scholarly journals Real-Time PCR with an Internal Control for Detection of All Known Human Adenovirus Serotypes

2008 ◽  
Vol 46 (12) ◽  
pp. 3997-4003 ◽  
Author(s):  
M. Damen ◽  
R. Minnaar ◽  
P. Glasius ◽  
A. van der Ham ◽  
G. Koen ◽  
...  
2009 ◽  
Vol 47 (3) ◽  
pp. 875-875
Author(s):  
M. Damen ◽  
R. Minnaar ◽  
P. Glasius ◽  
A. van der Ham ◽  
G. Koen ◽  
...  

2020 ◽  
Author(s):  
Guilan Lu ◽  
Xiaomin Peng ◽  
Renqing Li ◽  
Yimeng Liu ◽  
Zhanguo Wu ◽  
...  

Abstract Background: Twelve students experienced symptoms of acute respiratory infection (ARI) at a training base in Beijing from August 26 to August 30, 2015. We investigated the cause of this ARI outbreak. Methods: In partnership with the local center for disease control, we collected a total of twelve pharyngeal swab specimens as well as demographic information for the affected patients. We used multiplex real-time PCR to screen for sixteen common respiratory viruses in these samples. To isolate HAdV, we inoculated Hep-2 cells with the human adenovirus (HAdV)-positive samples and then carried out sequencing and phylogenetic analysis of the hexon, fiber, and penton genes of the isolated adenoviruses. In addition, we analyzed the entire genome of one strain isolated from the index case to identify single-nucleotide substitutions. Results: We identified ten HAdV-positive students using multiplex real-time PCR. None of the students were co-infected with other viruses. We successfully isolated seven HAdV strains from the pharyngeal swab specimens. The coding sequences of the hexon, fiber, and penton genes of these seven HAdV strains were identical, suggesting that they represented seven strains from a single virus clone. One HAdV isolate obtained from the index case, BJDX-01-2015, was selected for whole genome analysis. From this isolate, we obtained a 34,774-nucleotide sequence. The genome of BJDX-01-2015 clustered with HAdV-B55 in phylogenetic analyses and had 99.97% identity with human adenovirus 55 isolate HAdV-B/CHN/BJ01/2011/55 (GenBank accession no. JX491639). Conclusions: We identified HAdV-B55 as the strain associated with the August 2015 ARI outbreak at a training base in Beijing. This was the first reported outbreak in Beijing due to HAdV-B55. Continuous surveillance of respiratory adenoviruses is urgently needed to understand the epidemiological and evolutionary features of HAdV-B55, and an epidemiological modeling approach may provide further insights into this emerging public health threat. Furthermore, the clinical laboratory data from this outbreak provides important reference for the clinical diagnosis and may ultimately aid in informing the development of strategies to control and prevent respiratory tract infections caused by HAdV-B55. Keywords: Outbreak, Human adenovirus, Acute Respiratory Infection, Phylogenetic Analysis, Whole Genome Sequencing


Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 31-32
Author(s):  
Guanfang Shi ◽  
Kiron Nair ◽  
Preethi Ramachandran ◽  
Chi Chen ◽  
Ching Wong ◽  
...  

