Pathology

Disease

Coronavirus disease 2019 (COVID-19)

Infectious disease (medical specialty)

Biology

Gene

Nanopore sequencing

Genome

Virology

Coronavirus

Minion

DNA sequencing

Computational biology

Multiplex

Sanger sequencing

Genetics

Medicine

Emerging infectious diseases

We describe validated protocols for generating high-quality, full-length severe acute respiratory syndrome coronavirus 2 genomes from primary samples. One protocol uses multiplex reverse transcription PCR, followed by MinION or MiSeq sequencing; the other uses singleplex, nested reverse transcription PCR and Sanger sequencing. These protocols enable sensitive virus sequencing in different laboratory environments.

Rapid, Sensitive, Full-Genome Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2