Speeding up delivery of an effective vaccine for a new swine flu

Influenza A viruses infect a wide range of animals, and can sometimes move from these animal hosts to infect humans, with potentially serious effects; the 2009 H1N1 flu pandemic arose from a swine-human virus transmission event. Since then, there have been hundreds of known human cases of swine-origin influenza in the United States, most commonly from exposure at agricultural fairs.

Part of routine work to limit the risks of a future flu pandemic is genomic surveillance of circulating viruses in swine and other animals. Genomic data can be used to develop new candidate vaccine viruses to form the basis for a new vaccine before an outbreak occurs in humans; however, collecting data typically takes weeks or even months — precious response time lost, should an unexpected new strain with pandemic potential emerge.

In 2018, a mobile genome sequencing station was set up at a large US swine exhibition. Scientists analysed samples from animals that had tested positive for influenza A virus (and neighbouring pigs) with a commercially available rapid testing kit. Using the rapid, portable genome sequencing platform and an automated, real-time data analysis pipeline — requiring neither a laboratory facility nor an internet connection — they were able to assess the viral genome sequences and immediately compare them with known swine flu viruses, including current candidate vaccine viruses.

Three different swine influenza A viruses were identified. The most common, an H1N2 viral subtype, was found to be genetically distinct to the most similar World Health Organization candidate vaccine virus — including differences in parts of the genome known to determine vaccine efficacy. That meant that if this virus subtype did start to infect humans, there was no rapid path to producing an effective vaccine against it.

As an exercise in pandemic preparedness, all genomic sequence data were sent to the US Centers for Disease Control and Prevention (CDC), who used it to develop a synthetic candidate vaccine virus. Importantly, the actionable genomic analysis results were obtained within 18 hours of setting up the mobile testing facility¹. This unprecedented speed could offer a critical time advantage in mobilising design and production of a new vaccine to protect against a new influenza virus threat.