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

Details

• Alternative Title:
  Science
• Personal Author:
  Deng, Xianding ; Gu, Wei ; Federman, Scot ; du Plessis, Louis ; Pybus, Oliver G. ; Faria, Nuno ; Wang, Candace ; Yu, Guixia ; Bushnell, Brian ; Pan, Chao-Yang ; Guevara, Hugo ; Sotomayor-Gonzalez, Alicia ; Zorn, Kelsey ; Gopez, Allan ; Servellita, Venice ; Hsu, Elaine ; Miller, Steve ; Bedford, Trevor ; Greninger, Alexander L. ; Roychoudhury, Pavitra ; Starita, Lea M. ; Famulare, Michael ; Chu, Helen Y. ; Shendure, Jay ; Jerome, Keith R. ; Anderson, Catie ; Gangavarapu, Karthik ; Zeller, Mark ; Spencer, Emily ; Andersen, Kristian G. ; MacCannell, Duncan ; Paden, Clinton R. ; Li, Yan ; Zhang, Jing ; Tong, Suxiang ; Armstrong, Gregory ; Morrow, Scott ; Willis, Matthew ; Matyas, Bela T. ; Mase, Sundari ; Kasirye, Olivia ; Park, Maggie ; Masinde, Godfred ; Chan, Curtis ; Yu, Alexander T. ; Chai, Shua J. ; Villarino, Elsa ; Bonin, Brandon ; Wadford, Debra A. ; Chiu, Charles Y.
• Description:
  The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning nine counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least seven different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington state, with lack of a predominant lineage and limited transmission among communities. Lineages associated with outbreak clusters in two counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain the spread of SARS-CoV-2 in California and other states.
• Subjects:
  Betacoronavirus Coronavirus Infections COVID-19 Epidemiological Monitoring Genome, Viral Humans Pandemics Phylogeny Pneumonia, Viral Sequence Alignment Ships Travel

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• Source:
  Science. 2020;
• Pubmed ID:
  32513865
• Pubmed Central ID:
  PMC7286545
• Document Type:
  Journal Article
• Funding:
  Wellcome Trust/United Kingdom ; K08 CA230156/CA/NCI NIH HHS/United States ; R21 AI129455/AI/NIAID NIH HHS/United States
• Place as Subject:
  California ; Washington
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:9c45311673fcb4d68cea4fcb95293c615dd281e16fa4cf7c1a4bd224f38a7947
• Download URL:
  https://stacks.cdc.gov/view/cdc/89349/cdc_89349_DS1.pdf
• File Type:
  [PDF - 2.20 MB ]