Newswise — Researchers from the University of Birmingham are working with health partners in Brazil to combat the spread of Zika virus by deploying a pair of mobile DNA sequencing laboratories on a medical ‘road trip’ through the worst-hit areas of the country.
Focusing on areas with the highest reported rates of microcephaly, a team of global experts will use portable, USB-powered genome sequencing equipment to analyse virus samples. They will use data gathered to track the spread of the virus and spot its emergence in large towns and cities.
Working with the Instituto Evandro Chagas, in Belém – part of the Brazilian Ministry of Health which is supporting the project, the Institute of Tropical Medicine, University of São Paulo and the Fundação Oswaldo Cruz (FIOCRUZ), in Salvador, Bahia – over the 30-day sampling period, mobile testing teams will travel to north-eastern Brazil and test samples from 750 patients in coastal Brazil - from Belém itself in the north to Salvador in the east.
Led by the University of Birmingham, the project is supported by the Medical Research Council (MRC) and draws together experts from Public Health England, the Universities of Oxford, Nottingham and Edinburgh, as well as the University of Sydney, Australia and the Ontario Institute for Cancer Research, in Toronto, Canada.
Dr Nick Loman, from the Institute of Microbiology and Infection at the University of Birmingham, said: “Zika is spreading across the Americas and the Pacific and geneticists are playing catch-up. There are very few publicly available DNA sequences and hardly any from the regions where cases of microcephaly are most prevalent.
“Using the mobile laboratories, we can take to the roads of north-east Brazil to detect and characterise the early emergence of Zika in large urban centres. The data we gather will help to understand how the virus has spread across Brazil, Latin America, and make better predictions about how it might spread to other regions in the future. We are also able to bring cutting-edge genomic surveillance technology to public health laboratories previously unequipped with this capability.
“The portable DNA sequencing systems allow us to do outbreak genome sequencing in real-time, impacting directly on the response to the virus on the ground, as well as helping to build a picture of its evolution.
“I hope our work in Brazil will reveal more about Zika’s origins, how often it has entered the Americas, how it interacts with the immune system, how many strains there are, and whether it interacts with other viruses such as Dengue and Chikungunya. We have no real feel for that at the moment. Even though the volume of knowledge is increasing, there is much remaining to be learnt about Zika virus.”
He added that genome sequencing in outbreaks is useful to understand how the virus evolves, but the information had to be available quickly in order for this information to guide control efforts. This method and technology has already shown to be useful in the surveillance of Ebola in Guinea during the 2014-2016 epidemic[i].
The team will adopt an open data policy on the project – making information collected freely available to researchers and public health analysts investigating the spread of the virus as it is generated. Interested parties can find information and data here http://zibraproject.github.io/.
Experts at the World Health Organisation (WHO) believe the mosquito-borne virus can cause the birth defect microcephaly, which can result in abnormal smallness of the head - a congenital condition associated with incomplete brain development. The virus is also associated with Guillain-Barre syndrome - a rare neurological disorder that can result in paralysis.
The WHO has also reported the first signs of a possible rise in microcephaly cases outside Brazil, which is the hardest-hit country so far in an outbreak spreading rapidly across Latin America and the Caribbean. The research team in Brazil will use a lightweight MinION DNA sequencer from Oxford Nanopore Technologies, which weighs less than 100g and is powered by the USB of a laptop. The device is currently being used by more than 1,500 researchers worldwide.Following an initial training period, the genome surveillance laboratory will set out from Belém, visiting Natal, Joao Pessoa, Recife and Salvador.
The MinION equipment was first used successfully for remote disease surveillance by University of Birmingham-led teams in Conakry, Guinea, in April 2015 where Ebola samples from patients could be sequenced as soon as new cases were diagnosed. Information was available more quickly as samples could be analysed on site, in real time, rather than being shipped to traditional genome laboratories often located on a different continent.
By sequencing 142 samples from Ebola patients in Guinea, they were able to provide very detailed information about how cases were related, providing important clues to World Health Organisation epidemiologists battling to halt transmission of the virus.
ENDSPHOTO CAPTIONS – please credit Ricardo Funari:
• Zibra Joao Pessoa - Science on the road bus - Jaqueline Goes de Jesus (Fundacao Oswaldo Cruz – Salvador) and Nuno Faria (University of Oxford – UK) use the Oxford Nanopore MinION device in front of the minibus equipped with lab in Joao Pessoa, Brazil. (002 & 003/005)• The mobile Zika surveillance project, ZIBRA, is using DNA sequencing technology in the back of a bus. (004)• Dr Nick Loman, left, and the Zibra team work while travelling from Natal to Joao Pessoa in north-east Brazil in the minibus equipped with lab. (006)• Entomologists from the Evandro Chagas Institute collect mosquitos in Natal to be tested for Zika virus. (010)• The MinION portable DNA sequencer is used to analyse the Zika virus in north-east Brazil. (021)
Images can be accessed here: https://www.dropbox.com/sh/5n80xuvhdycdoxd/AAClsNjSdYIHWH4jFTto7il5a?dl=0
Notes to editors
• The University of Birmingham is ranked amongst the world’s top 100 institutions, its work brings people from across the world to Birmingham, including researchers and teachers and more than 5,000 international students from over 150 countries.
• The research project in Brazil will address a number of questions:
(i) What are the origins and patterns of virus spread of Zika in Brazil? This allows identification of main hubs of virus transmission and routes of entry into cities.
(ii) Do genetic strains of the virus circulating differ in epidemic and transmission potential? This will help to predict the likelihood of spread of Zika.
(iii) What are the main ecological and epidemiological drivers of Zika spread across Brazil? This will help public health authorities focus prevention efforts in higher risk locations.
(iv) Is there an association between specific Zika lineages and microcephaly? This will help to better understand the complex nature of the disease aetiology and develop treatment and vaccines.
• More information on the project can be found at http://zibraproject.github.io/roadtrip• More information on Oxford Nanopore and the MinION can be found at http://www.nanoporetech.com or https://www.publications.nanoporetech.com
For further information or to arrange an interview, please contact Tony Moran in the University of Birmingham press office on +44 (0)121 414 8254 / +44 (0) 782 783 2312 or email [email protected].
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