Antiviral Drug Development Support

Viral Sequencing, Resistance Monitoring and Analysis 

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Viral Sequencing, Resistance Monitoring and Analysis

Does your antiviral candidate reduce viral load? Are genetic changes emerging during treatment? And if a variant is identified, how do you determine if it matters?  

Answering these questions requires more than a single laboratory test. Antiviral developers need to understand how viral levels change throughout a study, characterise the virus’s genetic profile and investigate whether any observed changes could be relevant to treatment.  

hVIVO brings together molecular testing, next-generation sequencing (NGS), bioinformatics and specialist virology expertise in a unique combination of capabilities to support antiviral development programmes. This allows us to go beyond generating laboratory data to help you investigate viral genetic variation, assess potential resistance and interpret findings in the context of the virus, treatment and study.  

From preclinical investigation to clinical resistance monitoring, we can help you identify the scientific questions that really matter and determine the appropriate analytical approaches. 

Discuss your antiviral development programme with hVIVO

From viral detection to investigating potential resistance

Different techniques all answer different questions. Understanding what each can tell you, and what additional evidence may be needed, is essential when investigating antiviral activity and potential resistance. These approaches are complementary, not interchangeable. Detection and quantification do not explain why a virus may be changing; likewise, identifying a genetic variant does not, by itself, confirm antiviral resistance. 

01 – Detect the virus

BioFire can provide rapid, qualitative detection of selected respiratory pathogens. qPCR can also support viral detection, depending on the assay and study requirements.

02 – Quantify viral nucleic acid

qPCR and ddPCR can both measure selected viral genetic targets, supporting the assessment of viral load and changes over time.

03 – Characterise genetic variation

NGS can characterise viral genetic material and identify genetic variation, including changes that emerge or change in frequency during a study. 

04 – Analyse and interpret the findings

Bioinformatics can analyse sequence data and identify variants. Specialist virology expertise then helps assess their potential significance using relevant reference data, existing evidence and study context. 

05 – Investigate potential functional effects

Where a finding may warrant further investigation, phenotypic or functional testing can help assess whether an identified genetic change is associated with a measurable effect.

Why viral sequence interpretation matters

Viruses such as influenza are constantly evolving. A genetic difference identified through sequencing may reflect expected background variation, an analytical artefact, or a change potentially linked to treatment. Distinguishing between these possibilities requires an understanding of both the virus and the context in which the sample was collected.

For antiviral developers, that distinction has practical implications. Comparing study sequences with an inappropriate reference can produce large numbers of apparent variants that are difficult to interpret. Each finding that requires investigation can then add to the analytical workload and, where relevant, the evidence you need to explain in a regulatory submission. The challenge is therefore not simply to identify genetic differences, but to understand which findings are meaningful and which warrant further investigation.

We combine NGS and bioinformatics expertise with in-depth virology experience to help you assess findings in the context of the virus, treatment exposure, study design and available evidence. This supports a more informed investigation of potential resistance-associated variants without assuming that every detected change is biologically significant.

Ultimately, a detected variant is a finding to investigate—not proof of resistance. If a genetic change may be significant, further analysis can help clarify its potential effect.

Reference data that reflects the virus being studied 

The right reference can make the difference between identifying variation and truly understanding it.

Viral genomes vary between strains, geographical regions and time periods. When analysing an evolving virus like influenza, comparing study sequences with an unsuitable or outdated reference can make naturally occurring variation appear more significant than it is.

For influenza studies, hVIVO constructs season-matched reference panels from circulating strains, with selection informed by factors such as viral clade, geography and clinical trial timing. This helps contextualise observed differences against a more relevant picture of circulating viral variation, supporting a more meaningful interpretation of potential treatment-associated changes.  

Depending on the study design and requirements, we can also develop bespoke databases of circulating influenza strains for field trials in which participants may be exposed to viruses circulating in the wider community. The need for a bespoke database is assessed on a project-by-project basis, rather than assuming the same reference approach is appropriate for every programme.  

We can support both influenza and RSV studies, with the precise methods and requirements assessed for each project.

