Discover how targeted sequence capture delivers complete orthohantavirus genomes from complex host tissues, enabling novel virus discovery, outbreak tracing, and genome-wide diversity assessment.
In May 2026, the World Health Organization issued a Disease Outbreak News report documenting a cluster of Andes hantavirus (ANDV) cases among passengers aboard the MV Hondius, a cruise ship operating in the South Atlantic.1 As of May 27, 2026, the outbreak has resulted in 13 confirmed cases and three deaths.2 Investigations into the source and transmission circumstances remain ongoing.
The MV Hondius cluster is a reminder that hantaviruses, though rare in many parts of the world, carry significant clinical consequences and pose real challenges for public health response. Andes virus is the only orthohantavirus species known to be capable of limited human-to-human transmission, and the capacity to rapidly sequence and characterize viral strains during an outbreak is central to understanding transmission dynamics and guiding containment efforts.
The challenge: Obtaining viral sequence data from complex samples
Genomic surveillance of orthohantaviruses is technically demanding. Hantavirus titers in host tissue and environmental samples are typically low, and viral RNA degrades rapidly under field conditions. In practice, sequence data are frequently limited to short genomic fragments, which are insufficient for phylogenetic resolution or outbreak tracing. Compounding these issues is the overwhelming abundance of host RNA in primary tissue samples, which means that the viral signal is buried under a background that can exceed the viral fraction by several orders of magnitude.
Traditional approaches to this problem have their own constraints:
- Culture isolation requires biosafety level 3 or 4 infrastructure, is time-consuming, and not all hantavirus strains are readily cultivated.
- Amplicon sequencing via PCR is fast but limited by short read lengths and the requirement for primers that match the target sequence exactly. Strains with mutations at primer binding sites are effectively invisible to PCR-based methods.3
- Shotgun metagenomics can capture novel sequences without prior knowledge but requires extraordinary sequencing depth to recover rare viral reads from a high-host-background sample, making it cost-prohibitive for routine surveillance.
The solution: Hybridization capture for targeted viral RNA sequencing
Targeted sequence capture addresses these challenges by using biotinylated RNA probes (baits) that hybridize directly to viral sequences of interest in a complex nucleic acid library. Probe-bound fragments are physically pulled down and selectively enriched prior to sequencing, dramatically increasing the proportion of on-target reads without requiring high-titer isolates or perfect primer matches.
The myBaits® platform from Daicel Arbor Biosciences implements this approach with RNA bait sets designed from published reference sequences. Because probe-target hybridization tolerates partial sequence divergence, capture panels designed from known orthohantavirus genomes can detect and enrich divergent strains, novel variants, and sequences that would evade PCR-based detection. This makes targeted capture suitable not only for surveillance of known strains but also for novel pathogen discovery.
Research highlights: Orthohantavirus case studies
The following peer-reviewed studies illustrate how myBaits targeted capture has been applied across diverse orthohantavirus research contexts.
Discovering a novel hantavirus in bats
In a 2022 study, Weiss et al. identified a previously unknown hantavirus species, designated Kiwira virus, in African free-tailed bats (Mops condylurus) collected in Tanzania and Democratic Republic of Congo.4 Bat spleen samples were processed into sequencing libraries, and myBaits in-solution hybridization capture was performed using RNA baits based on available hantavirus genomic sequences, following the myBaits hybridization capture protocol. The capture panel successfully pulled down and assembled large portions of the L and S genomic segments of this divergent, previously unknown species from complex animal tissue.
The Kiwira virus discovery demonstrates that probe sets designed from known hantavirus sequences retain sufficient cross-reactivity to enrich divergent strains, enabling their detection without complete prior knowledge of the target sequence. This has direct implications for wildlife surveillance programs, where the discovery of novel zoonotic viruses is a primary objective.
Key takeaway: Targeted capture using conserved hantavirus bait sequences can recover large genomic segments from divergent, previously unknown strains in complex wildlife tissue, supporting novel virus discovery without culture-based isolation.
Tracing zoonotic outbreaks
A 2023 study by Heuser et al. investigated the first autochthonous human Seoul orthohantavirus (SEOV) infection documented in Germany, traced to a pet rat.5 A custom myBaits panel designed for rodent-associated orthohantaviruses was used to enrich amplified cDNA libraries prepared from total rat spleen and liver RNA. The enrichment yielded complete coding sequences for all three viral genomic segments (S, M, and L), providing a high-resolution, full-genome dataset obtained directly from host tissue.
