NEW ORLEANS (GenomeWeb) – Through next-generation sequencing, researchers are teasing out viral origins and tracking their spread, with the hopes of preventing outbreaks in the future.
"NGS shows great potential for diagnosis, surveillance, and outbreak investigation," said New York Medical College's Victoria Gilrane at this year's American Society for Microbiology meeting here.
She and researchers like the University of Washington's Alex Greninger are tracking respiratory infections circulating among hospital patients, while on a more global scale, Broad Institute's Nathan Yozwiak and the Scripps Research Institute's Kristian Andersen have been using sequencing to determine how the Ebola and Zika viruses have spread. With such an approach, they reported that they've been able to identify relatedness among viruses, uncover a new transmission route, and track movements into a new location, as well as rule out a common infection source.
For example, by sequencing samples from the West African Ebola outbreak, the Broad's Yozwiak noted that sequencing — which had about a 10-day turnaround time in his research — could determine that all the strains were related.
Analyzing mutation patterns among Ebola samples also enabled researchers to find that the virus could be spread sexually, added Scripps' Andersen. Generally, the viruses followed the same trend of mutations accumulating over time, but occasionally an isolate would pop up that was much more similar to earlier isolates. These instances, they determined, were due to sexual transmission. Andersen noted that the longest time between someone seemingly being cured of the virus and transmitting it sexually has been 500 days.
Similarly, with the Zika virus outbreak, sequencing could confirm the origin and spread of the virus. Yozwiak and his colleagues sequenced about 100 Zika viruses and, along with 64 Zika virus samples from GenBank, created a phylogeny that was consistent with a Brazilian origin and a rapid, early spread, as they reported in Nature in May. A series of papers in that issue examined the introduction and spread of the Zika virus in the Americas.
Yozwiak's analysis also clustered the Colombia, Puerto Rico, and Honduras isolates together, and suggested that the virus arrived in Brazil months before it was reported.
Sequencing likewise enabled a more zoomed-in view of Zika transmission. In Florida, there have been 250 locally transmitted cases and about 1,000 travel-associated cases. Scripps' Andersen and his colleagues sequenced 35 Zika virus isolates from Florida, mostly from Miami Beach, as he and his colleagues also reported in Nature in late May. The majority of the isolates were from human cases, though some were collected from mosquitoes.
From their analysis, Andersen and his colleagues found that the virus likely entered Florida a few months before it was first detected in July 2016 in Miami, and that there were likely multiple introductions, at least four and possibly as many as 30 times to 40 times that.
They also found that the Caribbean was the main source of Zika in Miami, which he said match travel patterns, particularly those of cruise ships.
Sequencing has also been able to determine whether apparent clusters of infection are actually related. In particular, the University of Washington's Greninger has used sequencing in his clinical lab to gauge whether respiratory infections affecting hospital patients have a common source.
For instance, he and his colleagues investigated three human parainfluenza virus 3 infections that cropped up within 12 days among three long-term inpatients. They collected swabs from those patients and 10 controls from the emergency room or community clinic for sequencing on the Illumina MiSeq platform. For the two inpatients with enough sequencing coverage, phylogenetic analysis showed that there was complete overlap between the samples, which Greninger said was consistent with the infection being acquired in the hospital.
He and his colleagues similarly investigated a cluster of human rhinoviruses that arose among four long-term inpatients within 20 days. For two of the patients, the analysis indicated that there had been 172 years since their common ancestor, suggesting that this cluster was actually due to simultaneous infections from people visiting from the community where there was a high burden of rhinovirus.
Sequencing can also be used to monitor an ongoing outbreak and uncover population shifts. At New York Medical College in Westchester, New York, Gilrane and her colleagues have been testing for enterovirus D68 and noticed that the strain infecting patients in 2016 differed from the one behind a 2014 outbreak.
The enterovirus D68 outbreak, which causes severe respiratory illness and sometimes acute flaccid myelitis, was first noted in 2014 in 49 states, including New York. Gilrane and her colleagues collected 160 nasopharyngeal samples in 2016 from patients in the Lower Hudson Valley in New York for analysis using both an EV-D68-specific rRT-PCR assay and a metagenomic next-generation sequencing assay.
When they compared these 2016 samples to 94 samples from 2014, the researchers noted some differences in their clinical characteristics. For instance, the age of the infected patients was slightly younger for the newer samples. The samples also belonged to different subclades: B1 and B3, respectively.
This, Gilrane noted, is the first time subclade B3 has been seen in the US, adding that sequencing enabled them to see this shift in the dominant clade as well as the decrease in diversity.
"Viral genomics is now in the outbreak response kit," the Yozwiak said.
However, Greninger noted that sequencing is only actionable if it is quick, adding that the definition of quick keeps becoming faster and faster.
Andersen said that in the past outbreaks haven't been prevented because of failure to diagnose them rapidly. He noted that the Ebola outbreak began in December 2013, but it wasn't recognized until March 2014. He acknowledged, though, that the delay was due in part to the Lassa virus being endemic in the area, Ebola never before being seen there, and a poor healthcare infrastructure in the region.
But in the future, he said that early diagnosis could help head off an outbreak. "The way to do that is with sequencing," he said. He described a vision in which single blood samples are collected from patients and tested "for everything with a genome."