From tracking pandemics to personalized treatments, discover how cutting-edge sequencing technologies are transforming our understanding of viruses
Imagine having a tool that could identify unknown viruses, track mutations in real-time, and help develop life-saving treatments—all within days. This is not science fiction but the reality of next-generation sequencing (NGS), a technology that has fundamentally transformed our approach to understanding viruses.
In the wake of the COVID-19 pandemic, millions witnessed the power of this technology as scientists across the globe sequenced SARS-CoV-2 genomes at unprecedented speeds, enabling rapid vaccine development and variant tracking 2 .
These sequencing technologies have changed how we understand viruses, particularly in the areas of genome sequencing, evolution, ecology, discovery, and transcriptomics 1 .
An exciting era of viral exploration has begun, allowing researchers to detect viral threats with precision and speed that were unimaginable just two decades ago. As we stand on the brink of new discoveries, this technology continues to reveal the invisible viral world that surrounds us—a world that holds both threats to human health and clues to preventing future pandemics.
Complete viral genomes sequenced in hours instead of weeks
Monitor mutations and emerging variants in real-time
Identify novel viruses without prior knowledge of their existence
Next-generation sequencing represents a radical departure from earlier sequencing methods. Unlike traditional Sanger sequencing, which was time-intensive and costly, NGS enables simultaneous sequencing of millions of DNA fragments 4 .
This high-throughput approach has democratized genomic research, making large-scale sequencing projects accessible to researchers worldwide.
This approach uses primers that target a specific gene region of interest, followed by NGS. It's ideal for situations where researchers need to accurately measure virus diversity or target specific viruses.
However, primers don't have equal affinity for all sequences, which can introduce bias during amplification 9 .
Targeted High SensitivityIn this method, hybridization-based capture is applied after nucleic acid extraction and library preparation. Randomly sheared overlapping fragments are captured by DNA or RNA single-stranded oligonucleotides.
This approach is particularly useful for enriching viral genomes when sequencing complex samples 5 9 .
Enrichment Complex SamplesThis comprehensive approach captures all potential pathogen genes present in a sample without selective enrichment. It allows researchers to analyze all genes in a complex sample simultaneously.
With adequate sequencing depth, scientists can assemble entire viral genomes from short sequences 9 .
Hypothesis-Free Broad DetectionThe journey of virus discovery has undergone dramatic transformation over the past century.
Classical approaches relied on filtering samples to remove host cells and other microbes, inoculating the filtrate in suitable cell cultures, then purifying and characterizing viruses based on morphological changes in the cultured cells 3 .
Limitations: Time-consuming, often requiring days to weeks for identification, and many viruses couldn't be cultured using standard techniques 3 .
The development of PCR and microarray technologies represented a significant leap forward, making detection faster and eliminating the strict dependency on cell cultures.
Limitations: These methods still required prior sequence information to design primers and probes, making them unsuitable for discovering truly novel viruses 3 .
The emergence of NGS has marked a revolutionary advance—a sequence-independent approach that requires no prior knowledge about the viruses being sought.
This technology can rapidly recover nearly full genome sequences of viruses with relatively small amounts of starting material, offering an extremely wide dynamic detection range that has dramatically accelerated the pace of virus discovery 3 .
| Method | Time Required | Prior Knowledge Needed? | Key Limitations |
|---|---|---|---|
| Classical (Cell Culture) | Days to weeks | No | Many viruses cannot be cultured; time-consuming |
| PCR-Based Methods | Days | Yes | Limited to known virus families; small genome fragments |
| NGS Approaches | Hours to days | No | High equipment cost; complex data analysis |
To understand how NGS is revolutionizing viral safety testing, let's examine a crucial multi-laboratory study published in 2025 that evaluated NGS for detecting adventitious viruses in biological products like vaccines 7 .
