• HOME
  • NEWS
  • EXPLORE
    • CAREER
      • Companies
      • Jobs
    • EVENTS
    • iGEM
      • News
      • Team
    • PHOTOS
    • VIDEO
    • WIKI
  • BLOG
  • COMMUNITY
    • FACEBOOK
    • INSTAGRAM
    • TWITTER
Saturday, August 2, 2025
BIOENGINEER.ORG
No Result
View All Result
  • Login
  • HOME
  • NEWS
  • EXPLORE
    • CAREER
      • Companies
      • Jobs
        • Lecturer
        • PhD Studentship
        • Postdoc
        • Research Assistant
    • EVENTS
    • iGEM
      • News
      • Team
    • PHOTOS
    • VIDEO
    • WIKI
  • BLOG
  • COMMUNITY
    • FACEBOOK
    • INSTAGRAM
    • TWITTER
  • HOME
  • NEWS
  • EXPLORE
    • CAREER
      • Companies
      • Jobs
        • Lecturer
        • PhD Studentship
        • Postdoc
        • Research Assistant
    • EVENTS
    • iGEM
      • News
      • Team
    • PHOTOS
    • VIDEO
    • WIKI
  • BLOG
  • COMMUNITY
    • FACEBOOK
    • INSTAGRAM
    • TWITTER
No Result
View All Result
Bioengineer.org
No Result
View All Result
Home NEWS Science News Health

Harnessing next generation sequencing to detect SARS-CoV-2

Bioengineer by Bioengineer
May 25, 2021
in Health
Reading Time: 5 mins read
0
Share on FacebookShare on TwitterShare on LinkedinShare on RedditShare on Telegram

…and prepare for the next pandemic

IMAGE

Credit: Peter Duchek

Researchers at the Vienna BioCenter designed a testing protocol for SARS-CoV-2 that can process tens of thousands of samples in less than 48 hours. The method, called SARSeq, is published in the journal Nature Communications and could be adapted to many more pathogens.

The COVID-19 pandemic has lasted more than a year and continues to impact our lives tremendously. Although some countries have launched speedy vaccination campaigns, many still await large-scale immunization schemes and effective antiviral therapies – before that happens, the world urgently needs to regain a semblance of normalcy.

One way to bring us closer to that point is massive parallel testing. Molecular tests that detect the presence of SARS-CoV-2 have become the best way to isolate positive cases and contain the spread of the virus. Several methods have come forward, some that detect viral proteins from nasopharyngeal swabs (such as antigen tests), and some that detect the presence of viral RNA from swabs, gargle samples, or saliva samples (such as reverse transcription and polymerase chain reaction tests, or RT-PCR).

Although antigen tests facilitate some logistical aspects of mass testing, their detection power is relatively weak – infected individuals carrying low amounts of virus remain undetected and can continue to infect other people. PCR tests, on the other hand, are more sensitive because they multiply fragments of the viral genome before scanning samples for the virus. However, they rely on the detection of fluorescent labels that tag viral sequences, which means that pooling samples coming from different people makes the process rather inefficient: if a pool tests positive, all the samples within the pool must be tested again individually to identify the source of the fluorescent signal. Too many machines needed, too expensive, too slow.

During the very first lockdown, scientists at the Vienna BioCenter were mulling over the situation: there had to be a way to scale up testing. Ulrich Elling, group leader at the Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), and Luisa Cochella, group leader at the Research Institute of Molecular Pathology (IMP), decided to channel their frustration into an innovative solution. IMP group leader Alexander Stark and IMBA postdoc Ramesh Yelangandula joined their efforts, and the project took off.

Combining their expertise in genomics, RNA biochemistry and data analysis, they developed a method that could enable large groups to be tested for SARS-CoV-2 with the same sensitivity as regular PCR tests. SARSeq, or ‘Saliva Analysis by RNA sequencing’, achieves high sensitivity, specificity, and the power to process up to 36,000 samples in less than 48 hours. The method is now published in the journal Nature Communications.

The testing principle is conceptually simple: individual patient samples are collected into the wells of a testing plate – one well for each sample. Then, a fragment of viral RNA unique to SARS-CoV-2 – the nucleocapsid gene – is selectively converted to DNA and PCR-amplified in any well that contains it.

“Amplifying the viral material from individual samples to a maximum homogenizes its quantity across positive samples, making SARSeq highly sensitive,” explains Luisa Cochella. “Within the thousands of samples that we could test simultaneously, some may contain up to 10 million times more coronavirus particles than others – if we pooled such samples before amplification, those with high amounts of viral material could mask other positive cases.”

What distinguishes this first step to the usual PCR test is that each sample receives a unique set of short DNA sequences – or barcodes – that attach to the amplifying viral DNA. In a second amplification step, all the samples from one plate are pooled into one well, which receives a second set of unique DNA barcodes. The contents of multiple plates can be pooled once more, as the DNA molecules from each sample carry a unique combination of two sets of barcodes. This pooling and barcoding strategy makes SARSeq highly specific and scalable.

“We combine the sensitivity of PCR with the high throughput of Next Generation Sequencing technology, or NGS, the same used to sequence the human genome. The NGS machine processes the pooled samples and tells us which samples contained any SARS-CoV-2 material. The barcodes allow us to distinguish each positive sample from the others, and trace it back to a patient,” says Ramesh Yelagandula, first author of the study. Moreover, the NGS-based method allows to test several RNAs in parallel, including RNAs that control the sample quality or RNAs from other pathogens for differential diagnostics.

