Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England.

@article{Volz2021AssessingTO,
  title={Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England.},
  author={Erik M. Volz and Swapnil Mishra and Meera Chand and Jeffrey C. Barrett and Robert Johnson and Lily Geidelberg and Wes Hinsley and Daniel J. Laydon and Gavin Dabrera and {\'A}ine Niamh O'toole and Roberto Amato and Manon Ragonnet-Cronin and Ian Harrison and Ben Jackson and Cristina V. Ariani and Olivia Boyd and Nicholas James Loman and John T. McCrone and S{\'o}nia Gonçalves and David Jorgensen and Richard Myers and Verity Hill and David K. Jackson and Katy A. M. Gaythorpe and Natalie Groves and John Sillitoe and Dominic P. Kwiatkowski and Seth Flaxman and Oliver Ratmann and Samir Bhatt and Susan Hopkins and Axel Gandy and Andrew Rambaut and Neil M. Ferguson},
  journal={Nature},
  year={2021}
}
The SARS-CoV-2 lineage B.1.1.7, designated a Variant of Concern 202012/01 (VOC) by Public Health England1, originated in the UK in late Summer to early Autumn 20202. Whole genome SARS-CoV-2 sequence data collected from community-based diagnostic testing shows an unprecedentedly rapid expansion of the B.1.1.7 lineage during Autumn 2020, suggesting a selective advantage. We find that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S-gene target… 

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References

SHOWING 1-9 OF 9 REFERENCES

Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020

TLDR
Two new SARS-CoV-2 lineages with the N501Y mutation in the receptor-binding domain of the spike protein spread rapidly in the United Kingdom and were estimated to be more transmissible than the 501N lineage.

Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy

TLDR
A mouse model in which a SARS-CoV-2 strain was infectious and could cause an inflammatory response and moderate pneumonia is developed, and a panel of adaptive mutations potentially associated with the increased virulence are revealed.

Viral Phylodynamics

TLDR
Viral phylogenies can be used to investigate important epidemiological, immunological, and evolutionary processes, such as epidemic spread, spatio-temporal dynamics including metapopulation dynamics, zoonotic transmission, tissue tropism, and antigenic drift, and quantitative investigation of these processes through the consideration of viral phylogenies is the central aim of viral phylodynamics.

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

TLDR
Large-scale virus genome sequencing reveals the genetic structure and importation dynamics of a national COVID-19 epidemic, which was one of world’s largest and was unusually well represented by virus genomic sampling.

Evolutionary analysis of the dynamics of viral infectious disease

TLDR
This Review outlines the questions that can be answered using viral evolutionary analysis across a wide range of biological scales and describes the current state of the art in such analysis.