As part of a series of profiles of recent academic appointments at LSTM, we sat down with Dr Kayla Barnes, a Senior Lecturer and genomics researcher based at the Malawi Liverpool Wellcome Programme (MLW). She spoke to us about LSTM and MLW's work in Malawi, her important research into surveillance of pathogens and vaccine effectiveness in infancy, and the legacy of her work during COVID.
Can you tell us a bit about your background and current research focus?
I’m based at Malawi Liverpool Wellcome Programme in Malawi (we’re part of Kamuzu University of Health Sciences) and my work focuses on two main projects - surveillance of viral pathogens and immune development over the first year of life of Malawi’s infants and how this relates to vaccine failure. These programmes may appear unlinked, but they really bookend an important pipeline. Vaccines are arguably the most cost-effective gains for human health but to identify the pathogens that we need vaccines for and to understand how well vaccines are working, you really need to look at both ends of that spectrum. The surveillance work we’ve been doing identifies what pathogens are circulating, and then at the other end of that spectrum we're trying to understand why some vaccines are not working well. So we’re trying to get a holistic picture of vaccine needs in Malawi and this can be related to other low-income countries (LICs).
The hallmark example of a vaccine that underperforms in LICs is the rotavirus vaccine which is about 95% effective in high-income countries but in Malawi it's only about 40% effective. There are still huge benefits to having this vaccine in Malawi - you still get herd immunity and it has led to a dramatic decrease in infant mortality globally - but the vaccine could be a lot better and it's still unclear what is drivering poor vaccine response.
What are the issues involved? Is it the same vaccine?
Yeah, it’s the same vaccine used in both Malawi and many global north countries. There has been a 20 plus year rotavirus programme in Malawi led by Nigel Cunliffe and more recently Khuzwayo Jere. They’ve shown that vaccine failure doesn't seem to be linked to the viruses circulating in Malawi versus high-income countries. Our hypothesis is that even before children get their first vaccine they have been exposed to pathogens and this, coupled with maternal nutrition, creates an immune state that is not as receptive to a live oral attenuated vaccine like the rotavirus vaccine. The Rotavirus vaccine needs to go through the gut immune system for infants to properly mount a long-term memory response known as an antibody response. Since rotavirus vaccine success broadly correlates with a country’s development status, to me that seems like a pathogen burden, hygiene, sanitation issue. The causality of poor vaccine efficacy is complex, but there is an interplay there that’s leading to this kind of low vaccine efficacy.
Is your new role with LSTM going to see a continuation of that work?
Yes, absolutely. The environmental surveillance work and viral genomic epidemiology I also carry out really came out of the COVID-19 pandemic and leveraged both direct funding from the Wellcome Trust to build sequencing capacity in the Africa Asia Programmes and Nick Feasey’s existing S. typhi and antimicrobial resistance environmental surveillance programme. Focusing on our environmental surveillance work which can be a tool for population level surveillance identified viruses in wastewater, specifically SARS-CoV-2. And since then, we've expanded the wastewater surveillance programme to identify multiple enteric pathogens to get a high-level view of circulating pathogens in urban Malawi.
I will also continue my single cell programme in Malawi and expand this work at LSTM. The goal of both of these studies is to inform the next vaccine, be it new vaccines or next generation vaccines. I have links with GSK, so the information we get from the infant immunity study will feed into the development of the next rotavirus vaccine.
It sounds like you are already working in the field and country or your choice. Why move from Harvard to LSTM?
I think the biggest benefit to moving to LSTM - Harvard aside – is its strong links with Malawi. I did my PhD at LSTM and spent a lot of that time in Malawi and southern Africa and that time really informed the study I'm doing today. In Malawi, there have been many important studies around disease burden and vaccine efficacy, including the rotavirus vaccine largely led or co-led by researchers at LSTM and University of Liverpool. Through previous work of many others and my experience in Malawi I understood that there was an at-risk population of infants with high pathogen exposure, and we didn’t really understand how this was affecting the immune development and therefore vaccine response. I plan to be located in Malawi so I felt that those strong links were important to this next phase of my career. Also, one of my big focuses is building my team - students, PhDs, post-doc level individuals, even to the master’s level - and there's already precedent within LSTM of fostering students and programmes to provide higher education, and that was really attractive.
During our 125 anniversary year celebrations we are also looking to the future and how we work equitably with our partners – your post is part of LSTM’s commitment to MLW. What do you see as the big issues that we should be addressing in the coming years if we are to achieve that equity?
There are many ways to try and achieve equity and I can only speak to how I do this in my programme. The phrase ‘capacity building’ gets thrown around a lot, but for me that means providing the highest level of training for the teams I work with in Malawi and other countries I partner with. I've done this in a few ways. First, we have a robust single cell programme running in Malawi where we can do everything except for sequencing (sequencing will come in the future) and we're just getting the sequencing up and running for pathogens. And I think from setting up the first single cell work in this country, there's now many other single cell studies occurring and this capacity in being supported at the institutional level. Next, through links at LSTM I aim to foster more trainees, so they are competitive for international academic schemes. We have had some successes and I think it's just making sure that bright, excited students get those opportunities. And in the coming years I hope to create opportunities for PhD and post-doc level early career researchers from Malawi to spend a chunk of time training in the US and the UK to hone their skills by learning from world experts. Getting to learn from people in that space is so crucial. As a PhD student at LSTM, I was so lucky to be in a highly collaborative environment with cutting edge techniques, and it was that experience that gave me the confidence to be an academic researcher. So, fostering that environment for trainees from LICs so they can do their own research in their own country is vital.
So skills, confidence and access to facilities?
Yeah, getting to spend time in different people’s labs or where there are lots of researchers. MLW has excellent research, but we are small and it takes a team of academics to build a researcher.