Performance Evaluation of the Maxwell 16 System for Extraction of Influenza Virus RNA from Diverse Samples

Liu, Hongbo; Gan, Yunhua; Yang, Bo; Weng, Hui; Huang, Chuanfeng; Yang, Di; Lei, Ping; Shen, Guanxin

doi:10.1371/journal.pone.0048094

Cited by 11 publications

(6 citation statements)

References 21 publications

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“…The mean Ct values of the baseline samples were 29.6 and 30.1, respectively, for the Maxwell 16 System and QIAamp extraction methods, and the respective standard deviation (SD) was 0.5 and 0.6, which was in accordance with our previous study [10]. It was considered to be a significant change in RNA yield when a mean Ct value goes beyond the possible variation range (more or less than 1.96 SD) of the assay method by comparison with the corresponding baseline value.…”

Section: Resultssupporting

confidence: 90%

“…The samples treated with buffer B were extracted with the QIAamp Kit and eluted in 60 μl Buffer AVE (Qiagen). Although having different starting and elution volumes (200-μl input and 50-μl output vs 140-μl input and 60-μl output), the two extraction methods in conjunction with either of the two RT-PCR assays below exhibited close detection limits (∼10 -0.3 TCID 50 /ml of the virus) according to our previous study [10] and the preliminary experiments in this study [Liu H,…”

Section: • • Virus Preparationsupporting

confidence: 53%

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Effects of Different Lysis Buffers of Nucleic Acid Purification Kit on the Stability of Influenza Virus RNA

Liu

Gan

et al. 2014

Future Virol.

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aims: Under suboptimal storage and transport conditions, influenza virus (flu-v) RNA is prone to degradation and lysis buffers from RNA extraction kits have a potential to stabilize RNA. The aim of this study was to investigate the effects of different lysis buffers on the stability of flu-v RNA. Materials & methods: Aliquots of flu-v suspension were processed in parallel with two lysis buffers, and then underwent cyclic freeze-thaw or prolonged storage at 4, 22 and -20°C. The viral RNA was analyzed by using real-time and conventional RT-PCR amplifying, respectively, partial and full-length sequences of the flu-v matrix gene. Results: The viral RNA remained intact in samples treated with either of the two lysis buffers for at least 7 days at 4°C, 90 days at -20°C or following seven freeze-thaw cycles, but buffer A was superior to buffer B in protecting RNA from degradation at 4°C and 22°C, or following a further increase of freeze-thaw cycles. conclusion: Lysis buffer preservatives provide viral RNA stabilization, whereas different lysis buffers vary in their ability to stabilize viral RNA, and thus their performance characteristics should be evaluated prior to their application in clinical practice. KeywordsNucleic acid (NA)-based techniques are now widely used in influenza surveillance and diagnosis [1,2]. However, suboptimal storage and transport conditions of influenza virus (flu-v) samples will most likely result in viral RNA degradation [3][4][5], and in some settings it is difficult to ensure certain sample conditions required by WHO, such as ultra-low-temperature freezing, especially for resource-limited areas; consequently, the efficacy of the NA-based assays will be compromised. Thus, inexpensive, simple and efficient sample stabilization methods need to be developed for facilitating flu surveillance and diagnosis.Earlier studies have shown that lysis buffers of NA extraction kits have the potential to be used as RNA stabilization agents at adverse temperatures and over an extended period of time [6,7], and have potential to inactivate viruses completely [8], which would reduce the biohazard risk from sample leakage during transit and simplify transportation requirements while preserving the integrity of viral RNA before testing. Nevertheless, these studies did not give a comprehensive picture of the abilities of lysis buffers in protecting viral RNA from degradation and there are still some questions that remain unanswered. First, could intact viral RNA be recovered from the samples preserved in lysis buffer at adverse temperatures and over an extended period of time, considering that a real-time RT-PCR (rRT-PCR) targeting a shorter fragment was only employed to evaluate the presence, quantity and/or quality of viral RNA in these studies [6,7]? Second, what is the consequence of virus samples preserved in lysis buffer and subjected to repeated freeze-thaw cycles, For reprint orders, please contact: reprints@futuremedicine.com

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Section: Resultssupporting

confidence: 90%

Section: • • Virus Preparationsupporting

confidence: 53%

Effects of Different Lysis Buffers of Nucleic Acid Purification Kit on the Stability of Influenza Virus RNA

Liu

Gan

et al. 2014

Future Virol.

