Discriminating lineages of Batrachochytrium dendrobatidis using quantitative PCR

Novel chytrid pathogen variants and the global amphibian pet trade

Global wildlife trade spreads emerging infectious diseases that threaten biodiversity. The amphibian chytrid pathogen Batrachochytrium dendrobatidis (Bd) has caused population declines and species extinctions worldwide except in Asia. Fire-bellied toads (Bombina orientalis), exported in large numbers from Asia, are tolerant of Bd and carry hypervirulent ancestral chytrid BdAsia-1 variants. We assayed the virulence of a new isolate of BdAsia-1 on the model Australasian frog host Litoria caerulea. Infected individuals (n = 15) all showed rapid disease progression culminating in death, whereas sham-inoculated individuals (n = 10) presented no clinical signs of disease and all survived (log rank test, χ² = 15.6, df = 1, p < 0.0001). The virulence of the new isolate of BdAsia-1 is comparable to the one we assayed previously (χ² = 0.0, df = 1, p = 0.91). Internationally traded wildlife, even when they appear healthy, can carry hypervirulent variants of pathogens. Once new pathogen variants escape into the environment, native species that have had no opportunity to evolve resistance to them may perish. Our study suggests that hypervirulent pathogens are being spread by the international pet trade. Notifiable wildlife diseases attributable to locally endemic pathogens often fail to generate conservation concern so are rarely subject to border surveillance or import controls. Because of the danger novel variants pose, national border control agencies need to implement disease screening and quarantine protocols to ensure the safety of their endemic fauna.

A Review of Non-Invasive Sampling in Wildlife Disease and Health Research: What’s New?

Simple Summary

The interest in wildlife research has increased in the last decades as more scientists work within a One Health framework that regards human, livestock and wildlife health as connected entities. To minimise the impact of research on wildlife, collecting samples with as little disturbance of the animals as possible is important. In our review, we assess the use of so-called non-invasive sampling and summarise which samples can be used successfully when carrying out research on wildlife diseases and health status. Our results show that interest in minimally invasive sampling has steadily increased since the 2010s. Topics able to employ these methods include disease research, but also stress and other hormone assessments, pollution studies, and dietary studies. At the moment, such methods are mainly used to collect samples from land mammals, however, they can also be used in a wide range of other animals. Ever more capable analytical methods will allow for an even wider use of such “animal-friendly” sampling methods.

Abstract

In the last decades, wildlife diseases and the health status of animal populations have gained increasing attention from the scientific community as part of a One Health framework. Furthermore, the need for non-invasive sampling methods with a minimal impact on wildlife has become paramount in complying with modern ethical standards and regulations, and to collect high-quality and unbiased data. We analysed the publication trends on non-invasive sampling in wildlife health and disease research and offer a comprehensive review on the different samples that can be collected non-invasively. We retrieved 272 articles spanning from 1998 to 2021, with a rapid increase in number from 2010. Thirty-nine percent of the papers were focussed on diseases, 58% on other health-related topics, and 3% on both. Stress and other physiological parameters were the most addressed research topics, followed by viruses, helminths, and bacterial infections. Terrestrial mammals accounted for 75% of all publications, and faeces were the most widely used sample. Our review of the sampling materials and collection methods highlights that, although the use of some types of samples for specific applications is now consolidated, others are perhaps still underutilised and new technologies may offer future opportunities for an even wider use of non-invasively collected samples.

HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes

Background

Identifying haplotypes is central to sequence analysis in diploid or polyploid genomes. Despite this, there remains a lack of research and tools designed for physical phasing and its downstream analysis.

Results

HaplotypeTools is a new toolset to phase variant sites using VCF and BAM files and to analyse phased VCFs. Phasing is achieved via the identification of reads overlapping ≥ 2 heterozygous positions and then extended by additional reads, a process that can be parallelized across a computer cluster. HaplotypeTools includes various utility scripts for downstream analysis including crossover detection and phylogenetic placement of haplotypes to other lineages or species. HaplotypeTools was assessed for accuracy against WhatsHap using simulated short and long reads, demonstrating higher accuracy, albeit with reduced haplotype length. HaplotypeTools was also tested on real Illumina data to determine the ancestry of hybrid fungal isolate Batrachochytrium dendrobatidis (Bd) SA-EC3, finding 80% of haplotypes across the genome phylogenetically cluster with parental lineages BdGPL (39%) and BdCAPE (41%), indicating those are the parental lineages. Finally, ~ 99% of phasing was conserved between overlapping phase groups between SA-EC3 and either parental lineage, indicating mitotic gene conversion/parasexuality as the mechanism of recombination for this hybrid isolate. HaplotypeTools is open source and freely available from https://github.com/rhysf/HaplotypeTools under the MIT License.

Conclusions

HaplotypeTools is a powerful resource for analyzing hybrid or recombinant diploid or polyploid genomes and identifying parental ancestry for sub-genomic regions.

Not just a pathogen: The importance of recognizing genetic variability to mitigate a wildlife pandemic

Emerging infectious diseases (EIDs) are increasingly recognized as a threat to both biodiversity and human health (Scheele et al., 2019; Wells et al., 2020). But pathogens cannot been seen as unique entities; their intraspecific genetic variability represented in variants, strains, antigenic types or genetic lineages may cause different impacts at the population level (Nelson and Holmes, 2007; Greenspan et al., 2018). The global spread of pathogens has been largely facilitated by globalization of transport, which particularly intensified during the last century (O'Hanlon et al., 2018). As seen with SARS-CoV-2, air travel can rapidly spread a pathogen globally (Wells et al., 2020). Furthermore, after initial introduction subsequent translocations of a pathogen may cause the contact of different variants facilitating the rise of novel genotypes that may have higher pathogenicity or transmissibility (Nelson and Holmes, 2007; Greenspan et al., 2018). Chytridiomycosis is an EID caused by the fungus Batrachochytrium dendrobatidis (Bd), that infects amphibian skin causing population declines to extinction in susceptible species. Now a wildlife pandemic, Bd has been recognized as the single pathogen causing the greatest loss of biodiversity on Earth (Scheele et al., 2019). Recent advances in genetics have made novel tools for pathogen detection and characterization more accessible and reliable (Boyle et al., 2004; Byrne et al., 2019). In this issue of Molecular Ecology Resources, Ghosh et al. (2021) report the development of a new genotyping qPCR assay targeting mitochondrial DNA (mtDNA) of Bd, and based on noninvasive swab samples (Figure 1), discriminate between the two most globally widespread and pathogenic genetic lineages of Bd. Having a better understanding of how the genetic diversity of a pathogen is distributed is crucial to understand their spread patterns and develop timely mitigation strategies.