This is the second installment of a two-part series. Part 1 was published on July 27, 2023.

A number of vaccines and monoclonal antibody drugs aimed at combating respiratory syncytial virus (RSV) have finally yielded results after years of unsuccessful attempts. In Part 1 of this blog post, we covered how the recent FDA approvals, including those from GSK, Pfizer, and AstraZeneca, are shaping the future of RSV prevention. We also traced the history of RSV vaccines and detailed other promising new frontiers that are in the clinical development pipeline, including mRNA and intranasal live attenuated virus vaccine candidates.

In this follow-up installment, we’re exploring how real-world pathogen testing data and pathogen genome sequencing data can accelerate the development of RSV vaccines and drugs from discovery through post-licensure. 

Journey of Vaccine Development: An Overview

On average, vaccine development takes a decade or more, with an investment ranging from $200 to $900 million, and a market entry probability of 6% (1, 2). This journey encompasses five main phases: discovery, pre-clinical, clinical development, approval, and phase IV/post-licensure (Figure 1).

 

The longevity of vaccine development is primarily due to the emphasis on safety. Given that vaccines are administered to healthy individuals as preventative measures, extensive clinical trials are necessary. These trials assess vaccine efficacy and uncover potential safety issues while encompassing a vast demographic, from infants to the elderly (3).

Yet, before entering human clinical trials, years of research and development are dedicated to creating and refining these vaccines. The success of the vaccine depends on how well the mechanism of infection is understood, so it can induce a similar, but safe, response to incur protection from the actual virus. Understanding how these mechanisms work is a slow and laborious process that requires teasing apart complex biological interactions. Pathogens can also mutate which requires close monitoring of the virus and potentially changes to the vaccine formulation over time to maintain efficacy (3).

In the quest for faster and more effective vaccine development, real-world pathogen testing data and pathogen genome sequencing have emerged as invaluable assets. These tools not only expedite vaccine discovery but also optimize clinical trial operations and enhance post-licensure monitoring.

Vaccine Discovery and Pathogen Genome Sequencing Data

During the discovery stage, which may last between two to five years, researchers work to understand the biologic nature of the viral pathogen, including its structure, virulence mechanisms, and antigenic properties (3). Equipped with this knowledge, researchers can pinpoint potential antigens that can be used to stimulate the immune response. These antigens are typically viral surface proteins that are highly conservative, virus-like particles (as was the case for Hepatitis B) or attenuated virus, an inactivated or weakened form of the pathogen itself (4).

Over the past 15 years, next-generation sequencing (NGS) technology has made a massive impact on increasing our understanding of these mechanisms, leading to a new approach called “reverse vaccinology.” Reverse vaccinology uses genomic information to uncover novel antigens. This approach, first employed in  2000 for the meningococcus B vaccine (5), has shifted the vaccine development paradigm and been used to create most vaccines during the last two decades (6). 

Reverse vaccinology uses pathogen genome sequencing to help researchers better understand the generic composition of the pathogen. Viral DNA and RNA are extracted from a human sample (e.g. a nasopharyngeal swab from a patient who is infected with the virus) and NGS is performed on that sample. When a pathogen genome is sequenced, the order of the individual nucleotides at each position are interrogated, and the subsequent informatic analysis allows scientists to uncover valuable information about the genetic organization. This information can be reverse engineered to determine what proteins these genes code for, some of which become potential antigens for vaccine candidates (7).

Pathogen genome sequencing has helped researchers better understand RSV as a single-stranded, negative-sense RNA virus with two distinct subgroups: RSV-A and RSV-B. Each subgroup can be further subdivided into genotypes based on sequence variation with 15 genotypes for RSV A and 29 genotypes for RSV B (8).

The envelope of RSV contains two glycosylated surface proteins: F (Fusion) and G (attachment glycoprotein). These proteins are central to the virus’s infectivity and subsequent respiratory disease they can cause. They also induce the neutralizing antibody immune response by the host (9). Vaccine candidates against RSV use different antigenic targets, but the recent FDA-approved vaccines have zeroed in on the pre-F protein because it is highly conserved (e.g. is present in most, if not all, strains of RSV and remains relatively unchanged over time) and facilitates viral fusion with host cells (10).