Recent evidence of increased constitutional symptoms and inflammatory cytokines in Philadelphia chromosome negative (Ph (-)) MPN suggests that an inflammatory response is important in the pathogenesis of Ph (-) MPN. Toll-like receptors (TLR), Receptor for Advanced Glycation End products (RAGE) and High mobility group protein B1 (HMGB1) are the important pathways for the inflammatory response. All these three important pathway proteins were studied in MPN diseases in the current studies. Materials and Methods: TLR assay. TLR 2,3, 4, 7, 9 quantification was performed by immuno-staining of 1×106 mononuclear cells (peripheral blood) which were incubated with fluorescence-conjugated anti-TLR-2,3, 4, 7, 9 antibodies and assayed by flow cytometry. HMGB1assay:HMGB1 ELISA kit from Immuno-Biological Laboratories, Inc. (IBL-America) were used. The plasma samples were diluted four times with the provided sample dilution buffer, and assayed in duplicate according to the manufacturer's suggestion. RAGE (RT-PCR) Assay: Total RNA was extracted from normal control or patient mononuclear cells. Predesigned primers for RAGE, and internal control genes were ordered from Qiagen (Germantown, MD). Real-time PCR was performed using SsoAdvanced™ Universal SYBR® Green Supermix (Bio-Rad, Hercules, CA) on Bio-Rad iQ5 Multicolor Real-Time PCR Detection System. At least three house-keeping genes (ribosomal protein L4, TATA box binding protein, and tubulin-α 1b) were used as normalization controls. The expression of RAGE were compared with each internal control. Average of three was used to calculate the ratio of final patient to normal Results: Total of 97 patients with MPN were studied 1) TLR: TLR 3,7,9 was not significantly different from controls. But TLR 2 was significantly increased in both PV, as well as in the MPN group when PV, ET and MF were grouped together as MPN (Fig A). TLR 4 was not significantly increased in PV, ET, MF individually but was found to be significantly increased than the controls, when they are grouped together as MPN (Fig B). 2) RAGE: No significant difference was found between ET, PV, MF individually or when they were grouped together as MPN than the controls (Fig C). 3) HMGB1: No significant difference was seen between ET, PV, MF or when they were grouped as MPN (Fig D). Conclusion: Current study suggests that TLR pathway especially TLR2, and to a lesser extent TLR4 are the important pathways for inflammatory response with increased inflammatory cytokines in MPN, while HMGB1 and RAGE pathways were not different from controls. Figure Disclosures No relevant conflicts of interest to declare.


2020 ◽  
Vol 67 (6) ◽  
pp. 2446-2454 ◽  
Author(s):  
Yin Wang ◽  
Lizhe Xu ◽  
Lance Noll ◽  
Colin Stoy ◽  
Elizabeth Porter ◽  
...  

2005 ◽  
Vol 51 (12) ◽  
pp. 2404-2406 ◽  
Author(s):  
Christoph Koidl ◽  
Michael Bozic ◽  
Jörg Berg ◽  
Markus Stöcher ◽  
Gerhard Mühlbauer ◽  
...  

2008 ◽  
Vol 54 (3) ◽  
pp. 491-499 ◽  
Author(s):  
Sara Bruce ◽  
Katariina Hannula-Jouppi ◽  
Cecilia M Lindgren ◽  
Marita Lipsanen-Nyman ◽  
Juha Kere

Abstract Background: Epigenetic studies, such as the measurement of DNA methylation, are important in the investigation of syndromes influenced by imprinted genes. Quick and accurate quantification of methylation at such genes can be of appreciable diagnostic aid. Methods: We first digested genomic DNA with methylation-sensitive restriction enzymes and used DNA without digestion as a control and nonmethylated λ DNA as an internal control for digestion efficiency. We then performed quantitative real-time PCR analyses with 6 unique PCR assays to investigate 4 imprinting control regions on chromosomes 7 and 11 in individuals with uniparental disomy of chromosome 7 (UPD7) and in control individuals. Results: Our validation of the method demonstrated both quantitative recovery and low methodologic imprecision. The imprinted loci on chromosome 7 behaved as expected in maternal UPD7 (100% methylation) and paternal UPD7 (<10% methylation). In controls, the mean (SD) for percent methylation at 2 previously well-studied restriction sites were 46% (6%) for both H19 and KCNQ1OT1, a result consistent with the previously observed methylation rate of approximately 50%. The methylation percentages of all investigated imprinted loci were normally distributed, implying that the mean and SD can be used as a reference for screening methylation loss or gain. Conclusion: The investigated loci are of particular importance for investigating the congenital Silver–Russell and Beckwith–Wiedemann syndromes; however, the method can also be applied to other imprinted regions. This method is easy to set up, has no PCR bias, requires small amounts of DNA, and can easily be applied to large patient populations for screening the loss or gain of methylation.


