Discovery of a Novel Merbecovirus DNA Clone Contaminating Agricultural Rice Sequencing Datasets from Wuhan, China

Author(s): Adrian Jones, Daoyu Zhang, Steven E. Massey, Yuri Deigin, Louis R. Nemzer, Steven C. Quay

HKU4-related coronaviruses belong to the same merbecovirus subgenus as Middle Eastern Respiratory Syndrome coronavirus (MERSCoV), which causes severe respiratory illness in humans with a mortality rate of over 30%. The high genetic similarity between HKU4-related coronaviruses and MERS-CoV makes them an attractive subject of research for modeling potential zoonotic spillover scenarios. In this study, we identify a novel coronavirus contaminating agricultural rice RNA sequencing datasets from Wuhan, China. The datasets were deposited with NCBI by the Huazhong Agricultural University in early 2020. We were able to assemble the complete viral genome of a novel HKU4-related merbecovirus. The assembled genome is 98.38% identical to the closest known full genome sequence, Tylonycteris pachypus bat isolate BtTp- GX2012. Using in silico modeling, we show that the novel HKU4-related coronavirus spike protein likely binds to human dipeptidyl peptidase 4 (DPP4), the receptor used by MERS-CoV. We further show that the novel HKU4-related coronavirus genome has been inserted into a bacterial artificial chromosome in a format consistent with previously published coronavirus infectious clones. Additionally, we have found a near complete read coverage of the spike gene of the MERS-CoV reference strain, and identify the likely presence of a HKU4-related-MERS chimera in the datasets.