Volume 546 Issue 7658, 15 June 2017

Three papers in this issue provide a plethora of new genome sequences for the Zika virus and offer insights into its genetic epidemiology. On page 401, Kristian Anderson and his colleagues reveal 39 new genome sequences obtained from infected patients and Aedes aegypti mosquitoes. Using phylogenetic analysis they conclude that the virus has been introduced to Florida on multiple separate occasions and that most of these events were linked to travel from the Caribbean. Their work also suggests that Zika transmission chains in Florida are unlikely to persist, indicating that future outbreaks would depend on transmission dynamics in the Americas. On page 406, Nuno Faria and his colleagues provide 54 new virus genomes, mostly from northeast Brazil, several sequenced in real time using portable DNA sequencers and a mobile genomics laboratory. Using these and other available sequences they trace the spatial origins and spread of the virus in Brazil and the Americas, revealing that northeast Brazil played a crucial role in establishing the epidemic and the spread of the virus on the continent. And on page 411, Bronwyn MacInnis and her colleagues analyse 110 Zika virus genomes derived from clinical and mosquito samples from ten countries and territories. Their work affirms the rapid expansion of the epidemic within Brazil and multiple introductions to other geographical regions. They also describe the ongoing evolution of the virus and look at how the accumulation of mutations might affect the future performance of diagnostic tests. Cover image: Jasiek Krzysztofiak/Nature

Editorial

World View

Seven Days

Correction

News

News Feature

Comment

Books & Arts

Correspondence

News & Views

  • News & Views |

    Most state-of-the-art methods of wireless energy delivery are inherently limited to static devices. An approach based on fundamental physics could overcome this limitation, opening up a wealth of applications. See Letter p.387

    • Geoffroy Lerosey
  • News & Views |

    Evolutionary trees constructed using both newly sequenced and previously available Zika virus genomes reveal how the recent outbreak arose in Brazil and spread across the Americas. See Letters p.401 , p.406 & p.411

    • Michael Worobey
  • News & Views |

    Cell division requires the action of key regulator proteins called cyclins and CDKs. It emerges that a cyclin–CDK complex can regulate cell metabolism, and targeting this metabolic regulation causes tumour regression in mice. See Letter p.426

    • Abigail S. Krall
    •  & Heather R. Christofk
  • News & Views |

    Rubber sheets that reversibly bind and release substrates have been made by copying a subtlety in the shape of octopus suckers. The findings reveal how macro-scale biological structures can influence function. See Letter p.396

    • Jonathan J. Wilker
  • News & Views |

    A paper that analysed genetic variants in 14,000 people to identify disease-associated regions set the standard for collaborative genome-wide association studies and provided methodological advances whose effects are still felt today.

    • Teri A. Manolio
  • News & Views |

    Production of the metabolite acetyl-CoA near specific regions of DNA modulates gene expression in mouse neurons during cellular differentiation and memory formation. See Article p.381

    • L. Ashley Watson
    •  & Li-Huei Tsai

Correction

Perspective

  • Perspective |

    The current and expected environmental consequences of built dams and proposed dam constructions in the Amazon basin are explored with the help of a Dam Environmental Vulnerability Index.

    • Edgardo M. Latrubesse
    • , Eugenio Y. Arima
    • , Thomas Dunne
    • , Edward Park
    • , Victor R. Baker
    • , Fernando M. d’Horta
    • , Charles Wight
    • , Florian Wittmann
    • , Jansen Zuanon
    • , Paul A. Baker
    • , Camila C. Ribas
    • , Richard B. Norgaard
    • , Naziano Filizola
    • , Atif Ansar
    • , Bent Flyvbjerg
    •  & Jose C. Stevaux

Article

  • Article |

    Genetic and phenotypic analysis reveals expression quantitative trait loci in human induced pluripotent stem cell lines associated with cancer and disease.

    • Helena Kilpinen
    • , Angela Goncalves
    • , Andreas Leha
    • , Vackar Afzal
    • , Kaur Alasoo
    • , Sofie Ashford
    • , Sendu Bala
    • , Dalila Bensaddek
    • , Francesco Paolo Casale
    • , Oliver J. Culley
    • , Petr Danecek
    • , Adam Faulconbridge
    • , Peter W. Harrison
    • , Annie Kathuria
    • , Davis McCarthy
    • , Shane A. McCarthy
    • , Ruta Meleckyte
    • , Yasin Memari
    • , Nathalie Moens
    • , Filipa Soares
    • , Alice Mann
    • , Ian Streeter
    • , Chukwuma A. Agu
    • , Alex Alderton
    • , Rachel Nelson
    • , Sarah Harper
    • , Minal Patel
    • , Alistair White
    • , Sharad R. Patel
    • , Laura Clarke
    • , Reena Halai
    • , Christopher M. Kirton
    • , Anja Kolb-Kokocinski
    • , Philip Beales
    • , Ewan Birney
    • , Davide Danovi
    • , Angus I. Lamond
    • , Willem H. Ouwehand
    • , Ludovic Vallier
    • , Fiona M. Watt
    • , Richard Durbin
    • , Oliver Stegle
    •  & Daniel J. Gaffney
  • Article |

