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New technology that quickly, easily and economically reveals the genomes of viruses and pathogens transforms public health and medicine.

Influenza sweeps around the world on an annual path of destruction. According to the World Health Organization, one year’s epidemic generates 3–5 million severe cases of influenza and kills 250,000–500,000 people. Moreover, the influenza season drains healthcare budgets. According to a 2007 article in Vaccine—written by experts at the US Centers for Disease Control and Prevention (CDC)—an influenza epidemic in the United States costs more than $87 billion. Many of these costs, in lives and dollars, can now be spared with advances from next-generation sequencing (NGS).

In brief, NGS quickly and relatively inexpensively determines an organism’s genome—the order of nucleic acids called bases. For example the Ion Torrent™ Personal Genome Machine (PGM) from Life Technologies (Carlsbad, California) can churn out as many as 2 billion bases in about seven hours. For comparison, the entire human genome consists of only about 3 billion bases.

As explained by Dan Didier, director of Public Health at Life Technologies: “Next-generation sequencing is used around the world to monitor viruses, as well as pathogens in food.” New viral and pathogenic challenges emerge constantly. In May 2013, for example, a novel respiratory virus related to SARS (severe acute respiratory syndrome) emerged in Saudi Arabia and quickly killed 18 people. Out of 44 cases worldwide, at the time of writing, this virus killed half of the people infected. NGS helps public-health officials identify such a new virus, learn to treat it and even reveals ways to prevent future outbreaks.

Souped-Up Surveillance
To fight the flu, healthcare experts and scientists need tools for tracking the disease. To help with that, Life Technologies established a Global Influenza Network, which consists of scientists around the world who collect data with the Ion PGM™ System. This technology will be used to sequence samples from influenza-infected patients to determine the most widespread strains. “This information can be used to not just catch up with the virus but get ahead of it to save lives and money,” says Didier.

Many people call this approach molecular diagnostics, but molecular surveillance might be more accurate in some circumstances. “Diagnosis means that someone is coming in sick,” says Didier, “but surveillance means looking at everyone out there.” NGS can detect new bacterial or viral strains and help to develop a test for them. This can also be used for known bacteria or viruses because they develop drug resistance by rearranging their DNA.

Beyond identifying causes of outbreaks, NGS can be used to improve treatments, especially when patients suffer from multiple strains of a virus. For example, someone infected with HIV could carry several forms of it. If a drug fights off one, than another strain of HIV can take over and grow. NGS could reveal all of the types of HIV that someone carries, and a personalized treatment plan could be developed based on the results of the molecular diagnostics.

Technology and Teamwork
Keeping track of diseases depends on using the right technology plus teamwork. Some groups collect specimens, others test them and sometimes others still analyze the data. This chain of action also requires organizations that connect the right groups. For example, Scott Becker, executive director of the Association of Public Health Laboratories, says, “We work very hard to support our members in their role in state and local public-health agencies and to connect them with federal partners at the CDC, FDA, corporate community and so on.” He adds, “It’s a local, state and federal continuum, and they all depend on each other.”

Becker says that today is the early stage of using NGS in public health. Beyond using NGS for communicable diseases, like influenza, Becker sees this technology teaching us more about chronic diseases. “Chronic disease is not something that public-health labs have been involved with,” he says. “It’s a new opportunity.” He also points out that these labs are looking to use NGS to screen newborns for a wide range of disorders.

For communicable diseases in particular, the teamwork must wrap around the world. For instance, Steve Glavas, head of the NGS platform at the Swedish Institute for Communicable Disease Control (SMI), says, “We keep an eye out for infectious diseases around the world and within the borders of Sweden.”

To perform that job, Glavas sees an increasingly important role for NGS. “It’s becoming more and more valuable to differentiate between one source or another in an outbreak,” he says. “In some cases, we can couple a strain with a previous outbreak in another place and maybe even associate it with a traveler who came into the country.” For such tracking, scientists at SMI use an Ion Torrent. “It’s high number of reads lets you pick up single reads that may be associated with another outbreak,” Glavas says. “With previous technology there were some things that you just couldn’t do, and we did lots of it without molecular techniques.”

Beating Outbreaks
In 2011, a strain of the bacteria Escherichia coli entered Germany on fenugreek seeds, which are used in some spice blends and other foods. This deadly strain killed 51 people there. To identify the killer, Dag Harmsen of the University of Münster in Germany and his colleagues applied NGS. As Harmsen says, “I got involved because I had early access to the Ion PGM™ System in Europe, and I could apply next-generation sequencing really quick.” In fact, Harmsen and his colleagues sequenced the outbreak strain in just 62 hours.

Thinking back on that work, Harmsen says, “Until then, larger machines had been applied to outbreaks and the turnaround for sequencing took from 10 days to several weeks.” He adds, “The exciting part was not the next-generation sequencing but the small desktop machine that is rather speedy.” So the Ion PGM™ System allows smaller labs to compete with larger ones. “This work was regarded by many as the proof of principle that it is technically feasible to apply these machines in nearly real time,” Harmsen explains. Based on the information from NGS, polymerase chain reaction (PCR) was used to develop a test to screen for the deadly strain of E. coli.

Similar approaches can go one step farther with viral outbreaks. In the May 15, 2013, Science Translational Medicine, a team of researchers from Novartis Vaccines and Diagnostics in Cambridge, Massachusetts, and colleagues used sequence information to make an influenza vaccine in just a few days. With traditional technology, it takes months to make such a vaccine.

Undoubtedly, much more lies ahead in sequencing’s impact on world health. From disease surveillance and vaccine production to chronic-disease treatment and personalized medicine, unraveling the genomic sequences of organisms promises to protect us from many diseases and save us from ones that we contract. In large part, these advances arise from one thing: smaller, faster and more affordable NGS machines. These machines already help to ensure our future health.