Innovation and discovery: The application of nucleic acid-based technology to avian virus detection and characterization

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.

Download Full-text

Virus detection via programmable Type III-A CRISPR-Cas systems

Nature Communications ◽

10.1038/s41467-021-25977-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Sagar Sridhara ◽

Hemant N. Goswami ◽

Charlisa Whyms ◽

Jonathan H. Dennis ◽

Hong Li

Keyword(s):

Nucleic Acid ◽

Detection Method ◽

Virus Detection ◽

High Sensitivity ◽

Nucleic Acid Detection ◽

Immune Effector ◽

Type Iii ◽

System A ◽

Acid Cleavage

AbstractAmong the currently available virus detection assays, those based on the programmable CRISPR-Cas enzymes have the advantage of rapid reporting and high sensitivity without the requirement of thermocyclers. Type III-A CRISPR-Cas system is a multi-component and multipronged immune effector, activated by viral RNA that previously has not been repurposed for disease detection owing in part to the complex enzyme reconstitution process and functionality. Here, we describe the construction and application of a virus detection method, based on an in vivo-reconstituted Type III-A CRISPR-Cas system. This system harnesses both RNA- and transcription-activated dual nucleic acid cleavage activities as well as internal signal amplification that allow virus detection with high sensitivity and at multiple settings. We demonstrate the use of the Type III-A system-based method in detection of SARS-CoV-2 that reached 2000 copies/μl sensitivity in amplification-free and 60 copies/μl sensitivity via isothermal amplification within 30 min and diagnosed SARS-CoV-2-infected patients in both settings. The high sensitivity, flexible reaction conditions, and the small molecular-driven amplification make the Type III-A system a potentially unique nucleic acid detection method with broad applications.

Download Full-text

Effect of large-scale testing platform in prevention and control of the COVID-19 pandemic: an empirical study with a novel numerical model

10.31219/osf.io/c6xzd ◽

2020 ◽

Author(s):

xie qing ◽

wang jing ◽

you jianling ◽

zhu shida ◽

zhou rui ◽

...

Keyword(s):

Nucleic Acid ◽

Large Scale ◽

Ad Hoc ◽

Virus Detection ◽

Nucleic Acid Testing ◽

Transfer Coefficients ◽

Differential Model ◽

Large Scale Testing ◽

Novel Coronavirus ◽

And Control

A large-scale (>20,000 tests per day) standardized and fully-automated laboratory (Huo-Yan) was built as an ad-hoc measure to meet the requirement of virus detection after the novel coronavirus (COVID-19) outbreak in Wuhan, China. We integrated the brief data from Health Commission of Hubei Province and the real-world operation data of Huo-Yan laboratory, into a novel differential model with non-linear transfer coefficients and competitive compartments, to evaluate the trend of suspected cases under different nucleic acid testing capacities, including suspected cases with/without coronavirus infection, to evaluate the achievement of “daily settlement” condition of suspected cases and the control of the epidemic under different nucleic acid testing capacities.

Download Full-text

Application of Gene Probes to Virus Detection in Water

Water Science & Technology ◽

10.2166/wst.1989.0093 ◽

1989 ◽

Vol 21 (3) ◽

pp. 147-154 ◽

Cited By ~ 7

Author(s):

Charles P. Gerba ◽

Aaron B. Margolin ◽

Martinez J. Hewlett

Keyword(s):

Cell Culture ◽

Nucleic Acid ◽

Virus Detection ◽

Enteric Viruses ◽

Serological Tests ◽

Nucleic Acid Probes ◽

Gene Probes ◽

Detection Capabilities ◽

Further Development ◽

A Current

Gene probes offer a rapid and sensitive method for the detection of viruses in water and other environmental samples. Gene probes are small strands of nucleic acid labeled with radioactive or nonradioactive compounds for their detection. The target organism is identified by the hybridization of the probe to the organism's nucleic acid. Nucleic acid probes are at least 1000-fold more sensitive than serological tests such as enzyme-linked-immunoassay and do not first require cultivation of the virus for detection. Gene probes have been developed for organisms that do not grow in cell culture, and probes have been constructed for most of the major groups of enteric viruses. Gene probes have been applied to the detection of enteric viruses in water, marine sediment and shellfish. Radioactively labeled probes can detect as little as 1-10 infectious units of virus within 48 hours. A current disadvantage of probes is that they cannot determine the infectivity of the viruses; however, they can be used to quickly determine the growth of viruses in cell culture. Further development of nonradioactive probes should place virus detection capabilities into the hands of most water quality laboratories.

