With its greater than 99% accuracy and long-read capabilities, Sanger sequencing is the gold-standard sequencing technology. And to further enable your research, fragment analysis by capillary electrophoresis (CE) provides DNA sizing, relative quantitation, and genotyping information. With our simple workflows, Sanger sequencing and fragment analysis can be completed in less than one workday—from sample to answer—helping to make your research of SARS-CoV-2 (the coronavirus that causes COVID-19) fast and cost-effective.Speak to sales
Protocol for finding and using Sanger sequencing primers for any location in the SARS-CoV-2 genome, including new Variants of Concern
Download protocol | Visualize SARS-CoV-2 genome and Order Primers | Search SARS-CoV-2 genome and Order Primers
Variant Analysis using Variant Reporter | Files for Variant Reporter (zip)
Variant Analysis using SeqScape | Files for SeqScape (zip)
Protocol to quickly confirm S-gene dropouts seen with the TaqPath COVID-19 assay by identifying if the S gene 69/70 deletion is present
Download protocol | Order primers
Flexible protocol to confirm the presence of the highly transmissible SARS-CoV-2 B.1.1.7, B.1.351, B.1.1.28, B.1.427 or B.1.429 strain lineages in your sample. Pick and choose primers pairs that best suit your needs.
Download protocol | Download primers sequences for B.1.1.7 | Download primers sequences for B.1.351 | Download primers sequences for B.1.1.28 | Download primers sequences for B.1.427 | Download primers sequences for B.1.429
Protocol to identify new variants in the Spike gene by sequencing the entire S-gene for vaccine development and epidemiological research.
Download protocol | Download primer sequences
Learn more about which protocol to choose ›
Sanger sequencing is the gold standard for sequencing single genes, confirming gene variants, detecting repeat sequences, copy number variation, and single nucleotide changes. Sanger sequencing is perfect for:
While NGS technologies are common in research labs due to higher throughput capabilities, Sanger sequencing offers a cost-effective solution for your research needs. It does not require expensive equipment and can generate high quality data even for low viral titer samples that do not yield high genome coverage for some NGS technologies.
As you work to understand SARS-CoV-2 to rapidly identify future treatment options and develop possible vaccine targets, our comprehensive portfolio of Sanger sequencing and fragment analysis research solutions is here to help advance your research.
In the context of an outbreak, where high numbers of samples need to be processed quickly and accurately, Sanger sequencing and fragment analysis can significantly help you to get answers quickly.
At the start of the SARS-CoV-2 outbreak, Sanger sequencing was used by several labs to confirm the causative pathogen as being SARS-CoV-2 1-4. Additionally, by analyzing these genomes and comparing to other known coronaviruses, it was determined that the virus originated in an animal reservoir that evolved from bats, with a likely intermediate animal host 5,6.
|RT-PCR/qPCR result confirmation||Rapid testing for multiple targets|
|Sanger sequencing is being used to confirm RT-PCR/qPCR results and provide confidence in distinguishing SARS-CoV-2 from other respiratory pathogens. In a simplified workflow, PCR product is purified and sequencing primers bind to known sequences in the target region, allowing the sequence to be extended using capillary electrophoresis (CE) 1,3.||Multiplexed qPCR solutions test for small numbers of pathogens, and its relatively small capacity can limit throughput when large numbers of targets or pathogens need to be detected. Fragment analysis by CE can be used to test multiple pathogens associated with different syndromes in a single sample 9. For example, a respiratory multiplex panel can detect viral and bacterial pathogens to help rule in/out common pathogens as the cause of infection.|
Learn about a simple method for detecting SARS-CoV-2 viral sequences through fragment analysis-based target multiplexing solutions:
Low-cost Sanger sequencing is considered the gold standard sequencing method for confirming the sequence of specific genes, including those already sequenced through NGS. It can be used to:
An understanding of the type and subtype of viruses is essential for effective crisis response. Surveillance also plays a role in understanding cross-species transmission of the virus and its spatial spread over evolutionary time and at human-wildlife interfaces. Monitoring helps detect the presence of different variants of the virus obtained from samples with different degrees of symptoms, including asymptomatic samples.
