Hidden Herpesvirus Found in Sea Turtles From Singapore’s Urban Waters

In the crowded coastal waters of Singapore, where land reclamation and urban runoff have reshaped shorelines for decades, scientists have uncovered the first molecular evidence of a tumor-associated herpesvirus in the city-state’s sea turtles. A research team from Nanyang Technological University screened whole-genome sequencing data from green turtles and hawksbill turtles and detected Scutavirus chelonidalpha5, formerly known as chelonid alphaherpesvirus 5 or ChHV5, in every single animal tested. The virus is the leading candidate agent behind fibropapillomatosis, a disease that produces debilitating tumors in sea turtles around the world, yet had never been confirmed in wild turtles from Singapore.

Fibropapillomatosis is among the most consequential infectious diseases affecting marine turtles globally. It strikes green turtles most often, although cases have been documented in all sea turtle species, and its external tumors can grow around the eyes, neck, and flippers, impairing vision, movement, and feeding so severely that animals may starve or drown. The precise cause of the disease has never been fully resolved. Decades of research point to Scutavirus chelonidalpha5 as a key player, but the emergence and prevalence of fibropapillomatosis appear to be shaped by environmental conditions as well, particularly degraded water quality, eutrophication, and nutrient enrichment in coastal habitats.

Crucially, infection with the virus does not automatically mean illness. Numerous studies have found viral DNA in turtles that appear completely healthy, supporting the view that fibropapillomatosis is a multifactorial disease in which viral presence, host immunity, and environmental stressors interact to trigger tumor growth. This subtlety is what makes the Singapore findings so revealing: the virus was present not only in tumored animals but also in every apparently healthy individual sampled, suggesting that subclinical infections may be common in both species in the region.

The study began with two stranded green turtles found floating near East Coast Park and Lazarus Island in 2021 and 2022, both carrying multiple large external lesions on the neck and flippers. Internal examination revealed extensive pulmonary tumors that compromised lung integrity and buoyancy. Because veterinary diagnostic records were unavailable, the researchers classified the lesions based on gross morphology alone and describe them as suggestive of fibropapillomatosis rather than definitively diagnosed. The team then widened the net, analyzing whole-genome sequencing datasets from a total of four green turtles and four hawksbill turtles stranded or nesting in Singapore between 2020 and 2022, including individuals both with and without visible tumors.

The sequencing strategy was technically elegant. The team constructed Illumina TruSeq Nano paired-end libraries and sequenced them to roughly thirty-fold genome coverage on the HiSeq X platform. Because the viral genome is tiny, around 170 kilobases, compared with the roughly 2.1 gigabase turtle genome, viral sequences were expected to make up only a vanishingly small fraction of each dataset. To pull this signal out, the researchers used two complementary pipelines. The first, a reference-based approach using the BWA-MEM algorithm, aligned all quality-filtered reads against the reference viral genome, then filtered the results with SAMtools to retain only primary mapped read pairs. The second used Kraken2 metagenomic classification: host reads were subtracted, and the remaining reads were queried against the RefSeq viral database to count matches to the genus Scutavirus.

Both approaches told the same story. Viral sequences turned up in all eight genome datasets. After normalizing read counts to the smallest library size of roughly 223.8 million reads, reference-based viral counts ranged from about 30,869 to 98,326 reads, with the highest abundance found in a tumored green turtle from Lazarus Island. Kraken2 counts, between 178 and 488 normalized reads, mirrored the same pattern, and a Spearman’s rank correlation between the two methods was significant, indicating that the independent pipelines were capturing the same underlying viral signal. The concordance gives strong confidence that the detections are real rather than artifacts of any single analytical approach.

Perhaps the most striking result was what the statistics did not show. There was no significant difference in viral load between turtles with tumors and turtles without, and while green turtles carried somewhat higher counts than hawksbills, that difference also fell just short of significance with the small sample size. All four hawksbill turtles, none of which had visible tumors, still harbored detectable viral sequences. The authors caution that the sample sizes are small and unbalanced, and one green turtle muscle sample was excluded from statistical analysis because post-mortem contamination produced an unreliable taxonomic profile. Even so, the pattern is consistent with studies elsewhere showing that visual surveys based on tumors alone likely underestimate true infection rates.

That finding matters for conservation because turtles without symptoms may act as cryptic carriers, quietly maintaining the virus within populations. Viral infection can remain latent, and loads may drop below detection thresholds depending on tissue type, infection stage, and species, further limiting the reliability of external examinations. The researchers argue that host whole-genome sequencing, by enabling unbiased viral detection in both sick and healthy animals, offers a sensitive complement to existing viral, histological, and environmental DNA monitoring methods. Combined approaches of this kind could catch infections long before tumors appear.

Singapore’s urban coastline makes the discovery especially poignant. Land reclamation, urban runoff, and pollution have drastically altered the island nation’s natural shores, and pollution is known to weaken immune function in marine organisms, potentially raising susceptibility to diseases like fibropapillomatosis. Globally, higher disease prevalence has been linked to eutrophic, polluted coastal habitats. The study’s authors are careful to note that environmental parameters were not measured in this work, so no direct link between pollution and viral presence can be drawn from the data. Still, the hypothesis that heavily impacted coastal ecosystems elevate disease risk fits the emerging picture that fibropapillomatosis reflects an interaction among viral exposure, host immune status, microbiome composition, and environmental stress rather than pathogen presence alone.

There are also broader geographic implications. Southeast Asia has long been a surveillance gap for this disease. The earliest known regional record dates to 1958, when fibropapillomatosis was reported in nesting green turtles at Malaysia’s Sarawak Turtle Islands, and subsequent studies have documented cases in Indonesia and Taiwan along with molecular evidence of the virus in green, hawksbill, and olive ridley turtles in Borneo. The Singapore data now fill in a missing piece of that map in one of the most heavily urbanized marine environments on Earth. The team calls for comprehensive health assessments across Singapore and the wider region, integrating water quality and pollutant monitoring with molecular and clinical surveillance, alongside more systematic sampling across species, life stages, and tissue types, and histopathological confirmation of lesions in future work. If the virus proves to be a sentinel of cumulative environmental stress, then tracking it genomics-first could benefit not just the turtles but the ecosystems they inhabit.

Subject of Research: Detection of Scutavirus chelonidalpha5, the virus linked to fibropapillomatosis, in green and hawksbill turtles from Singapore using host whole-genome sequencing

Article Title: Host whole-genome sequencing reveals Scutavirus chelonidalpha5 infection in sea turtles from Singapore

Article References: Tanabe, L. K., Espinosa, A. G., Tiong, R. H. Y., & Kim, H. L. (2026). Host whole-genome sequencing reveals Scutavirus chelonidalpha5 infection in sea turtles from Singapore. Frontiers in Amphibian and Reptile Science, 4, Article 1814588. https://doi.org/10.3389/famrs.2026.1814588

Image Credits: AI Generated

DOI: 10.3389/famrs.2026.1814588

Keywords: sea turtles, Scutavirus chelonidalpha5, fibropapillomatosis, herpesvirus, whole-genome sequencing, metagenomics, Singapore, green turtle, hawksbill turtle, marine conservation, urbanization, wildlife disease