“The Next Generation Sequencing facility and other colleagues at the Vienna BioCenter were of tremendous help to develop and optimize the method,” says Alexander Stark. “With our machines, home-made enzymes, and analysis pipeline, we expect each test to cost less than five Euro.”

The testing procedure can run in parallel to existing diagnostics, while being independent of the bottlenecks in supply chains. Therefore, it does not compete with other testing methods for reagents or equipment.

“We developed SARSeq to try and circumvent the limitations of other tests, and to process thousands of samples in parallel. Not only is it an excellent method to detect SARS-CoV-2, but it can also be applied to other respiratory pathogens like the flu virus, the common cold rhinoviruses, and potentially many others,” says Ulrich Elling.

The principles behind SARSeq are simple and adaptable to any respiratory pathogen. As the world’s population skyrockets along with our proximity to animals, cutting-edge diagnostic methods like SARSeq will be crucial to prevent future diseases from spreading like wildfire.

###

Original publication

Yelagandula, R., Bykov, A., Vogt, A., Heinen, R., Özkan, E., Strobl, M. M., Baar, J. C., Uzunova, K., Hajdusits, B., Kordic, D., Suljic, E., Kurtovic-Kozaric, A., Izetbegovic, S., Schaeffer, J., Hufnagl, P., Zoufaly, A., Seitz, T., VCDI, Födinger, M., Allerberger, F., Stark, A., Cochella, L., Elling, U.: “Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq”. Nature Communications, 2021. DOI: http://dx.doi.org/10.1038/s41467-021-22664-5

Further information

News & Updates on our SARS-CoV-2 Research: https://www.viennabiocenter.org/research/covid-19/news/

About the Vienna BioCenter

The Vienna BioCenter is a leading life sciences hub in Europe, offering an extraordinary combination of research, business and education in a single location. Over 2,000 employees, 90 research groups, 35 biotech companies, 1,300 students and scientists from 70 countries create a highly dynamic and stimulating environment.

http://www.viennabiocenter.org

About IMBA at the Vienna BioCenter

IMBA – Institute of Molecular Biotechnology – is one of the leading biomedical research institutes in Europe focusing on cutting-edge stem cell technologies, functional genomics, and RNA biology. IMBA is a subsidiary of the Austrian Academy of Sciences, the leading national sponsor of non-university academic research. The stem cell and organoid research at IMBA is being funded by the Austrian Federal Ministry of Science and the City of Vienna.

http://www.oeaw.ac.at/imba

About the IMP at the Vienna BioCenter

The Research Institute of Molecular Pathology (IMP) in Vienna is a basic life science research institute largely sponsored by Boehringer Ingelheim. With over 200 scientists from 40 countries, the IMP is committed to scientific discovery of fundamental molecular and cellular mechanisms underlying complex biological phenomena.

http://www.imp.ac.at

Media Contact

Mehdi Khadraoui

T: +43 664 808 473 625

E: [email protected]

Media Contact
Daniel F. Azar
[email protected]

Original Source

http://bit.ly/SARSeq-VBC

Related Journal Article

http://dx.doi.org/10.1038/s41467-021-22664-5

Tags: BiotechnologyEpidemiologyGeneticsHealth Care Systems/ServicesInfectious/Emerging DiseasesMedicine/HealthMicrobiologyMolecular BiologyVirology
Share12Tweet8Share2ShareShareShare2

Related Posts

blank

Serum Markers Predict Atrial Fibrillation in Diabetes

August 2, 2025
blank

Amyloid Fibrils Connect CHCHD10, CHCHD2 to Neurodegeneration

August 2, 2025

Mapping the Human Hippocampus: Single-Nucleus to Spatial Transcriptomics

August 2, 2025

Boosting ADMET Predictions for Key CYP450s

August 2, 2025
Please login to join discussion

POPULAR NEWS

  • Blind to the Burn

    Overlooked Dangers: Debunking Common Myths About Skin Cancer Risk in the U.S.

    60 shares
    Share 24 Tweet 15
  • Neuropsychiatric Risks Linked to COVID-19 Revealed

    45 shares
    Share 18 Tweet 11
  • Dr. Miriam Merad Honored with French Knighthood for Groundbreaking Contributions to Science and Medicine

    46 shares
    Share 18 Tweet 12
  • Study Reveals Beta-HPV Directly Causes Skin Cancer in Immunocompromised Individuals

    38 shares
    Share 15 Tweet 10

About

We bring you the latest biotechnology news from best research centers and universities around the world. Check our website.

Follow us

Recent News

Serum Markers Predict Atrial Fibrillation in Diabetes

Intrapleural Anti-VEGF Boosts Nab-Paclitaxel Efficacy

Amyloid Fibrils Connect CHCHD10, CHCHD2 to Neurodegeneration

  • Contact Us

Bioengineer.org © Copyright 2023 All Rights Reserved.

Welcome Back!

Login to your account below

Forgotten Password?

Retrieve your password

Please enter your username or email address to reset your password.

Log In
No Result
View All Result
  • Homepages
    • Home Page 1
    • Home Page 2
  • News
  • National
  • Business
  • Health
  • Lifestyle
  • Science

Bioengineer.org © Copyright 2023 All Rights Reserved.