Supplementary Materials

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

Xianding Deng, Wei Gu, Scot Federman, Louis du Plessis, Oliver G. Pybus, Nuno Faria, Candace Wang, Guixia Yu, Brian Bushnell, Chao-Yang Pan, Hugo Guevara, Alicia Sotomayor-Gonzalez, Kelsey Zorn, Allan Gopez, Venice Servellita, Elaine Hsu, Steve Miller, Trevor Bedford, Alexander L. Greninger, Pavitra Roychoudhury, Lea M. Starita, Michael Famulare, Helen Y. Chu, Jay Shendure, Keith R. Jerome, Catie Anderson, Karthik Gangavarapu, Mark Zeller, Emily Spencer, Kristian G. Andersen, Duncan MacCannell, Clinton R. Paden, Yan Li, Jing Zhang, Suxiang Tong, Gregory Armstrong, Scott Morrow, Matthew Willis, Bela T. Matyas, Sundari Mase, Olivia Kasirye, Maggie Park, Godfred Masinde, Curtis Chan, Alexander T. Yu, Shua J. Chai, Elsa Villarino, Brandon Bonin, Debra A. Wadford, Charles Y. Chiu

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 and S2
  • Captions for Tables S1 to S5
  • Caption for Data S1
  • References
Table S1
List of all 62 SARS-CoV-2 samples analyzed in the study along with sequencing controls.
Table 2
Patient epidemiologic metadata and sequencing metrics for 36 SARS-CoV-2 genomes recovered from COVID-19 infected patients.
Table S3
Custom primer sequences for the MSSPE method.
Table S4
Tiling multiplex PCR primers.
Table S5
PCR primers and Sanger sequencing reads obtained for confirmation of SNV G29711T from SARS-CoV-2 respiratory nasal swab samples.
Data S1
Tree file for the global phylogeny of 789 SARS-CoV-2 genomes.