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;..., Data analysis follows 4 main steps:

Data Collection and Curation. GenBank Accesion Numbers of Hantavirus sequences were obtained from a BLAST query, metadata was collected, taxonomic names homogenized, and sequences found in wild animals were selected.

Genetic Sequence Alignment and Phylogenetic Inference. Genetic data was aligned and used to infer the phylogenetic relationships among the samples.

Phylogenetic Network analysis on the genetic links of Hantaviruses among hosts. Phylogenetic network was built from the phylogentic tree of New World Hantavirus.

Geographic analysis on the habitat suitability of hosts linked in the phylogenetic network. Habitat suitability within the distribution areas of each species was modeled with classification trees. Historical records on the species presence were used to assess the land use change in the time of sampling, and train a model to predict the presence of the species based on 12 land use variables. These models were used to predict the a..., , ## **Unveiling the Impacts of Land Use on the Phylogeography of Zoonotic New World Hantaviruses**

Gabriel E García-Peña and André V. Rubio. Ecography 2024. DOI: 10.1111/ecog.06996

##### *Supplementary Material*

## Description of the data and file structure

Analysis presented in the main article was performed in R (R Core Team 2022); MAFFT (Katoh 2005) and JModelTest2 (Darriba et al. 2012), following 4 main steps:

##### 1. Data Collection and Curation.

**BLAST_Nprot.csv** : Accession numbers from the BLAST search for Hanatavirus. With this list of accesion numbers, it is possible to download the genetic sequences in R, by using the function read.GenBank() from the library ape. Metadata of these sequences can be accesed with the R code presented in the file: **fetch.metadata.R** (see code section).

##### 2. Genetic Sequence Alignment and Phylogenetic Inference.

**Nprot_MaxAlign.fas**: Fasta file with Multiple sequence alignment of the genetic sequences. Fasta file can be read in R...