Tracking the origin and spread of emerging epidemics

It took just a few months for Zika to spread across over 50 countries and territories in the Americas. The virus was first detected in the continent in May 2015, following a series of explosive outbreaks in the Pacific islands. But where and when did the recent epidemic begin, and how rapidly is the virus evolving? Were the birth defects seen since October 2015 the consequence of newly acquired virus mutations?

To answer these and other questions we designed the ZiBRA project and set out to trace the evolutionary history of Zika across the Americas, identify the origins of the epidemic and track patterns of virus transmission in the most severely affected areas. In June 2016, our team equipped and drove a mobile molecular and genomic laboratory for 2,000km across the Atlantic coast of Brazil. In two weeks we tested 1,400 samples from pregnant women and their newborns in the main central public health laboratories. 

We used a new pocket-size genome sequencing device, called a MinION, developed by Oxford Nanopore Technologies (a spin-out company of Oxford University). This revolutionary piece of kit allowed us share analyses of whole virus genomes with local and national public health agencies in less than 48h upon arrival to a new laboratory. When combined with epidemiological and climatic data, our genetic analyses revealed that Zika was first established in the northeast Brazil at least one year before its detection in the country.We found that temperature and humidity determine the abundance of the urban mosquitoes that transmit Zika, and that we should expect a lag of approximately five months between peaks in Zika infection and microcephaly incidence. We have also identified a small set of candidate mutations that are unique to the Zika virus strain in the Americas. 

What started as a pilot project is now expanding towards a global system of genomic pathogen surveillance in human, insect and animal populations. The ZiBRA team has now generated more than half of all publically available Zika virus genome sequences and trained over 50 young researchers in Brazil.

The project pioneered in real-time data sharing, and our interdisciplinary team brings together researchers from the University of Birmingham, reference institutes in Brazil, Ministry of Health (MoH) of Brazil, Angola, Cabo Verde and Mozambique, and the World Health Organization. 

The world is becoming increasingly connected through air travel, road networks and commercial shipping. The main scientific aim is to improve outbreak prevention and prediction of virus epidemic spread – by building a framework capable of incorporating mobility and ecological suitability measures with insights from a synchronized genomic surveillance in areas at risk for disease emergence.