    The establishment of a drug-discovery screening pipeline for cryptosporidiosis, and identification of pyrazolopyridines as selective ATP-competitive inhibitors of the Cryptosporidium lipid kinase PI(4)K.

    • Ujjini H. Manjunatha
    • , Sumiti Vinayak
    • , Jennifer A. Zambriski
    • , Alexander T. Chao
    • , Tracy Sy
    • , Christian G. Noble
    • , Ghislain M. C. Bonamy
    • , Ravinder R. Kondreddi
    • , Bin Zou
    • , Peter Gedeck
    • , Carrie F. Brooks
    • , Gillian T. Herbert
    • , Adam Sateriale
    • , Jayesh Tandel
    • , Susan Noh
    • , Suresh B. Lakshminarayana
    • , Siau H. Lim
    • , Laura B. Goodman
    • , Christophe Bodenreider
    • , Gu Feng
    • , Lijun Zhang
    • , Francesca Blasco
    • , Juergen Wagner
    • , F. Joel Leong
    • , Boris Striepen
    •  & Thierry T. Diagana
  • Article |

    The metabolic enzyme acetyl coenzyme A synthetase directly regulates gene expression during memory formation by binding to specific genes and providing acetyl coenzyme A for histone acetylation.

    • Philipp Mews
    • , Greg Donahue
    • , Adam M. Drake
    • , Vincent Luczak
    • , Ted Abel
    •  & Shelley L. Berger

Letter

  • Letter |

    Molecular dynamics simulations of the Pb(Mg1/3,Nb2/3)O3–PbTiO3 relaxor reveal a multi-domain state analogous to the slush state of water that provides an explanation for the unusual properties of relaxors.

    • Hiroyuki Takenaka
    • , Ilya Grinberg
    • , Shi Liu
    •  & Andrew M. Rappe
  • Letter |

    Genome sequencing of Zika virus samples from infected patients and Aedes aegypti mosquitoes in Florida shows that the virus was probably introduced into the United States on multiple occasions, and that the Caribbean is the most likely source.

    • Nathan D. Grubaugh
    • , Jason T. Ladner
    • , Moritz U. G. Kraemer
    • , Gytis Dudas
    • , Amanda L. Tan
    • , Karthik Gangavarapu
    • , Michael R. Wiley
    • , Stephen White
    • , Julien Thézé
    • , Diogo M. Magnani
    • , Karla Prieto
    • , Daniel Reyes
    • , Andrea M. Bingham
    • , Lauren M. Paul
    • , Refugio Robles-Sikisaka
    • , Glenn Oliveira
    • , Darryl Pronty
    • , Carolyn M. Barcellona
    • , Hayden C. Metsky
    • , Mary Lynn Baniecki
    • , Kayla G. Barnes
    • , Bridget Chak
    • , Catherine A. Freije
    • , Adrianne Gladden-Young
    • , Andreas Gnirke
    • , Cynthia Luo
    • , Bronwyn MacInnis
    • , Christian B. Matranga
    • , Daniel J. Park
    • , James Qu
    • , Stephen F. Schaffner
    • , Christopher Tomkins-Tinch
    • , Kendra L. West
    • , Sarah M. Winnicki
    • , Shirlee Wohl
    • , Nathan L. Yozwiak
    • , Joshua Quick
    • , Joseph R. Fauver
    • , Kamran Khan
    • , Shannon E. Brent
    • , Robert C. Reiner Jr
    • , Paola N. Lichtenberger
    • , Michael J. Ricciardi
    • , Varian K. Bailey
    • , David I. Watkins
    • , Marshall R. Cone
    • , Edgar W. Kopp IV
    • , Kelly N. Hogan
    • , Andrew C. Cannons
    • , Reynald Jean
    • , Andrew J. Monaghan
    • , Robert F. Garry
    • , Nicholas J. Loman
    • , Nuno R. Faria
    • , Mario C. Porcelli
    • , Chalmers Vasquez
    • , Elyse R. Nagle
    • , Derek A. T. Cummings
    • , Danielle Stanek
    • , Andrew Rambaut
    • , Mariano Sanchez-Lockhart
    • , Pardis C. Sabeti
    • , Leah D. Gillis
    • , Scott F. Michael
    • , Trevor Bedford
    • , Oliver G. Pybus
    • , Sharon Isern
    • , Gustavo Palacios
    •  & Kristian G. Andersen

    Special:

  • Letter |

    Virus genomes reveal the establishment of Zika virus in Brazil and the Americas, and provide an appropriate timeframe for baseline (pre-Zika) microcephaly in different regions.

