# Phylogenetic and Proteomic Analyses of Segment 2 Sequence Reveals the Presence of Two Variants of a Divergent Amnoonvirus (Family: Amnoonviridae) Infecting Nile Tilapia (Oreochromis niloticus)

## TL;DR

This study identifies two new variants of a divergent amnoonvirus infecting Nile tilapia in Egypt and explores their genetic and protein differences.

## Contribution

The discovery of two distinct amnoonvirus variants and their detailed phylogenetic and proteomic characterization.

## Key findings

- Two genetic variants, AmnoonvirusEGY1F and -H, were identified in Nile tilapia from Egypt.
- The Egyptian strains formed distinct clades and showed divergence from other tilapia lake virus (TiLV) strains.
- Mutations in the PB2 protein of AmnoonvirusEGY1H were predicted to affect its function and immunogenicity.

## Abstract

Illumina sequencing of segment 2, which encodes the polymerase basic subunit 2 (PB2) of the RNA-dependent RNA polymerase of a divergent amnoonvirus recently detected in tissues of Nile tilapia farmed in Egypt, revealed the presence of two genetic variants of the same virus: AmnoonvirusEGY1F and -H. The phylogenetic and genetic analyses presented in this study support the inclusion of both variants in the genus Tilapinevirus, family Amnoonviridae, order Articulavirales. The Egyptian strains formed distinct, well-supported clades in both nucleotide- and amino acid-based trees, showing a notable divergence from unclassified amnoonviruses and clustered with members of the genus Tilapinevirus. Within the genus Tilapinevirus, both Egyptian strains were divergent from all tilapia lake virus (TiLV) strains, whose full RNA segment 2 sequences are available in public databases, as well as the newly isolated Tilapinevirus poikilos from the fancy-tailed guppy. The Egyptian strains were also divergent from TiLV strains identified in Israel and Lake Victoria. Although the PB2 proteins of AmnoonvirusEGY1F and -H exhibited striking similarity, several mutations were detected that altered the sequence of their antigenic cell epitopes. Some of these mutations in the AmnoonvirusEGY1H strain were predicted to affect PB2-encoded functions. Collectively, findings of this study aid in the growing understanding of viral diversity and PB2 evolution in emerging amnoonviruses, particularly the role of amino acid substitutions in affecting the encoded protein structure, function, and immunogenicity.