Characterizing geographical and temporal dynamics of novel coronavirus SARS-CoV-2 using informative subtype markers

Zhengqiao Zhao; Bahrad A. Sokhansanj; Gail L. Rosen

. CC-BY-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.07.030759 doi: bioRxiv preprint event. An example of this is the number of sequences from cruise vessels in the database. We expect that the 208 impact of any such clustering will be diminished in time as more comprehensive sequencing efforts take place. 209 there would be high selection pressure (i.e., due to exposure to the human immune response or need to gain 215 entry to host cells). ambiguities. We expect that as the number of publicly available sequences increases, there will likely be 220 additional samples that will allow resolution of base-call ambiguities. That said, it is possible that the 221 ambiguity symbols in the ISMs reflect genomic regions or sites that are difficult to resolve using sequencing 222 methods, in which case the ISMs will never fully resolve. Importantly, however, because of the application of 223 the error correction algorithm, there are fewer spurious subtypes which are defined due to variants arising 224 from sequencing errors, and all remaining ISMs are still usable as subtype identifiers.