Nature paper

Genomic Epidemiology Reveals Multiple Introductions of Zika virus into the United States

Nature. 2017 Jun 15;546(7658):401-405. doi: 10.1038/nature22400.

Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Luo C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC Jr, Lichtenberger PN, Ricciardi MJ, Bailey VK, Watkins DI, Cone MR, Kopp EW 4th, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG.

Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016-several months before its initial detection. By analyzing surveillance and genetic data, we show that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions were linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. Our study provides an understanding of how ZIKV initiates transmission in new regions.

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