Zika: Open genomic surveillance of Zika virus in Brazil using a novel portable real-time sequencing device

Lead Research Organisation: University of Birmingham
Department Name: UNLISTED


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Technical Summary

A major epidemic of Zika virus (ZIKV) is ongoing in Latin America. Critically, there is
evidence for an association between infection with ZIKV and both microcephaly in newborns
and Guillain-Barré syndrome. Currently there is a paucity of complete genome sequences for
this virus, in part due to difficulties in transporting material outside of Brazil for sequencing,
hindering attempts to determine virus origins, epidemiology and any genomic basis to
microcephaly. We have recently established real-time portable genome sequencing using the
Oxford Nanopore MinION device, and successfully used this to characterize Ebola virus
genetic diversity in Guinea during the 2014-2015 outbreak [1]. We propose to extend this
ground-breaking achievement to ZIKV by establishing two portable genome sequencing
laboratories in Brazil. Through collaboration with the Oswaldo Cruz Foundation (FIOCRUZ)
and the Instituto Evandro Chagas public health laboratory in Brazil we will sequence 750
complete genomes of ZIKV, covering a broad geographical region including historical
samples, and from patients with a range of clinical presentations. These novel genomic data
will provide key information on how and when ZIKV was introduced to Brazil, the pattern and
determinants of spread through the country and to neighbouring localities, the extent of
genetic diversity (of importance to vaccine and diagnostic design), and whether there are any
associations between changes in the virus genome and the likelihood of ZIKV complications
such as microcephaly. Crucially these data will provide a surveillance framework for tracking
further spread into other geographic regions. In common with our previous efforts, this effort
will serve as a beacon for open science during a public health emergency [1-4]. Data will be
subject to open release as it is generated.
Description In 2016 the world urgently needed to understand the origins of Zika virus with was associated with cases of newborn microcephaly in the Americas.

To do this we worked with Brazilian colleagues to develop an entirely new method of sequencing virus genomes rapidly.

We were able to show that Zika had been circulating in Brazil for a full year before it was detected, and demonstrated how it had spread from Asia across the Pacific.

We continue to work closely with our Brazilian colleagues using our methods to understand new and emerging mosquito-transmitted viruses.

Our new method became ultimately famous globally, as it set the standard for how the SARS-CoV-2 virus was sequenced during the COVID-19 pandemic.
Exploitation Route This project has formed the basis of a global standard for sequencing viruses and other microbial pathogens and is available as a freely available open source toolkit for that purpose. It will be of use for future pathogen surveillance projects and pandemic preparedness.
Sectors Environment


Pharmaceuticals and Medical Biotechnology

URL http://www.zibraproject.org
Description ZIBRA 2 - ZIKV in Brazil Real-Time Analysis - Second Round
Amount R$ 1,100,000 (BRL)
Funding ID MCTIC/FNDCT-CNPq/MEC-CAPES/MS-Decit/No.14/2016 - Preventing and Combating Zika Virus 
Organisation National Council for Scientific and Technological Development (CNPq) 
Sector Public
Country Brazil
Start 03/2017 
End 03/2019
Description World Health Organization Global Advisory Alert and Response Network - Technical Expert/Outbreak Response Participation 
Organisation World Health Organization (WHO)
Department WHO Global Outbreak Alert and Response Network
Country France 
Sector Charity/Non Profit 
PI Contribution We have been included as technical experts on next-generation molecular diagnostics (by sequencing) to assist the WHO in outbreak and epidemic response when required in-country.
Collaborator Contribution WHO are the recognised international agency responsible for the management and containment of outbreaks and epidemics.
Impact In the past weeks this has included serving in an advisory function to support an outbreak of necrotising cellulitis in Sao Tome. We provided rapid response sequencing facility, in collaboration with Ian Goodfellow (University of Cambridge) to the island and provided real-time pathogen diagnostics and epidemiology using nanopore sequencing.
Start Year 2016
Title The Zibra Pipeline 
Description The Zibra Pipeline provides the bioinformatics component of the Zika real-time sequencing project. This open source package was designed to simplify the process of bioinformatics analysis using standard laptops when performing in-field sequencing. It supports both nanopore and Illumina platforms. It is packaged as a Docker container which means it can run on Windows, Linux and Mac computers. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This software was pivotal in the ability to give local stakeholders in Brazil the ability to generate their own sequences with limited bioinformatics support. 
URL https://github.com/zibraproject/zika-pipeline