LONDON – A multinational effort to sequence and analyze 174 Zika genomes has shown exactly how the virus spread across the Americas and demonstrates how whole genome sequencing could be applied in the surveillance of disease outbreaks and to rapidly identify conserved viral DNA that can be targeted by vaccines.

The research, published in a series of papers in Nature and Nature Protocols, found that in each of the regions where Zika circulated the virus was undetected for many months before any cases were reported.

Reconstructing the spread of the virus by following a trail of mutations showed northeast Brazil was the hub of the outbreak. It was here that the researchers tracked down the common ancestor of Zika in the Americas and dated it to January 2014, more than a year before the first confirmed human infection in May 2015.

From taking hold in Brazil, its spread to other regions occurred before Zika transmission in the Americas was first detected.

In the case of Florida, it is shown Zika was introduced at least four times by travelers from the Caribbean, but each introduction failed to sustain a permanent infection.

The researchers built on partnerships formed and experience gained in the response to the 2013-2016 Ebola virus epidemic in west Africa, where it was shown to be feasible to do whole genome sequencing in the field.

Building on this, a total of 110 Zika virus genomes were sequenced from patient and mosquito samples from 11 countries and analyzed with 64 existing sequences held in NIH's genetic sequence database Genbank.

When the epidemic began in the Americas, little was known about the genetic make-up of Zika, said Bronwyn MacInnis, associate director of malaria and viral genomics at the Broad Institute, of Boston. "Collectively, our goal was to capture as complete a picture of the genetic underpinnings of the epidemic as we could."

The sequences can be used to identify conserved genes in rapidly mutating viruses, informing the design of vaccines. "We can also use genome sequences at scale to evaluate vaccines during [clinical testing]," MacInnis told BioWorld Today. "It is possible to track if particular strains of the virus escape the effect of a vaccine and cause breakthrough infections."

The findings will also provide a framework to understand the origin of any fresh outbreak. Comparing Zika sequences from new cases to the reference database will show if they are imported, isolated cases or if the spread is local, in which case public health measures are required.

"Genomics allowed us to track and to reconstruct how the virus traveled and changed across the epidemic, which also means that genomics could have helped detect it much earlier,"MacInnis said. "We were way behind the curve on Zika. We need to be well ahead of the next emerging viral threat and genomics can have a role in achieving this."

The slow response to the Zika outbreak is attributed the fact that the symptoms are both mild and similar to those caused by other mosquito-transmitted infections, including dengue and chikungunya, both of which were spreading at the same time.

It was not until a rise in the number of babies born with microencephaly and the subsequent understanding this was linked to maternal Zika infection, that the serious nature of the epidemic was recognized.

A total of 200,000 cases of Zika virus infection and 2,366 cases of microencephaly were confirmed in Brazil up to December 2016.

One of the key advances described by the researchers is a new protocol for sequencing viral DNA directly from blood or serum samples, without the need to isolate and culture the virus first.

That means it is now practicable, speedy and inexpensive enough to use real-time genome sequencing for disease surveillance, according to Nicholas Loman of the school of biosciences at Birmingham University, U.K.

During the Ebola epidemic he worked with Oliver Pybus, professor of the evolution of infectious diseases at Oxford University, to show it is possible to use portable sequencing machines to do whole genome analyses in the field.

In June 2016 the two were joined by 13 other researchers in a mobile laboratory on a 2,000 km road trip to the areas of northeast Brazil where the most cases of microencephaly occurred.

The high viral load seen in Ebola virus infection makes it possible to sequence the virus without isolating it first, but that is not possible in Zika where the viral load is low.

Loman got around this by using the polymerase chain reaction to amplify Zika virus directly in the blood and serum samples, generating enough copies of the virus for its genome to be sequenced on the road in remote areas of northeast Brazil, using handheld sequencing machines developed by the Oxford University spin-out Oxford Nanopore Ltd.

The machines weigh less than 100 gm, are powered via the USB port of a laptop computer and do not require an Internet connection. "We could do emergency epidemiology research quickly and get immediate results. . . . The new protocol will be hugely beneficial to researchers working in remote areas around the world during viral outbreaks," Pybus said.

The project is now expanding to other areas of Brazil, looking not only at Zika, but also dengue and chikungunya viruses and yellow fever, building a fuller picture of the epidemiology of viruses transmitted by mosquitoes.

Pybus has looked at the sequences of a handful of Zika samples from babies born with microencephaly. "Based on the limited data we don't see any particular viral mutations associated with this form of the disease, but we do need more samples to study that properly," he said.