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

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

China and Singapore, as indicated in Figure 6 . An additional observation to note from 6 is that the most 352 abundant subtype in Italy (TCGTCCACGGGTGGG) is found proportionately much more in France and Spain 353 than the second-most abundant subtype (TCGTCCACGGGTAAC), detected later. Conversely, the second-most 354 abundant subtype is found more uniformly in other countries. These observations give rise to two potential 355 hypotheses for further study: (1) An outbreak centered in Italy moved earlier to France and Spain, and cases 356 elsewhere are connected to a combination of earlier and later exposures. Or, (2) the second-most abundant 357 subtype in Italy is linked to potential exposure from another country in Europe. Overall, the foregoing 358 results are consistent with phylogenetic tree-based analyses, such as that illustrated on NextStrain's website 359 (http://www.nextstrain.org/ncov), which suggest a flow of the infection from Asia, to Italy, and then 360 subsequently export from Italy to other countries in Europe. It is important to note, however, that the ISMs 361 also resolve potentially significant differences in the subtype distributions in European countries outside of 362 Italy as the virus continues to progress, indicated in Figure 4 . The copyright holder for this preprint (which was not peer-reviewed) is the .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 subtype in the United States (CCCCGCCCACAGTTGGG). The plot in Figure 8 further shows that the putative endogenous U.S. subtype was expanding prior to the first detection of the New York major subtype, further 415 supporting the theory that New York's outbreak is not linked to the dominant subtype elsewhere in the 416 United States, particularly Washington state (see Figure 5 ).