Paragon Genomics has developed a whole-genome targeted sequencing panel for Andes virus using CleanPlex® amplicon sequencing chemistry in response to growing public health concerns surrounding recent hantavirus outbreaks.
To support the scientific and public health community, Paragon Genomics plans to make primer sequences publicly available for research use while also offering optimized primer pools and library preparation kits for laboratories seeking streamlined sequencing workflows.
Free Research Primer Set Available for Download
Rising Interest in Andes Virus Surveillance
Recent international attention surrounding hantavirus infections — including reports tied to cruise ship-associated exposure events and continued monitoring by the CDC and WHO — has highlighted the importance of rapid genomic surveillance tools for emerging infectious diseases.
Among hantaviruses, Andes virus is particularly important because it is the only hantavirus known to demonstrate well-documented human-to-human transmission.
Recent public health discussions surrounding the Andes virus have increased interest in:
- Outbreak preparedness
- Genomic surveillance
- Mutation monitoring
- Transmission analysis
- Rapid sequencing workflows
Why Does Genomic Sequencing Matter?
Genomic sequencing serves an important role in infectious disease surveillance and outbreak response.
Sequencing can support:
- Outbreak tracking
- Mutation monitoring
- Phylogenetic analysis
- Transmission mapping
- Lineage identification
- Epidemiological surveillance
Additionally, whole-genome sequencing data may help researchers better understand:
- Viral evolution
- Transmission dynamics
- Geographic spread
- Genomic variation between outbreaks
Advantages of Targeted Sequencing
Targeted sequencing workflows allow laboratories to focus sequencing reads on viral genomes of interest while maintaining high sensitivity and efficient sequencing utilization. Compared to broader metagenomic approaches, targeted sequencing may offer:
Higher Sequencing Depth
Targeted enrichment concentrates sequencing reads directly on viral genomes of interest, enabling deeper genome coverage and more efficient sequencing utilization compared to untargeted metagenomic workflows.
Lower Sequencing Cost
By reducing off-target sequencing reads, targeted sequencing workflows can support more cost-efficient viral sequencing across larger sample volumes and surveillance studies.
Faster Turnaround
Streamlined CleanPlex® library preparation workflows support rapid sequencing deployment during active outbreak investigations and infectious disease surveillance efforts.
Simplified Workflows
Highly multiplexed amplification workflows reduce sequencing complexity while supporting scalable whole-genome viral sequencing applications.
Scalable Surveillance Deployment
Targeted sequencing workflows can be scaled across research laboratories, public health programs, and infectious disease surveillance initiatives requiring consistent high-throughput sequencing performance.
Why Amplicon Sequencing?
Amplicon-based sequencing workflows are particularly attractive for outbreak response and surveillance applications because they are:
Fast
Scalable
Low Input
Cost-Effective
Portable
Rapidly Deployable
Andes Virus Panel Design
Paragon Genomics developed a whole-genome Andes virus sequencing panel using publicly available outbreak reference genomes that are associated with the recent 2026 outbreak response.
| Feature | Details |
|---|---|
| Panel ID | PGD40 |
| Target Species | Andes Virus |
| Number Of Pools | 2 |
| Total Amplicons | 137 |
| Pool 1 | 69 Amplicons |
| Pool 2 | 68 Amplicons |
| Amplicon Size | 123–175 Bp |
| Overall Genome Coverage | 98.21% |
| Covered Bases | 11,844 / 12,060 Bp |
Genome Coverage
The panel was designed to cover nearly the entire viral genome across all three segments.
| Segment | Coverage | Covered Region |
|---|---|---|
| Segment S | 96.38% | 36–1820 |
| Segment M | 97.7% | 53–3616 |
| Segment L | 99.01% | 34–6528 |
The uncovered regions are limited primarily to terminal genomic ends where primer placement occurs.
Reference Genome Used
The panel design utilized the publicly available outbreak reference listed below, which was associated with the recent outbreak investigations.
ANDV-Switzerland-Hu-3337-2026
It was published publicly through virological surveillance resources.
