Location: Zoonotic and Emerging Disease Research
Project Number: 3022-32000-027-032-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jun 15, 2025
End Date: May 31, 2028
Objective:
Henipaviruses are transboundary animal pathogens that can result in animal and human disease. The 1998 Nipah virus outbreak in Malaysia is predicted to have cost $580 million across several industries including pork production. To better understand the sources, transmission cycles, and identify reservoirs to mitigate such outbreaks and prevent introduction of henipaviruses into the U.S., we plan a series of international, multi-taxon expeditions to South Pacific Islands to comprehensively sample terrestrial vertebrate communities with the goal of understanding regional species diversity to identify potential pathogenic threats and to gain a better understanding of transmission cycles of pathogens that threaten agriculture interests, public health and national security. The Cooperator has established positive in-country collaborations. We will use high-throughput molecular methods to characterize host diversity and biogeographic structure, with a focus on insular bat communities. Additional sequencing will focus on characterizing the microbial communities of bats with the goal of pathogen discovery, characterizing distributions and sharing patterns of known taxa, and to refine understanding of host-pathogen associations. We have two main objectives for this project:
Resolve diversity and distributions of vertebrate hosts in the Philippines, and Papua New Guinea.
Identify host-vector-pathogen communities and sharing networks among islands within those Archipelagos.
Approach:
We propose a 3-year project, with 2 expeditions per country with ARS and Cooperator staff: Philippines and Papua New Guinea. We will start in the Philippines where the Cooperator has an established Memorandum of Understanding and permits with the Philippines government that allow for multi-taxon sampling, exportation, and use of material in non-commercial research. The Cooperator has led regular expeditions, research, and training in the Philippines for the last three decades and has strong in-country collaborations that will aid in the success of this investigation. The Cooperator will coordinate field sampling in Papua New Guinea (PNG) and the neighboring Solomon Islands.
Sampling: We will sample and analyze specimens vertebrate communities in the Philippines Summer of 2025. The first Philippines expedition will target an elevational gradient on Mt. Isarog on Luzon Island. PNG expeditions will mirror those in the Philippines with a focus on bat and small mammal communities and will target previously unsampled islands to complement ongoing research. Specifically, we aim to sample Bougainville Island, the easternmost island in PNG adjacent to the Solomon, and a key locality in understanding faunal exchange between continental Australia.
Host sequencing: A subset of collected animals will be sequenced to confirm molecular identity, using in-house reduced representation methods (Sanger, RADseq). Bat and rodents will be sequenced more deeply, given their outsized role in the transmission of zoonotic diseases. RADseq will be used to characterize the distribution of diversity across the landscape and understand the directionality and extent of gene flow between islands and populations. RADseq libraries will be sequenced on an Illumina NextSeq 2000 at the Cooperator Genome Sequencing Core. RADseq data will further be used to identify samples, representative of species, islands, and demographic groups (males, females), for whole-genome sequencing (WGS). Library preparation for WGS will be conducted in house and shipped to the cooperators for sequencing.
Microbial sequencing: We will use Nanopore Adaptive Sampling (NAS) and metagenomic sequencing to characterize the microbial communities of mammals, refine host distributions and exchange networks, and resolve host-pathogen associations. NAS allows for the real-time retention or rejection of DNA (or cDNA) molecules based on a user-defined reference file. In that way, NAS can be used to enrich for pathogens of interest. Metagenomic sequencing characterizes the total microbial community within a sample. Library preparation and Nanopore sequencing will be conducted at the Cooperator facility. Metagenomics sequencing will be run through the OMRF. Pathogen sequence data will be used to build phylogenies, infer mutation rates, and identify instances of host-switching and island hopping.