PCR Is Not Enough — Go Further with Hantavirus Whole-Genome NGS
Reliable Whole-Genome Sequencing Even from Low Viral Load Clinical Samples
Recent reports of Hantavirus infections across multiple regions have renewed global attention toward emerging and re-emerging infectious diseases. Hantavirus is a zoonotic RNA virus primarily transmitted through rodents and is known to cause Hemorrhagic Fever with Renal Syndrome (HFRS) and Hantavirus Pulmonary Syndrome (HPS), both associated with high fatality rates. As a result, continuous genomic surveillance and variant monitoring have become increasingly important.
In real-world clinical specimens, however, viral load is often very low while host-derived nucleic acids vastly outnumber viral sequences. Under these conditions, obtaining reliable whole-genome sequencing data beyond simple detection becomes technically challenging.
In this post, we introduce validation data generated using the Celemics Hemorrhagic Fever Syndrome Panel applied to Hantaan virus clinical specimens, and highlight the advantages of NGS-based Hantavirus whole-genome analysis.
Why PCR-Based Detection Alone Is Not Enough
Conventional PCR-based diagnostics provide rapid and sensitive pathogen detection, but they remain limited by their narrow target scope.
- Mutations Outside Primer-Binding Regions May Be Missed
Hantavirus possesses a tripartite RNA genome consisting of S, M, and L segments, with antigenic variation distributed across all three segments. Variants occurring outside primer-binding regions may therefore remain undetected. - Limited Resolution for Phylogenetic Analysis
Outbreak investigation and transmission tracking require whole-genome-level information, whereas PCR assays typically analyze only limited genomic regions. - Difficulty in Species-Level Discrimination
Multiple Hantavirus species circulate globally, making broad species-level discrimination difficult with conventional single-target PCR assays.
NGS Target Enrichment for Whole-Genome Hantavirus Analysis
NGS-based target enrichment (hybridization capture) addresses these limitations by selectively enriching viral sequences from complex clinical backgrounds, enabling detection of SNVs, InDels, and all genomic variants across the full viral genome in a single experiment. This approach is especially advantageous in clinical specimens with high host background, where enrichment efficiency directly impacts sequencing sensitivity and data quality.
Celemics Hemorrhagic Fever Syndrome Panel
The Celemics Hemorrhagic Fever Syndrome Panel is a syndrome-based NGS target enrichment panel designed for broad differential diagnosis of hemorrhagic fever-associated pathogens. For Hantavirus analysis, the panel offers several key advantages.
- Simultaneous Detection of 10 Hantavirus Species
The panel covers a broad range of Hantavirus species, from endemic strains such as Seoul orthohantavirus and Hantaan virus to high-risk imported species including Andes orthohantavirus. - Validation Through Collaboration with National Institutions
The panel was co-developed and validated through collaborative research with national public health institutions to ensure both clinical and epidemiological utility. - Species-Specific Blocker Technology
Species-specific blockers minimize interference from host-derived nucleic acids and maximize on-target enrichment efficiency. - Whole-Genome Analysis Support
The panel supports SNV/InDel analysis and phylogenetic analysis across all S/M/L segments of the viral genome.
💡 Key Point
The Hemorrhagic Fever Syndrome Panel is a syndrome-based panel capable of simultaneously screening for multiple hemorrhagic fever-associated viruses beyond Hantavirus. This enables broad differential diagnosis even when the causative pathogen is initially unknown.
Clinical Sample Validation Results
To evaluate real-world panel performance, Hantaan virus-positive clinical specimens were serially diluted to simulate a range of viral load conditions.
Samples were analyzed at Ct values of 24.3, 27.6, and 30.9 (approximately 10-fold dilution steps), with two independent replicates per condition to assess reproducibility
- Whole-Genome Coverage at Low Viral Load
Despite decreasing viral load, the panel achieved ≥95% 10x whole-genome coverage at Ct 30.9 (low viral load) in both replicates, demonstrating robust performance across a clinically relevant range of sample conditions.
- Depth-of-Coverage Profile
Coverage uniformity was assessed across increasing sequencing depths. At Ct 24.3 and 27.6, genome coverage exceeded 97% even at 50x depth, indicating data quality sufficient for variant calling and phylogenetic analysis beyond simple detection.
- Limit of Detection (LoD)
Across all replicate experiments, all samples from Ct 24.3 through Ct 30.9 were consistently called as ‘Detected’, confirming that the panel reliably covers the viral load range most commonly observed in clinical practice. These results confirm that Celemics panels can reliably deliver whole-genome sequencing data even from low-titer clinical specimens.• ≥95% 10x whole-genome coverage achieved at Ct 30.9 (low viral load)
• Consistent results across two independent replicates, confirming high reproducibility
• Simultaneous analysis of 10 Hantavirus species — from endemic strains to high-risk imported variants
What Sets Celemics Apart
- End-to-End Validated Workflow
Celemics’ proprietary Probe Design Technology, Probe Manufacturing, and Optimization capabilities underpin a fully integrated workflow — from library preparation and sequencing to bioinformatics analysis. - Species-Specific Blocker Technology
Clinical specimens contain overwhelmingly more host-derived DNA/RNA than viral sequences. Celemics’ species-specific blockers minimize host nucleic acid interference and maximize on-target enrichment efficiency for reliable results even at low viral loads. - Syndrome-Based Panel Lineup
Beyond the Hemorrhagic Fever panel, Celemics offers a flexible range of syndrome- and scenario-specific NGS panels:• Hemorrhagic Fever Syndrome Panel — Hantavirus and other hemorrhagic fever pathogens
• Respiratory Syndrome Virus Panel — SARS-CoV-2, Influenza, RSV, and more
• Hantavirus Dedicated Panel — Deep-dive analysis at the Orthohantavirus genus level
Beyond COVID-19: Expanding Pathogen Genomics Capabilities
Building on SARS-CoV-2 whole-genome sequencing expertise accumulated during the COVID-19 pandemic, Celemics has continuously expanded its validated NGS panel portfolio for major respiratory pathogens — including Influenza A/B, RSV, Adenovirus, Coronavirus, Parainfluenza, Rhinovirus, and Enterovirus.
Celemics also maintains panels for livestock pathogens such as African Swine Fever Virus (ASFV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), and Porcine Epidemic Diarrhea Virus (PEDV), enabling integrated pathogen surveillance from a One Health perspective — spanning human, animal, and environmental domains
Explore Celemics Custom NGS Panel Solutions
Celemics provides pathogen-specific and syndrome-based NGS panel portfolios optimized for whole-genome pathogen surveillance, low viral load specimen analysis, and outbreak monitoring.
From respiratory viruses to zoonotic pathogens, Celemics supports integrated pathogen genomics workflows from a One Health perspective.
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