Viral RNA and COVID Research Workflow Standardization

Ensure your precious samples are prepared to the high-quality gold standard with Adaptive Focused Acoustic ® technology

AFA-Energetics® for Viral RNA

The COVID-19 pandemic has highlighted many challenges that researchers face in their journey to discover a cure amid the urgency and worldwide demand.
More than ever, excellence is required because there isn’t time to lose. When working with viral specimens, reproducibility, consistency, and scalability are critical.
Covaris Adaptive Focused Acoustics® (AFA®) is a proven technology for active extraction of labile, low-frequency biomolecules from complex, difficult biological samples.

Sequencing the virus and human DNA

Covaris Adaptive Focused Acoustics (AFA) is the gold standard for mechanical shearing prior to sequencing. Advantages include:
  • Standardized, automatable sample prep
  • Reproducible workflow for consistent high-quality yields
  • High-throughput scalability
  • Better size control as compared to enzymatic shearing

Scalability for COVID-19 Sequencing

Covaris offers three platforms with a range of scalability and automation for all needs utilizing the AFA-TUBE TPX Plate and Strips.

AFA-TUBE with Compatible Instruments

AFA enables unique workflows

AFA technology is uniquely positioned to help with new workflows such as:
    • Amplicon Sequencing: Customers at deCODE Genetics [2] were able to use the Covaris AFA-TUBE TPX Plate to enable DNA amplicon fragmentation to sequence SARS-CoV-2 efficiently and allowed them to complete multiple preparation steps in their NGS library construction without transfer steps, reducing sample loss.
    • High-throughput Sequencing: Covaris offers scalability for labs processing high volumes of samples as compared to enzymatic workflows that are slower and lack scalability for high volume processing.
    • Low volume shearing for epigenetics: Covaris is an ideal methodology for the shearing of low volume samples for epigenetic profiling through genome-wide DNA methylation [6] to determine biomarkers that could predict the course of the disease or stratify clinical subgroups. Exploring the epigenetics of the COVID-19 disease could open up new pathways towards accurate risk detection and precision medicine treatment options for the disease.

Improved Desiccated Stabilized Viral Specimen Transport

Covaris has developed a robust workflow that reduces the dependence on cold-chain logistics for shipment and storage of viral RNA swab samples that enables superior rehydration, extraction, and purification for downstream analysis. This is critically important in pandemic situations such as the current COVID-19 crisis which involves extremely large numbers of samples. In the containment of an epidemic, accurate diagnostics are critical for the foundation of the epidemiologic studies used by authorities to decide on the best course of action.
Current transportation techniques require swab specimens to be sent in liquid or gel transport media. This creates logistic challenges to maintain the specimen integrity prior to extraction for RT-PCR analysis. In addition to temperature and time requirements of the current technique, the viral particles are also diluted. This may result in a higher risk of false negative results.

The Covaris Desiccated Stabilized Transport Solution:

    • Utilizes FDA approved Nasopharyngeal Dry Synthetic flocked swabs which are readily available (customer to supply)
    • Simplifies logistics complexity and reduces shipping and storage cost
    • No cold chain logistics required – ambient temperature storage and shipping for up to 7 days.
    • Active sample rehydration and release for improved sensitivity and reproducibility
    • Sample collection, stabilization, and rehydration is compatible with most FDA EUA RT-PCR based SARS CoV-2 assays

Current Wet transport Vs. Covaris Desiccated Stabilized Transport System

Advantages of a Desiccated Stabilized Transport System

Improved Sensitivity to Reduce False Negatives

Cq values (blue-red) obtained after RT-qPCR of RNA extracted from dry-stabilized swabs following the AFA-truXTRAC protocol as compared to Cq values (green-purple) obtained from RNA extracted from swabs stored in liquid transport media and extracted using the Competitor Q Viral RNA kit.

Simplified Transport and Long-term Storage Without Compromise

Cq values obtained after RT-qPCR of RNA extracted with the AFA-truXTRAC protocol from dry-stabilized swabs stored at RT for 1 (blue), 3 (red), 7 (green) days.

Extraction of Viral RNA from Dry-Stabilized Specimens

Cq values obtained after RT-PCR of RNA extracted from dry-stabilized MS2 phage spiked human cells as compared to a direct RT-PCR control.

Extraction and Purification of Viral RNA from Dry-Stabilized Whole Blood and Blood Plasma


Ct values obtained after RT-PCR of MS2 Phage dilutions (Control) vs. RNA extracted and purified from MS2 phage-spiked dry-stabilized whole blood & plasma and fresh whole blood & plasma.


Sequencing SARS-CoV-2

  1. Van der made CI, Simons A, Schuurs-hoeijmakers J, et al. Presence of Genetic Variants Among Young Men With Severe COVID-19. JAMA. 2020; DOI: 10.1001/jama.2020.13719
  2. Akello JO, Leib SL, Engler O, Beuret C. Evaluation of Viral RNA Recovery Methods in Vectors by Metagenomic Sequencing. Viruses. 2020;12(5). Covaris DOI: 10.3390/v12050562. Utilized a Covaris M220 Focused-ultrasonicator for DNA Shearing.
  3. Gudbjartsson DF, Helgason A, Jonsson H, et al. Early Spread of SARS-Cov-2 in the Icelandic Population; 2020. DOI: 10.1101/2020.03.26.2004444 Utilized a Covaris LE220-plus Focused-ultrasonicator for amplified DNA Shearing in a 96 AFA-TUBE TPX Plate.
  4. Harilal D, Ramaswamy S, Loney T, et al. SARS-Cov-2 Whole Genome Amplification and Sequencing for Effective Population Based Surveillance and Control of Viral Transmission; 2020. DOI: 10.1101/2020.06.06.138339 Utilized a Covaris LE220-plus Focused-ultrasonicator for amplified DNA Shearing.
  5. Tayoun AA, Loney T, Khansaheb H, et al. Whole genome sequencing and phylogenetic analysis of SARS-Cov-2 strains from the index and early patients with COVID-19 in Dubai, United Arab Emirates, 29 January to 18 March 2020; 2020. DOI: 10.1101/2020.05.06.080606. Utilized a Covaris LE220-plus Focused-ultrasonicator for DNA Shearing
  6. Alfano N, Dayaram A, Axtner J, et al. Non-invasive surveys of mammalian viruses using environmental DNA; 2020. DOI: 10.1101/2020.03.26.009993
  7. Schäfer A, Baric RS. Epigenetic Landscape during Coronavirus Infection. Pathogens. 2017;6(1):8. Published 2017 Feb 15. doi:10.3390/pathogens6010008