NCM 2022: Genomic investigation into yellow fever virus spread at the animal–human interface

Zoonotic viruses that originate in wildlife harm global human health and economic prosperity. Zoonotic disease emergence is highest in biodiverse, tropical forests undergoing intensive land-use change. Phylodynamic analyses of virus genomes can powerfully test epidemiological hypotheses but are rarely applied to viruses of animals inhabiting these habitats, because virus genomes are typically unavailable. In 2016–2021, the densely populated Atlantic Forest and Cerrado region in Brazil experienced an explosive human outbreak of sylvatic yellow fever, caused by repeated virus spillover from wild neotropical primates. Using a portable nanopore sequencing approach, we generated 498 yellow fever virus genomes, resulting in an exceptionally well-sampled dataset of zoonotic virus genomes sampled from wild mammals. We used yellow fever virus genome sequences and epidemiological data from neotropical primates, humans, and mosquito vectors to identify the environmental, demographic, and climatic factors that influence virus spread.