Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19

Shona C Moore; Rebekah Penrice-Randal; Muhannad Alruwaili; Xiaofeng Dong; Steven T Pullan; Daniel Carter; Kevin Bewley; Qin Zhao; Yani Sun; Catherine Hartley; En-min Zhou; Tom Solomon; Michael B. J. Beadsworth; James Cruise; Debby Bogaert; Derrick W T Crook; David A Matthews; Andrew D. Davidson; Zana Mahmood; Waleed Aljabr; Julian Druce; Richard T Vipond; Lisa Ng; Laurent Renia; Peter Openshaw; J Kenneth Baillie; Miles W Carroll; Calum Semple; Lance Turtle; Julian Alexander Hiscox

The copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2020.03.05.20032011 doi: medRxiv preprint 8 made no prior assumptions as to what nucleic acid was present in the RNA extracted from the oropharyngeal swabs. Here, amplification by sequence-independent single primer amplification (SISPA) was used. This had previously been used to identify dengue, chikungunya, influenza and Lassa fever viruses in clinical samples [7] [8] [9] . To provide an internal control, samples were spiked with nucleic acid from a plasmid expressing the VP35 RNA from Ebola virus (EBOV) [10] . Samples were not bar coded Reads mapping to viruses could also be identified and these included SARS-CoV-2 and human betaherpes virus 5 (human cytomegalovirus) (Fig. 1D) . Coverage of the SARS-CoV-2 genome in the three samples was not uniform (Fig. 1E ) and unsurprisingly the read depth was much lower than with the amplicon-based approach (Fig. 1C) .