fluctuations in blood hormone and substrate concentrations.

Investigation of episodic endocrine secretion has been hampered by inadequate analytical techniques for describing patterns of blood concentrations over time. Although standard time series methods, such as autocorrelation and power spectral analysis, are available, their use is limited to special cases in which rhythms are regular. To facilitate the analysis of our own episodic LH data, we have developed a process for determining the frequency and amplitude of both regular and irregular endocrine rhythms (signals) in the presence of high levels of random measurement errors (noise). This process, called cycle detection, engages an iterative, computerized procedure which scans data identifying sequential increases and decreases greater than an initial, preset threshold value. One complete cycle is defined as two increases greater than threshold separated by a decrease which is also greater than threshold. For an initial first pass estimate of frequency and amplitude, the threshold is set at 2.7 times the noise standard deviation. On the next pass, the threshold is readjusted, based on an empirically derived formula, and the data are scanned again. This process is repeated until the threshold reaches a stable value. We have tested the reliability of the cycle detection process by simulating irregular rhythm fluctuations of different frequencies, corrupted by various levels of noise and evaluating the signal characteristics with cycle detection analysis. These tests indicate that cycle detection provides excellent estimates of cycle frequency and amplitude, even with signal to noise ratios as low as 1.5. The ability of this process to analyze cyclic signals of almost any shape, with either regular or irregular rhythms, should make it a valuable tool in the hands of endocrine researchers.

Animals↗
PubMed2001

KAI1 metastasis suppressor gene is frequently down-regulated in cervical carcinoma.

KAI1 is a metastasis suppressor gene located on human chromosome 11p11.2. It belongs to a structurally distinct family of cell surface glycoproteins. Decreased KAI1 expression has been observed in several common solid epithelial tumors, including prostatic, pancreatic, lung, hepatic, colorectal, ovarian, and esophageal cancers. A recent study also observed frequent loss of KAI1 expression in a number of squamous cell carcinomas of the cervix by immunohistochemical technique. To further confirm whether this gene is altered in this malignancy, we analyzed KAI1 expression in various stages of cervical carcinoma by a molecular method. Total cellular RNA was extracted from 84 primary invasive cervical carcinomas and 6 metastatic or recurrent lesions. cDNA was synthesized and was used for real-time quantitative polymerase chain reaction analysis. The level of KAI1 expression was obtained as the value of threshold cycle (Ct) and was quantitated with a comparative Ct method. In addition, paraffin blocks of the tumors were selected and prepared for immunohistochemical study with an anti-KAI1 polyclonal antibody, C-16. Both the real-time quantitative polymerase chain reaction method and immunohistochemical study revealed a frequent decrease in KAI1 expression in invasive cervical cancers and metastatic or recurrent lesions. However, the reduction in KAI1 was not related to progression of the disease. When tumor cell differentiation was analyzed, poorly differentiated tumors showed a greater decrease in KAI1 expression than well or moderately differentiated tumors (P < 0.001). Histologically, KAI1 loss was observed equally in both squamous cell carcinoma and adeno-/adenosquamous carcinoma. Since down-regulation of KAI1 occurs in both early and late stages of cervical cancer, we suggest that its involvement in the progression of this malignancy is an early event.

Adenocarcinoma↗
PubMed2004

Use of real-time PCR for determining copy number and zygosity in transgenic plants.

This review examines how real-time PCR can be used to determine copy number and zygosity in transgenic plants. Distinguishing between plants that harbor one and two copies of a transgene or are hemizygous and homozygous requires the ability to routinely distinguish twofold differences, a detection difference which approaches the resolution of PCR-based quantification methods. After explaining the basic principles, especially the threshold cycle (Ct value) as the basic measuring unit in real-time PCR, we introduce three quantitation methods currently in use. While the absolute and relative standard curve approaches are qualitative methods that distinguish high-copy from low-copy transformants, the comparative (2(-DeltaDeltaCt)) method with double-dye oligonucleotides (TaqMan probes) is able to detect twofold differences. In order to obtain reliable results, Ct values for an amplicon should be below 25 and the standard deviation below 0.3. Although real-time PCR can deliver exact copy number determinations, the procedure is not fail-safe. Therefore, real-time PCR should to be viewed as complementary to--rather than as a replacement of--other methods such as Southern analysis, but it is particularly useful as a preliminary screening tool for estimating copy numbers of a large number of transformants.

DNA, Plant↗
PubMed2006

Comparison of relative mRNA quantification models and the impact of RNA integrity in quantitative real-time RT-PCR.

Relative quantification in quantitative real-time RT-PCR is increasingly used to quantify gene expression changes. In general, two different relative mRNA quantification models exist: the delta-delta Ct and the efficiency-corrected Ct model. Both models have their advantages and disadvantages in terms of simplification on the one hand and efficiency correction on the other. The particular problem of RNA integrity and its effect on relative quantification in qRT-PCR performance was tested in different bovine tissues and cell lines (n = 11). Therefore different artificial and standardized RNA degradation levels were used. Currently fully automated capillary electrophoresis systems have become the new standard in RNA quality assessment. RNA quality was rated according the RNA integrity number (RIN). Furthermore, the effect of different length of amplified products and RNA integrity on expression analyses was investigated. We found significant impact of RNA integrity on relative expression results, mainly on cycle threshold (Ct) values and a minor effect on PCR efficiency. To minimize the interference of RNA integrity on relative quantification models, we can recommend to normalize gene expression by an internal reference gene and to perform an efficiency correction. Results demonstrate that innovative new quantification methods and normalization models can improve future mRNA quantification.

