Museum collections and machine learning guide discovery of novel coronaviruses and paramyxoviruses

Tissue samples from specimens at the Field Museum of Natural History screened for coronavirus (n = 1330) and paramyxovirus (n = 491) RNA by RT-PCR. Natural history museum collections are valuable but underutilized resources for viral discovery, offering opportunities to test hypotheses about viral occurrence across space, time, and taxonomic groups. We developed machine learning models of bat host suitability to guide coronavirus and paramyxovirus screening of 1330 and 491 archival tissues, respectively, in a museum collection. For the first time, we recovered coronavirus (n = 16) and paramyxovirus (n = 3) sequences from museum tissues, confirming three novel coronavirus host species and three novel paramyxovirus host species (3% and 33% prediction success rate, respectively). These sequences included a SARS-like coronavirus and an orthoparamyxovirus from Angolan Rhinolophus fumigatus specimens collected in June 2019, suggesting that viruses with epidemic potential may be more widespread in sub-Saharan Africa than previously believed. Our study demonstrates the value of combining predictive modeling and collections-based viral discovery, particularly for filling outstanding sampling gaps and investigating changes in host–virus associations over time.

The data in this deposit are structured as a frictionless data pacakge (https://datapackage.org/standard/data-package/).

The datapackage.json file contains descriptive metadata (i.e. metadata related to the project) and structural metadata (i.e. metadata describing the structure and contents of the data). This means that field descriptions can be found in the datapackage.json file.

Coronavirus and Paramyxovirus data are stored in cov_pmv_wdds.csv.
The project_metadata.json file contains richer project metadata.
Both the data and metadata conform to the Wildlife Disease Data Standard version 1.0.3.

Some sequence data did not meet GenBank criteria for deposition. See fmnh244607_fmnh244565.fasta for those sequences. 

Nucleotide alignments for phylogenetic trees can be found in *_alignment.fasta.