Charles Agoti: Bug reinfection: why, when, how

I'm Dr Charles Agoti. I am a Senior Research Scientist in the Programme. I work on respiratory viruses, in particular SARS-CoV-2, influenza, and respiratory syncytial virus. My area of work is molecular epidemiology. I'm particularly interested in patterns of infection of these viruses, not only in very sick cases, but actually how they occur - starting from the infections occurring in the community, those that are symptomatic, those that are asymptomatic, who is infected, why they are infected, how often they are infected, the seasonality of those infections, so in terms of informing the general patterns that lead to regular or irregular outbreaks that you observe eventually, that are captured through either hospital surveillance or sometimes even actually through severe infections that might be fatal from these infections.

My most recent research project is around respiratory virus reinfections in the community. A project that we call RESVER. In this project we are tracking about 500 individuals in the Kilifi community, visiting them every week to collect respiratory samples for detailed testing, to identify these infections. The goal is to be able to identify the rates and timings of repeat infections, and because we know, generally fast infections are not troublesome, but when you start seeing people getting repeat infections, that has implications. So, we are interested to understand how often that occurs, why it occurs, whether it's because the viruses are changing, or if the host immunity is not sustained, it's waning, or is it the environment which they live in for instance crowded household, is that playing a role? And actually, what's the role of these repeat infected individuals in the overall patterns of the viruses that we observe in terms of the epidemics, and in terms of their persistence in the long term.

In my area of research at the moment, one of the big questions that we have is how frequently do repeat infections with different respiratory viruses occur. We know they are not occurring at the same rate or at the same interval. For instance, flu, SARS-CoV, RSV, they have different patterns, and that influences how we are going to administer interventions. If I gave an example flu, we know there's a recommendation of annual vaccination, depending on the strain in circulation. We don't know whether for instance for SARS-CoV-2, we need to do the same thing. Do we need to administer vaccines annually? So, understanding how frequently repeat infections occur and their prevalence, will inform eventually how these interventions are applied in the general population.

The difference in my work might be more at the population level rather than at the individual patient level, because I don't work at the clinic. I work with populations and my work does inform actually how interventions are going to be rolled out to populations. For instance, indicated some of the different risk factors we are looking for in reinfections are things like, is it due to waning of immunity? Is it due to changes of the virus? Is it due to environment? For instance, if you are seeing crowded households getting more infections, that has implications, for instance how, then you think about interventions in crowded environment. If you think it's waning immunity, then that means you have to apply the intervention more repeatedly. If you think it's change in the virus, then you have to update the intervention to be relevant to the upcoming wave or upcoming epidemic, so that the intervention can be still working.

It's really important to look at this in the lens of interventions. My research matters because repeat infections are really critical in understanding the longevity of interventions that we have in place, especially vaccines. The fact that repeat infection occurs means interventions, like vaccines, are unlikely to work in the long term, or are likely to work to cause sterilising immunity in our specific world in the field. So, lack of that means you have to understand their nature so that the interventions can be able to emulate the natural infections and even be better. I give you an example, for instance, for RSV the occurrence of repeat infections informed the fact that immunity that is mounted by natural infection is not adequate. So, vaccines had to be designed to be better than natural infection. As much as really important to prevent infections, or control infections at the patient level, it's better actually to address this in the community. Interventions that protect people from getting either the infection, or people that get severe infection or severe disease following infection. So, if we don't actually stop it in the community, then it will be much more resources-required to prevent it at the hospital, and I feel that's really important in the spirit of prevention is better than control.

This interview was recorded in September 2025.