Vaccine researchers can get a head start on their reverse vaccinology process by using RSV genome sequencing data. Ovation generates pathogen genome sequencing data from our network of clinical laboratories, who contribute consented, de-identified remnant samples from patient RSV testing. RSV-positive samples are selected to be whole-genome sequenced based on phenotypic criteria. The sequencing data is packaged together with de-identified patient demographics and longitudinal clinical data and delivered directly to the researcher’s environment. Here, they can use their own data analysis tools to achieve their research insights.

Leveraging Real-World Pathogen Testing Data During Vaccine Clinical Development

Once in-depth testing of the vaccine candidate’s safety in lab and animal models is complete, a three-phase sequence of clinical trials in humans begins.

• • Phase 1: The vaccine is tested on a small number of healthy individuals to assess safety, determine a dosage range that is safe and provides optimal immune response, and identify any side effects.
  • Phase 2: The vaccine is tested in a larger participant group, including those at risk of contracting the disease (like RSV). This phase explores optimal doses, delivery methods, and vaccination schedules, all while continuing to monitor safety and immune response. Phase 2 trials are randomized and well controlled and include a placebo group.
  • Phase 3: During this phase, the vaccine is tested in tens of thousands of individuals, focusing on its protection against the target infection and its safety. Concomitant administration with other vaccines may also be tested (3).

Carrying out these clinical trials is an intricate and costly process. Starting from the first steps of participant recruitment, screening, and securing informed consent to the conclusion of the study, the vaccine developer must undertake a wide array of complex and closely monitored operations. Clinical trials for RSV vaccines are especially time-constrained and challenging as the virus is seasonal in nature, and its seasonality has been disrupted in recent years by the COVID-19 pandemic (11). RSV testing data has helped life sciences organizations develop enrollment strategies and accelerate trial timelines for late-stage case-driven clinical trials. 

This testing data is available as clinical testing is common during the temperate RSV season. When a patient presents with RSV symptoms (cough, wheezing, fever, sneezing) that are worsening, their healthcare provider will order a laboratory diagnostic test because clinical symptoms of RSV can be nonspecific and easily confused with other common respiratory viruses. Molecular diagnostic tests for RSV include rapid antigen or reverse transcriptase-polymerase chain reaction (RT-PCR); the latter is considered the gold standard and is most commonly used due to the fact that it has higher levels of sensitivity than antigen-based versions (12, 13). De-identified versions of these laboratory test results, along with their demographic and clinical information, plus genetic characterization of the virus (if included with the test), can be made available to researchers while protecting patient privacy. 

For example, Ovation collaborates with clinical laboratories performing high-throughput infectious disease testing, including for RSV. These labs use Ovation’s laboratory information management system (LIMS) to manage their clinical testing. Ovation’s technology de-identifies the clinical information from thousands of patients and curates it into a high-quality real-world dataset. This dataset can then be delivered independently or packaged with other linked de-identified clinical data. Researchers can also link their own RWD assets using universal patient tokens.

During their Phase 2/3 pivotal vaccine efficacy trial (ConquerRSV), Moderna leveraged RWD, including Ovation’s RSV Testing Data, to pinpoint areas of active RSV infection within the U.S. Unlike standalone claims and hospital data, Ovation’s data, being derived from laboratory tests, captured infections with geographical granularity (ZIP-3 level) and provided near real-time surveillance throughout the enrollment period.

 

Access to testing data was also cited by the consulting firm McKinsey as an innovation that drove the unprecedented development timeline of the COVID-19 vaccines. During the height of the pandemic, COVID-19 vaccine developers opened clinical sites in locations where testing data identified emerging hot spots (14).

Testing data for RSV is especially important as preventative measures enacted during the height of the COVID-19 pandemic led to a disruption in the seasonality of the virus in recent years. Whether or not the season will kick off early this year remains uncertain. Having a strategy to pinpoint infection hot spots with regional specificity can help mitigate the risk of case-driven clinical trial enrollment success. The comprehensive lab data that Ovation provides allows researchers to access a highly accurate and near real-time picture of infection rates so that they can select ideal trial sites.

