A Half-Day Genome Sequencing Protocol for Middle East Respiratory Syndrome Coronavirus

Kwan Woo Kim; Sungmi Choi; Su-Kyoung Shin; Imchang Lee; Keun Bon Ku; Seong Jun Kim; Seil Kim; Hana Yi

doi:10.3389/fmicb.2021.602754

A Half-Day Genome Sequencing Protocol for Middle East Respiratory Syndrome Coronavirus

Front Microbiol. 2021 Feb 19:12:602754. doi: 10.3389/fmicb.2021.602754. eCollection 2021.

Authors

Kwan Woo Kim¹, Sungmi Choi², Su-Kyoung Shin², Imchang Lee², Keun Bon Ku³, Seong Jun Kim³, Seil Kim^{3

4

5}, Hana Yi^{1

2

6}

Affiliations

¹ Interdisciplinary Program in Precision Public Health, Korea University, Seoul, South Korea.
² Institute for Biomaterials, Korea University, Seoul, South Korea.
³ Korea Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.
⁴ Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea.
⁵ Department of Bio-Analysis Science, University of Science and Technology, Daejeon, South Korea.
⁶ School of Biosystems and Biomedical Sciences, Korea University, Seoul, South Korea.

Abstract

Recent coronavirus (CoV) outbreaks, including that of Middle East respiratory syndrome (MERS), have presented a threat to public health worldwide. A primary concern in these outbreaks is the extent of mutations in the CoV, and the content of viral variation that can be determined only by whole genome sequencing (WGS). We aimed to develop a time efficient WGS protocol, using universal primers spanning the entire MERS-CoV genome. MERS and synthetic Neoromicia capensis bat CoV genomes were successfully amplified using our developed PCR primer set and sequenced with MinION. All experimental and analytical processes took 6 h to complete and were also applied to synthetic animal serum samples, wherein the MERS-CoV genome sequence was completely recovered. Results showed that the complete genome of MERS-CoV and related variants could be directly obtained from clinical samples within half a day. Consequently, this method will contribute to rapid MERS diagnosis, particularly in future CoV epidemics.

Keywords: MERS (Middle East respiratory syndrome); MinION long-read sequencing; coronavirus; universal primer; whole-genome sequencing.