Evaluation of a novel direct capture method for virus concentration n wastewater from COVID-19 infectious ward and correlation analysis with the number of inpatients.

The global outbreak of the SARS-CoV-2 pandemic has increased the focus of Wastewater-based epidemiology (WBE) studies as a tool for understanding the epidemic and risk management. A highly sensitive and rapid method for the virus concentration from wastewater is needed to obtain the accurate information for early detection of SARS-CoV-2 outbreak and epidemic. In this study, we evaluated the efficiency of the direct capture method provided from Promega, based on column adsorption using the wastewater from actual infectious diseases ward. The efficiency of the nucleic acid extraction-purification process was also evaluated by Maxwell RSC instrument (fully automated extraction) and QIAamp Viral RNA mini kit (manual extraction). The obtained SARS-CoV-2 data from wastewater were analyzed with the number of inpatients which is the consideration of the severity and the days of onset. The combination of direct capture and Maxwell's method (DC-MW) was suggested to be a highly sensitive and simple method with better concentration efficiency and quantification than other methods. Moreover, the inpatient conditions (severity and days of after onset) should be considered to accurately understand the actual status of the correlation between the number of inpatients and SARS-CoV-2 concentration in wastewater. The highly sensitive method of DC-MW was suggested to assess more actual situation of SARS-CoV-2 shedding into the wastewater.

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Comparison of Automated Nucleic Acid Extraction Methods with Manual Extraction

Journal of Molecular Diagnostics ◽

10.2353/jmoldx.2008.070149 ◽

2008 ◽

Vol 10 (4) ◽

pp. 311-316 ◽

Cited By ~ 64

Author(s):

Nicola Dundas ◽

N. Kristine Leos ◽

Midori Mitui ◽

Paula Revell ◽

Beverly Barton Rogers

Keyword(s):

Nucleic Acid ◽

Extraction Methods ◽

Acid Extraction ◽

Nucleic Acid Extraction ◽

Manual Extraction

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Differing Effects of Standard and Harsh Nucleic Acid Extraction Procedures on Diagnostic Helminth Real-Time PCRs Applied to Human Stool Samples

Pathogens ◽

10.3390/pathogens10020188 ◽

2021 ◽

Vol 10 (2) ◽

pp. 188

Author(s):

Tanja Hoffmann ◽

Andreas Hahn ◽

Jaco J. Verweij ◽

Gérard Leboulle ◽

Olfert Landt ◽

...

Keyword(s):

Nucleic Acid ◽

Real Time ◽

Real Time Pcr ◽

Acid Extraction ◽

Nucleic Acid Extraction ◽

Pcr Assay ◽

Bead Beating ◽

Stool Samples ◽

Pcr Assays ◽

Human Stool

This study aimed to assess standard and harsher nucleic acid extraction schemes for diagnostic helminth real-time PCR approaches from stool samples. A standard procedure for nucleic acid extraction from stool and a procedure including bead-beating as well as proteinase K digestion were compared with group-, genus-, and species-specific real-time PCR assays targeting helminths and nonhelminth pathogens in human stool samples. From 25 different in-house and commercial helminth real-time PCR assays applied to 77 stool samples comprising 67 historic samples and 10 external quality assessment scheme samples positively tested for helminths, higher numbers of positive test results were observed after bead-beating-based nucleic acid extraction for 5/25 (20%) real-time PCR assays irrespective of specificity issues. Lower cycle threshold values were observed for one real-time PCR assay after the standard extraction scheme, and for four assays after the bead-beating-based scheme. Agreement between real-time PCR results after both nucleic acid extraction strategies according to Cohen’s kappa ranged from poor to almost perfect for the different assays. Varying agreement was observed in eight nonhelminth real-time PCR assays applied to 67 historic stool samples. The study indicates highly variable effects of harsh nucleic acid extraction approaches depending on the real-time PCR assay used.

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Forensic evaluation of two nucleic acid extraction systems and validation of a RT-qPCR protocol for identification of SARS-CoV-2 in post-mortem nasopharyngeal swabs

Forensic Science International ◽

10.1016/j.forsciint.2021.110775 ◽

2021 ◽

pp. 110775

Author(s):

Pedro A. Barrio ◽

Amparo Fernández-Rodríguez ◽

Pablo Martín ◽

Coro Fernández ◽

Lourdes Fernández ◽

...

Keyword(s):

Nucleic Acid ◽

Forensic Evaluation ◽

Acid Extraction ◽

Post Mortem ◽

Nucleic Acid Extraction

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Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR

Viruses ◽

10.3390/v13040615 ◽

2021 ◽

Vol 13 (4) ◽

pp. 615

Author(s):

Allen Wing-Ho Chu ◽

Cyril Chik-Yan Yip ◽

Wan-Mui Chan ◽

Anthony Chin-Ki Ng ◽

Dream Lok-Sze Chan ◽

...

