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

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

For example, the subtree colored dark-yellow (labeled D and E in Figure 16 contains the subtypes that 511 are close to the reference sequence ISM subtype (CCCCGCCCACAGGTGGG). Other subtypes in this subtree are 512 also found in Asia, as well as in other countries with links to travel exposure to Asia and, as discussed above, 513 Iran (i.e. with the subtype CCCCTCCCACAGGTGGG). The closest subtree to the dark-yellow (labeled D and E) is 514 the purple-colored subtree (labeled C). This cluster "C" includes many subtypes that first were observed in 515 the United States, including the endogenous U.S. subtype described above, CCCTGCCTGTAGGCGGG. (This 516 subtype is labeled as being first observed in Canada, though that first sequence was found from a case linked 517 to U.S. exposure.) Clusters labeled A (green) and B (cyan and red), on the other hand, primarily include 518 subtypes first found in Europe or (as indicated for Brazil) due to exposure from travelers to Europe.