Identification of SARS-CoV-2 in wastewater can provide near real-time information about virus spread and could be an important approach for monitoring the virus spread 18,19. This method, known as wastewater-based epidemiology (WBE), may be able to act as an early warning system for infectious disease outbreaks in general, and in the immediate future could help predict the second wave of SARS-CoV-2 infections. Multiple researchers around the world have used Sanger sequencing to confirm the identify of SARS-CoV-2 in wastewater following viral identification by RT-PCR or qPCR 20-22.
Read more: SARS-COV-2 in Wastewater: A Potential Early Warning Method
Research indicates that the pharyngeal microbiota (PM) may influence susceptibility to different respiratory viral infections 23,24 making it possible that it may be important in understanding the epidemiology of SARS-CoV-2. Fragment analysis by CE can be used identify microbial signatures associated with different disease phenotypes 25. It relies on amplification of 16S-23S rRNA interspace (IS) regions in bacteria to produce PCR fragments that vary in length and frequency depending upon bacterial species. Each PCR fragment can be separated and detected on a genetic analyzer. The resulting fragment patterns are compared to a curated database to determine the species present in the sample 25.
Read more: Could Differences in Microbiota Explain Variability in SARS-CoV-2 Susceptibility?
There is an urgent need to develop safe and specific anti-viral treatments and/or vaccines for SARS-CoV-2. Vaccines provide a long-term solution to reduce the risk of infection by training the immune system to respond quickly and effectively. Therefore, it is critical to select a vaccine approach and begin with basic lab research to identify the pathogen and antigen candidates that could cause an immune response.
The simple, fast, cost-effective Sanger sequencing workflow is ideal at different steps of the vaccine development workflow:
Vaccine research is often performed with cultured human cells obtained from major repositories or fellow researchers. An estimated 15–20% of the time, cells used in experiments have been misidentified or cross-contaminated with another cell line. Although major repositories now authenticate cell line identity, many are calling for all researchers to test and authenticate cell line identity using standard genotyping techniques like Short Tandem Repeat (STR) genotyping with CE.
We offer products to authenticate cell line identity:
Emerging viruses pose a great challenge to global health care and economic systems. Given their pandemic potential, as witnessed in the case of the SARS-CoV-2 virus, rapid development and screening of drugs is needed to combat and contain the infection spread.
“Sanger sequencing can accomplish what some other new platforms can’t, especially when you want to look at minor allele frequency haplotypes from contagious viral genes that might not get captured in some of the higher throughout platforms.”
Dr. Lillian Seu
Center for Infectious Disease Control, Zambia
Read how Sanger sequencing was used to help detect drug resistance mutation in HIV research in Zambia
“The high-precision and sensitivity of Sanger sequencing make it irreplaceable in confirming point mutations, determining the position of cloned DNA, sequencing short internal gaps, or missing data at the genome termini.”
Dr. Iryna Goraichuk
USDA-ARS Exotic and Emerging Avian Viral Unit
Read how new avian viruses have been discovered with the help of Sanger sequencing
Our simple and fast Sanger sequencing workflow can be completed in less than one workday, from sample to answer. We offer products that support many steps of our recommended workflow, from PCR amplification to data analysis.
Order primers for pre-amplification and PCR to sequence the S gene 69/70 deletion variant and verify S gene dropout in the TaqPath COVID-19 assay. (Download protocol)
From straightforward sample preparation to peak analysis, we offer a wide range of products and services to simplify each step of the fragment analysis workflow.
Sanger sequencing and fragment analysis protocols are referenced in the publications below:
Get bite-sized answers to your everyday Sanger sequencing and fragment analysis questions
Learn about the history of sequencing and how to pick the right platform for your research needs
For Research Use Only. Not for use in diagnostic procedures.