Supplementary Materials

The PDF file includes:

  • Fig. S1. Number of lineages through time for different local transmission clusters.
  • Fig. S2. Workplace mobility trends of different counties in Washington State compared to King county.
  • Fig. S3. Re estimates using the coalescent skygrowth model compared to Google mobility data.
  • Fig. S4. Effective reproduction number and workplace mobility in Yakima County.
  • Fig. S5. Substitutions and success of a SARS-CoV-2 introduction.
  • Fig. S6. Probability that a newly sampled case reveals a new introduction.
  • Fig. S7. Histogram of primers used by UW Virology across time.
  • Fig. S8. Comparison of cycle threshold (Ct) across SARS-CoV-2 Spike variant.
  • Fig. S9. Symptom and cycle threshold (Ct) values across time.
  • Fig. S10. Comparing cycle threshold (Ct) by viral clade.
  • Fig. S11. Cycle threshold by number of substitutions.
  • Fig. S12. Age of infected individuals by 614D or 614G variant over time.
  • Fig. S13 Dependence of the local outbreak clusters and the number of background sequences used.
  • Fig. S14. Principle of the multi-tree coalescent.
  • Fig. S15. Estimation of effective population sizes and rates of introductions from simulations.
  • Fig. S16. Estimation of the percentage of new cases due to introductions from simulations.
  • Table S1. GLM of Ct with N1, N2 primers in patients at UW affiliates
  • Table S2. GLM of Ct with ORF1ab primers in patients at UW affiliates

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Other Supplementary Material for this manuscript includes the following: