Cryptic transmission of SARS-CoV-2 in Washington State

Bedford, Trevor; Greninger, Alexander L.; Roychoudhury, Pavitra; Starita, Lea M.; Famulare, Michael; Huang, Meei‐Li; Nalla, Arun Kumar; Pepper, Gregory; Reinhardt, Adam; Xie, Hong; Shrestha, Lasata; Nguyen, Truong N.; Adler, Amanda; Brandstetter, Elisabeth; Cho, Shari; Giroux, Danielle; Han, Peter D.; Fay, Kairsten; Frazar, Chris; Ilcisin, Misja; Lacombe, Kirsten; Lee, Jover; Kiavand, Anahita; Richardson, M; Sibley, Thomas H.; Truong, Melissa; Wolf, Caitlin R; Nickerson, Deborah A.; Rieder, Mark J.; Englund, Janet A.; Investigators, Seattle Flu Study; Hadfield, James; Hodcroft, Emma B.; Huddleston, John; Moncla, Louise H.; Müller, Nicola F.; Neher, Richard A.; Deng, Xianding; Gu, Wei; Federman, Scot; Chiu, Charles Y.; Duchin, Jeff; Gautom, Romesh; Melly, Geoff; Hiatt, Brian; Dykema, Philip; Lindquist, Scott; Queen, Krista; Tao, Ying; Uehara, Anna; Tong, Suxiang; MacCannell, Duncan; Armstrong, Gregory L.; Baird, Geoffrey S.; Chu, Helen Y.; Shendure, Jay; Jerome, Keith R.

doi:10.1101/2020.04.02.20051417

Cited by 141 publications

(164 citation statements)

References 30 publications

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“…As the epidemic has progressed, samples have been increasingly obtained across Europe and 20 from the United States (Figure 1A, 1C). The tree shows multiple introductions of different variants across the globe with introductions from distant locations seeding local epidemics, where infections sometimes went unrecognized for several weeks and allowed wider spread (17). The tree topology shows minimal structure, even at the genome level, indicating that SARS-CoV-2 viruses have not diverged significantly since the beginning of the pandemic.…”

Section: Indicators Of Viral Evolution Have Been Shown To Be Robust Pmentioning

confidence: 99%

A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains

Dearlove

Lewitus

Bai

et al. 2020

Preprint

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The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine. Here we analyzed SARS-CoV-2 sequence diversity across 5,700 sequences sampled since December 2019. The Spike protein, which is the target immunogen of most vaccine 5 candidates, showed 93 sites with shared polymorphisms; only one of these mutations was found in more than 1% of currently circulating sequences. The minimal diversity found among SARS-CoV-2 sequences can be explained by drift and bottleneck events as the virus spread away from its original epicenter in Wuhan, China. Importantly, there is little evidence that the virus has adapted to its human host since December 2019. Our findings suggest that a single vaccine 10

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Section: Indicators Of Viral Evolution Have Been Shown To Be Robust Pmentioning

confidence: 99%

A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains

Dearlove

Lewitus

Bai

et al. 2020

Preprint

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show abstract

“…It is reasonable to ask if 12 to 14 million of the US population could be infected by April 2.4 -5.1) days during the outbreak in Washington state. 16 Other countries' experiences also inform whether a CIR of 4.2% could be reached in the US. Iceland has a robust nationwide testing program and 5.7% of over 27,000 tests (representing 7.5% of the nation's population) were positive through April 6, 2020.…”

Section: Professor Neil Ferguson Director Of the Mrc Centre For Globmentioning

confidence: 99%

COVID-19 Excess Deaths in the United States, New York City, and Michigan During April 2020

Wetzler¹,

Wetzler

2020

Preprint

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“…For the rest of the clades (B, B1, and B4), we identified four putative SARS-CoV-2 virus introductions to NYC as early as February 20 (90%CI: January 29 to February 26) ( Table 1). Notably, two of these introductions were inferred to be of domestic origin based on their close relationship with US isolates, including those from the main community transmission in Washington state (Clade B1) (Bedford et al 2020). The introduction of this clade to the East Coast was recently reported (Fauver et al 2020).…”

Section: Phylogenetic Analysis Reveals Multiple Introductions To Nyc mentioning

confidence: 99%

Introductions and early spread of SARS-CoV-2 in the New York City area

Gonzalez‐Reiche

Hernandez

Sullivan

et al. 2020

Preprint

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New York City (NYC) has emerged as one of the epicenters of the current SARS-CoV2 pandemic. To identify the early events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus causing COVID19 in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV2 genomes indicates multiple, independent but isolated introductions mainly from Europe and other parts of the United States. Moreover, we find evidence for community transmission of SARS-CoV2 as suggested by clusters of related viruses found in patients living in different neighborhoods of the city.

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Cryptic transmission of SARS-CoV-2 in Washington State

Abstract: Following its emergence in Wuhan,

Cited by 141 publications

References 30 publications

A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains

A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains

COVID-19 Excess Deaths in the United States, New York City, and Michigan During April 2020

Introductions and early spread of SARS-CoV-2 in the New York City area

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