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

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

and then subsequently to a greater degree in Europe. A critical point to keep in mind while interpreting 439 these time series data is that they are based on the reported date of sequences. The sequences of individuals 440 who test SARS-CoV-2 positive will likely lag the actual infection date, since many of those individuals will 441 be tested because they have symptoms -although some were almost certainly tested while presymptomatic 442 due to contacts, such as passengers on the Diamond Princess cruise ship. is simply being missed. In those cases, it appears from Figures 8, 11 , and 12 that in later times, other 450 subtypes have emerged over time and are becoming increasingly abundant. One potential explanation is that 451 because the SARS-CoV-2, is an RNA virus and thus highly susceptible to mutation as transmissions 452 occur [20] . Therefore, as transmissions have continued, the ISM associated with the reference sequence has 453 been replaced by different ISMs due to these mutations. Another plausible explanation for such leveling off 454 in a region is that the leveling off in relative abundance of the subtype represents containment of that 455 subtype's transmission while other subtypes continue to expand in that country or region. The latter could 456 plausibly explain the pattern observed in the United States, where earlier subtypes connected to Asia did not 457 increase in abundance while a putative endogenous subtype, as well as the dominant New York subtype, have 458 significantly increased in abundance (see Figure 8 and accompanying discussion above). Further investigation 459 and modeling of subtype distributions, as well as additional data, will be necessary to help resolve these questions -particularly in view of the caveats described below.