Suggested Workflow
Simplified Sequencing Workflow
Applications
This workflow may support applications including:
Outbreak Surveillance
Support rapid genomic characterization of Andes virus samples during outbreak investigations using targeted whole genome sequencing workflows optimized for high coverage viral sequencing.
Genomic Epidemiology
Generate sequencing data for phylogenetic analysis, viral lineage tracking, transmission mapping, and comparative analysis across outbreak-associated Andes virus samples.
Mutation Monitoring
Monitor genomic changes across circulating Andes virus strains using highly multiplexed CleanPlex® amplicon sequencing designed for deep coverage across all three viral genome segments.
Public Health Preparedness
Support emerging pathogen surveillance initiatives with rapidly deployable amplicon sequencing workflows that can be designed, optimized, and scaled for infectious disease genomics research.
Research Sequencing
Enable targeted whole genome sequencing of Andes virus for virology research, genomic surveillance studies, assay development efforts, and viral evolution analysis.
Open Research Initiative
Supporting the Scientific Community
To support public health and research efforts, Paragon Genomics plans to make the Andes virus primer sequences publicly available for research use.
The goal is to support:
- Scientific collaboration
- Genomic surveillance efforts
- Assay development research
- Outbreak preparedness initiatives
Researchers may use the published primer sequences within:
- Custom sequencing workflows
- Internal research applications
Research Use Only
The published primer sequences are intended for Research Use Only (RUO). The sequences are not intended for:
- In vitro diagnostic (IVD) use
- Clinical diagnostic deployment
- Commercial resale
- Integration into competing commercial library preparation kits
Commercial Solutions Available
In addition to publicly available primer designs, Paragon Genomics can provide:
- Optimized primer pools
- CleanPlex® library preparation kits
- Custom sequencing workflows
- Automation-compatible solutions
- OEM assay development support
Why This Matters
Rapid assay development remains increasingly valuable for genomic preparedness initiatives and outbreak surveillance programs, as well as for emerging infectious disease research. The ability to quickly design and optimize highly multiplexed CleanPlex® amplicon panels demonstrates how targeted sequencing workflows can be adapted for new pathogens, evolving outbreak investigations, and infectious disease genomics applications requiring scalable viral sequencing deployment.
Interested in Andes Virus Sequencing Workflows?
Contact Paragon Genomics to learn more about primer pools, sequencing kits, custom panel development, infectious disease surveillance workflows, and OEM assay development partnerships.
Frequently Asked Questions
-
The panel was developed using publicly available reference material tied to the recent Andes virus outbreak response. Paragon Genomics evaluated earlier outbreak sequences, closely related Argentine sequences, and other available Andes virus sequences to support broad genome coverage across all major genome regions.
-
Because viruses naturally accumulate mutations over time, sequencing enables scientists to monitor changes within the outbreak virus. They can evaluate if the virus remains associated with a stable viral lineage or shows emerging variation during ongoing surveillance efforts involving Andes virus.
-
The workflow was designed for near whole-genome coverage across the S, M, and L genome segments of Andes virus.
-
Yes. The published primer sequences were developed to support Andes virus sequencing research workflows using CleanPlex® chemistry.
Research groups involved in tropical medicine investigations, viral surveillance studies, and infectious disease genomics can incorporate the primers into internal sequencing workflows, assay evaluation projects, or even custom viral sequencing applications.
-
Generated sequence data can help researchers evaluate genetic differences compared with previously reported strains, study the outbreak's evolutionary history, and then better understand transmission patterns associated with Andes virus surveillance efforts.
-
Yes. Since Andes virus is the only hantavirus with well-documented human-to-human transmission, targeted sequencing workflows can help researchers analyze genomic data tied to suspected transmission chains and compare viral genomes across linked cases.
-
Amplicon workflows allow for enrichment of viral genomes while supporting rapid deployment, scalable throughput, and lower RNA input requirements. This generates consensus sequences across challenging infectious disease samples that are tied to Andes virus surveillance.
