Digital PCR for Hantavirus research

The Andes virus cluster aboard the MV Hondius in the spring of 2026 pulled this virus – the one hantavirus with documented person-to-person transmission – into the spotlight. (1) Inactivated vaccines exist for Hantaan and Seoul viruses in China and South Korea against HFRS (Hemorrhagic Fever with Renal Syndrome), but there is no licensed vaccine for New World hantaviruses like Andes, no licensed antiviral for any hantavirus infection, and no widely available certified reference material for hantavirus RNA. Active research spans countermeasure development, reservoir and environmental surveillance, and reference-material work.

Labs working in these areas face a familiar bottleneck. Human efficacy trials are not feasible for sporadically emerging hantaviruses, so regulatory agencies recognize reduction of viral load in animal models as evidence of countermeasure efficacy. But at low copy numbers, RT-qPCR results can vary between runs, instruments and labs, so an identical log reduction in viral load can read differently depending on when and where it was measured – calling the efficacy result into question.

Reverse-transcription digital PCR (RT-dPCR) overcomes this issue because it provides absolute quantification of hantavirus RNA by partitioning each sample into thousands of fixed nanowells and counting positive reactions directly. Since the readout is an endpoint yes or no, dPCR doesn't require a standard curve and is less influenced by PCR inhibitors common in blood, tissues and rodent excretions. (2) It produces a viral load measurement that is meaningful over experiments and across facilities.

Applications of digital PCR in hantavirus research

Advanced hantavirus research workflows require deep analytical precision. RT-qPCR works well across reservoir surveys, exploratory work and many efficacy studies. But for applications where that's not enough, dPCR adds rigor that qPCR can't match.

Measuring antiviral and vaccine efficacy by viral load reduction

In the Andes virus Syrian hamster challenge model – the only system that reproduces HPS-like disease among the New World hantaviruses – the primary readout of whether a candidate works is survival, measured alongside the change in serum and tissue viral load over time. (3) RT-qPCR has long been used for these measurements, but it is limited by the absence of certified reference material for hantavirus RNA and potential for the standard curves to drift, making it impossible to distinguish whether a drug drove the number down or whether the measurement itself just moved.

Since digital PCR counts target molecules directly without a standard curve, a reduction in viral load in a hantavirus animal model is meaningful over a long study, across sites, and across the regulatory filings built on it – the same absolute count, no matter which instrument runs the plate.

Quantifying virus in reservoir hosts and the environment

Digital PCR counts hantavirus copies directly in wild rodent and environmental samples – samples that have too little virus, or too much interfering material, for RT-qPCR's standard curves to track reliably. Most published hantavirus surveillance still uses RT-qPCR or serology; the case for adding dPCR is sharpest in three contexts.

Rodent surveillance networks. The US National Ecological Observatory Network (NEON) logged 104,379 rodent captures and 14,004 blood samples across 49 species between 2014 and 2019, with 296 seropositive samples identified across 15 species – a structured surveillance backbone that turns rodent ecology into a quantitative record. (4) That backbone reads antibodies, not virus, and adding viral-load measurement would identify current shedders, not just past infections.

Archived and retrospective samples. A 2025 New Mexico study used RT-qPCR to quantify Sin Nombre viral loads across multiple rodent species and demonstrated that archived frozen lungs can be retro-screened years after collection, extending the temporal reach of the same surveillance approach. (5) Degraded RNA in archived samples is exactly where dPCR's partition-based detection holds up and standard curves slip.

Environmental and wastewater surveillance. France's RatSWIM pilot, run under the PREZODE One Health initiative, samples urban wastewater for Seoul virus shed by commensal Rattus populations – a low-copy, inhibitor-rich matrix where amplification efficiency falls before the signal does. (6) That makes wastewater a textbook case for using dPCR, because partition-level dilution keeps each well's call intact as efficiency drops.

Across rodent tissue, oral swabs, and sewage, the question is the same: how much virus is here, and is that number rising. Digital PCR returns that number as an absolute count that holds over time and across sites.

Detecting long-term Andes virus RNA in immune-privileged sites

Persistence research lives at the regime digital PCR is built for. At a few copies per reaction, standard-curve quantification can be unreliable, and a steadily decaying signal becomes hard to separate from a flat plateau. Counting molecules directly gives the tight error bars needed to distinguish a steadily declining viral load from a flat plateau at the limit of detection. A small longitudinal cohort can then be followed across years with enough confidence to say whether the virus is clearing, holding, or gone.

