Metagenomics and the Etiology of Zoonotic Disease: Deciphering Bat-to-Human Viral Transmission in Madagascar

Cara Brook, Jean-Michel Héraud, and Soa Fy Andriamandimby of the Pasteur Institute in Madagascar, and Jessica Metcalf of Princeton University in the U.S. will establish metagenomic next generation sequencing (NGS) in Madagascar to analyze samples from undiagnosed fever patients and from bats to identify bat-derived viruses that cause human infectious diseases and help develop new diagnostics. It is estimated that up to 75% of emerging human diseases are derived from an animal reservoir. The majority of these zoonoses emerge in low-resource settings in equatorial regions likely due to living conditions and limited access to healthcare. Madagascar has long been geographically isolated, and Madagascan fruit bats are considered potential major sources of several different zoonotic diseases such as Ebola. However, identifying disease-causing viruses using traditional diagnostic methods requires the development of targeted assays and is laborious and inefficient. In contrast, metagenomic NGS is a powerful diagnostic tool that can simultaneously assay many viruses and identify new ones. Their institution serves as a national reference laboratory for several diseases in Madagascar, and to help develop local next generation sequencing and data analysis capacity, they will pilot the approach with a subset of 380 human clinical samples already collected. They will then process an additional 410 human samples for NGS library preparation, sequencing, and pathogen analysis in Madagascar.