-
Potentially. In outbreak investigations involving Andes virus, researchers often will look at how much genetic variation exists between the samples collected from different patients, locations, or exposure settings. Comparing consensus sequences may help clarify whether cases are connected through a shared transmission event or whether the sequencing data points toward separate spillover events occurring independently.
-
Yes. Researchers can evaluate genetic differences between circulating strains to determine if the data suggest a dramatically altered virus or whether the sequences remain relatively conserved across monitored Andes virus samples.
-
No. The workflow is intended for Research Use Only applications focused on genomic characterization and surveillance. It is not intended to replace existing diagnostic assays, nor is it based on a single complete genome sequence alone.
-
Potentially, yes. Comparing genomes across outbreak-associated samples may help researchers determine if sequenced isolates remain consistent with a known viral lineage or suggest the emergence of a highly divergent new strain. Analysis of the virus's genetic code may also provide a valuable early signal during ongoing outbreak surveillance efforts, reconstructing transmission chains, and informing public health responses.
-
Because Andes virus belongs to a class of segmented viruses, researchers often want sequencing coverage across all viral genome segments rather than just partial genomic regions alone. Broader coverage can support comparative analysis across clinical samples and provide additional context when investigating potential animal reservoirs or genomic relationships linked to the natural reservoir host.
-
The panel was developed using publicly available reference material tied to the recent Andes virus outbreak response. Paragon Genomics evaluated earlier outbreak sequences, closely related Argentine sequences, and other available Andes virus sequences to support broad genome coverage across all major genome regions.
-
Because viruses naturally accumulate mutations over time, sequencing enables scientists to monitor changes within the outbreak virus. They can evaluate if the virus remains associated with a stable viral lineage or shows emerging variation during ongoing surveillance efforts involving Andes virus.
-
The workflow was designed for near whole-genome coverage across the S, M, and L genome segments of Andes virus.
-
Yes. The published primer sequences were developed to support Andes virus sequencing research workflows using CleanPlex® chemistry.
Research groups involved in tropical medicine investigations, viral surveillance studies, and infectious disease genomics can incorporate the primers into internal sequencing workflows, assay evaluation projects, or even custom viral sequencing applications.
-
Generated sequence data can help researchers evaluate genetic differences compared with previously reported strains, study the outbreak's evolutionary history, and then better understand transmission patterns associated with Andes virus surveillance efforts.
-
Yes. Since Andes virus is the only hantavirus with well-documented human-to-human transmission, targeted sequencing workflows can help researchers analyze genomic data tied to suspected transmission chains and compare viral genomes across linked cases.
-
Amplicon workflows allow for enrichment of viral genomes while supporting rapid deployment, scalable throughput, and lower RNA input requirements. This generates consensus sequences across challenging infectious disease samples that are tied to Andes virus surveillance.
-
Potentially. In outbreak investigations involving Andes virus, researchers often will look at how much genetic variation exists between the samples collected from different patients, locations, or exposure settings. Comparing consensus sequences may help clarify whether cases are connected through a shared transmission event or whether the sequencing data points toward separate spillover events occurring independently.
-
Yes. Researchers can evaluate genetic differences between circulating strains to determine if the data suggest a dramatically altered virus or whether the sequences remain relatively conserved across monitored Andes virus samples.
-
No. The workflow is intended for Research Use Only applications focused on genomic characterization and surveillance. It is not intended to replace existing diagnostic assays, nor is it based on a single complete genome sequence alone.
-
Potentially, yes. Comparing genomes across outbreak-associated samples may help researchers determine if sequenced isolates remain consistent with a known viral lineage or suggest the emergence of a highly divergent new strain. Analysis of the virus's genetic code may also provide a valuable early signal during ongoing outbreak surveillance efforts, reconstructing transmission chains, and informing public health responses.
-
Because Andes virus belongs to a class of segmented viruses, researchers often want sequencing coverage across all viral genome segments rather than just partial genomic regions alone. Broader coverage can support comparative analysis across clinical samples and provide additional context when investigating potential animal reservoirs or genomic relationships linked to the natural reservoir host.