Nature paper

Zika virus Evolution and Spread in the Americas.

Nature. 2017 Jun 15;546(7658):411-415. doi: 10.1038/nature22402.

Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A, Lin AE, Tomkins-Tinch CH, Ye SH, Park DJ, Luo CY, Barnes KG, Shah RR, Chak B, Barbosa-Lima G, Delatorre E, Vieira YR, Paul LM, Tan AL, Barcellona CM, Porcelli MC, Vasquez C, Cannons AC, Cone MR, Hogan KN, Kopp EW, Anzinger JJ, Garcia KF, Parham LA, Ramírez RMG, Montoya MCM, Rojas DP, Brown CM, Hennigan S, Sabina B, Scotland S, Gangavarapu K, Grubaugh ND, Oliveira G, Robles-Sikisaka R, Rambaut A, Gehrke L, Smole S, Halloran ME, Villar L, Mattar S, Lorenzana I, Cerbino-Neto J, Valim C, Degrave W, Bozza PT, Gnirke A, Andersen KG, Isern S, Michael SF, Bozza FA, Souza TML, Bosch I, Yozwiak NL, MacInnis BL, Sabeti PC.

Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analysed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental United States. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of surveillance of viral infections. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those that might be relevant to the effectiveness of diagnostic tests.

Molecular Mapping of Zika Spread
Mike Worobey, Nature (background commentary)

Open Science Combats Zika
Nate Grubaugh, Nature Microbiology (blog)

A Sequencing Road Trip At The Heartland Of Zika Virus In The Americas
Nuno Faria, Nature Microbiology (blog)

Genomic Epidemiology To Combat Virus Outbreaks
Nate Grubaugh, The STEM Lab and Field Blog (blog)

Genomic Epidemiologi – Zika Virus
Kristian Andersen, Future of Genomic Medicine 2017 (talk)

Media Coverage (selected)
The Atlantic – How Zika Conquered The Americas
Associated Press – Zika Hit Florida Months Before Infections Found, Study Says
KBPS – San Diego Lab Takes ‘Open Science’ Approach To Tracking Zika’s Arrival In US
Los Angeles Times – What The DNA Of The Zika Virus Tells Scientists About Its Rapid Spread
NPR – Miami’s Zika Outbreak Began Months Before It Was First Detected
WIRED – Virus Hunters Draw A Map Of Zika’s Spread With DNA
Miami Herald – Miami Zika Linked To Caribbean Outbreak, Study Finds
Time – Zika Was Spreading Long Before Experts Realized It
Financial Times – Scientists ‘Way Behind The Curve’ On Threat Of Zika Virus
Mashable –  How The Zika Virus Stealthily Swept The Americas
San Diego Tribune – Zika Struck Florida Up To 40 Times Before Detection
NBC News – Zika Virus Was Spreading Quietly A Year Before Anyone Knew, Gene Study Shows
Fox News – Tracking Zika: Virus Hit Earlier Than Thought In Brazil, Florida
CIDRAP News – Zika Studies Uncover Early Spread, Factors Fueling Florida Outbreak
GenomeWeb – Genomic Studies Untangle Zika Virus Introduction, Spread Across Americas
Science News – The Zika Epidemic Began Long Before Anyone Noticed (Danish) – Zika-Udbruddet Kortlagt: Fremover Kan Epidemier Fanges I Opløbet

Press Releases
Scripps Research – Zika Reached Miami At Least Four Times, Caribbean Travel Likely Responsible
Florida Gulf Coast University – FGCU Virologists Publish Study That Finds Zika Invaded Florida Multiple Times In 2016
USAMRIID – Near Real-Time Genomic Sequencing Maps Introduction And Spread Of Zika Virus In US
Colorado State University – Zika Reached Miami At Least Four Times In 2016, New Study Finds
University of Miami – Zika Virus Was Introduced In South Florida Multiple Times In 2016, Study In Nature Reveals
Oxford University – Zika Spread Secrets Tracked Through New Gene Sequencing Study
Fred Hutch – On The Zika Trail
Broad Institute – Zika Virus Likely Circulated In Americas Long Before Detection During 2015-16 Epidemic