Figure S4.

Two Exceptions to the Pattern of Increasing Frequency of the G614 Variant over Time, from Figure 1B, Related to Figure 1

A. Details regarding Santa Clara county, the only exceptional pattern at the county/city level in Figure 1B. Many samples from the Santa Clara County Department of Public Heath (DPH) were obtained from March into May, and D614 has steadily dominated the local epidemic among those samples. The subset of Santa Clara county samples specifically labeled “Stanford,” however, were sampled over a few weeks mid-March through early April, and have a mixture of both the G614 and D614 forms. These distinct patterns suggest relatively little mixing between the two local epidemics. Why Santa Clara county DPH samples should maintain the original form is unknown, but one possibility is that they may represent a relatively isolated community that had limited exposure to the G614 form, and G614 may not have had the opportunity to become established in this community – though this may be changing, see Part C. The local stay-at-home orders were initiated relatively early, March 16, 2020. B. Details regarding Iceland, the only country with an exceptional pattern from Figure 1B. All Icelandic samples are from Reykjavik, and only G614 variants were initially observed there, with a modest but stable introduction of the original form D614 in mid-March. This atypical pattern might be explained by local sampling. The Icelanders conducted a detailed study of their early epidemic (Gudbjartsson et al., 2020), and all early March samples were collected from high risk travelers from Europe and people in contact with people who were ill; the majority of the traveler samples from early March were from people coming in from Italy and Austria, and G614 dominated both regions. On March 13, they began to sequence samples from local population screening, and on March 15, more travelers from the UK and USA with mixed G614/D614 infections began to be sampled in the high-risk group, and those events were coincident with the appearance of D614. C. Updated data regarding California from the June 19, 2020 GISAID sampling. Most of the analysis in this paper was undertaken using the May 29, 2020 GISAID download, but as California was an interesting outlier, and more recent sampling conducted while the paper was under review was informative, we have included some additional plots from California data that were available at the time of our final response to review, on June 19^th. Informative examples from well-sampled local regions are shown. Stay-at-home order dates are shown as a pink line, followed by a light pink block indicating the maximum two-week incubation time. N indicates the number of available sequences. Overall California, and specifically, San Diego and San Joaquin, show a clear shift from D614 to G614. The transition for San Joaquin was well after the stay-at-home orders and incubation period had passed. San Francisco shows a trend toward G614. Santa Clara DPH, which was essentially all D614 in our May 29^th GISAID download, had 7 G614 forms sampled in late May that were evident in our June 19^th GISAID download. Ventura is an example of a setting that was essentially all G614 when it began to be sampled significantly in early April, so a transition cannot be tracked; i.e., we cannot differentiate in such cases whether the local epidemic originated as a G614 epidemic, or whether it went through a transition from D614 to G614 prior to sampling. The figures in Parts A, B, and C can be recreated with more current data at http://cov.lanl.govcontent/index.