The findings demonstrated remarkable sensitivity and breadth of virus detection across participating laboratories:
| Spike Level (GC/mL) | Targeted Analysis Detection | Non-targeted Analysis Detection |
|---|---|---|
| 10â´ GC/mL | All 5 viruses detected by all laboratories | All 5 viruses detected by all laboratories |
| 10³ GC/mL | All 5 viruses detected by all testing laboratories | Reo1 and EBV detected by all laboratories; variable detection of others |
| 10² GC/mL | Variable detection; one lab detected 3 viruses | Variable detection; one lab detected 4 viruses |
All laboratories successfully detected all five spiked viruses at 10ⴠgenome copies/mL using both targeted and non-targeted bioinformatic analyses. Even at the lower concentration of 10³ genome copies/mL, all five testing laboratories detected all viruses using targeted analysis 7 .
This experiment provided crucial validation for using NGS as an alternative method to supplement or replace conventional adventitious virus tests, enhancing the safety of biologics including vaccines 7 .
Implementing NGS in virology requires a sophisticated array of laboratory reagents and technologies.
| Reagent/Technology | Function | Application Examples |
|---|---|---|
| Amplification Reagents | Enable clonal amplification of DNA fragments for sequencing | Emulsion PCR (454, Ion Torrent), bridge amplification (Illumina) 1 |
| Sequencing Chemistries | Determine the sequence of nucleotides | Pyrosequencing (454), reversible terminators (Illumina), detection of released H+ (Ion Torrent) 1 |
| Target Enrichment Kits | Enrich for viral sequences before sequencing | xGen SARS-CoV-2 Amplicon Panel, xGen SARS-CoV-2 Hyb Panel 5 |
| Library Preparation Kits | Prepare nucleic acid fragments for sequencing | Fragmentation, end repair, adapter ligation, size selection 5 |
| Bioinformatic Tools | Analyze and interpret sequencing data | DeepVariant for variant calling, Stanford HIVdb for resistance interpretation 2 4 |
The NGS landscape features several competing platforms, each with distinct characteristics. Illumina systems dominate the market with their high-accuracy reversible terminator chemistry, while Oxford Nanopore Technologies offers long-read, real-time sequencing capabilities. Other players like PacBio and Ion Torrent provide alternative technologies suitable for different applications 1 4 .
Each technology represents trade-offs between read length, accuracy, throughput, and cost—factors that researchers must balance based on their specific viral research questions.
The applications of NGS in virology extend far beyond virus discovery.
In clinical settings, NGS provides high-resolution characterization of individual mutations in viral genomes, some of which affect disease progression or response to therapy 2 .
In HIV management, NGS has revolutionized treatment by identifying drug resistance mutations that guide antiretroviral therapy selection.
Unlike traditional methods, NGS can detect minority variants present in as little as 1% of the viral population, which may increase the risk of treatment failure 2 .
The technology enables sequencing of multiple genomic regions simultaneously, providing a comprehensive resistance profile that informs personalized treatment strategies 2 .
This approach allows clinicians to tailor antiviral regimens based on the specific genetic makeup of the infecting virus.
AI and machine learning algorithms analyze complex genomic datasets, uncovering patterns that traditional methods might miss.
Combining genomics with transcriptomics, proteomics, and metabolomics provides a comprehensive view of virus-host interactions 4 .
Single-cell genomics reveals cellular heterogeneity in response to viral infections, while spatial transcriptomics maps gene expression in tissue context 4 .
CRISPR technology enables precise editing and interrogation of viral and host genes to understand their roles in infection and disease 4 .
Next-generation sequencing has fundamentally transformed virology, providing researchers with an unprecedented ability to detect, characterize, and track viral pathogens.
From revealing the genetic blueprint of unknown viruses to guiding personalized treatment for infected patients, this technology has become an indispensable tool in our ongoing battle against viral diseases.
As sequencing technologies continue to evolve—becoming faster, cheaper, and more accessible—their potential to reshape virology and clinical practice grows exponentially.
The integration of NGS with artificial intelligence, multi-omics approaches, and novel molecular biology techniques promises to unlock even deeper understanding of the complex interactions between viruses and their hosts.
While challenges remain, including data management complexities and the need for standardized workflows, the future of NGS in virology is exceptionally bright. This technology continues to push the boundaries of scientific discovery, offering new hope for tackling both existing and emerging viral threats in an increasingly interconnected world.