    • N. R. Faria
    • , J. Quick
    • , I.M. Claro
    • , J. Thézé
    • , J. G. de Jesus
    • , M. Giovanetti
    • , M. U. G. Kraemer
    • , S. C. Hill
    • , A. Black
    • , A. C. da Costa
    • , L. C. Franco
    • , S. P. Silva
    • , C.-H. Wu
    • , J. Raghwani
    • , S. Cauchemez
    • , L. du Plessis
    • , M. P. Verotti
    • , W. K. de Oliveira
    • , E. H. Carmo
    • , G. E. Coelho
    • , A. C. F. S. Santelli
    • , L. C. Vinhal
    • , C. M. Henriques
    • , J. T. Simpson
    • , M. Loose
    • , K. G. Andersen
    • , N. D. Grubaugh
    • , S. Somasekar
    • , C. Y. Chiu
    • , J. E. Muñoz-Medina
    • , C. R. Gonzalez-Bonilla
    • , C. F. Arias
    • , L. L. Lewis-Ximenez
    • , S. A. Baylis
    • , A. O. Chieppe
    • , S. F. Aguiar
    • , C. A. Fernandes
    • , P. S. Lemos
    • , B. L. S. Nascimento
    • , H. A. O. Monteiro
    • , I. C. Siqueira
    • , M. G. de Queiroz
    • , T. R. de Souza
    • , J. F. Bezerra
    • , M. R. Lemos
    • , G. F. Pereira
    • , D. Loudal
    • , L. C. Moura
    • , R. Dhalia
    • , R. F. França
    • , T. Magalhães
    • , E. T. Marques Jr
    • , T. Jaenisch
    • , G. L. Wallau
    • , M. C. de Lima
    • , V. Nascimento
    • , E. M. de Cerqueira
    • , M. M. de Lima
    • , D. L. Mascarenhas
    • , J. P. Moura Neto
    • , A. S. Levin
    • , T. R. Tozetto-Mendoza
    • , S. N. Fonseca
    • , M. C. Mendes-Correa
    • , F. P. Milagres
    • , A. Segurado
    • , E. C. Holmes
    • , A. Rambaut
    • , T. Bedford
    • , M. R. T. Nunes
    • , E. C. Sabino
    • , L. C. J. Alcantara
    • , N. J. Loman
    •  & O. G. Pybus

    Special:

  • Letter |

    One hundred and ten Zika virus genomes from ten countries and territories involved in the Zika virus epidemic reveal rapid expansion of the epidemic within Brazil and multiple introductions to other regions.

    • Hayden C. Metsky
    • , Christian B. Matranga
    • , Shirlee Wohl
    • , Stephen F. Schaffner
    • , Catherine A. Freije
    • , Sarah M. Winnicki
    • , Kendra West
    • , James Qu
    • , Mary Lynn Baniecki
    • , Adrianne Gladden-Young
    • , Aaron E. Lin
    • , Christopher H. Tomkins-Tinch
    • , Simon H. Ye
    • , Daniel J. Park
    • , Cynthia Y. Luo
    • , Kayla G. Barnes
    • , Rickey R. Shah
    • , Bridget Chak
    • , Giselle Barbosa-Lima
    • , Edson Delatorre
    • , Yasmine R. Vieira
    • , Lauren M. Paul
    • , Amanda L. Tan
    • , Carolyn M. Barcellona
    • , Mario C. Porcelli
    • , Chalmers Vasquez
    • , Andrew C. Cannons
    • , Marshall R. Cone
    • , Kelly N. Hogan
    • , Edgar W. Kopp
    • , Joshua J. Anzinger
    • , Kimberly F. Garcia
    • , Leda A. Parham
    • , Rosa M. Gélvez Ramírez
    • , Maria C. Miranda Montoya
    • , Diana P. Rojas
    • , Catherine M. Brown
    • , Scott Hennigan
    • , Brandon Sabina
    • , Sarah Scotland
    • , Karthik Gangavarapu
    • , Nathan D. Grubaugh
    • , Glenn Oliveira
    • , Refugio Robles-Sikisaka
    • , Andrew Rambaut
    • , Lee Gehrke
    • , Sandra Smole
    • , M. Elizabeth Halloran
    • , Luis Villar
    • , Salim Mattar
    • , Ivette Lorenzana
    • , Jose Cerbino-Neto
    • , Clarissa Valim
    • , Wim Degrave
    • , Patricia T. Bozza
    • , Andreas Gnirke
    • , Kristian G. Andersen
    • , Sharon Isern
    • , Scott F. Michael
    • , Fernando A. Bozza
    • , Thiago M. L. Souza
    • , Irene Bosch
    • , Nathan L. Yozwiak
    • , Bronwyn L. MacInnis
    •  & Pardis C. Sabeti
  • Letter |

