Sequencing (e.g. Sanger, Illumina or Nanopore technologies) provides a deeper insight into the genome of SARS-CoV-2 and can be used for many different purposes during an outbreak, such as the path of transmission through a community, monitoring the evolution of strains both geographically and temporally and identifying whether a patient may have co-infections. The number of samples you wish to sequence, plus the availability of each platform in your country is likely to affect the sequencing platform you choose. The following table should help to break down the differences between the main platforms currently available:

Sequencing platform




Sequencing type

First generation

Third generation

Fourth generation

Principle of sequencing

chain-termination method

Sequencing by synthesis


Read length

Short read (~900 nt)

Short read (50-300 nt)

Long read  (variable <1,000 kb)


Large: ~96 samples

Large: each MiSeq machine can run ~96 samples

Small – large: a few samples up to approximately 550 samples

Paired reads?

Not applicable (overlapping strategy)



Run time

30 minutes – 3 hours

Between 4 hours – 6 days, depending on the machine and throughput capacity

Dependent on the application as sequencing is in real time: can be run up to 48 hours

Error rate





High quality

High throughput, low cost per sample

Rapid and almost ‘point of care’ sequencing


Low throughput, high cost per sample

Short read assembly, depending on desired outcome. Potentially high cost and large infrastructure required

Higher error rate, higher cost per sample (dependent on equipment)

DNA requirements

50-500 ng

50-1000 ng

400-1000 ng

Nanopore webinar on SARS-CoV-2 sequencing

The Artic Network have published a SARS-CoV-2 Nanopore sequencing protocol on their website.

Sample collection

Sequencing relies on high quality nucleic acid, so it is important to ensure good extraction. 

Oxford Nanopore Technologies extraction web page  |  Illumina extraction web page