Post-Licensure Monitoring: Linking RSV Testing Data and Pathogen Genome Sequencing

Once a vaccine is approved and on the market, the responsibility shifts to continuous post-market monitoring of vaccine safety and efficacy. Any side effects or issues observed and reported after the vaccine is administered are carefully assessed. These studies will also examine the evidence of protection given by the vaccine to ensure it is long-lasting, and also to investigate new indications or administration schedules (3). For RSV, the challenge is to induce an antibody response of sufficient titre and duration to protect vulnerable populations from severe disease during the entire RSV season (17).

Pathogen genome sequencing is vital during vaccine rollout to ensure that the vaccines are still effective in the face of ongoing genetic changes to the virus. For a vaccine to be protective, there must be a good match between the antigens included in the vaccine and those expressed by the circulating form of the pathogen. If the circulating form of the antigen mutates, it can evade neutralizing antibodies, like the Omicron variant evaded the COVID-19 vaccines (18).

While RSV does not show the abrupt antigenic changes that are seen in other viruses such as COVID-19 or influenza, research has shown that rolling out vaccination programs can cause evolutionary changes in the virus (19). Pathogen genome sequencing can be used to monitor the ongoing evolution of RSV for signs of escape from the protection of the new vaccines.

Once genetic changes in the virus have been identified, it’s crucial to determine whether these variants reduce vaccine effectiveness and to what extent. This requires linking immunization records to pathogen genomic sequencing on vaccine-evading strains. This data can then be used to help enhance or redesign the existing vaccines by enabling the discovery of novel serotypes and previously unrecognized resistance determinants (20).

Post-licensure studies can utilize pathogen testing data to locate infection hotspots and define enrollment strategies, akin to the process for late-stage clinical trials. This may include co-administration studies, like GSK’s RSVPreF3 (Arexy) trials investigating concomitant RSV vaccination with pneumococcal, influenza, or shingles vaccination.

Pathogen testing data can also be linked to de-identified clinical data and serve as another efficacy source in addition to a vaccine developer’s phase 3 trials that continue to run post-licensure. This could include tracking RT-PCR confirmed diagnoses, respiratory illness complications, patient-reported outcomes, and more in relation to an individual’s date of vaccination.

Pathogen Testing and Genome Sequencing Data: Revolutionizing RSV Vaccine Development

Utilizing insights from previous challenges with infectious diseases like COVID-19, life sciences organizations are significantly accelerating vaccine development timelines by integrating real-world laboratory testing data and pathogen genomic sequencing data at pivotal junctures: discovery, clinical trials, and post-licensure observation.

Ovation offers a robust toolset to expedite vaccine development. Our exhaustive RSV Testing Data incorporates ~745,000 retrospective tests with approximately 16,000 new tests added monthly. The dataset is inclusive of pediatric and adult populations, and delivered through an intuitive surveillance dashboard that provides near real-time insight into patient testing counts, positive test counts, geographic dispersal, and more. 

Ovation’s pathogen genome sequencing data is generated using commercially available library preparation kit designed to achieve greater than 95% breadth and approximately 100x median depth of coverage of viromes to ensure accuracy of genetic calls. 

Beyond vaccine development, Ovation’s infectious disease data has served public health surveillance efforts such as the National Institutes of Health (NIH) Rapid Acceleration of Diagnostics (RADx®) Tech program and the COVID-19 Research Database.

For more insights and opportunities to use Ovation’s data for vaccine development, connect with our team. We also invite you to learn more about our data from the following resources:

• RSV Testing Data available on AWS Data Exchange
• Case Study: Real-world RSV testing data supports clinical trial enrollment strategies for the ConquerRSV vaccine trial
• About Ovation RSV Testing Data (PDF)