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“…During this study, Isohelix swabs were selected over Copan swabs due to easier handling and higher sensitivity for sample collection, and this approach has been successfully used by other studies (12). Furthermore, our results demonstrated that automated RNA extraction was as efficient (13,14) as manual kits for extracting SARS-CoV-2, which has been previously noted using phenol-chloroform (15).…”

Section: Discussionsupporting

confidence: 53%

End-to-End Protocol for the Detection of SARS-CoV-2 from Built Environments

et al. 2020

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019, is a respiratory virus primarily transmitted person to person through inhalation of droplets or aerosols, laden with viral particles. However, as recent studies have shown, virions can remain infectious for up to 72 h on surfaces, which can lead to transmission through contact. Thus, a comprehensive study was conducted to determine the efficiency of protocols to recover SARS-CoV-2 from surfaces in built environments. This end-to-end (E2E) study showed that the effective combination for monitoring SARS-CoV-2 on surfaces includes using an Isohelix swab collection tool, DNA/RNA Shield as a preservative, an automated system for RNA extraction, and reverse transcriptase quantitative PCR (RT-qPCR) as the detection assay. Using this E2E approach, this study showed that, in some cases, noninfectious viral fragments of SARS-CoV-2 persisted on surfaces for as long as 8 days even after bleach treatment. Additionally, debris associated with specific built environment surfaces appeared to inhibit and negatively impact the recovery of RNA; Amerstat demonstrated the highest inhibition (>90%) when challenged with an inactivated viral control. Overall, it was determined that this E2E protocol required a minimum of 1,000 viral particles per 25 cm2 to successfully detect virus from test surfaces. Despite our findings of viral fragment longevity on surfaces, when this method was employed to evaluate 368 samples collected from various built environmental surfaces, all samples tested negative, indicating that the surfaces were either void of virus or below the detection limit of the assay. IMPORTANCE The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (the virus responsible for coronavirus disease 2019 [COVID-19]) pandemic has led to a global slowdown with far-reaching financial and social impacts. The SARS-CoV-2 respiratory virus is primarily transmitted from person to person through inhalation of infected droplets or aerosols. However, some studies have shown that virions can remain infectious on surfaces for days and can lead to human infection from contact with infected surfaces. Thus, a comprehensive study was conducted to determine the efficiency of protocols to recover SARS-CoV-2 from surfaces in built environments. This end-to-end study showed that the effective combination for monitoring SARS-CoV-2 on surfaces required a minimum of 1,000 viral particles per 25 cm2 to successfully detect virus from surfaces. This comprehensive study can provide valuable information regarding surface monitoring of various materials as well as the capacity to retain viral RNA and allow for effective disinfection.

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“…For example, in the anthrax mailing attack of 2001 in the US, Bacillus anthracis was cultured from the victim's cerebral spinal fluid and blood, and subsequently genotyped to identify the source of the microorganism (Keim, Budowle, & Ravel, 2011). Chemical‐, mechanical‐, or heat‐based DNA extraction methods are generally effective for bacteria and viruses (Alessandrini et al, 2019; Brauge et al, 2018; Cho et al, 2014; Hennechart‐Collette, Niveau, Martin‐Latil, Fraisse, & Perelle, 2019; Liu et al, 2012; Thomas et al, 2013), with the exception of bacteria endospores.…”

Section: Dna Extraction From Human Remains and Non‐conventional Samplesmentioning

confidence: 99%

Recent trends and developments in forensic DNA extraction

Chong

Thong

Syn

2020

WIREs Forensic Science

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The extraction of DNA is a fairly standard procedure routinely undertaken in biological academic and research settings. In a forensic DNA context, DNA extraction is the crucial first step toward the generation of DNA profiles used to support convictions or exonerations in the criminal justice system. However, it is often complicated by the additional challenge of yielding sufficient quantities of clean DNA that is free from environmental inhibitors, from a wide spectrum of sample types which may contain limited quantities of biological material. While improvements in methods and technology over the decades have sped up and simplified the process of DNA extraction, several issues remain to be fully addressed—such as the incomplete separation of spermic DNA from sperm‐epithelial cell mixtures, increasing demands for ever‐faster DNA results, or even on‐scene DNA processing, and processing of difficult samples such as skeletal remains or samples contaminated by Chemical, Biological, or Radiological (CBR) agents. These challenges are often compounded by high work volumes and limited quantities of starting material. As such, this review focuses on recent trends and developments in four areas of forensic DNA extraction: (a) analysis of sexual assault evidence which often represents a significant portion of a forensic DNA laboratory's casework, (b) use of portable rapid DNA instruments which has gained much traction among law enforcement in recent times, (c) DNA extraction from difficult and CBR‐contaminated samples which, albeit rare, would be essential in a DNA laboratory's toolbox in the event of an incident, and (d) bypassing DNA extraction altogether. This article is categorized under: Forensic Biology > Forensic DNA Technologies

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Performance Evaluation of the Maxwell 16 System for Extraction of Influenza Virus RNA from Diverse Samples

Cited by 11 publications

References 21 publications

Effects of Different Lysis Buffers of Nucleic Acid Purification Kit on the Stability of Influenza Virus RNA

Effects of Different Lysis Buffers of Nucleic Acid Purification Kit on the Stability of Influenza Virus RNA

End-to-End Protocol for the Detection of SARS-CoV-2 from Built Environments

Recent trends and developments in forensic DNA extraction

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