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SeqMatic provides next-generation sequencing (NGS) for viral genomes, including sequencing of known viruses with an existing reference genome and de novo sequencing of novel or uncharacterized viruses. Our team has sequenced viral genomes including SARS-CoV-2, influenza, and polio for academic, public health, and biopharma research.
Viral genome sequencing helps researchers characterize viral genomes, identify genetic variation, study viral evolution, and track emerging or circulating strains. SeqMatic supports sequencing across major viral genome types, including single- and double-stranded DNA (ssDNA/dsDNA) and RNA (ssRNA/dsRNA) viruses, as well as viruses infecting different hosts, including bacteriophages, plant viruses, and animal viruses. SeqMatic’s BSL2+ certified laboratory is equipped to safely handle and sequence applicable viral samples.
Viral genome sequencing supports work at every stage, from characterizing a single isolate to tracking a variant across an outbreak.
| Application | What It Enables |
| Individual isolate characterization | Virulence assessment, drug/antiviral resistance mechanisms, molecular marker discovery |
| Vaccine & diagnostic design | Target identification from viral genome structure |
| Outbreak surveillance & transmission tracking | Population-level epidemiological monitoring |
| Variant & mutation tracking | Monitoring evolutionary changes in circulating strains over time |
| Pathogen identification | Species- and strain-level identification |
For individual isolate research: virulence characterization, drug/antiviral resistance mechanisms, molecular marker discovery, vaccine and diagnostic target design.
For population-level research: evolutionary relationships between strains, epidemiological surveillance, outbreak transmission mapping, viral population dynamics over time.
| Virus | Application |
| SARS-CoV-2 | Outbreak surveillance, variant tracking |
| Influenza | Mutation tracking, seasonal strain monitoring |
| Polio | Molecular surveillance |
| Sample Category | Examples |
| Viral isolates & cultures | Cultured viral isolates, low-titer viral samples |
| Swabs | Nasal, oropharyngeal, and similar collection types |
| Environmental & wastewater surveillance | Wastewater, water, and other environmental samples for viral surveillance |
For exact input amounts and purity thresholds by platform, refer to the Sample Input Recommendations.
Handling a live pathogen isolate takes different lab infrastructure than routine, non-infectious sequencing work.
Libraries are sequenced across SeqMatic’s full platform lineup, matched to each project’s read length and depth requirements: Illumina or Ultima Genomics for short read sequencing, and PacBio or Oxford Nanopore for long read sequencing.
SeqMatic’s team helps determine the right platform for each project during consultation, based on the read length, depth, and accuracy the research question requires.
Step 1. Project consultation and planning. Your science shouldn’t have to fit our workflow. The SeqMatic workflow should fit your scientific question. SeqMatic’s scientific team reviews study objectives, sample types, and target sequencing depth before work begins, with assurance of confidential sample submission and handling throughout.
Project Planning & Consultation page →
Step 2. Sample submission and extraction. SeqMatic accepts a wide range of sample types and performs nucleic acid extraction in house, with viability and quality checkpoints before any library preparation begins.
Extraction Services page →
Step 3. Library preparation. Libraries are constructed directly from genomic DNA/cDNA through fragmentation and adapter ligation, validated through quality control at multiple points before committing to a full sequencing run.
Step 4. Sequencing. Libraries are sequenced on the platform best matched to the project’s read length and depth requirements.
Multiomics Technology Sequencing Platforms →
Step 5. Data analysis and delivery. Custom bioinformatics turns raw sequencing data into an interpretable result set.
Bioinformatics services →
BSL-2+ containment covers most viruses used in routine research, diagnostic, and outbreak-surveillance work, including agents like SARS-CoV-2. It does not cover higher-risk agents that require BSL-3 or BSL-4 containment.
That’s fine. SeqMatic’s Extraction Services handle nucleic acid extraction from the sample itself.
Sample-specific handling and shipping guidance is covered in SeqMatic’s Sample Submission Instructions.
Yes. The viruses listed above are examples of what SeqMatic has sequenced to date, not a complete list of what we can handle. Because de novo assembly builds a genome without needing an existing reference to align to, novel, emerging, or less-common viruses can be sequenced the same way even ones that SeqMatic hasn’t worked with before.
The right method depends on the goal: whole-genome sequencing captures the complete viral genome; targeted sequencing focuses on specific regions of interest; metagenomic sequencing detects and characterizes viruses directly from complex environmental or clinical samples without prior knowledge of what’s present; and meta transcriptomic sequencing captures actively expressed viral RNA within a host or community. Our scientific team can guide you during the Project Planning & Consultation for the best possible method.
Yes. SeqMatic provides custom bioinformatics at three tiers — Primary (alignment and quantification), Secondary (QC, normalization, and differential expression), and Tertiary (pathway, gene ontology, and functional interpretation) and can go deeper per customer request.
See Sample and Data Storage and Data Transfer Options for storage duration and secure delivery options.
