Cryo-EM structures of HKU2 and SADS-CoV spike glycoproteins and insights into coronavirus evolution

Jinfang Yu; Shuyuan Qiao; Runyu Guo; Xinquan Wang

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.23.961912 doi: bioRxiv preprint suggested that the presence of two NTDs in HCoV-NL63 is a result of gene 363 duplication 31 . However, the sequence identity between these two NTDs is only 15.7% 364 in HCoV-NL63 and 12.9% in PEDV. Considering that HKU2 (SADS-CoV) and 365 HCoV-229E have one NTD belonging to either subtype I or subtype II, a more plausible 366 evolution way of the NTD in α-coronaviruses is the recombination of two separate 367 primitive domains into the genome, resulting in the presence of two NTDs in the S1 368 subunit α-coronaviruses including HCoV-NL63 and PEDV. To be note, these two NTD However, we argue that the evolution pathways may not be in the order of α-, δ-, γ-, 384 and β-genus. A more plausible pathway is that the β-, γ-and δ-coronavirus NTDs may 385 evolve independently and parallelly from subtype I (β-and γ-coronavirus NTDs) or 386 subtype II (δ-coronavirus NTDs) (Supplementary Fig. 7b ).