Photo by Ricardo Funari
Nick Loman, PhD, uses the Oxford Nanopore MinION device in front of a minibus equipped with a lab in Joao Pessoa, Brazil.
Researchers say they have uncovered the origin of Zika virus in Brazil and tracked the spread of the virus across the country.
The team traveled across northeast Brazil in a mobile genomics lab, analyzing samples from Zika patients.
The researchers found that Zika’s establishment within Brazil—and its spread from there to other regions—occurred before Zika transmission in the Americas was first discovered.
The team reported their findings in Nature.
To gain insight into the epidemiology and evolution of Zika virus, the researchers traveled 2000 km across northeast Brazil in June of last year. The team traveled in a minibus equipped with mobile DNA sequencing capabilities and tested samples from more than 1300 patients infected with the virus.
“Despite there being probably millions of cases of the Zika virus in Brazil, there was only a handful of known virus genomes prior to our work,” said Nuno Faria, PhD, of the University of Oxford in the UK.
“A better understanding of Zika virus genetic diversity is critical to vaccine design and also to identify areas where surveillance is most needed.”
“We generated Zika virus genomes to establish the virus epidemic history in the Americas,” said Oliver Pybus, DPhil, also of the University of Oxford.
“We showed that the virus was present in Brazil for a full year prior to the first confirmed cases in May 2015. We also found that northeast Brazil, which was the region with the most recorded cases of Zika and microcephaly, was the nexus of the epidemic in Brazil and played a key role in its spread within Brazil to major urban centers, such as Rio de Janeiro and São Paulo, before spreading across the Americas. We now have a better understanding of the epidemiology of the virus.”
During the genome sequencing journey across Brazil, the researchers used the portable MinION DNA sequencer from the company Oxford Nanopore Technologies, which started as an Oxford University spinout company. The device weighs less than 100 g and is powered by the USB port of a laptop.
“Genome sequencing has become a powerful tool for studying emerging infectious diseases,” said Nick Loman, PhD, of the University of Birmingham in the UK.
“However, genome sequencing directly from clinical samples without isolation remains challenging for viruses such as Zika. We developed a new protocol that allows for real-time genomic sequencing—something of vital importance when managing viral outbreaks, as it can provide real insight into how a virus is spreading, transmitting and evolving.”
“What’s more, using equipment like portable nanopore sequencing, we were able to carry out emergency epidemiological research more quickly, to get immediate results when working in the field, as on the road in Brazil. This new protocol will doubtless prove hugely beneficial to researchers working in remote areas around the world during times of viral outbreaks.”
