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What is coronavirus?

Coronaviruses are a large family of single-stranded RNA viruses that can infect humans as well as animals. In humans, coronavirus infection is typically associated with mild to moderate respiratory illnesses such as the common cold. The most common coronaviruses associated with human illness are 229E, NE63, OC43, and HKU1. There are hundreds of other coronaviruses, most of which circulate in animals, including cats, camels, and bats. Sometimes these viruses can mutate and jump to humans, which results in severe respiratory illness, as in the outbreak of Severe Acute Respiratory Syndrome (SARS-CoV) in 2002 and, more recently, Middle East Respiratory Syndrome (MERS-CoV) in 2012.

How was Sanger sequencing used to identify SARS-CoV-2?

Sanger sequencing played an important role in identifying the novel coronavirus SARS-CoV-2. Following next-generation sequencing, where partial and full genomes were obtained, Sanger sequencing was used in the connection of viral contigs, resulting in acquisition of the sequence of full length genomes [1]. 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.

Based on the genome sequences obtained using Sanger sequencing, a real-time PCR pathogen detection assay was developed by the CDC. In a recent study, Sanger sequencing was used to confirm results following positive identification by RT-PCR [2].


Why use Sanger sequencing to identify SARS-CoV-2?

Sanger sequencing can provide further confidence in identifying SARS-CoV-2 RNA to distinguish it from other respiratory viruses with easy-to-use genetic analyzers and simplified workflows. From sample to answer, the workflow can be completed in one day.


Sanger sequencing workflow

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Cycle sequencing kits

Choose from a variety of Sanger sequencing research kits to meet your workflow and throughput needs.

BigDye Direct Cycle Sequencing Kit

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The Applied Biosystems BigDye Direct Cycle Sequencing Kit simplifies the Sanger sequencing workflow by combining post-PCR cleanup and cycle sequencing into a single step. The kit requires PCR primers with M13 tails, which are available through the Primer Designer Tool.

BigDye Terminator v3.1 Cycle Sequencing Kit

The Applied Biosystems BigDye Terminator v3.1 Cycle Sequencing Kit's robust, highly flexible chemistry is ideal for de novo sequencing, resequencing, and finishing with PCR product, plasmid, fosmid, and BAC templates.


Related products

PCR clean up

ExoSAP-IT Express reagent: fastest PCR cleanup method

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The Applied Biosystems ExoSAP-IT Express reagent offers rapid turnaround times and improved efficiency of resource use while delivering the same superior cleanup as the original ExoSAP-IT reagent. Eliminate spin columns, magnetic beads, sedimentation, filtration, and gel purification. The novel ExoSAP-IT technology allows for a significant reduction in sample cleanup time with minimal steps, providing the simplest workflow.

  • 5 min protocol
  • One-tube, one-step PCR cleanup
  • Novel enzyme technology
  • 100% recovery of PCR

Cycle sequencing cleanup

Centri-Sep 96's hydrated matrix enables effective and reliable high-throughput removal of excess BigDye terminators from DNA sequencing reactions, giving you clean sequencing reads with uniform signal intensity starting with the first base. The plate's 96-well format enables you to purify 96 research samples simultaneously, either manually or by robotics, within 15 minutes.

Genetic analyzers

A range of platforms to meet your throughput’s need
 
Throughput Low Med High
  Learn more › Learn more › Learn more ›

Featured instrument consumables

On-instrument consumables are critical research components of your sequencing run. Using the right Applied Biosystems products can help reduce your re-run rate and enables high-quality, reproducible data.

SeqStudio-cartridge

The Applied Biosystems SeqStudio Cartridge is an easy-to-use reagent cartridge that includes capillaries, POP-1 universal polymer, buffer, and pump. The POP-1 universal polymer allows for flexibility to perform Sanger sequencing and fragment analysis on the SeqStudio Genetic Analyzer System with one cartridge. Just load your samples, click in the cartridge, and go.

POP polymers dynamically coat the capillary wall to control electro-osmotic flow. Their definite quality and uniform consistency eliminate guesswork and help to ensure reproducibility. POP polymers are specifically formulated to separate DNA fragments of a known size range at a desired resolution and run time.

We offer a wide portfolio of Applied Biosystems software solutions for viewing and interpreting your Sanger sequencing and fragment analysis results. Learn about our free tools and commercially available products below.



References

Thermo Fisher Scientific Sanger sequencing products are referenced in the protocols below:
  1. Lu R, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020 Jan 30. pii: S0140-6736(20)30251-8. doi: 10.1016/S0140-6736(20)30251-8. [Epub ahead of print] PubMed PMID: 32007145.
  2. Chan JF, et al. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet. 2020 Feb 15;395(10223):514-523. doi: 10.1016/S0140-6736(20)30154-9. Epub 2020 Jan 24. PubMed PMID: 31986261.

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