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

Abstract

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.

Evaluation of Seegene Allplex Respiratory Panel 1 kit for the detection of influenza virus and human respiratory syncytial virus

“…It is well known that NA amplification tests are thought to be superior in many aspects as sensitivity or specificity among other parameters compared to conventional diagnostic techniques such as cell culture or antigen based assays [9,10]. However, in addition to the variability of these parameters between the different commercial kits available in the market, the need for the automation of extraction and PCR setup is also demanded to minimize the user-related biased [11]. In this study, the novel Allplex RP1 assay was compared with ProFlu+ and GeneXpert assays for the detection of FLUV and HRSV, and with ProFAST+ to determine the FLUAV subtype.…”

Comparison of an automated nucleic acid extraction system with the column-based procedure

“…Those approaches comprise virus diagnostics for cytomegalovirus [13,16,20], hepatitis virus B and C [18], human immunodefi ciency virus [12,18], PCRs for bacterial [15] and viral [4,15] respiratory pathogens, stool pathogens [14] or commensalic bacteria from stool [7], and biothreat agents [5], as well as PCR diagnostics for parasitic diseases like toxoplasmosis [17] and for fungal pathogens like Aspergillus fumigatus [3]. EZ1 extraction is affected by various preanalytic factors like sample type and chosen preprocessing protocol In-house according to [29] n.a.…”

Clinical consequences of polymerase chain reaction‐based diagnosis of intestinal parasitic infections

“…Naturally, these costs are dependent on the amount of stool samples processed, cost of labor, and current technology in place. As an additional benefit of automation of PCR procedures, the influence of human errors on test results can be minimized . For this reason, the amount of cases in which human errors can occur is already smaller for PCR detection compared with microscopy detection.…”