Zika papers in Nature

nature-grubaugh-coverIn a series of papers in the journals Nature and Nature Protocols, we used Zika virus sequencing from patients and mosquitos to show how the virus has spread across South America and into Florida. This work was performed as a large (huge!) collaboration of national and international institutions, which was made possible because of open science and open data.

Over the last couple of years, Zika virus has been causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, local Zika virus transmission was reported for the first time in the continental United States. The ensuing outbreak led to more than 250 locally acquired infections. A couple of months after the Florida outbreak was detected, a few cases were also reported in Brownsville, Texas.

zika_spread

Spread of Zika across the Americas (from M. Worobey)

Over the past year – together with a large group of international collaborators – we have been investigating how Zika virus is spreading across the Americas. In the primary paper from our group “Genomic epidemiology reveals multiple introductions of Zika virus into the United States”, we show how Zika virus spread from South America, and via the Caribbean into Florida. By tracking the virus from its first detection in Florida, we show that at least 4 introductions – and likely as many as 30 to 40 – contributed to the outbreak in Florida. We show that local transmission likely started in the spring of 2016 – several months before its initial detection. Our Zika virus genomic data provides a strong link showing that the majority of the Florida introductions were rooted in the Caribbean. We further corroborated this finding by integrating Zika infection rates in potential source countries, with traffic volumes coming into the Miami area.

A common theme from all studies, is that Zika virus has been circulating in endemic countries several months or years before initially being detected. Mike Worobey wrote a very nice News & Views commentary where he summarized this and other findings from the studies (see Figure). Together, these studies provide other key examples of how virus sequencing combined with large-scale analyses can be used to gain critical insights into the emergence, transmission, and spread of viruses during public health emergencies.

Articles

Genomic Epidemiology Reveals Multiple Introductions Of Zika Virus Into The United States
Grubaugh et al., Nature

Establishment And Cryptic Transmission Of Zika Virus In Brazil And The Americas
Faria et al., Nature

Zika Virus Evolution And Spread In The Americas
Metsky et al., Nature

Multiplex PCR Method For MinION And Illumina Sequencing Of Zika And Other Virus Genomes Directly From Clinical Samples
Quick et al., Nature Protocols

Epidemiology: Molecular Mapping Of Zika Spread
Worobey, Nature (News & Views)

Background

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
Videnskab.dk (Danish) – Zika-Udbruddet Kortlagt: Fremover Kan Epidemier Fanges I Opløbet

Press Releases

The Scripps Research Institute – 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

Data Repos

Andersen Lab GitHub
USAMRIID/Jason Ladner GitHub
ZiBRA GitHub
BioProject – Scripps #1
BioProject – Scripps #2
BioProject – USAMRIID
BioProject – Broad

Primary Collaborating Institutions

Colorado State University
Florida Department of Health
Florida Gulf Coast University
Fred Hutchinson Cancer Research Center
Miami-Dade County Mosquito Control
National Center for Atmospheric Research
The Broad Institute of MIT and Harvard
Tulane University
University of Birmingham
University of Edinburgh
University of Florida
University of Miami
University of Oxford
University of Toronto
US Army Medical Research Institute for infectious diseases