Virological Sampling of Inaccessible Wildlife with Drones

Abstract

There is growing interest in characterizing the viromes of diverse mammalian species, particularly in the context of disease emergence. However, little is known about virome diversity in aquatic mammals, in part due to difficulties in sampling. We characterized the virome of the exhaled breath (or blow) of the Eastern Australian humpback whale (Megaptera novaeangliae). To achieve an unbiased survey of virome diversity, a meta-transcriptomic analysis was performed on 19 pooled whale blow samples collected via a purpose-built Unmanned Aerial Vehicle (UAV, or drone) approximately 3 km off the coast of Sydney, Australia during the 2017 winter annual northward migration from Antarctica to northern Australia. To our knowledge, this is the first time that UAVs have been used to sample viruses. Despite the relatively small number of animals surveyed in this initial study, we identified six novel virus species from five viral families. This work demonstrates the potential of UAVs in studies of virus disease, diversity, and evolution.

Challenges of collecting blow from small cetaceans

“…In both of these circumstances, drones enable the collection of the appropriate samples (Geoghegan et al. ) and could potentially benefit particularly small populations in contaminated waters, which are already vulnerable to stressors. Nonetheless, research efforts should be mindful of minimizing the disturbance on dolphins in any attempts to obtain samples (Hodgson and Koh , Ramos et al.…”

“…Poor water quality prevents biopsy sampling of humpback dolphins in some locations, for example, Taiwan, because the resulting open wounds could compromise the health of the individuals being sampled (Wang et al 2008) and, additionally, health assessments are not possible as samples of viruses and microbiome cannot be obtained through biopsy. In both of these circumstances, drones enable the collection of the appropriate samples (Geoghegan et al 2018) and could potentially benefit particularly small populations in contaminated waters, which are already vulnerable to stressors. Nonetheless, research efforts should be mindful of minimizing the disturbance on dolphins in any attempts to obtain samples Koh 2016, Ramos et al 2018).…”

“…), and viruses (Geoghegan et al. ). Such studies have been successfully executed on large cetaceans such as baleen whales (Domínguez‐Sánchez et al.…”

“…Blow samples collected from cetaceans can be analyzed for DNA to investigate population structure (Fr ere et al 2010), analyzed for hormones for stress (Hunt et al 2014, Thompson et al 2014) and health (Apprill et al 2017), and screened for epizootics, microbiota (Pirotta et al 2017), and viruses (Geoghegan et al 2018). Such studies have been successfully executed on large cetaceans such as baleen whales (Dom ınguez-S anchez et al 2018, Harcourt et al 2019) as these animals have proven the most suitable to approach and sample with this emerging technology.…”

Methods for Monitoring for the Population Consequences of Disturbance in Marine Mammals: A Review

“…Remote sampling methods have been used to measure reproductive hormone levels in blubber samples from delphinid species (e.g., Kellar et al, 2009;Trego et al, 2013), baleen whales (e.g., bowhead whales, Kellar et al, 2013;humpback whales, Vu et al, 2015) and deep diving cetaceans such as sperm whale (Sinclair et al, 2015). Sampling the blow from respiring animals has been increasing in the recent decade (e.g., Hogg et al, 2009;Dunstan et al, 2012;Hunt et al, 2013;Thompson et al, 2014;Bennett et al, 2015;Apprill et al, 2017;Pirotta et al, 2017;Geoghegan et al, 2018;Nelsons et al, 2019). Along with fecal sampling it provides a non-invasive technique for monitoring the health of pinnipeds (Harvey, 1989;Fossi et al, 1997;Trites and Joy, 2005;Deagle and Tollit, 2007), killer whales (Hanson et al, 2010;Ford et al, 2011;Ayres et al, 2012) and baleen whale species (reviewed in Hunt et al, 2013).…”