After South Africa introduced the vaccine to combat rotavirus-induced diarrhea in 2009, hospital admissions fell and symptoms from the deadly disease became less severe. However, Martin Nyaga’s research discovered another trend: After the vaccine was launched, variants of the same genotype of the virus that had disappeared more than a decade ago started to re-emerge.

Martin uses whole-genome sequencing to understand how viruses evolve, particularly in the aftermath of vaccine introductions, to help determine novel strains and inform disease surveillance strategies.

"I have a big passion for genetics because the information you get from it is invaluable in informing public health strategies," said Martin, a virology professor and the head of the UFS-Next Generation Sequencing Unit at the University of Free State in South Africa.

Martin studies enteric viruses, respiratory viruses, and the viral communities in African children’s gut, respiratory tract and environmental surfaces using whole genome and metagenomics next generation sequencing. But the rotavirus is perhaps his favorite thorn to study because it indiscriminately infects nearly every child in the world, irrespective of their social economic status.

In 2008, Martin moved to Pretoria, South Africa looking for opportunities after finishing his undergraduate studies in Kenya. His first job was at the Medical Research Council-Diarrhoeal Pathogens Research Unit where he was part of the team that ran the clinical trials for the Rotarix rotavirus vaccine in South Africa. The following year, the WHO recommended the vaccine be given to every child.

His fascination took off during his doctorial fellowship at the J. Craig Venter Institute in Rockville, MD. He participated in an NIH-funded study that genetically sequenced and compared rotavirus samples from across 15 African countries, giving him a detailed view into the diversity of strains circulating in Africa and the chance to work with U.S. genomic experts at a time when it was still an emerging field.

He has since expanded on that work, analyzing rotavirus strains that cross the species barrier from animals to humans, understanding how it has shapeshifted in countries like South Africa, and contributing data to regional surveillance networks.

There are four WHO prequalified rotavirus vaccines available today, and notably all of them are less effective in sub-Saharan Africa, where a disproportionate number of deaths from the virus occur. Rotarix, for example, is only about 60% effective in Africa compared to 90% in the U.S. and Europe. Martin has been trying to figure out how to close that gap. One potential solution would be improving current vaccines by identifying local strains that are specific to Africa. The Rotarix vaccine uses a strain from Belgium.

Today, Martin is also focused on growing genomic surveillance systems across the entire continent. To do that, he is expanding the annual training workshops he has been hosting since 2018 and is also working to standardize the data quality that is entered into national databases so that scientists throughout Africa can use each other’s data without compromising the quality of results.

"The point is sustainability. We need to make sure we can continue to see what is happening because the viruses are continuously changing. Strengthening the surveillance systems is key and to do that we need to enhance quality and proficiency," said Martin.