Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States.
Tara Alpert,Anderson F. Brito,Erica Lasek-Nesselquist,Erica Lasek-Nesselquist,Jessica E. Rothman,Andrew L Valesano,Matthew MacKay,Mary E. Petrone,Mallery I. Breban,Anne E. Watkins,Chantal B.F. Vogels,Chaney C. Kalinich,Simon Dellicour,Simon Dellicour,Alexis Russell,John P. Kelly,Matthew Shudt,Matthew Shudt,Jonathan Plitnick,Jonathan Plitnick,Erasmus Schneider,Erasmus Schneider,William J. Fitzsimmons,Gaurav Khullar,Jessica Metti,Joel T. Dudley,Megan Nash,Nike Beaubier,Jianhui Wang,Chen Liu,Pei Hui,Anthony Muyombwe,Randy Downing,Jafar Razeq,Stephen M. Bart,Stephen M. Bart,Ardath Grills,Stephanie Morrison,Steven Murphy,Caleb Neal,Eva Laszlo,Hanna Rennert,Melissa M. Cushing,Lars F. Westblade,Priya Velu,A. Craney,Lin Cong,David R. Peaper,Marie L. Landry,Peter W. Cook,Joseph R. Fauver,Christopher E. Mason,Adam S. Lauring,Kirsten St. George,Kirsten St. George,Duncan MacCannell,Nathan D. Grubaugh +56 more
TLDR
In this paper, the emergence and spread of SARS-CoV-2 lineage B.1.7 in the United States has been investigated and the extent of establishment is relatively unknown.About:
This article is published in Cell.The article was published on 2021-05-13 and is currently open access. It has received 90 citations till now.read more
Citations
More filters
Journal ArticleDOI
Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence.
Moritz U. G. Kraemer,Verity Hill,Christopher Ruis,Simon Dellicour,Simon Dellicour,Sumali Bajaj,John T. McCrone,Guy Baele,Kris V Parag,Anya Lindström Battle,Bernardo Gutierrez,Ben Jackson,Rachel M. Colquhoun,Áine O'Toole,Brennan Klein,Alessandro Vespignani,Erik M. Volz,Nuno R. Faria,Nuno R. Faria,Nuno R. Faria,David M. Aanensen,Nicholas J. Loman,Louis du Plessis,Simon Cauchemez,Andrew Rambaut,Samuel V. Scarpino,Samuel V. Scarpino,Samuel V. Scarpino,Oliver G. Pybus,Oliver G. Pybus +29 more
TL;DR: In this paper, the authors investigated the spatial invasion dynamics of lineage B.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data.
Journal ArticleDOI
COVID-19 vaccine development: milestones, lessons and prospects
Maochen Li,Han Wang,Lili Tian,Zehan Pang,Qingkun Yang,Tianqi Huang,Junfen Fan,Lihua Song,Yigang Tong,Huahao Fan +9 more
TL;DR: In this article , the safety and efficacy of COVID-19 vaccines were evaluated, including the possible complications and different effects on pregnant women, the elderly, people with immune diseases and acquired immunodeficiency syndrome (AIDS), transplant recipients, and cancer patients.
Posted ContentDOI
Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA
Rebecca Earnest,Rockib Uddin,Nicholas Matluk,Nicholas Renzette,Katherine J. Siddle,Christine Loreth,Gordon Adams,Christopher Tomkins-Tinch,Mary E. Petrone,Jessica E. Rothman,Mallery I. Breban,Robert Tobias Koch,Kendall Billig,Joseph R. Fauver,Chantal B.F. Vogels,Sarah E Turbett,Kaya Bilguvar,Kaya Bilguvar,Bony De Kumar,Marie L. Landry,David R. Peaper,Kevin Kelly,Greg Omerza,Heather Grieser,Sim Meak,John Martha,Hannah H. Dewey,Susan Kales,Daniel Berenzy,Kristin Carpenter-Azevedo,Ewa King,Richard C Huard,Sandra Smole,Catherine M. Brown,Timelia Fink,Andrew S. Lang,Glen R. Gallagher,Pardis C. Sabeti,Stacey Gabriel,Bronwyn MacInnis,New England Variant Investigation Team,Ryan Tewhey,Ryan Tewhey,Ryan Tewhey,Mark D. Adams,Daniel J. Park,Jacob E. Lemieux,Jacob E. Lemieux,Nathan D. Grubaugh +48 more
TL;DR: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha as discussed by the authors.
