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

Sequencing of viral genomes during outbreaks provides much needed information in terms of viral adaptation [4] and informs molecular epidemiological studies [11] . Due to recombination in coronaviruses (e.g. [12, 13] ) current diagnostics may not remain fit for purpose and therefore metagenomic approaches provide independent verification of the presence of viral genomes as well information on the underlying microbiome -which may contribute to severe disease in COVID-19. One limitation of the metagenomic approach is the limit of detection and in this study, not all of the SARS-CoV-2 genome was sequenced using the SISPA approach. For diagnostic purposes, RT-qPCR generally is more sensitive, provided that the primer binding sites remain conserved in the pathogen being tested. In this case, RT-qPCR diagnostic reagents can be revaluated based upon using sequencing as sentinel for these events.