Viral metagenomic analysis of the upper respiratory tract virome and identification of novel viruses in giant pandas

Abstract

The giant panda (Ailuropoda melanoleuca) is a flagship species for biodiversity conservation, yet the viral communities inhabiting its upper respiratory tract (URT) remain poorly characterized. In this study, we performed viral metagenomic sequencing on 13 pooled libraries derived from 130 nasopharyngeal swabs collected from giant pandas between 2018 and 2021. The assembly yielded 16 complete or near-complete viral genomes, predominantly of DNA viruses belonging to the families Papillomaviridae, Genomoviridae, and Parvoviridae. Notably, we identified the complete genome of a novel Parvoviridae species within the subfamily Densovirinae. Phylogenetic analysis revealed that this virus clusters with invertebrate-infecting viruses, suggesting that it likely represents an arthropod-associated viral element derived from respiratory parasites rather than a direct vertebrate pathogen. Although the alpha diversity remained stable, beta diversity analysis revealed significant temporal shifts in viral community composition (P = 0.02). This study provides the first systematic characterization of the giant panda URT virome, establishing a critical baseline for disease surveillance and highlighting the complex interplay between the host and its environment-associated viral elements.

Keywords

Giant panda / Upper respiratory tract / Virome / Phylogenetic analysis / Parvoviridae

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Funding

Chongqing Municipal Key Research and Development Program of China(2023YFD1801300)

National Natural Science Foundation of China(82550118)

Chengdu Research Base of Giant Panda Breeding(202503KY0001)

RIGHTS & PERMISSIONS

The Author(s)