The resulting genomic data enabled precise phylogenetic analyses that linked the German pet rat strains to SEOV lineages circulating in France, Great Britain, the United States, and the Netherlands. Reconstructing these geographic connections from primary animal tissue, without relying on cultured virus, illustrates the practical value of targeted capture for rapid outbreak source attribution.
Key takeaway: Custom targeted capture panels can yield complete multi-segment viral genomes directly from host tissue, providing the resolution needed for phylogenetic outbreak tracing across international lineages.
Assessing genome-wide hantavirus diversity
Hiltbrunner and Heckel (2020) examined the genetic diversity of Tula (TULV) and Puumala (PUUV) orthohantaviruses in natural European rodent populations, working with highly degraded wild rodent RNA samples (RNA integrity numbers (RIN) below 2).6 An in-solution sequence capture kit (myBaits) was employed, with RNA baits designed from 91 published hantavirus sequences. The targeted enrichment generated a 120- to 184-fold increase in the proportion of virus reads compared to equivalent shotgun sequencing libraries.
This depth of enrichment enabled contiguous de novo assemblies covering more than 99% of each viral genome and allowed researchers to resolve co-infections in individual hosts without reference-biased assembly approaches. The ability to work with severely degraded field samples is particularly significant for ecological surveillance, where sample quality is often outside the researcher’s control.
Key takeaway: Targeted capture increases viral reads over background by multiple orders of magnitude, enabling efficient near-complete de novo genome assembly from degraded field samples and accurate detection of co-infections within individual hosts.
Monitoring for genetic changes during in vitro viral culture
Binder et al. (2020) focused on the isolation and molecular characterization of Central European PUUV strains from bank voles collected in Germany.7 A custom myBaits target capture panel containing biotinylated RNA probes against all GenBank PUUV sequences at the time of the study was applied to total cellular cDNA libraries prepared from both primary lung tissue and cell culture supernatants. The targeted enrichment facilitated rapid complete genome determination across both sample types.
Importantly, direct comparison of sequences from primary tissue and cell culture passages allowed the researchers to track viral adaptation and detect mutations arising during in vitro passage. This capacity to monitor genetic change during culture is valuable for researchers who need to understand how their working viral stocks relate to field isolates.
Key takeaway: Targeted capture enables complete genome determination from both primary tissue and cell culture materials, allowing direct detection of adaptive mutations introduced during in vitro passaging.
Proven technology for hantavirus genomic surveillance
Across wildlife surveillance, outbreak investigation, population-level diversity studies, and strain characterization, targeted sequence capture with myBaits delivers the depth and resolution that standard metagenomics cannot consistently achieve in high-background, low-titer samples. The four studies highlighted above span diverse geographic settings, host species, and research objectives, yet they share a common finding: hybridization capture produces high-quality, comprehensive orthohantavirus genomic data where other methods fall short.
Daicel Arbor Biosciences has applied these same proven capture principles to the development of our new Orthohantavirus panel, designed to support high-resolution orthohantavirus genomic surveillance from complex primary samples. Learn more about this new panel and explore our full myBaits microbial offerings.
References
- 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
- Soucheray, S. Hantavirus outbreak linked to cruise ship grows to 13 cases. CIDRAP. https://www.cidrap.umn.edu/hantavirus/hantavirus-outbreak-linked-cruise-ship-grows-13-cases#:~:text=Over%20the%20past%20five%20days,three%20of%20which%20were%20fatal
- Ceballos-Garzon A, et al. Applying targeted gene hybridization capture to viruses with a focus on SARS-CoV-2. (2024) Virus Research. doi: 10.1016/j.virusres.2023.199293
- Weiss,S. et al. Kiwira virus, a newfound hantavirus discovered in free-tailed bats (Molossidae) in East and Central Africa. (2022) doi: 10.3390/v14112368
- Heuser E, et al. Pet Rats as the likely reservoir for human Seol Orthohantavirus infection (2023) https://doi.org/10.3390/v15020467
- Hiltbrunner, M. and Heckel G. Assessing genome-wide diversity in European hantaviruses through sequence capture from natural host samples. (2020) https://doi.org/10.3390/v12070749
- Binder F, et al. Isolation and characterization of new Puumala orthohantavirus strains from Germany. (2020) Virus Genes. https://doi.org/10.1007/s11262-020-01755-3
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