Rothstein, A. P. | bioRxiv Science

bioRxiv2023

Bayesian phylogenetics on globally emerging SARS-CoV-2 variant BA.2.86 suggest global distribution and rapid evolution

Using bioinformatic pipelines and Bayseian phylogenetic analyses, we characterized a SARS-CoV-2 variant designated by the World Health Organization as a variant under monitoring in August 2023. Here we analyze the genomes of this SARS-CoV-2 variant, BA.2.86, deposited into GISAID within the two weeks of its emergence (2023-08-14 first submission to 2023-08-31), including the first BA.2.86 genome reported from a traveler originating from Japan. We present bioinformatics methods using publicly available tools to help analysts identify the lineage-defining 12 nucleotide insertion (S:Ins16MPLF), which is often masked by most bioinformatics pipelines. We also applied maximum-likelihood and Bayesian phylogenetics to demonstrate the high mutational rate of the tree branch leading to the emergence of BA.2.86, hinting at possible origins, and predict that BA.2.86 emerged around May 2023 and spread globally rapidly. Taken together, these results provide a framework for more rigorous bioinformatics approaches for teams performing genomic surveillance on viral respiratory pathogens.

bioinformatics↗

bioRxiv2023

Evolutionary rescue and reintroduction of resistant frogs allows recovery in the presence of a lethal fungal disease

Vast alteration of the biosphere by humans is causing a sixth mass extinction, driven in part by an increase in emerging infectious diseases. The emergence of the lethal fungal pathogen (Batrachochytrium dendrobatidis; "Bd") has devastated global amphibian biodiversity, with hundreds of species experiencing declines or extinctions. With no broadly applicable methods available to reverse these impacts in the wild, the future of many amphibians appears grim. The once-common mountain yellow-legged (MYL) frog is emblematic of amphibians threatened by Bd. Although most MYL frog populations are extirpated following disease outbreaks, some persist and eventually recover. Frogs in these recovering populations have increased resistance against Bd infection, consistent with evolution of resistant genotypes and/or acquired immunity. We conducted a 15-year landscape-scale reintroduction study and show that frogs collected from recovering populations and reintroduced to vacant habitats can reestablish populations despite the presence of Bd. In addition, results from viability modeling suggest that many reintroduced populations have a low probability of extinction over 50 years. To better understand the role of evolution in frog resistance, we compared the genomes of MYL frogs from Bd-naive and recovering populations. We found substantial differences between these categories, including changes in immune function loci that may confer increased resistance, consistent with evolutionary changes in response to Bd exposure. These results provide a rare example of how reintroduction of resistant individuals can allow the landscape-scale recovery of disease-impacted species. This example has broad implications for the many taxa worldwide that are threatened with extinction by novel pathogens. Significance StatementUnderstanding how species persist despite accelerating global change is critical for the conservation of biodiversity. Emerging infectious diseases can have particularly devastating impacts, and few options exist to reverse these effects. We used large-scale reintroductions of disease-resistant individuals in an effort to recover a once-common frog species driven to near-extinction by a disease that has decimated amphibian biodiversity. Introduction of resistant frogs allowed reestablishment of viable populations in the presence of disease. In addition, resistance may be at least partially the result of natural selection at specific immune function genes, which show evidence for selection in recovering populations. The evolution of resistance and reintroduction of resistant individuals could play an important role in biodiversity conservation in our rapidly changing world.

ecology↗