Environmental DNA‐derived pathogen gene sequences can expand surveillance when pathogen titers are decoupled in eDNA and hosts

Abstract

Abstract Environmental DNA (eDNA) collection has emerged as a powerful and noninvasive wildlife population and pathogen‐monitoring tool. Ranavirus is an emerging pathogen linked to die‐offs in amphibian species. Applications of eDNA detection for ranavirus surveillance have shown promise, but it is unclear how reliably eDNA represents viral pressure on host populations. We evaluated the relationship of ranavirus titers in hosts and eDNA in four New York vernal pools from May to October 2016. We compared ranavirus titers in aquatic eDNA samples (n = 562) and liver samples (n = 362) of wood frog (Lithobates sylvaticus) and green frog (Lithobates clamitans) larvae from pools with past ranavirus die‐offs. We detected low‐quantity Ranavirus DNA (<Log10 0.7 copies) in larval liver samples from two pools but observed no signs of clinical disease or die‐offs in any frog population. Despite low ranavirus quantities in hosts, we observed sustained moderate titers of Ranavirus eDNA in all pools with peak titers (<Log10 3 copies/ml) occurring after observed host infections. We identified the viral strain in the pool network, compared viral populations between host and environment, and identified longitudinal genetic changes in the virus by assembling five complete viral gene sequences from host and eDNA samples collected in 2016 and archived host samples from a past outbreak. The Ranavirus at this site was closely related to both Frog Virus 3 (FV3) reference isolate and FV3—Spotted Salamander—Maine isolate. We identified polymorphisms in 2016 host‐derived Ranavirus sequences that were rare in 2016 eDNA‐derived gene sequences and absent from archived host sequences, suggesting that ranavirus in resident hosts has changed over time within our field site and is not the primary source of Ranavirus DNA detected in environmental samples. We therefore suggest that vernal pools may function as catchment basins of eDNA from surrounding uplands.

Keywords

• amphibians
• biological monitoring
• communicable diseases
• emerging
• nonlethal sampling
• ponds