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

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

States. The colors shown on the charts are also keyed to the colors used in Figure 4 , which allows for the The copyright holder for this preprint (which was not peer-reviewed) is the .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 Belgium. California, on the other hand, includes as a dominant subtype, CCCCGCCCACAGGTGGG, which is also 314 a major subtype in Mainland China, as shown in Figure 4 . The most abundant subtype in Washington, 315 CCCTGCCTGTAGGCGGG, is also the most abundant in the United States as a whole, likely as the result of 316 Washington state having the most subtypes overall. The same CCCTGCCTGTAGGCGGG subtype is also found in 317 substantial abundance in Canada as well. Consistent with the hypothesis that this subtype is endogenous to 318 the US, the ISM was found in the sequence of one suspected case of exposure in the United States found in 319 The copyright holder for this preprint (which was not peer-reviewed) is the .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 (CCCCTCCCACAGTTGGG) corresponds to cases that were linked to original exposure from China, which is consistent with the ISM being in common with one found in Hong Kong.) Figure 6 shows the relative 333 abundance (proportion of total sequences in that country/region) of each of these two dominant subtypes in 334 Italy in other countries/regions. As the plot shows, the outbreak in other European countries have generally 335 involved the same viral subtypes as those which are most abundant in Italy, as defined by ISM. Indeed, 336 initial reports of cases in various other European countries in late February 2020 were linked to travellers 337 from Italy [2] . The Italy subtypes are found, however, at lower yet still significant abundance in countries 338 including Japan, Canada, the United States, and Australia. in New York (TTTCGTCCACGTGTGGG) was detected in one sequence in Iceland linked to exposure in Italy. 346 However, that same subtype was found in Iceland in sequences from 27 cases linked to exposure in Austria, 2 347 from Denmark, and 1 from Germany. This further suggests that it was unlikely that the incidence of the 348 TTTCGTCCACGTGTGGG subtype in New York is connected to Italy rather than elsewhere in Europe, but limited 349 sequence coverage prevents more definitive inference.