Research Article | 31 Dec 2025

Whole-genome characterization and evolutionary analysis of a novel duck reovirus isolated from Cairina moschata in Vietnam

Phan Nhan1,2 , Nguyen Tran Phuoc Chien3 , Nguyen Trong Ngu4 , Truong Quynh Nhu3 , and Nguyen Phuc Khanh3 Show more
VETERINARY WORLD | pg no. 4172-4183 | Vol. 18, Issue 12 | DOI: 10.14202/vetworld.2025.4172-4183
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Abstract

          
Background and Aim: Novel duck reovirus (NDRV) is an emerging Orthoreovirus infecting domestic waterfowl, particularly Cairina moschata (Muscovy duck), and is associated with arthritis, immunosuppression, and economic losses. Despite its circulation in Southeast Asia, whole-genome data from Vietnam are lacking, restricting molecular surveillance and regional vaccine development. This study aimed to sequence and characterize the complete genome of a Vietnamese NDRV isolate and evaluate its evolutionary relationship with global strains, with particular emphasis on lineage-specific mutations and entropy-based variability. 
Materials and Methods: Liver and spleen tissues from diseased C. moschata ducklings were used for virus isolation in specific-pathogen-free embryos. Viral RNA was extracted and subjected to whole-genome sequencing using the Illumina NovaSeq 6000 platform. Genome assembly, annotation, and quality assessment were performed through metaSPAdes, Ragtag, Prokka, and Geneious. Phylogenetic trees for all 10 segments were reconstructed using maximum-likelihood methods, and amino acid (aa) variability was quantified using Shannon entropy. 
Results: The Vietnamese isolate CTU/NDRV/TG.2024 possessed a 10-segment genome of 23,423 bp, with conserved terminal untranslated regions and canonical Orthoreovirus gene organization. Sequencing generated ~43.1 million paired-end reads with 100% genome coverage and a mean depth of 177×. The S1 segment was bicistronic, encoding P10, P18, and σC. Phylogenetic analyses of all segments consistently clustered the isolate within the NDRV lineage, closely related to Chinese isolates (2011–2023), notably J18 and SD-12, indicating recent regional dissemination. Aa identity across segments ranged from 89.2% to 99.6%, with the highest variability observed in S1 (particularly σC) and S4. High-entropy sites were concentrated within σC (positions 88N, 132A, 149A, 152Q), suggesting immune-driven antigenic drift. A unique substitution, L3-1248A, exhibited maximum entropy (H(x)=0.93), indicating a potential regional molecular signature. Complete genome sequences were deposited in GenBank (PV034361–PV034370). 
Conclusion: This study provides the first complete NDRV genome from Vietnam, revealing a close relationship to contemporary Chinese strains and highlighting mutation hotspots linked to immune-evasion and host-adaptation. These findings underscore the need for continued genomic surveillance and support the development of regionally appropriate vaccines for Southeast Asian waterfowl populations. 
          
Keywords: amino acid variability, Cairina moschata, cross-border dissemination, genomic surveillance, novel duck reovirus, Orthoreovirus, phylogenetic analysis, shannon entropy whole-genome sequencing.