Streamlining diagnostic workflows for common respiratory diseases, such as SARS-CoV-2, influenza and RSV

Updated : Tue, November 30, 2021 @ 10:29 PM

A fourth wave of COVID-19 has already emerged in many countries and a newly classified variant of concern, Omicron (B.1.1.529), has recently been discovered.¹ The expected impact of this is so far unknown, but early indications show an increased risk of reinfection. In addition, there have been a series of warnings regarding the severity of expected outbreaks of respiratory syncytial virus (RSV) and flu this autumn and winter.^2,3,4 Due to the low incidence of RSV and influenza since the start of the SARS-CoV-2 pandemic, there will be larger numbers of young children than in previous years who have never been exposed to these viruses. This is concerning as both viruses can cause severe complications in young children, so could add significant pressure to hospitals as infections rebound. The latest World Health Organization (WHO) Influenza Update noted that RSV was currently elevated in many places worldwide.⁵ The European Centre for Disease Prevention and Control (ECDC) and the US Centers for Disease Control and Prevention (CDC) have so far reported the main influenza subtype this season to be A H3N2.^4,6 This subtype disproportionately affects older people, indicating this flu season could also be severe for the elderly.⁴

The WHO encourages routine influenza surveillance alongside SARS-CoV-2 testing,⁵ while the Academy of Medical Sciences recommends clinical labs should introduce multiplex testing for at least SARS-CoV-2, RSV and influenza.² As more countries are facing border closures, winter lockdowns and new SARS-CoV-2 variants spreading in their regions, PCR testing differentiating against the circulating respiratory viruses will remain crucial over the winter.

SARS-CoV-2 testing has forced many labs to increase their throughput of PCR diagnostics. As we move to a future scenario where SARS-CoV-2 becomes endemic and there are fewer peaks in infections, there is an opportunity for maximising this extra capacity. Outbreaks of other respiratory infections could be monitored more closely and there is potential for more patient testing, resulting in more appropriate treatments for better clinical outcomes and more responsible use of antibiotics. If laboratory managers continue to maintain and optimise their workflows, this will also result in communities being better prepared for future outbreaks and pandemics.

Purification of high-quality DNA and RNA for high-throughput downstream applications

At the beginning of the SARS-CoV-2 pandemic, LGC, Biosearch Technologies™ launched sbeadex™ viral RNA purification kit to support the overwhelming demand for testing reagents. Our R&D team reacted quickly to verify the kit* using AccuPlex™ Reference Material (LGC Clinical Diagnostics, formerly LGC SeraCare), to replicate clinical samples. We’re pleased to announce that the application of this kit has now been extended to include a range of bacteria and viruses that cause common respiratory diseases (see Table 1), including RSV and influenza as well as bacteria causing atypical pneumonia.

Our renamed sbeadex Pathogen Nucleic Acid Purification Kits can now be incorporated more widely into respiratory workflows, thereby simplifying sample accessioning and enabling efficient purification of high-quality DNA and RNA from swabs and sputum. The absence of organic solvents in the final wash step results in a PCR inhibitor-free final eluate, meaning that purified samples are optimal for downstream PCR and real-time PCR applications as well as next generation sequencing (NGS), a critical method to sequence positive COVID-19 samples to discover any mutations. The expanded list of pathogens verified for use with the kit is well suited for multiplexing for viral and bacterial pathogens causing respiratory infections. 

Table 1: Pathogens verified using the sbeadex Pathogen Nucleic Acid Purification Kit.

Please see our application note for full details of the verification studies.

How sbeadex works

Biosearch Technologies’ sbeadex purification kits use magnetic separation for the purification of nucleic acids. They are versatile and can be used with a wide variety of sample types and automation instruments. Superparamagnetic particles coated with sbeadex surface chemistry use a novel two-step binding mechanism which, when combined with the washing steps, removes impurities from the preparation. The absence of organic solvents in the final wash step means no drying step is needed, which reduces time to results. After washing, the nucleic acid is eluted from the magnetic particles and is ready for use in downstream PCR, RT-PCR and NGS applications.

Comparable to market-leading purification kits

The sbeadex Pathogen Nucleic Acid Purification Kit was compared to two market-leading competitor purification kits using control panels of viral respiratory pathogens and bacterial atypical pneumonia pathogens. For each of the chemistries, three purification replicates were performed using a magnetic particle processor. The purified nucleic acids were then used as templates in qPCR and RT-qPCR reactions with appropriate primers and probes for each of the pathogens tested. Quantification cycles (C_q) were determined for each reaction and the average C_q value for each pathogen and purification chemistry combination was calculated.

qPCR and RT-qPCR results for both the viral and bacterial control panels demonstrated that the performance of the sbeadex Pathogen Nucleic Acid Purification Kit was equivalent to the competitor purification chemistries, with no significant differences observed in the C_q values.

Serial dilutions of the sbeadex purified Influenza B standard were used to demonstrate a linear correlation between dilution factor and the amount of isolated nucleic acid, confirming that the kit works well across a broad nucleic acid concentration range.

Flexibility in automated processing for high-throughput workflows

The sbeadex Pathogen Nucleic Acid Purification Kit portfolio can be used for all scales of nucleic acid preparation; however, it is particularly well suited for incorporation into automated high-throughput workflows. The verification studies were performed efficiently using the KingFisher™ Flex open automation platform (Thermo Fisher Scientific) and the oKtopure™ fully automated, high-throughput platform (Biosearch Technologies) and protocols are available for both instruments. High-throughput batch sizes of the kits are available (5,000 and 10,000 purifications), simplifying the ordering process.

Watch how sbeadex purifies DNA from nose swabs on the oKtopure instrument

Why stop at respiratory pathogens?

The sbeadex Pathogen Nucleic Acid Purification Kit is a simple renaming of our proven sbeadex Viral RNA Purification Kit to reflect its continuously expanding usability to purify good yields of high-quality DNA and RNA from a variety of viral and bacterial pathogens. However, we don’t intend to stop there. Testing of additional pathogens and sample matrices is underway.

See our website for up-to-date information or stay tuned for our next blog post about further verifications of pathogens and matrices using sbeadex Pathogen Nucleic Acid Purification Kit.

*For Research Use Only. Not for use in diagnostic procedures.

References:

1. World Health Organization. Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern. https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern. Published November 26, 2021. Accessed November 29, 2021.
2. The Academy of Medical Sciences. COVID-19: Preparing for the future – Looking ahead to winter 2021/22 and beyond.  https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1007597/ams-preparing-for-winter.pdf. Published 2021. Accessed November 19, 2021.
3. Press Briefing by White House COVID-⁠19 Response Team and Public Health Officials. https://www.whitehouse.gov/briefing-room/press-briefings/2021/10/06/press-briefing-by-white-house-covid-19-response-team-and-public-health-officials-60/. Published October 6, 2021. Accessed November 19, 2021.
4. European Centre for Disease Prevention and Control. Early influenza cases indicate the possibility of severe upcoming season for elderly. Press release. https://www.ecdc.europa.eu/en/news-events/early-influenza-cases-indicate-possibility-severe-upcoming-season-elderly. Published October 26, 2021. Accessed November 19, 2021.
5. World Health Organization. Influenza Update N° 406. https://www.who.int/publications/m/item/influenza-update-n-406. Published November 8, 2021, based on data up to October 24, 2021. Accessed November 19, 2021.
6. Centers for Disease Control and Prevention. FluView Summary ending on November 6, 2021 – A weekly Influenza Surveillance Report Prepared by the Influenza Division.https://www.cdc.gov/flu/weekly/weeklyarchives2021-2022/week44.htm. Accessed November 19, 2021.