References

1. André FE. How the research-based industry approaches vaccine development and establishes priorities. Dev Biol (Basel). 2002;110:25-29.
2. Pronker ES, Weenen TC, Commandeur H, Claassen EH, Osterhaus AD. Risk in vaccine research and development quantified. PLoS One. 2013;8(3):e57755. doi:10.1371/journal.pone.0057755.
3. International Federation of Pharmaceutical Manufacturers & Associations. The complex journey of a vaccine: the steps behind developing a new vaccine. https://www.ifpma.org/publications/the-complex-journey-of-a-vaccine-the-steps-behind-developing-a-new-vaccine/. Accessed August 10, 2023. 
4. Pathogen genomics leading to vaccines. Nat Genet. 2019;51(6):923. doi:10.1038/s41588-019-0441-8.
5. Masignani V, Pizza M, Moxon ER. The Development of a Vaccine Against Meningococcus B Using Reverse Vaccinology. Front Immunol. 2019;10:751. Published 2019 Apr 16. doi:10.3389/fimmu.2019.00751.
6. Rappuoli R, De Gregorio E, Del Giudice G, et al. Vaccinology in the post−COVID-19 era. PNAS. 2021;118(3):e2020368118. https://doi.org/10.1073/pnas.2020368118.
7. Rappuoli R, Bottomley MJ, D’Oro U, Finco O, De Gregorio E. Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design. J Exp Med. 2016;213(4):469-481. doi:10.1084/jem.20151960.
8. Lin GL, Golubchik T, Drysdale S, et al. Simultaneous Viral Whole-Genome Sequencing and Differential Expression Profiling in Respiratory Syncytial Virus Infection of Infants. J Infect Dis. 2020;222(Suppl 7):S666-S671. doi:10.1093/infdis/jiaa448.
9. Biagi C, Dondi A, Scarpini S, et al. Current State and Challenges in Developing Respiratory Syncytial Virus Vaccines. Vaccines (Basel). 2020;8(4):672. Published 2020 Nov 11. doi:10.3390/vaccines8040672.
10. Kingwell K. RSV vaccines score landmark FDA approvals. Nat Rev Drug Discov. 2023;22(7):523-525. doi:10.1038/d41573-023-00085-x.
11. Biagi C, Dondi A, Scarpini S, et al. Current State and Challenges in Developing Respiratory Syncytial Virus Vaccines. Vaccines (Basel). 2020;8(4):672. Published 2020 Nov 11. doi:10.3390/vaccines8040672.
12. Centers for Disease Control and Prevention. RSV Symptoms and Care. https://www.cdc.gov/rsv/about/symptoms.html. Accessed August 8, 2023.
13. Centers for Disease Control and Prevention. RSV For Healthcare Professionals. https://www.cdc.gov/rsv/clinical/index.html. Accessed August 8, 2023.
14. Fast-forward: Will the speed of COVID-19 vaccine development reset industry norms? McKinsey & Company. https://www.mckinsey.com/industries/life-sciences/our-insights/fast-forward-will-the-speed-of-covid-19-vaccine-development-reset-industry-norms. Published May 13, 2021. Accessed August 8, 2023.
15. Reichert H, Suh M, Jiang X, et al. Mortality Associated With Respiratory Syncytial Virus, Bronchiolitis, and Influenza Among Infants in the United States: A Birth Cohort Study From 1999 to 2018. J Infect Dis. 2022;226(Suppl 2):S246-S254. doi:10.1093/infdis/jiac127.
16. Wadman M. FDA advisers agree maternal RSV vaccine protects infants, but are divided on its safety. Science. https://www.science.org/content/article/fda-advisers-agree-maternal-rsv-vaccine-protects-infants-divided-safety. Published May 19, 2023. Accessed August 8, 2023.
17. Battles MB, McLellan JS. Respiratory syncytial virus entry and how to block it. Nat Rev Microbiol. 2019;17(4):233-245. doi:10.1038/s41579-019-0149-x.
18. Cao Y, Wang J, Jian F, et al. Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature. 2022;602(7898):657-663. doi:10.1038/s41586-021-04385-3.
19. Mas V, Nair H, Campbell H, Melero JA, Williams TC. Antigenic and sequence variability of the human respiratory syncytial virus F glycoprotein compared to related viruses in a comprehensive dataset. Vaccine. 2018;36(45):6660-6673. doi:10.1016/j.vaccine.2018.09.056.
20. Bentley SD, Lo SW. Global genomic pathogen surveillance to inform vaccine strategies: a decade-long expedition in pneumococcal genomics. Genome Med. 2021;13(1):84. Published 2021 May 17. doi:10.1186/s13073-021-00901-2.