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
Genomic sequencing effort for SARS-CoV-2 by country during the pandemic.
TL;DR: Although many developing countries have high numbers of SARS-CoV-2 infected cases but few published sequences, good performance on sequencing efforts for some low- and middle-income countries is observed.
92
Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda.
Daniel Lule Bugembe,My V. T. Phan,Isaac Ssewanyana,Patrick Semanda,Hellen Nansumba,Beatrice Dhaala,Susan Nabadda,Áine O'Toole,Andrew Rambaut,Pontiano Kaleebu,Pontiano Kaleebu,Matthew Cotten,Matthew Cotten +12 more
TL;DR: The A.23.1 spike-protein-coding region has changes similar to VOCs including a change at position 613, a change in the furin cleavage site that extends the basic amino acid motif and multiple changes in the immunogenic N-terminal domain this paper.
Phylogeny of the SARS coronavirus.
Markus Eickmann,Stephan Becker,Hans-Dieter Klenk,Hans Wilhelm Doerr,Konrad Stadler,Stefano Censini,Silvia Guidotti,Vega Masignani,Maria Scarselli,Marirosa Mora,Claudio Donati,Jang H. Han,Hyun Chul Song,Sergio Abrignani,Antonello Covacci,Rino Rappuoli +15 more
TL;DR: The nucleotide sequence of the SARS coronavirus FRA isolate is determined and the overall genome organization is found.
86
Evidence for strong mutation bias towards, and selection against, U content in SARS-CoV-2: implications for vaccine design.
Alan M. Rice,Atahualpa Castillo Morales,Alexander T Ho,Christine Mordstein,Christine Mordstein,Stephanie Mühlhausen,Semir Watson,Laura Cano,Bethan Young,Bethan Young,Grzegorz Kudla,Laurence D. Hurst +11 more
TL;DR: An evolutionarily informed approach to attenuation is proposed that, unusually, seeks to increase usage of the already most common synonymous codons in SARS-CoV-2 genes.
In-Flight Transmission of SARS-CoV-2.
Man-Lik Choi Edward,Daniel K.W. Chu,Peter K.C. Cheng,Dominic N.C. Tsang,Malik Peiris,Daniel G. Bausch,Leo L.M. Poon,Deborah Watson-Jones +7 more
TL;DR: Four persons with severe acute respiratory syndrome coronavirus 2 infection had traveled on the same flight from Boston, Massachusetts, USA, to Hong Kong, China, which strongly suggests that the virus can be transmitted during air travel.