scholarly journals Evaluation of Nasopharyngeal Swab Collection Techniques for Nucleic Acid Recovery and Participant Experience: Recommendations for COVID-19 Diagnostics

2020 ◽  
Vol 7 (11) ◽  
Author(s):  
Natalie N Kinloch ◽  
Aniqa Shahid ◽  
Gordon Ritchie ◽  
Winnie Dong ◽  
Tanya Lawson ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Copy Number ◽  
Respiratory Infections ◽  
Nasopharyngeal Swab ◽  
Human Dna ◽  
Acid Recovery ◽  
Participant Experience ◽  
Nasal Anatomy ◽  
Adult Volunteers

Abstract Nasopharyngeal swabs are critical to the diagnosis of respiratory infections including coronavirus disease 2019, but collection techniques vary. We compared 2 recommended nasopharyngeal swab collection techniques in adult volunteers and found that swab rotation following nasopharyngeal contact did not recover additional nucleic acid (as measured by human DNA/RNA copy number). Rotation was also less tolerable for participants. Notably, both discomfort and nucleic acid recovery were significantly higher in Asian participants, consistent with nasal anatomy differences. Our results suggest that it is unnecessary to rotate the swab in place following contact with the nasopharynx and reveal that procedural discomfort levels can differ by ethnicity.

scholarly journals Evaluation of nasopharyngeal swab collection techniques for nucleic acid recovery and participant experience: recommendations for COVID-19 diagnostics

2020 ◽  
Author(s):  
Natalie N Kinloch ◽  
Aniqa Shahid ◽  
Gordon Ritchie ◽  
Winnie Dong ◽  
Tanya Lawson ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Copy Number ◽  
Respiratory Infections ◽  
Nasopharyngeal Swab ◽  
Human Dna ◽  
Acid Recovery ◽  
Participant Experience ◽  
Nasal Anatomy ◽  
Adult Volunteers

Nasopharyngeal swabs are critical to the diagnosis of respiratory infections including COVID-19, but collection techniques vary. We compared two recommended nasopharyngeal swab collection techniques in adult volunteers and found that swab rotation following nasopharyngeal contact did not recover additional nucleic acid (as measured by human DNA/RNA copy number). Rotation was also less tolerable for participants. Notably, both discomfort and nucleic acid recovery were significantly higher in Asians, consistent with nasal anatomy differences. Our results suggest that it is unnecessary to rotate the swab in place following contact with the nasopharynx, and reveal that procedural discomfort levels can differ by ethnicity.

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

Viruses ◽  
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.

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

Diagnostics ◽  
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.

scholarly journals Influenza A and B viruses in the population of Vojvodina, Serbia

2014 ◽  
Vol 66 (1) ◽  
pp. 43-50 ◽  
Author(s):  
J. Radovanov ◽  
V. Milosevic ◽  
I. Hrnjakovic ◽  
V. Petrovic ◽  
M. Ristic ◽  
...  
Keyword(s):  
Influenza A ◽  
Respiratory Infections ◽  
Influenza Viruses ◽  
Influenza B Virus ◽  
Nasopharyngeal Swab ◽  
Influenza B ◽  
Influenza A Viruses ◽  
B Virus ◽  
Life Threatening ◽  
Seasonal Epidemic

At present, two influenza A viruses, H1N1pdm09 and H3N2, along with influenza B virus co-circulate in the human population, causing endemic and seasonal epidemic acute febrile respiratory infections, sometimes with life-threatening complications. Detection of influenza viruses in nasopharyngeal swab samples was done by real-time RT-PCR. There were 60.2% (53/88) positive samples in 2010/11, 63.4% (52/82) in 2011/12, and 49.9% (184/369) in 2012/13. Among the positive patients, influenza A viruses were predominant during the first two seasons, while influenza B type was more active during 2012/13. Subtyping of influenza A positive samples revealed the presence of A (H1N1)pdm09 in 2010/11, A (H3N2) in 2011/12, while in 2012/13, both subtypes were detected. The highest seroprevalence against influenza A was in the age-group 30-64, and against influenza B in adults aged 30-64 and >65.

scholarly journals Double emulsion flow cytometry with high-throughput single droplet isolation and nucleic acid recovery