2019 ◽  
Vol 82 (9) ◽  
pp. 1512-1523
Author(s):  
ODBERT A. TRIPLETT ◽  
JIEKUN XUAN ◽  
STEVEN FOLEY ◽  
RAJESH NAYAK ◽  
WILLIAM H. TOLLESON

ABSTRACT Having reliable methods for detecting Shiga toxin–producing Escherichia coli (STEC) in foods is an important food safety goal. The majority of STEC outbreaks have involved either the O157:H7 serotype or one of six non-O157 serogroups, O26, O45, O103, O111, O121, and O145, termed “The Big Six.” We have compared detection by PCR of the Shiga toxin genes stx1a and stx2a from STEC bacteria isolated from unclarified apple juice by simple centrifugation with the use of an immunocapture technique to minimize contaminants (such as pectin and polyphenols that may copurify with DNA) that may interfere with DNA amplification efficiencies and limit sensitivity. An internal control for successful immunocapture, DNA extraction, and PCR amplification was generated by introducing the pmRaspberry plasmid into an stx null strain, yielding an E. coli O45 pmRaspberry derivative that can be added to food samples directly. Using serial dilutions of a representative Big Six STEC in apple juice, our immunocapture method resulted in a 50% probability of detection value of 3.34, 2.25, and 4.25 CFU for detection by multiplex real-time PCR, growth on solid agar, and multiplex endpoint PCR, respectively. The time to result was 6.5 h, 9.5 h, and 1.5 days for immunocapture of Big Six STECs and detection by multiplex real-time PCR, endpoint PCR, and growth on solid agar, respectively. A set of 52 Big Six STEC isolates and 30 non–Big Six STEC strains was used to establish the inclusivity and exclusivity of the method. Finally, the ability to detect Big Six STEC contamination reliably was confirmed at 4.5 and 45 CFU/25-mL portions of refrigerated apple juice.


2019 ◽  
Vol 48 (5) ◽  
pp. 492-498
Author(s):  
D. B. Andreychuk ◽  
A. V. Andriyasov ◽  
Z. B. Nikonova ◽  
А. А. Kozlov ◽  
D. L. Suarez ◽  
...  

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Maria Francesca Peruzy ◽  
Yolande Thérèse Rose Proroga ◽  
Federico Capuano ◽  
Federica Corrado ◽  
Serena Santonicola ◽  
...  

The aim of the present study was to develop rapid qualitative and quantitative methods based on the use of Real-Time PCR and Droplet Digital PCR (ddPCR), in order to have reliable techniques to detect and quantify Campylobacter spp. in food samples. The gene 16S-rRNA was used as specific target for Campylobacter spp. Real- Time PCR evaluation assay and a not competitive internal control was ushered in it. To investigate the selectivity of the method, 26 Campylobacter strains and 40 non-Campylobacter strains were tested and in order to verify the application of Real-Time PCR method, 5 pork meat samples were experimentally inoculated with a Campylobacter jejuni strain. Subsequently, dilutions with a bacterial load of Campylobacter jejuni within 10-106 CFU/mL were chosen for the optimization of the ddPCR assay. Lastly, a total of 54 naturally contaminated foods samples were analyzed through molecular (Real-Time PCR and ddPCR) and traditional methods. The Real-Time PCR protocol demonstrated to amplify only the Campylobacter spp. strains and when Campylobacter jejuni was experimentally inoculated in meat samples the pathogen was always detected. The ddPCRs assay allowed to quantify a level of contamination of 10 CFU/mL, but it was unable to quantify levels of 105 – 106 CFU/mL. Lastly, Campylobacter spp. was never detected in the 54 samples tested. In conclusion, the novel analytic approach proposed, based on an initial screening of the samples with Real-Time PCR and then on quantification of Campylobacter spp. with a ddPCR on those positive, represents a quick monitoring tool and, if used correctly, it would allow the implementation of food safety.


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