Virome Analysis of Signal Crayfish (Pacifastacus leniusculus) along Its Invasion Range Reveals Diverse and Divergent RNA Viruses.

Katarina Bačnik,Ana Bielen,Sandra Hudina,Denis Kutnjak,Silvija Černi

doi:10.3390/v13112259

Abstract

Crayfish are a keystone species of freshwater ecosystems and a successful invasive species. However, their pathogens, including viruses, remain understudied. The aim of this study was to analyze the virome of the invasive signal crayfish (Pacifastacus leniusculus) and to elucidate the potential differences in viral composition and abundance along its invasion range in the Korana River, Croatia. By the high-throughput sequencing of ribosomal RNA, depleted total RNA isolated from the crayfish hepatopancreas, and subsequent sequence data analysis, we identified novel and divergent RNA viruses, including signal crayfish-associated reo-like, hepe-like, toti-like, and picorna-like viruses, phylogenetically related to viruses previously associated with crustacean hosts. The patterns of reads abundance and calculated nucleotide diversities of the detected viral sequences varied along the invasion range. This could indicate the possible influence of different factors and processes on signal crayfish virome composition: e.g., the differences in signal crayfish population density, the non-random dispersal of host individuals from the core to the invasion fronts, and the transfer of viruses from the native co-occurring and phylogenetically related crayfish species. The study reveals a high, previously undiscovered diversity of divergent RNA viruses associated with signal crayfish, and sets foundations for understanding the potential risk of virus transmissions as a result of this invader’s dispersal.

Highlights

Until recently, knowledge of invertebrate viruses was limited mostly to viral pathogens causing high mortalities and arboviruses, which are vectored by arthropods and cause disease in humans and other vertebrate species [1]
We have investigated the signal crayfish population in a recently invaded Korana river, Croatia, where signal crayfish range expansion is well monitored [27,28,29], and occurs in both upstream and downstream directions [27]
The signal crayfish was illegally introduced in the lower section of the river, and is spreading both upstream and downstream [28], with its invasion range currently stretching along 33 km [27]

Summary

Introduction

Knowledge of invertebrate viruses was limited mostly to viral pathogens causing high mortalities and arboviruses (arthropod-borne viruses), which are vectored by arthropods and cause disease in humans and other vertebrate species [1]. This view has changed, with metagenomics revealing remarkable levels of RNA virus diversity in invertebrates [2,3,4,5], and, in this perspective, the detection of invertebrate disease-causing viruses became the exception rather than the rule [1]. The existing literature on crayfish diseases is biased mostly towards the crayfish plague pathogen, the oomycete Aphanomyces astaci, while other disease agents, including fungi, bacteria, and viruses, are significantly understudied [20]

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