Viruses of Freshwater Mussels during Mass Mortality Events in Oregon and Washington, USA

Abstract

Freshwater mussels (Unionida) are globally imperiled, in part due to largely unexplained mass mortality events (MMEs). While recent studies have begun to investigate the possibility that mussel MMEs in the Eastern USA may be caused by infectious diseases, mussels in the Western USA have received relatively little attention in this regard. We conducted a two-year epidemiologic investigation of the role of viruses in ongoing MMEs of the Western pearlshell (Margaritifera falcata) and the Western ridged mussel (Gonidea angulata) in the Chehalis River and Columbia River watersheds in the Western USA. We characterized viromes of mussel hemolymph from 5 locations in 2018 and 2020 using metagenomic methods and identified 557 viruses based on assembled contiguous sequences, most of which are novel. We also characterized the distribution and diversity of a previously identified mussel Gammarhabdovirus related to pathogenic finfish viruses. Overall, we found few consistent associations between viruses and mussel health status. Variation in mussel viromes was most strongly driven by location, with little influence from date, species, or health status, though these variables together only explained ~1/3 of variation in virome composition. Our results demonstrate that Western freshwater mussels host remarkably diverse viromes, but no single virus or combination of viruses appears to be associated with morbidity or mortality during MMEs. Our findings have implications for the conservation of imperiled freshwater mussels, including efforts to enhance natural populations through captive propagation.

Genetic mechanisms underlying the structural elaboration and dissemination of viral internal ribosomal entry sites

“…We identified 193 -194 nt long type 6 IRESs that share 75-90% nucleotide sequence identity in Crogonang virus 17 isolate CGH03, Crogonang virus 61 isolate CGH03 and Picornavirales sp. isolate HPLV-37 [71, 72]. Their genomes encode proteins that are characteristic of marnaviruses, and the genomic location of the IRESs positions them to promote translation of the ORF2 capsid protein precursor.…”

“…Type 6i-like IRESs were identified in several members of the Marnaviridae family (order Picornavirales) (Table S12). Marnaviruses infect unicellular aquatic organisms and have monocistronic or dicistronic genomes that encode polyprotein precursors of capsid and non-structural proteins [70] [71,72]. Their genomes encode proteins that are characteristic of marnaviruses, and the genomic location of the IRESs positions them to promote translation of the ORF2 capsid protein precursor.…”

Viral Diversity in Samples of Freshwater Gastropods Benedictia baicalensis (Caenogastropoda: Benedictiidae) Revealed by Total RNA-Sequencing

“…As is known, the diversity of picorna-like viruses and the number of their genomes have been actively expanded in the last decade through the analysis of viromes and transcriptomes of invertebrates (including mollusks) [14,15,17,[24][25][26][27]50,51]. We also managed to uncover a new range of previously unknown picornaviruses.…”

“…Metagenomic analysis, including shotgun sequencing, is also employed to identify possible viral infections during mollusk diseases. Thus, during the mass mortality events of unknown etiology among freshwater mussels (Unionida) in the rivers of the USA, several dozen new viruses were identified [15,[25][26][27]. It was shown that some of them, for example, a novel densovirus (Clinch densovirus 1; family Parvoviridae), were epidemiologically linked to morbidity [25].…”

Performance Analysis of Cross-Assembly of Metatranscriptomic Datasets in Viral Community Studies

“…Информация о гипотетических вирусных геномах ускользает от внимания исследователей. В работе [44] авторы применили приложение CD-HIT-EST [45] для кластеризации и поиска сходства между скаффолдами раздельных геномных сборок при исследовании сообществ РНК-содержащих вирусов с помощью алгоритмов выравнивания нуклеотидных последовательностей. Подход с применением CD-HIT-EST в некоторой степени решает проблему сопоставления геномных сборок без таксономии, но может столкнуть с проблемой, когда одна геномная сборка содержит скаффолд -фрагмент генома какого либо вируса, а другая сборка содержит скаффолд -другой фрагмент этого же вируса.…”