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Research Article | 07 Oct 2026

First metagenomic detection and partial genomic characterization of Bossavirus delphinidgamma1 in captive common bottlenose dolphins in Southeast Asia

Augustine Natasha1 ORCID , Annisa Wening Maharani Putri2 ORCID , Nunak Nafiqoh3 ORCID , Sara Puspareni Prayitno1 ORCID , Lila Gardenia3 ORCID , Hessy Novita2 ORCID , Tanjung Penataseputro2 ORCID , Agustin Indrawati4 ORCID , Desy Sugiani2 ORCID , Uni Purwaningsih2 ORCID , Tuti Sumiati2 ORCID , Dewi Syahidah2 ORCID , Rifky Rizkiantino2 ORCID , Ji Eun Park1, Harimurti Nuradji2 ORCID , Angela Mariana Lusiastuti2 ORCID , and Won-Keun Kim1,5 ORCID Show more
VETERINARY WORLD | Article No. 10 | pg no. 4433-4445 | Vol. 19, Issue 10 | DOI: 10.14202/vetworld.2026.4433-4445
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ABSTRACT

                      
Background and Aim: Bossavirus delphinidgamma1 is a dolphin-associated gammaherpesvirus for which genomic information from tropical Asian marine mammal populations remains scarce. This study aimed to detect and partially characterize Bossavirus delphinidgamma1 in captive common bottlenose dolphins (Tursiops truncatus) in Indonesia and evaluate an integrated Oxford Nanopore Flongle–Illumina sequencing workflow for viral surveillance using non-invasive, low-biomass samples.
Materials and Methods: Fifteen blowhole, anal, and reproductive tract swabs were collected from five clinically healthy captive dolphins between January 2023 and January 2025. RNA and DNA were extracted from individual or pooled samples. RNA underwent sequence-independent single-primer amplification followed by Oxford Nanopore Flongle sequencing, whereas DNA from Dolphin 4 was sequenced using Illumina NovaSeq X. Metagenomic reads were subjected to taxonomic identification, reference mapping, consensus generation, coding sequence annotation, protein similarity analysis, multiple-sequence alignment, and maximum-likelihood phylogenetic analysis.
Results: Oxford Nanopore sequencing detected Bossavirus delphinidgamma1 sequences exclusively in the anal swab from Dolphin 4. The run generated 87,070 reads, of which 109 (0.12%) mapped to the viral reference genome, with a mean coverage depth of 0.28×. Subsequent DNA metagenomic sequencing of pooled Dolphin 4 swab extracts confirmed viral genetic material. Combined Oxford Nanopore and Illumina mapping covered 63.7% of the reference genome, with a median depth of 1×; 0.71% of the genome achieved ≥10× coverage. The recovered sequence contained a nearly complete DE1 gene and >50% coverage of several additional coding regions. Twelve predicted coding regions showed 68.9%–97.1% amino acid identity to Bossavirus delphinidgamma1 or a closely related dolphin gammaherpesvirus. Phylogenetic analysis placed the Indonesian sequence with the Sarasota reference strain, with 100% bootstrap support.
Conclusion: This study provides the first metagenomic evidence and partial genomic characterization of Bossavirus delphinidgamma1 in captive common bottlenose dolphins in Indonesia and Southeast Asia. The integrated sequencing approach enabled substantial partial-genome recovery from non-invasive samples and supports its application for exploratory marine mammal viral surveillance. Larger longitudinal studies incorporating targeted molecular confirmation, serology, and environmental sampling are warranted.
                      
Keywords: Bossavirus delphinidgamma1, bottlenose dolphin, gammaherpesvirus, marine mammal, metagenomic sequencing, non-invasive sampling, Southeast Asia, viral surveillance.