    The authors trace the emergence of porcine primordial germ cells and develop in vitro models of primordial germ cell development from human and monkey pluripotent stem cells in order to provide insight into early human development.

    • Toshihiro Kobayashi
    • , Haixin Zhang
    • , Walfred W. C. Tang
    • , Naoko Irie
    • , Sarah Withey
    • , Doris Klisch
    • , Anastasiya Sybirna
    • , Sabine Dietmann
    • , David A. Contreras
    • , Robert Webb
    • , Cinzia Allegrucci
    • , Ramiro Alberio
    •  & M. Azim Surani
  • Letter |

    Regulatory T cells expressing the transcription factor T-bet selectively suppress TH1 and CD8 T cells, but not TH2 or TH17 activation and associated autoimmunity.

    • Andrew G. Levine
    • , Alejandra Mendoza
    • , Saskia Hemmers
    • , Bruno Moltedo
    • , Rachel E. Niec
    • , Michail Schizas
    • , Beatrice E. Hoyos
    • , Ekaterina V. Putintseva
    • , Ashutosh Chaudhry
    • , Stanislav Dikiy
    • , Sho Fujisawa
    • , Dmitriy M. Chudakov
    • , Piper M. Treuting
    •  & Alexander Y. Rudensky
  • Letter |

    The cyclin D3–CDK6 kinase complex, which is overactive in some cancers, inhibits two key glycolysis enzymes and thereby enhances the levels of antioxidants in cells, promoting tumour cell survival.

    • Haizhen Wang
    • , Brandon N. Nicolay
    • , Joel M. Chick
    • , Xueliang Gao
    • , Yan Geng
    • , Hong Ren
    • , Hui Gao
    • , Guizhi Yang
    • , Juliet A. Williams
    • , Jan M. Suski
    • , Mark A. Keibler
    • , Ewa Sicinska
    • , Ulrike Gerdemann
    • , W. Nicholas Haining
    • , Thomas M. Roberts
    • , Kornelia Polyak
    • , Steven P. Gygi
    • , Nicholas J. Dyson
    •  & Piotr Sicinski
  • Letter |

    Through drug exposure, a rare, transient transcriptional program characterized by high levels of expression of known resistance drivers can get ‘burned in’, leading to the selection of cells endowed with a transcriptional drug resistance and thus more chemoresistant cancers.

    • Sydney M. Shaffer
    • , Margaret C. Dunagin
    • , Stefan R. Torborg
    • , Eduardo A. Torre
    • , Benjamin Emert
    • , Clemens Krepler
    • , Marilda Beqiri
    • , Katrin Sproesser
    • , Patricia A. Brafford
    • , Min Xiao
    • , Elliott Eggan
    • , Ioannis N. Anastopoulos
    • , Cesar A. Vargas-Garcia
    • , Abhyudai Singh
    • , Katherine L. Nathanson
    • , Meenhard Herlyn
    •  & Arjun Raj
  • Letter |

    The structure of the anti-CRISPR protein AcrIIA4, in complex with a single-guide RNA and Cas9, reveals that the protein inhibits DNA binding and blocks the Cas9 endonuclease active site.

    • De Dong
    • , Minghui Guo
    • , Sihan Wang
    • , Yuwei Zhu
    • , Shuo Wang
    • , Zhi Xiong
    • , Jianzheng Yang
    • , Zengliang Xu
    •  & Zhiwei Huang

Corrigendum

Feature

Column

  • Column |

    A safe haven for career support unlocks a range of non-academic options, says Nathan L. Vanderford.

    • Nathan L. Vanderford

Futures

  • Futures |

    How to live happily ever after.

    • Cassandra Khaw

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