Lab on a Chip ◽  
2020 ◽  
Vol 20 (12) ◽  
pp. 2062-2074 ◽  
Author(s):  
Kara K. Brower ◽  
Catherine Carswell-Crumpton ◽  
Sandy Klemm ◽  
Bianca Cruz ◽  
Gaeun Kim ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Nucleic Acid ◽  
High Throughput ◽  
Double Emulsion ◽  
Single Droplet ◽  
Emulsion Droplets ◽  
Acid Recovery ◽  
Emulsion Flow ◽  
Double Emulsion Droplets

We have developed a novel workflow (sdDE-FACS, s̲ingle d̲roplet D̲ouble E̲mulsion FACS) that allows robust production, screening, and sorting of single double emulsion droplets with complete nucleic acid recovery.

scholarly journals The Curious Strategy of Multipartite Viruses

2020 ◽  
Vol 7 (1) ◽  
pp. 203-218
Author(s):  
Yannis Michalakis ◽  
Stéphane Blanc
Keyword(s):  
Nucleic Acid ◽  
Host Species ◽  
Copy Number ◽  
Viral Particle ◽  
Genome Integrity ◽  
Genome Architecture ◽  
Genomic Integrity ◽  
Virus Genomes

Multipartite virus genomes are composed of several segments, each packaged in a distinct viral particle. Although this puzzling genome architecture is found in ∼17% of known viral species, its distribution among hosts or among distinct types of genome-composing nucleic acid remains poorly understood. No convincing advantage of multipartitism has been identified, yet the maintenance of genomic integrity appears problematic. Here we review recent studies shedding light on these issues. Multipartite viruses rapidly modify the copy number of each segment/gene from one host species to another, a putative benefit if host switches are common. One multipartite virus functions in a multicellular way: The segments do not all need to be present in the same cell and can functionally complement across cells, maintaining genome integrity within hosts. The genomic integrity maintenance during host-to-host transmission needs further elucidation. These features challenge several virology foundations and could apply to other multicomponent viral systems.

The use of one-step nucleic acid amplification (OSNA) and tumor-related factors in the axillary management of breast cancer: A predictive model.

2015 ◽  
Vol 33 (28_suppl) ◽  
pp. 61-61
Author(s):  
Shramana Mitul Banerjee ◽  
Norman R. Williams ◽  
Timothy Ian Davidson ◽  
Soha El-Sheikh ◽  
My-annh Tran-Dang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Lymph Node ◽  
Nucleic Acid ◽  
Sentinel Lymph Node ◽  
Copy Number ◽  
Nucleic Acid Amplification ◽  
Nodal Involvement ◽  
Related Factors ◽  
One Step ◽  
Node Metastases

61 Background: Recent trends in surgical practice advocate selective use of axillary nodal clearance (ANC) following sentinel lymph node biopsy (SNB) in the treatment of breast cancer. We aimed to determine the effectiveness of one-step nucleic acid amplification (OSNA) using CK19 mRNA copy number and tumor-related factors in predicting non-sentinel axillary nodal involvement, in order to formulate local guidelines for ANC. Methods: Patients due to have SNB at our institution for invasive breast cancer as well as selected patients with high grade ductal carcinoma in situ with negative assessment of the axilla on pre-operative imaging were included. Alternate slices of each node were sent for assessment by either OSNA or Histopathology. Immediate ANC was performed if OSNA was positive. The CK19 mRNA copy number, the total tumor load (summation of m RNA copy number of positive nodes,TTL), the total nodal status at ANC and tumor characteristics including grade, tumor size and lymphovascular invasion (LVI) for each patient were determined. A model of risk probability was constructed using TTL and tumor related factors. Results: 664 nodes were examined from 425 patients who had SNB performed between 2011 and 2014. After excluding 8 patients who did not meet the study criteria, 648 nodes from 417 patients were included for analysis. The concordance between OSNA and histology was 91.4%; positive predictive value (PPV) and negative predictive value (NPV) was 77% and 97% respectively. Patients with TTL less than 1400 did not have additional non sentinel lymph node involvement. TTL (p<0.01), and presence of LVI (p<0.05) were predictive for additional nodal involvement. The risk model identified all patients with more than 2 positive nodes as requiring ANC. All patients with non-sentinel node metastases at ANC were selected. Conclusions: OSNA is a sensitive and reliable intraoperative method for the detection of sentinel node metastases. Our study has shown it can also be used to predict the presence of non-sentinel metastases. Patients deemed high risk may be offered immediate ANC while axillary surgery in other groups may be omitted or be decision-based on risk stratification.

