One of the primary advantages next-generation sequencing (NGS) provides over other methods of analysis is that it is an effective and high-throughput solution for screening multiple samples and detecting viruses without prior knowledge of an infectious agent. Among its core capabilities, NGS workflows can be used to detect SARS-CoV-2 virus, perform surveillance and epidemiological studies, track mutational changes in the virus, enable unbiased pathogen discovery, and analyze potential susceptibility and human response to SARS-CoV-2 infection. The table below highlights which workflows are best suited for each application.


Targeted Sequencing WGS/Shotgun Sequencing Expression Analysis
Detect virus X X
Perform surveillance & epidemiology X X
Track Mutations X X
Discovery X X
Analyze human response to disease X X X


Automation supports a lab’s ability to rapidly and safely perform NGS analysis of SARS-CoV-2 samples. PerkinElmer’s workflow automates nucleic acid isolation right through to library-prep analysis, simplifying library preparation, mitigating risk of lab-acquired infections, increasing throughput, and reducing variability.

RNA isolation for SARS-CoV-2 NGS

Viral Nucleic Acid Extraction

Nucleic acid quality is of major importance when conducting molecular analysis since factors causing degradation and the presence of impurities and enzymatic inhibitors can have a significant impact on the quality of data. PerkinElmer’s chemagen™ technology addresses the challenges associated with viral nucleic acid extraction while offering high recovery of clean nucleic acids suitable for demanding downstream applications.

The PerkinElmer chemagic™ Viral DNA/ RNA 300 Kit H96 and the chemagic™ 360 instrument is recommended for the isolation of nucleic acids for use with NGS applications.

Library Preparation

Analysis of SARS-CoV-2
PerkinElmer’s NEXTFLEX® Rapid Directional RNA-seq kit 2.0 is ideal for coronavirus-related NGS studies including library preparation for targeted sequencing, whole genome and shotgun sequencing, and expression analysis. It provides high coverage uniformity, low duplication rates, strand specificity with a streamlined, automated protocol enabling rapid analysis of SARS-CoV-2 samples.

Additionally, the 1, 536 NEXTFLEX® UDI barcodes, which can be used with the NEXTFLEX® Rapid Directional RNA-seq kit 2.0 or other library preparation protocol, enable the multiplexing up to 1,536 samples onto one Illumina® flow cell significantly reducing the sequencing cost and time.

The ability to multiplex a large number of samples in a single run is one of the biggest benefits of using an amplicon-based approach for epidemiological sequencing studies of the SARS-CoV-2 virus as it significantly decreases the turnaround time and cost of analysis. With the ability to multiplex up to 1,536 amplicon libraries in a single run, the NEXTFLEX® DNA-seq kits along with the NEXTFLEX® UDI barcodes deliver a simple, cost-effective solution for adding adapters compatible with Illumina® sequencing to SARS-CoV-2 amplicon pools. For amplicon pools which need to be fragmented, we recommend using the NEXTFLEX® Rapid XP DNA-seq kit.  For those that do not need fragmentation, we recommend using the NEXTFLEX® Rapid DNA-seq kit 2.0.

RNA-seq library prep for SARS-CoV-2

Analysis of Human Response to SARS-CoV-2 Infection
The way different patients respond to coronavirus infections is also a critical field of study right now. The NEXTFLEX® Rapid XP DNA-Seq kit is ideal for the sequencing of human DNA to analyze how the clinical outcome in COVID-19 cases be explained by human genetic diversity. This allows researchers to determine which host genetic variants impact the pathogenesis of COVID 19 infection and to analyze the functional basis of these associations.

For small RNA-seq analysis of patients infected with SARS-CoV-2, we recommend the NEXTFLEX® Small RNA-seq kit v3. It is a reduced-bias small RNA library preparation solution for Illumina® sequencing platforms with gel-free and low-input options.

Increase your SARS-CoV-2 library prep throughput

Automation of Library Preparation

PerkinElmer has standardized and tested more than 150 push-button methods automating NGS library prep kits. This extensive library of automated methods offers labs unrivaled flexibility in choice of library prep. Together, with our suite of automated liquid handling solutions optimized for NGS applications, the PerkinElmer NGS application library provides the ability to adapt to your needs.

Library QC

The LabChip® GX Touch nucleic acid analyzer using the NGS 3K assay delivers automated analysis of the sizes and profiles of NGS libraries for required quality assessment prior to sequencing. With flexible throughput options and multiple data visualization choices, the LabChip® GX Touch nucleic acid analyzer simplifies library QC.

LabChip Instrument
Contact Us to Improve your NGS Coronavirus Workflows

For research use only. Not for use in diagnostic procedures.