Journal ArticleDOI
Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA
Rebecca Earnest,R. Uddin,Nicholas Matluk,Nicholas Renzette,Sarah E Turbett,Katherine J. Siddle,Christine Loreth,Gordon Adams,Christopher Tomkins-Tinch,Mary E. Petrone,Jessica E. Rothman,Mallery I. Breban,Robert Koch,K. Billig,Joseph R. Fauver,Chantal B.F. Vogels,Kaya Bilguvar,Bony De Kumar,Marie L. Landry,David R. Peaper,Kevin Kelly,Greg Omerza,Heather J. Grieser,Sim Meak,John Martha,Hannah B. Dewey,Susan Kales,Daniel Berenzy,Kristin Carpenter-Azevedo,Ewa King,Richard C. Huard,Vladimir Novitsky,Mark Howison,Josephine Darpolor,Akarsh Manne,Rami Kantor,Sandra Smole,Catherine M. Brown,Timelia Fink,A Lang,Glen R. Gallagher,Virginia E. Pitzer,Pardis C. Sabeti,Stacey Gabriel,Bronwyn MacInnis,Ryan Tewhey,Mark D. Adams,Daniel J. Park,Jacob E. Lemieux,Nathan D. Grubaugh +49 more
TL;DR: The SARS-CoV-2 Delta variant emerged 1.37-2.63 times faster than Alpha (state range) and 6.2 times more viral RNA copies per milliliter than Alpha as mentioned in this paper .
Posted ContentDOI
SARS-CoV-2 Spreads through Cell-to-Cell Transmission
Cong Zeng,John P. Evans,Tiffany King,Tiffany King,Yi-Min Zheng,Eugene M. Oltz,Sean P. J. Whelan,Linda J. Saif,Linda J. Saif,Shan-Lu Liu +9 more
TL;DR: Evidence that SARS-CoV-2 spreads through cell-cell contact in cultures, mediated by the spike glycoprotein is provided, with important implications for a better understanding of Sars-Cov-2 spread and pathogenesis.
References
More filters
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Book
ggplot2: Elegant Graphics for Data Analysis
TL;DR: This book describes ggplot2, a new data visualization package for R that uses the insights from Leland Wilkisons Grammar of Graphics to create a powerful and flexible system for creating data graphics.
Journal ArticleDOI
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh,Daron M. Standley +1 more
TL;DR: This version of MAFFT has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update.
Journal ArticleDOI
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.
TL;DR: The software package Tracer is presented, for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference, which provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more.
Related Papers (5)
Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England.
Nicholas G Davies,Sam Abbott,Rosanna C. Barnard,Christopher I Jarvis,Adam J. Kucharski,James D Munday,Carl A. B. Pearson,Timothy W Russell,Damien C. Tully,Alex D. Washburne,Tom Wenseleers,Amy Gimma,William Waites,Kerry L. M. Wong,Kevin van Zandvoort,Justin D. Silverman,Karla Diaz-Ordaz,Ruth H. Keogh,Rosalind M Eggo,Sebastian Funk,Mark Jit,Katherine E. Atkins,Katherine E. Atkins,W. John Edmunds +23 more
Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus.
Bette T. Korber,Will Fischer,Sandrasegaram Gnanakaran,Hyejin Yoon,James Theiler,Werner Abfalterer,Nick Hengartner,Elena E. Giorgi,Tanmoy Bhattacharya,Brian T. Foley,Kathryn M. Hastie,Matthew Parker,David G Partridge,Cariad Evans,Timothy M. Freeman,Thushan I de Silva,Adrienne Angyal,Rebecca Brown,Laura Carrilero,Luke R. Green,Luke R. Green,Luke R. Green,Danielle C. Groves,Katie Johnson,Alexander J Keeley,Benjamin B Lindsey,Paul J. Parsons,Mohammad Raza,Sarah Rowland-Jones,Nikki Smith,Rachel Tucker,Dennis Wang,Matthew Wyles,Charlene McDanal,Lautaro G. Perez,Haili Tang,Alex Moon-Walker,Alex Moon-Walker,Alex Moon-Walker,Sean P. J. Whelan,Celia C. LaBranche,Erica Ollmann Saphire,David C. Montefiori +42 more
Detection of a SARS-CoV-2 variant of concern in South Africa.
Houriiyah Tegally,Eduan Wilkinson,Marta Giovanetti,Marta Giovanetti,Arash Iranzadeh,Vagner Fonseca,Vagner Fonseca,Jennifer Giandhari,Deelan Doolabh,Sureshnee Pillay,Emmanuel James San,Nokukhanya Msomi,Koleka Mlisana,Anne von Gottberg,Sibongile Walaza,Mushal Allam,Arshad Ismail,Thabo Mohale,Allison J. Glass,Susan Engelbrecht,Gert U. van Zyl,Wolfgang Preiser,Francesco Petruccione,Alex Sigal,Alex Sigal,Diana Hardie,Gert Marais,Nei yuan Hsiao,Stephen N.J. Korsman,Mary-Ann Davies,Lynn Tyers,Innocent Mudau,Denis York,Caroline Maslo,Dominique Goedhals,Shareef Abrahams,Oluwakemi Laguda-Akingba,Arghavan Alisoltani-Dehkordi,Arghavan Alisoltani-Dehkordi,Adam Godzik,Constantinos Kurt Wibmer,B.T. Sewell,José Lourenço,Luiz Carlos Junior Alcantara,Luiz Carlos Junior Alcantara,Sergei L Kosakovsky Pond,Steven Weaver,Darren P. Martin,Richard J Lessells,Richard J Lessells,Jinal N. Bhiman,Carolyn Williamson,Carolyn Williamson,Tulio de Oliveira,Tulio de Oliveira,Tulio de Oliveira +55 more