Alpine lakes harbor diverse, endemic and structurally unique RNA viruses

Abstract

Alpine lakes, characterized by isolation, low temperatures, oligotrophic conditions, and intense ultraviolet radiation, remain a poorly explored ecosystem for RNA viruses. Here, we present the first comprehensive metatranscriptomic study of RNA viruses in Lake Nam Co, a high-altitude alkaline saline lake on the Tibetan Plateau. Using a combination of sequence- and structure-based homology searches, we identified 742 RNA virus species, including 383 novel genus-level groups and 84 novel family-level groups exclusively found in Lake Nam Co. These findings significantly expand the known diversity of the Orthornavirae, uncovering evolutionary adaptations such as permutated RNA-dependent RNA polymerase (RdRP) motifs and distinct RNA secondary structures. Notably, 14 previously unknown RNA virus families potentially infecting prokaryotes were predicted, broadening the known host range of RNA viruses and questioning the traditional assumption that RNA viruses predominantly target eukaryotes. The presence of auxiliary metabolic genes (AMGs) in viral genomes suggested that RNA viruses (families f.0102 and Nam-Co_family_51) exploit host energy production mechanisms in energy-limited alpine lakes. Low nucleotide diversity, SNP frequencies, and pN/pS ratios indicate strong purifying selection in Nam Co viral populations. Our findings offer insights into RNA virus evolution and ecology, highlighting the importance of extreme environments in uncovering hidden viral diversity, and further shed light into their potential ecological implications, particularly in the context of climate change. Significance StatementThis study unveils the hidden diversity and complexity of RNA viruses in the high-altitude ecosystem of Lake Nam Co, significantly expanding the known RNA virome. The discovery of novel viral clades, expanded potential host ranges, and unique evolutionary adaptations emphasizes the importance of exploring extreme environments to uncover viral diversity and evolutionary pathways. Our findings offer critical insights into viral evolution, host-virus interactions, and the ecological roles of RNA viruses, particularly in the context of climate change and environmental resilience.