Algorithms↗
PubMed2026

Lesion viral burden, multidrug-resistant superinfection, and HIV-associated haematological vulnerability in hospitalised clade Ib mpox: a prospective cohort study in Uganda.

BACKGROUND: Mpox has shifted to sustained human-to-human transmission across Africa, yet integrated triage incorporating viral burden, bacterial co-infection, antimicrobial resistance (AMR), HIV status, and routine biomarkers remain scarce. METHODS: At Uganda's national mpox referral hospital, we prospectively enrolled 155 adults at 14 &#xb1; 2 days post-symptom onset; mpox was confirmed by lesion-swab qPCR (F3L), with clade assignment by whole-genome sequencing in a prespecified subset (March-April 2025). Lesion viral DNA burden was estimated using qPCR cycle threshold (Ct) values. Purulent lesions underwent EUCAST-standardised culture and susceptibility testing. Routine laboratory assessments included complete blood counts, C-reactive protein, serum chemistries, HIV serostatus, and plasma HIV-1 RNA. FINDINGS: Median age was 30 years, and 73/155 (47%) had HIV infection. Multisite pain, particularly anogenital, was highly prevalent. Among 80 participants with purulent lesions selected for clinically suspected bacterial superinfection, all yielded bacterial growth; 35/80 (43.8%) were polymicrobial and predominantly multidrug-resistant Gram-negative bacilli. Susceptibility to first-line &#x3b2;-lactams and fluoroquinolones was low, whereas meropenem retained activity (51/61, 84%). Lesion viral burden did not differ by HIV serostatus and showed weak correlation with HIV-1 viraemia; higher burden was associated with leucocytosis, neutrophilia with left shift, elevated CRP, and hypoalbuminaemia. Genomes clustered within Clade Ib, without segregation by HIV status or clinical severity. INTERPRETATION: Hospitalised adults with acute Clade Ib mpox in Uganda exhibited high lesion viral burden, frequent multidrug-resistant bacterial co-isolation, and an inflammatory haematological profile accentuated in participants living with HIV-1. These findings support consideration of integrating diagnostic microbiology, HIV viral load assessment, and antimicrobial stewardship into mpox case-management in endemic settings. FUNDING: This study was supported by the Coalition for Epidemic Preparedness Innovations (CEPI; Project ID PRJ-8284).

Adult↗
PubMed2004

Detection of infectious salmon anaemia virus by real-time RT-PCR.

A one-tube real-time reverse transcription-polymerase chain reaction (RT-PCR) using LightCycler technology and SYBR Green chemistry that quantitatively detects infectious salmon anaemia virus (ISAV) in biological samples is described. The assay utilized primers targeting ISAV RNA segment 8, with ISAV isolate U5575-1 as template. The entire optimized assay, including one cycle of reverse transcription, 50 cycles of complementary DNA amplification, and data acquisition and analysis took only 80min. The melting curve and gel electrophoresis analyses of real-time RT-PCR showed harmony with each other as a virus-specific single melting peak and a product of the expected size of 211 bp were obtained. A regression line between the mean threshold cycle (Ct) values and viral template concentrations over a 1:10(5) dilution range with an r(2) value of 0.962 and a slope of -3.771 indicated that the assay was highly reproducible. This assay was 100 times more sensitive than the conventional one-tube RT-PCR assay when compared on the same sample. Analysis of different tissues from fish that survived an ISAV experimental infection further confirmed that real-time RT-PCR was more sensitive than regular RT-PCR for detection of ISAV nucleic acids. Temporal analysis of ISAV-infected TO cell cultures showed that the amount of the specific viral RNA increased more than 100-fold within 32 h post-inoculation (p.i.) and over 1200-fold by 144 h p.i. The melting curve analysis throughout the duration of the infection sampled had a single melting peak suggesting that the virus population was uniform in the targeted region. Quantitative analysis of CHSE-214 cell cultures infected with different ISAV isolates indicated that ISAV isolates, based on their ability to replicate and cause cytopathic effects in CHSE-214 cells, may be differentiated into three CHSE phenotypes: replicating cytopathic, replicating non-cytopathic, and non-replicating. Thus, the SYBR Green real-time RT-PCR is a sensitive, rapid, and highly reproducible assay that can be used to quantitate ISAV in biological samples.

Animals↗
PubMed2004

Detection and quantitation of bovine respiratory syncytial virus using real-time quantitative RT-PCR and quantitative competitive RT-PCR assays.

A single tube, fluorogenic probe-based, real-time quantitative reverse transcription-polymerase chain reaction (Q-RT-PCR) assay was developed for detection and quantitation of bovine respiratory syncytial virus (BRSV) using BioRad's iCycler iQ. Real-time Q-RT-PCR was compared with quantitative competitive RT-PCR (QC-RT-PCR) and viral titers. Viral mRNA levels were measured in BRSV-infected bovine turbinate cell lysate harvested at eight time points (1.5, 6, 12, 24, 36, 48, 60, 72 h) post-infection. A homologous BRSV cRNA standard was used for quantitation of the mRNA by plotting a standard curve of cycle threshold (Ct) values versus standard 10-fold dilutions of cRNA of known concentrations. Detection as low as 171 copies/microl of standard BRSV cRNA was possible. For QC-RT-PCR, a competitor RNA molecule having a deletion was designed and used for quantitation of the BRSV viral mRNA. The results of real-time Q-RT-PCR and QC-RT-PCR assays showed a positive correlation. Real-time Q-RT-PCR was a sensitive, specific, rapid, and efficient method that eliminates the post-PCR processing steps when compared to QC-RT-PCR. Quantitation of BRSV using real-time Q-RT-PCR will have application in studies aimed at understanding the pathogenesis of BRSV.

Animals↗