Download Full-text

Correction: Full Genome Virus Detection in Fecal Samples Using Sensitive Nucleic Acid Preparation, Deep Sequencing, and a Novel Iterative Sequence Classification Algorithm

PLoS ONE ◽

10.1371/journal.pone.0101921 ◽

2014 ◽

Vol 9 (7) ◽

pp. e101921

Author(s):

Keyword(s):

Nucleic Acid ◽

Deep Sequencing ◽

Virus Detection ◽

Classification Algorithm ◽

Iterative Sequence ◽

Sequence Classification ◽

Full Genome ◽

Fecal Samples ◽

Nucleic Acid Preparation

Download Full-text

Comparison of the ID Now Influenza A & B 2, Cobas Influenza A/B, and Xpert Xpress Flu Point-of-Care Nucleic Acid Amplification Tests for Influenza A/B Virus Detection in Children

Journal of Clinical Microbiology ◽

10.1128/jcm.01611-19 ◽

2020 ◽

Vol 58 (3) ◽

Cited By ~ 9

Author(s):

Neena Kanwar ◽

Jeffrey Michael ◽

Kathryn Doran ◽

Emily Montgomery ◽

Rangaraj Selvarangan

Keyword(s):

Nucleic Acid ◽

Influenza A ◽

Point Of Care ◽

Virus Detection ◽

Reference Method ◽

Nucleic Acid Amplification ◽

Molecular Assays ◽

B Virus ◽

Flu Virus ◽

Xpert Assay

ABSTRACT Early diagnosis of influenza (Flu) is critical for patient management and infection control. The ID Now influenza A & B 2 (ID Now) assay (Abbott Laboratories), Cobas influenza A/B nucleic acid test (LIAT; Roche Molecular Systems, Inc.), and Xpert Xpress Flu (Xpert; Cepheid) are rapid, point-of-care molecular assays for Flu virus detection. The study aim was to compare the performances of these three commercially available Clinical Laboratory Improvement Amendments (CLIA)-waived Flu virus assays. We prospectively enrolled 201 children <18 years old from January to April 2018 and collected nasopharyngeal swab specimens in viral medium. Aliquots were frozen for testing on different diagnostic platforms, as per the manufacturers’ instructions. CDC Flu A/B PCR was used as a reference method to evaluate the performances of these three platforms. Among the 201 specimens tested, the CDC Flu A/B PCR assay detected Flu A/B virus in 107 samples (Flu A virus, 73 samples; Flu B virus, 36 samples; dual Flu A/B virus positive, 2 samples), while the ID Now virus detected 102 samples (Flu A virus, 69 samples; Flu B virus, 37 samples; dual Flu A/B virus positive, 4 samples; invalid rate, 1/201 [0.5%]), the LIAT detected 112 samples (Flu A virus, 74 samples; Flu B virus, 38 samples; invalid rate, 11/201 [5.5%]), and the Xpert assay detected 112 samples (Flu A virus, 76 samples; Flu B virus, 36 samples; invalid rate, 6/201 [3.0%]). The overall sensitivities for the ID Now assay, LIAT, and Xpert assay for Flu A virus detection (93.2%, 100%, and 100%, respectively) and Flu B virus detection (97.2%, 94.4%, and 91.7%, respectively) were comparable. The specificity for Flu A and B virus detection by all methods was >97%. These molecular assays had higher sensitivity than did a historical standard-of-care test from the BD Veritor antigen test (Flu A virus, 79.5%; Flu B virus, 66.7%).

Download Full-text