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 It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the .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 nucleoprotein of the virus is significant in modulating the antibody response. [32] Additionally, Table 2 shows a high-entropy, informative site in the predicted coding region ORF8. Based 237 on structural homology analysis the ORF8 region in SARS-CoV-2 does not have a known functional domain 238 or motif [5] . In previously characterized human SARS coronavirus, ORF8 has been associated with an 239 enhanced inflammatory response, but that sequence feature does not appear to have been conserved in 240 SARS-CoV-2, and, in general, SARS-CoV-2 ORF8 appears divergent from other previously characterized 241 SARS-related coronaviruses [5, 40] . Previous entropy-based analysis of earlier and smaller SARS-CoV-2 242 sequence data sets have suggested that there is a mutational hotspot in ORF8, including early divergence 243 between sequences found in China, and large scale deletions found in patients in Singapore -which is 244 consistent with the results we have found here on a much more comprehensive analysis of genomes [4, 28, 30] . 245 Similarly, sites were identified in the ORF3a reading frame, which also appears to have diverged 246 substantially from other SARS-related viruses. In particular, the SARS-CoV-2 variant in the predicted 247 ORF3 region appear also to not contain functional domains that were responsible for increased inflammatory 248 response as they were in those viruses [5, 40] . Japan 2020-03-08 2020-03-11 2020-02-10 - though, Japan includes a number of sequences, of a subtype that is found extensively in European countries, 288 TCTCGTCCACGGGTAAC, first found in Japan on March 11, 2020 . This subtype has also been found in Canada 289