Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic
TL;DR: In this paper , the authors describe how phylogenetic and phylodynamic methods provide insight into viral evolution, focusing on the SARS-CoV-2 pandemic, and summarize their contributions to our understanding of SARS transmission and control.
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Abstract: Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic and to the design of effective control strategies. Phylogenies (evolutionary trees) have provided key insights into the international spread of SARS-CoV-2 and enabled investigation of individual outbreaks and transmission chains in specific settings. Phylodynamic approaches combine evolutionary, demographic and epidemiological concepts and have helped track virus genetic changes, identify emerging variants and inform public health strategy. Here, we review and synthesize studies that illustrate how phylogenetic and phylodynamic techniques were applied during the first year of the pandemic, and summarize their contributions to our understanding of SARS-CoV-2 transmission and control. In this Review, the authors describe how phylogenetic and phylodynamic methods provide insight into viral evolution, focusing on the SARS-CoV-2 pandemic. The approaches reveal routes and timings of transmission events, and they can assess the effectiveness of various intervention measures aimed at controlling the virus.
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Cryptic transmission of SARS-CoV-2 in Washington State.
Trevor Bedford,Trevor Bedford,Alexander L. Greninger,Alexander L. Greninger,Pavitra Roychoudhury,Pavitra Roychoudhury,Lea M. Starita,Michael Famulare,Meei-Li Huang,Arun K. Nalla,Gregory Pepper,Adam Reinhardt,Hong Xie,Lasata Shrestha,Truong N. Nguyen,Amanda L. Adler,Elisabeth Brandstetter,Shari Cho,Danielle Giroux,Peter D Han,Kairsten Fay,Chris D. Frazar,Misja Ilcisin,Kirsten Lacombe,Jover Lee,Anahita Kiavand,Matthew Richardson,Thomas R. Sibley,Melissa Truong,Caitlin R Wolf,Deborah A. Nickerson,Mark J. Rieder,Janet A. Englund,Janet A. Englund,Seattle Flu Study Investigators,James Hadfield,Emma B. Hodcroft,John Huddleston,John Huddleston,Louise H. Moncla,Nicola F. Müller,Richard A. Neher,Xianding Deng,Wei Gu,Scot Federman,Charles Y. Chiu,Jeff Duchin,Jeff Duchin,Romesh Gautom,Geoff Melly,Brian Hiatt,Philip Dykema,Scott Lindquist,Krista Queen,Ying Tao,Anna Uehara,Suxiang Tong,Duncan MacCannell,Gregory L. Armstrong,Geoffrey S. Baird,Helen Y. Chu,Jay Shendure,Jay Shendure,Keith R. Jerome,Keith R. Jerome +64 more
TL;DR: The large majority of SARS-CoV-2 infections sampled during this time frame appeared to have derived from a single introduction event into the state in late January or early February 2020 and subsequent local spread, strongly suggesting cryptic spread of COVID-19 during the months of January and February 2020, before active community surveillance was implemented.
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