Unveiling the impacts of land use on the phylogeography of zoonotic New World Hantaviruses

Billions of genomic sequences are stored in public repositories (NCBI) as
well as records of species occurrence (GBIF). By implementing analytical
tools from different scientific disciplines, data mining on these
databases can be a source of information to aid in the global surveillance
of zoonotic pathogens that circulate among wildlife. We illustrate this by
investigating the hantavirus-rodent system in the Americas, i.e. New World
Hantaviruses (NWH). First we draw the circulation of pathogenic NWH among
rodents; by inferring the phylogenetic links among 278 genomic samples of
the S segment (N protein) of NWH found in 55 species of Cricetidae
rodents. Second, machine learning was used to assess the impact of land
use on the probability of presence of the rodent species linked with
reservoirs of pathogenic hantaviruses. Our results show that hosts are
widely present across the Americas. Some hosts are present in the primary
forest and agricultural land, but not in the secondary forest; whereas
other hosts are present in secondary forest and agricultural land. The
diversity of host species allows Hantavirus to circulate on a wide
spectrum of habitats, in particular rural rather than urban. We highlight
that Public repositories of genomic data and species occurrence are very
useful resources for monitoring potential enzootic transmission and
spillover of zoonotic viruses in relation with the changes that humans
produce in the Biosphere.