scholarly journals Natural-product inhibitors of human DNA ligase I

1996 ◽  
Vol 314 (3) ◽  
pp. 993-1000 ◽  
Author(s):  
Ghee T. TAN ◽  
Sangkook LEE ◽  
Ik-Soo LEE ◽  
Jingwen CHEN ◽  
Pete LEITNER ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Natural Product ◽  
Conformational Changes ◽  
Enzyme Inhibitor ◽  
Enzymic Activity ◽  
Dna Ligase ◽  
Enzyme Active Site ◽  
Dna Relaxation ◽  
Human Dna ◽  
Dna Ligase I

Enzymic activity mediated by recombinant human DNA ligase I (hLI), in conjunction with tannin removal procedures, has been applied to a natural-product screen involving ~1000 plant extracts and various pure compounds. The primary hLI activity assay involved the measurement of the amount of radiolabelled phosphate in a synthetic nucleic acid hybrid that becomes resistant to alkaline phosphatase as a result of ligation. A bioactivity-guided fractionation scheme resulted in the isolation of ursolic [IC50 = 100 μg/ml (216 μM)] and oleanolic [IC50 = 100 μg/ml (216 μM)] acids from Tricalysia niamniamensis Hiern (Rubiaceae), which demonstrated similar DNA ligase inhibition profiles to other triterpenes such as aleuritolic acid. Protolichesterinic acid [IC50 = 6 μg/ml (20 μM)], swertifrancheside [IC50 = 8 μg/ml (11 μM)] and fulvoplumierin [IC50 = 87 μg/ml (357 μM)] represent three additional natural-product structural classes that inhibit hLI. Fagaronine chloride [IC50 = 10 μg/ml (27 μM)] and certain flavonoids are also among the pure natural products that were found to disrupt the activity of the enzyme, consistent with their nucleic acid intercalative properties. Further analyses revealed that some of the hLI-inhibitory compounds interfered with the initial adenylation step of the ligation reaction, indicating a direct interaction with the enzyme protein. However, in all cases, this enzyme–inhibitor interaction did not disrupt the DNA relaxation activity mediated by hLI. These results indicate that, although the same enzyme active site may be involved in both enzyme adenylation and DNA relaxation, inhibitors may exert allosteric effects by inducing conformational changes that disrupt only one of these activities. Studies with inhibitors are important for the assignment of specific cellular functions to these enzymes, as well as for their development into clinically useful antitumour agents.

scholarly journals Evaluation of Three Automated Nucleic Acid Extraction Systems for Identification of Respiratory Viruses in Clinical Specimens by Multiplex Real-Time PCR

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Yoonjung Kim ◽  
Mi-Soon Han ◽  
Juwon Kim ◽  
Aerin Kwon ◽  
Kyung-A Lee
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
False Negative ◽  
Virus Detection ◽  
Turnaround Time ◽  
Nasopharyngeal Swab ◽  
Acid Extraction ◽  
Analytical Sensitivity ◽  
Nucleic Acid Extraction ◽  
Negative Results

A total of 84 nasopharyngeal swab specimens were collected from 84 patients. Viral nucleic acid was extracted by three automated extraction systems: QIAcube (Qiagen, Germany), EZ1 Advanced XL (Qiagen), and MICROLAB Nimbus IVD (Hamilton, USA). Fourteen RNA viruses and two DNA viruses were detected using the Anyplex II RV16 Detection kit (Seegene, Republic of Korea). The EZ1 Advanced XL system demonstrated the best analytical sensitivity for all the three viral strains. The nucleic acids extracted by EZ1 Advanced XL showed higher positive rates for virus detection than the others. Meanwhile, the MICROLAB Nimbus IVD system was comprised of fully automated steps from nucleic extraction to PCR setup function that could reduce human errors. For the nucleic acids recovered from nasopharyngeal swab specimens, the QIAcube system showed the fewest false negative results and the best concordance rate, and it may be more suitable for detecting various viruses including RNA and DNA virus strains. Each system showed different sensitivity and specificity for detection of certain viral pathogens and demonstrated different characteristics such as turnaround time and sample capacity. Therefore, these factors should be considered when new nucleic acid extraction systems are introduced to the laboratory.

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