Partial RdRp sequences offer a robust method for Coronavirus subgenus classification

David A Wilkinson; Lea Joffrin; Camille Lebarbenchon; Patrick Mavingui

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.02.974311 doi: bioRxiv preprint Introduction: Covid-19) epidemic is ongoing and is regarded as a public health emergency of international 45 concern by the WHO, having resulted in more than 2,500 deaths. Thanks to molecular epidemiology 46 studies, we know that SARS, MERS and SARS-CoV-2 had their origins in wild animal reservoir 47 species before spilling over into humans. Indeed, numerous molecular studies have identified a 48 wealth of Coronavirus diversity harboured by equally diverse animal hosts (1-6), and phylogenetic 49 analysis of sequence data from these studies is helping in our understanding of many aspects of 50 disease ecology and evolution (7-9). This includes the role of reservoir hosts in disease maintenance 51 and transmission (3, 4, 6, 10-12), the evolutionary origins of human-infecting coronaviruses (3, 13), 52 the importance of bats as reservoirs of novel coronaviruses (14, 15), the role of intermediate hosts in 53 human disease emergence (3, 11, 16) , and the understanding of risk that might be related to 54 coronavirus diversity and distributions (17, 18 Betacoronaviruses related to MERS Coronavirus). Whole genome data from holotype specimens 72 selected to represent an exhaustive spectrum of coronavirus diversity was used to test the 73 phylogenetic repartition and support for each of these taxa (20). Due to the limited diversity of 74 holotype specimens classified into these subgenera, there is currently no method for attributing 75 subgenus to isolates with divergent sequences, and no proposed method for partial sequence data. 76