The study of rotavirus has taken a significant leap forward with the discovery that the whole rotavirus genome – not just its two surface proteins – affects how well vaccines work. Researchers have found that genetic differences between circulating rotavirus strains and vaccine strains may impact vaccine effectiveness, leading to a better understanding of why some strains are more likely to infect vaccinated individuals.

The study, published in eLife, used a novel approach to estimate rotavirus vaccine effectiveness by analyzing the full genetic code of each virus strain. The researchers found that individuals vaccinated with Rotarix (RV1) were more likely to be infected by rotavirus strains that were significantly genetically different from the vaccine – over 9.6% different in their full genome.

The study revealed that circulating viral strains that were genetically similar to the vaccine had a viral backbone called genogroup 1 (Wa-like), while those that were genetically distant tended to have a different viral backbone called genogroup 2 (DS-1-like) or had mix-and-match variants known as reassortant strains.

Vaccine effectiveness results also reflected this genetic pattern, with the Rotarix (RV1) vaccine providing strong protection against genetically similar viral strains but its protection dropping significantly for more genetically distant strains. The RotaTeq (RV5) vaccine followed a similar pattern, but differences in its effectiveness were less pronounced.

The researchers found that vaccination patterns in different locations influenced the rotavirus strains circulating in the population. They discovered that in places where more people used Rotarix (RV1), rotavirus strains that were genetically distant dominated. This suggests that over time, rotavirus is naturally adapting in response to vaccine-induced immunity, leading to shifts in the genetic makeup of circulating strains to favor those genetically different from the vaccine.

The study highlights the need to continually monitor viral evolution to maintain vaccine effectiveness in the long term. The researchers caution that their study is limited by a relatively small sample size of cases and call for future studies to further validate their findings in other settings where whole genome sequencing data is more widely available.

The team’s framework for using whole genome sequencing data to understand how all gene segments contribute to immune protection could be crucial for maintaining the long-term success of rotavirus vaccines. This study shows that looking at the entire genetic structure of rotavirus gives a much clearer picture of how well vaccines work compared to just looking at the two surface proteins, and highlights the importance of incorporating the full genomic structure of viruses when designing vaccines.

The COVID-19 pandemic has left an indelible mark on human history, underscoring the urgent need for effective strategies against future pandemics. The World Health Organization (WHO) and many nations have already begun preparations to address potential pandemics caused by “Disease X.” One such threat is the H5N1 avian influenza virus, which has been detected in humans since 1997 and has spread globally, causing cross-species infections.

Researchers at the State Key Laboratory for Emerging Infectious Diseases at the University of Hong Kong (HKU) and the InnoHK Centre for Virology, Vaccinology and Therapeutics (CVVT) have pioneered an influenza virus vector-based nasal spray vaccine platform. This innovative approach has been used to develop a nasal spray H5N1 avian influenza vaccine, offering a critical reserve against future outbreaks.

The COVID-19 pandemic highlighted the importance of rapid vaccine development and deployment. Current vaccines, including mRNA vaccines, effectively prevent severe disease and reduce mortality but fail to curb viral transmission. A nasal spray vaccine offering single-dose protection could play a pivotal role in outbreak control by rapidly inducing mucosal immunity at the primary site of viral entry.

The HKU and CVVT team’s research has shown that their nasal spray H5N1 avian influenza vaccine has a high safety profile and is able to induce comprehensive immunity, including neutralising antibodies, T-cell responses, and mucosal immunity in the upper respiratory tract. Crucially, a single dose provides robust protection against infection and sustains immune memory.

Further clinical trials could position this vaccine as a critical reserve for future H5N1 outbreaks, drastically shortening deployment timelines. Its nasal delivery mechanism also promises to curb viral transmission early in an outbreak. This research was funded by the InnoHK initiative of the Innovation and Technology Commission of Hong Kong Special Administrative Region Government, with key contributors including Professor Chen Honglin, Dr Wang Pui, Dr. Deng Shaofeng, Ph.D. candidate Liu Ying, and Professor Yuen Kwok Yung, Professor To Kai Wang Kelvin from the Centre for Virology, Vaccinology and Therapeutics, State Key Laboratory for Emerging Infectious Diseases and the Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine.