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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References
Scientists call for fully open sharing of coronavirus genome data.
TL;DR: Other researchers have shown that restrictions at the largest SARS-CoV-2 genome platform encourage fast sharing while protecting data providers' rights as mentioned in this paper. But they did not address the privacy concerns of data providers.
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Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy.
Francesca Di Giallonardo,Sebastián Duchêne,Ilaria Puglia,Valentina Curini,Francesca Profeta,Cesare Cammà,Maurilia Marcacci,Paolo Calistri,Edward C. Holmes,Alessio Lorusso +9 more
TL;DR: It is shown how importations were an important driver of the first wave of SARS-CoV-2 in Italy, with at least 124 instances of sequence clusters representing longer chains of transmission.
Genomic epidemiology of the early stages of SARS-CoV-2 outbreak in Russia
Andrey Komissarov,Ksenia R. Safina,Sofya K. Garushyants,Artem Fadeev,Mariia Sergeeva,Anna A. Ivanova,Daria Danilenko,Dmitry Lioznov,Olga V. Shneider,Nikita Shvyrev,Vadim Spirin,Dmitry Glyzin,Vladimir Shchur,Georgii A. Bazykin +13 more
TL;DR: It is estimated that the sampled viral diversity has originated from 67 closely timed introductions into Russia, mostly in late February to early March, suggesting that border closure with China has helped delay establishment of SARS-CoV-2 in Russia.
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Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America
TL;DR: In this paper , a detailed phylogenetic analysis of four SARS-CoV-2 lineages was performed to investigate the possibility of virus recombination among them, revealing well-supported phylogenetic differences between the Orf1ab region encoding viral non-structural proteins and the rest of the genome including Spike (S) protein and remaining reading frames.
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Emergence of an early SARS-CoV-2 epidemic in the United States.
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TL;DR: In this paper, the authors show that superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.
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