Relevant reference data can help: 

- Put observed genetic variation into biological context 

- Investigate whether changes may be associated with treatment 

- Avoid over-interpreting differences that reflect background viral diversity 

- Focus further analysis on findings that warrant investigation 

By improving the relevance of sequence comparisons, it can help reduce misleading variant findings and the unnecessary analytical and interpretive burden they create. It also supports the development of more informative datasets for scientific assessment.  

Encouraging robust, traceable workflows in antiviral development 

Generating useful sequence data depends on more than the sequencing technology itself. Sample integrity, consistent processing, reproducibility, and clear documentation all contribute to the quality and interpretability of the resulting data.  

Our NGS capability sits within our specialist virology laboratory rather than operating as a standalone sequencing service. This centralised model brings together sample processing, sequencing, bioinformatics and scientific interpretation all into a connected workflow, supporting consistency across stages and closer collaboration between the teams generating and interpreting results.

For sponsors, this integrated approach can reduce operational variability, help resolve issues, and clarify how the data generated relates to the scientific question it is intended to answer. 

The FDA’s updated guidance on submitting NGS data to the Division of Antiviral Products highlights the importance of robust methods, appropriate analysis, documentation and interpretation when NGS data is used to support antiviral development.

Our approach reflects these interconnected considerations: generating data through established workflows, interpreting sequence differences in their biological context and considering the evidence needed to assess potential resistance. 

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Investigating potential resistance beyond sequencing

NGS can identify genetic changes, but sequence data alone cannot establish whether a variant changes the virus’s susceptibility to an antiviral. A mutation may appear at a position of interest, or rise in frequency during treatment, without having any measurable effect on how the virus responds to the drug.

That’s why understanding the relationship between genotype and phenotype matters when investigating potential resistance. Linking a genetic change to a functional outcome, such as a shift in antiviral susceptibility, helps separate findings that warrant concern from those that reflect normal viral variation.

Where a finding may be significant, we can take the investigation further. Combining sequence analysis with laboratory testing builds a clearer, evidence-based picture of whether a variant is likely to matter for your antiviral, your study and your development programme.

ICON_Virology

Testing what a variant really does

We combine bioinformatics, specialist virology interpretation, and in-house phenotypic or functional testing when appropriate to the virus and scientific question. This enables further investigation of potentially significant findings and helps determine whether a genetic change is associated with a measurable functional effect. 

Virology Lab Solutions
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Support from the lab bench

Our wider laboratory capabilities can also support relevant preclinical questions. Depending on the programme, this can include investigating antiviral activity or exploring resistance under experimental conditions.

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Connecting laboratory findings to the wider development programme 

 

Antiviral development spans multiple stages, from preclinical investigation to clinical trials and resistance monitoring. The questions you need to answer change as the programme progresses, and the combination of capabilities used will depend on the virus, development stage and study design. We can support you through our complementary laboratory and clinical development capabilities.  

Preclinical development 

Laboratory investigations can help explore antiviral activity and investigate potential resistance mechanisms under experimental conditions.  

Early-phase clinical development 

Molecular and virological assessments can support investigations into viral detection, quantification, and genetic characterisation, aligned with the study's objectives.  

Later-stage clinical development and resistance monitoring 

Where relevant, viral sequence analysis helps investigate genetic changes observed during a study. Findings are considered alongside treatment exposure, sampling timepoints, viral kinetics, as well as other clinical outcomes.  

Human challenge trials and clinical research 

Our experience with human challenge trials and infectious disease research can complement laboratory capabilities when the virus and study design are relevant. Bringing together clinical and laboratory context helps interpret viral changes within the broader study. 

Wider development and regulatory consultancy

We can also support drug development strategy, regulatory advice and clinical development planning, which may be relevant depending on the programme’s needs.

Talk to our team about your antiviral programme

Whether you’re planning viral sequencing, investigating changes observed during treatment, or assessing a potential resistance-associated variant, we can discuss the scientific question or analytical approach that best fits your needs. 

Tell us about your virus, development stage and study objectives. Our team can then explore the relevant capabilities, project requirements and next steps with you.

Speak to the team today!

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This page was last updated 1 October 2026