Keyword(s):

Nucleic Acid ◽

High Throughput ◽

Rna Extraction ◽

Nasopharyngeal Swab ◽

Acid Extraction ◽

Rt Pcr ◽

Nucleic Acid Extraction ◽

Suitable Alternative ◽

Pcr Inhibitors ◽

Pcr Targeting

SARS-CoV-2 RT-PCR with pooled specimens has been implemented during the COVID-19 pandemic as a cost- and manpower-saving strategy for large-scale testing. However, there is a paucity of data on the efficiency of different nucleic acid extraction platforms on pooled specimens. This study compared a novel automated high-throughput liquid-based RNA extraction (LRE) platform (PHASIFYTM) with a widely used magnetic bead-based total nucleic acid extraction (MBTE) platform (NucliSENS® easyMAG®). A total of 60 pools of nasopharyngeal swab and 60 pools of posterior oropharyngeal saliva specimens, each consisting of 1 SARS-CoV-2 positive and 9 SARS-CoV-2 negative specimens, were included for the comparison. Real-time RT-PCR targeting the SARS-CoV-2 RdRp/Hel gene was performed, and GAPDH RT-PCR was used to detect RT-PCR inhibitors. No significant differences were observed in the Ct values and overall RT-PCR positive rates between LRE and MBTE platforms (92.5% (111/120] vs 90% (108/120]), but there was a slightly higher positive rate for LRE (88.3% (53/60]) than MBTE (81.7% (49/60]) among pooled saliva. The automated LRE method is comparable to a standard MBTE method for the detection of SAR-CoV-2 in pooled specimens, providing a suitable alternative automated extraction platform. Furthermore, LRE may be better suited for pooled saliva specimens due to more efficient removal of RT-PCR inhibitors.

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Assay System for Simultaneous Detection of SARS-CoV-2 and Other Respiratory Viruses

Diagnostics ◽

10.3390/diagnostics11061084 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1084

Author(s):

Ho-Jae Lim ◽

Jung-Eun Park ◽

Min-Young Park ◽

Joo-Hwan Baek ◽

Sunkyung Jung ◽

...

Keyword(s):

Respiratory Infections ◽

Simultaneous Detection ◽

Respiratory Viruses ◽

Analytical Performance ◽

Nasopharyngeal Swab ◽

Acid Extraction ◽

Nucleic Acid Extraction ◽

Significant Difference ◽

Z Scores ◽

Syncytial Virus

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggers disease with nonspecific symptoms that overlap those of infections caused by other seasonal respiratory viruses (RVs), such as the influenza virus (Flu) or respiratory syncytial virus (RSV). A molecular assay for accurate and rapid detection of RV and SARS-CoV-2 is crucial to manage these infections. Here, we compared the analytical performance and clinical reliability of Allplex™ SARS-CoV-2/FluA/FluB/RSV (SC2FabR; Seegene Inc., Seoul, South Korea) kit with those of four commercially available RV detection kits. Upon testing five target viral strains (SARS-CoV-2, FluA, FluB, RSV A, and RSV B), the analytical performance of SC2FabR was similar to that of the other kits, with no significant difference (p ≥ 0.78) in z-scores. The efficiency of SC2FabR (E-value, 81–104%) enabled reliable SARS-CoV-2 and seasonal RV detection in 888 nasopharyngeal swab specimens processed using a fully automated nucleic acid extraction platform. Bland–Altman analyses revealed an agreement value of 95.4% (SD ± 1.96) for the kits, indicating statistically similar results for all five. In conclusion, SC2FabR is a rapid and accurate diagnostic tool for both SARS-CoV-2 and seasonal RV detection, allowing for high-throughput RV analysis with efficiency comparable to that of commercially available kits. This can be used to help manage respiratory infections in patients during and after the coronavirus disease 2019 pandemic.

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Synergistic use of electroosmotic flow and magnetic forces for nucleic acid extraction

The Analyst ◽

10.1039/c9an02191d ◽

2020 ◽

Vol 145 (6) ◽

pp. 2412-2419 ◽

Cited By ~ 1

Author(s):

Rachel N. Deraney ◽

Lindsay Schneider ◽

Anubhav Tripathi

Keyword(s):

Nucleic Acid ◽

Electric Field ◽

Microfluidic Chip ◽

Applied Electric Field ◽

Electroosmotic Flow ◽

Acid Extraction ◽

Nucleic Acid Extraction ◽

Magnetic Forces ◽

Extraction And Purification

NA extraction and purification utilitzing a microfluidic chip with applied electric field to induce electroosmotic flow opposite the magnetic NA-bound bead mix.

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