Molecular epidemiology of Enterovirus A71 in Senegal between 2013–2021

Abstract

Enterovirus A71 (EV-A71) is a non-polio enterovirus that currently represents a major public health concern worldwide. To date, little is known about the molecular epidemiology of EV-A71 in Africa where resources and diagnostic capacities are limited. Although the laboratory diagnosis of non-polio enteroviruses is mainly based on molecular techniques, an implementation of genomic approaches into their surveillance will give a better understanding of their molecular epidemiology. To fill this gap in Senegal, a total of 521 non-polio enterovirus isolates collected from both acute flaccid paralysis (AFP) and environmental surveillance (ES) programs between 2013 and 2021 were screened for EV-A71 using real-time RT-PCR. Positive samples were sequenced using MinION (Oxford Nanopore Technologies) with an amplicon-based method targeting the entire coding region of the capsid protein. The generated sequences were analysed using phylogeny. An overall rate of 1.9% (10/521) of the isolates tested positive for EV-A71. All positive isolates originated from the AFP cases, and 40% (4/10) of them were isolated in 2016. The ten newly characterised EV-A71 sequences all belonged to the C genogroup, including eight C2 subgenotype sequences and two C1 subgenotype sequences. Our data provides not only new insights into the recent molecular epidemiology of enterovirus A71 in Senegal but also points to the crucial need to set up specific surveillance programs targeting non-polio enteroviruses, including sequencing such as the Oxford Nanopore Technologies platforms, which can be promoted for rapid identification of emerging or re-emerging enteroviruses and better characterization of public health concerns.

Biography

Ndack graduated in Animal Biology from the Cheikh Anta Diop University of Dakar. She went on to obtain her master’s degree in 2017, where she trained in molecular biology and other diagnostic techniques in the national reference center for poliomyelitis. Her PhD thesis focussed on the sequencing of non-polio enteroviruses from Senegal between 2013–2021. Since 2022, many of her studies have focussed on non-polio enteroviruses using next-generation sequencing (NGS) techniques such as nanopore sequencing. In 2023 Ndack underwent training in poliovirus sequencing techniques using nanopore sequencing methods in the context of poliovirus surveillance.