When the COVID-19 virus was first discovered and identified in late 2019, the race was on. As the virus caused a worldwide pandemic that has killed and sickened millions, scientists knew they needed to quickly develop a vaccine to deal with the deadly coronavirus.

Researchers turned to next generation sequencing (NGS) to solve the world health crisis. With NGS, scientists were able to quickly read the COVID-19 genome nearly immediately after the virus was discovered.

That sequencing became the foundation for vaccines that were introduced in record time. Today, it’s being used to map COVID-19 variants and create newer vaccines and boosters.

The COVID-19 story is just the best-known usage of next generation sequencing to combat viral threats with vaccines. NGS is a widely known and used approach to discovery that is leading to new vaccine development.

A Long History of Genotyping

Genotyping has been used for decades to understand the genetic makeup of new pathogens and track changes in genetic material. Those methods, however, were very labor-intensive. Successful mapping could take up to three years to complete.

With the completion of the Human Genome Project, next generation sequencing has revolutionized how researchers approach new viruses and vaccines.

The technology has made discovery faster and more economical. What took years now takes days.

NGS allows researchers to create genomes of hundreds of bacteria in weeks. Researchers can use NGS to develop population-level information on the genomes of pathogens. That information, combined with bioinformatics allows for the identification of genetic patterns related to a pathogen. Collectively, those insights can possibly lead to more effective vaccines.

Here are two ways that NGS technology is transforming the approach to vaccines.

Vaccine Design

When developing a vaccine, scientists need to determine which antigens to include. To do so, scientists look for the most prevalent strains of a disease that are in circulation around the world. They aspire to create a vaccine best able to meet those most frequently seen strains.

It doesn’t make sense to use strains that were isolated in a lab 50 years ago, given the prevalence of mutations in viruses. Instead, you need genotyping of the pathogen on a global level to understand what is in play.

In addition to the global reach of the COVID-19 genotyping and vaccine development, scientists are using the NGS approach for other vaccines. Recently scientists worked with reference labs around the world to gain sequencing information and track various bacterial strains of meningococcal group B. The NGS data allows for scientists to develop a vaccine with the most current, impactful coverage.

‘Carriage’ Microbes

Many people carry disease-causing pathogens in their mouth, nose or throat but never get sick themselves. However, they can still infect others by transmitting these pathogens, causing others to become ill.

Take, for example, Streptococcus pneumoniae. Thirty to 50 percent of children under 5 carry the bacteria in their noses but do not get sick themselves. For scientists, these asymptomatic carrier bacteria are critical, with major implications for how diseases operate and the impact on the population.

Scientists are using NGS to better understand the genetic diversity of carriage bacteria and have effective the pneumococcal conjugate vaccine (PCV) protects against infection.

NGS allows scientists to examine colonization and transmission of the carrier pathogens. It can also provide an early detection warning of emerging strains of a disease to provide more broad-spectrum vaccines.

The key is to use NGS early in the process of vaccine development to overcome a new pathogen. They help scientists understand where bacteria are circulating worldwide to develop vaccines that also can have a global reach.

NGS is revolutionizing vaccine development and will continue to do so as new pathogens emerge.