Aquatic Flaviviruses

Abstract

Flaviviruses are positive-sense single-stranded RNA viruses, including some well-known human pathogens such as Zika, dengue, and yellow fever viruses, which are primarily associated with mosquito and tick vectors. The vast majority of flavivirus research has focused on terrestrial environments; however, recent findings indicate that a range of flaviviruses are also present in aquatic environments, both marine and freshwater. These flaviviruses are found in various hosts, including fish, crustaceans, molluscs, and echinoderms. Although the effects of aquatic flaviviruses on the hosts they infect are not all known, some have been detected in farmed species and may have detrimental effects on the aquaculture industry. Exploration of the evolutionary history through the discovery of the Wenzhou shark flavivirus in both a shark and crab host is of particular interest since the potential dual-host nature of this virus may indicate that the invertebrate-vertebrate relationship seen in other flaviviruses may have a more profound evolutionary root than previously expected. Potential endogenous viral elements and the range of novel aquatic flaviviruses discovered thus shed light on virus origins and evolutionary history and may indicate that, like terrestrial life, the origins of flaviviruses may lie in aquatic environments.

Keywords: Flaviviridae; aquatic virology; evolutionary history; flavivirus; marine virology.

FIG 1

Maximum-likelihood phylogenetic tree of the NS5 (RNA-dependent RNA polymerase) amino acid sequences of flaviviruses, trimmed with BMGE v1.2 (66), under an LG+F+R8 protein substitution model in IQ-TREE v1.6.12 (67). Aquatic host-linked flaviviruses are highlighted in blue—light blue for freshwater hosts or dark blue for marine hosts. A, B, and C refer to clades that have not yet been tentatively named. The Tree file, alignment, and table containing accession numbers of used sequences are available on GitHub (https://doi.org/10.5281/zenodo.6980038).