In the one documented case, Andes virus RNA persisted in the male reproductive tract for almost six years after recovery, a trace-level target that sits at the very floor of what RT-qPCR can reliably quantify. (7) Another study followed Chilean Andes patients across blood, plasma, saliva, gingival crevicular fluid, urine, and nasopharyngeal swabs. (8) Andes is the one hantavirus with documented person-to-person transmission, which makes the persistence question a countermeasure-design question: you cannot design out transmission you cannot count.

Calibrating reference materials and validation panels

Reference material and assay-validation laboratories use digital PCR to assign absolute hantavirus RNA copy numbers to in-house validation panels, without leaning on a separately calibrated standard.

Building those panels with traditional PCR runs into circular logic: you use a calibrated assay to create the very tool that calibrates other assays. If your lab manufactures the validation panels that downstream CROs and network labs benchmark against, that circularity is a liability, because you are tracing a copy of a copy, and small measurement errors compound at every step.

Digital PCR breaks that chain because it gives the panel an independent baseline: an absolute ruler instead of an estimate carrying inherited uncertainty. That correction matters most in a small, concentrated field: HPS (Hantavirus Pulmonary Syndrome) case counts run an order of magnitude below HFRS, so molecular testing is concentrated in specialized reference and public health labs rather than spread across a routine clinical pipeline. (9) Those are the same laboratories most exposed to that inherited uncertainty – the reference labs preparing surveillance panels for regional and national networks, where every downstream RT-qPCR result is only as trustworthy as the panel it was benchmarked against.

Digital PCR assays for hantavirus research

QIAGEN QIAcuity nanoplate digital PCR assays are available for key Orthohantavirus research targets, supporting quantification workflows across countermeasure efficacy, reservoir and environmental surveillance, long-term persistence detection, and reference-material development.

If you're working across more than one pathogen, you can find the rest of the dPCR microbial detection range under digital PCR applications.

1. World Health Organization. Hantavirus cluster linked to cruise ship travel, Multi-country. Disease Outbreak News. 13 May 2026. https://www.who.int/emergencies/disease-outbreak-news/item/2026-DON601 (accessed August 12, 2026)
2. Sancha Dominguez L, Cotos Suárez A, Sánchez Ledesma M, Muñoz Bellido JL. Present and future applications of digital PCR in infectious diseases diagnosis. Diagnostics (Basel). 2024;14(9):931. doi:10.3390/diagnostics14090931
3. Safronetz D, Ebihara H, Feldmann H, Hooper JW. The Syrian hamster model of hantavirus pulmonary syndrome. Antiviral Res. 2012;95(3):282–292. doi:10.1016/j.antiviral.2012.06.002
4. Astorga F, Alkishe A, Paansri P, Mantilla G, Escobar LE. Hantavirus in rodents in the United States: temporal and spatial trends and report of new hosts. Ecosphere. 2025;16(3):e70209. doi:10.1002/ecs2.70209
5. Goodfellow SM, Nofchissey RA, Ye C, Banther-McConnell JK, Suriyamongkol T, Cook JA, et al. A human pathogenic hantavirus circulates and is shed in taxonomically diverse rodent reservoirs. PLoS Pathog. 2025;21(1):e1012849. doi:10.1371/journal.ppat.1012849
6. PREZODE Initiative. Rodents and hantaviruses: monitoring to prevent [project description]. RatSWIM (Rodent Assessment Through Sewers and Sewage Water Impact on Mammals), PEPR PREZODE. 2026. https://prezode-initiative.org/en/rodents-and-hantaviruses-monitoring-to-prevent/ [No peer-reviewed primary publication at time of citation; ongoing project.]
7. Züst R, et al. Presence and persistence of Andes virus RNA in human semen. Viruses. 2023;15(11):2266. doi:10.3390/v15112266
8. Ferrés M, Martínez-Valdebenito C, Henriquez C, et al. Viral shedding and viraemia of Andes virus during acute hantavirus infection: a prospective study. Lancet Infect Dis. 2024;24(7):775-782. doi:10.1016/S1473-3099(24)00142-7
9. World Health Organization. Hantavirus. Fact sheet. 6 May 2026. https://www.who.int/news-room/fact-sheets/detail/hantavirus (accessed July 31, 2026)