General information, not a diagnosis Method and limitations

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Genomic surveillance: understanding sequences without overinterpretation

Sequencing describes part of the genetic heritage of an infectious agent. Compared to clinical and epidemiological data, it can shed light on its circulation, changes and possible links between samples.

Topic updated:

Scientists examining sequencing data in a public health laboratory
AI-generated illustration, not evidence of a health event. A sequence only makes sense with the quality of the sampling, the date and the monitoring context.

EssentialShort answer

To be retained

The starting points

Genomic surveillance compares infectious agent sequences to track their diversity and support public health surveys. It does not alone prove that one person has transmitted an infection to another or that a mutation alters the severity of the disease.

Deepen ▼

01Reference

From sampling to signal

Each step can influence the representativeness of the result.

Sampling

The quality, date, location and selection of samples determine what can be observed.

Sequencing

The laboratory reads all or part of the genome according to the agent, method and question asked.

Quality control

Incomplete or contaminated sequences must be identified prior to any comparison.

Context

The results are reconciled with the available cases, exposures and monitoring series.

02Reference

What the data can shed light on

The level of confidence depends on the number and choice of samples.

Diversity of lineage

Follow the lines observed in a population and their evolution over time.

Home survey

Compare samples to guide a survey, without replacing known contacts and dates.

Diagnosis and treatment

Identify genetic changes that warrant functional studies or increased vigilance.

International sharing

Compare signals between territories according to compatible methods and metadata.

03Reference

Read the limits

A frequency among the received sequences is not necessarily a frequency throughout the population.

Selection Bias

Targeted sampling, laboratory capacity, and deposition delays can distort a trend.

Change and effect

An observed mutation does not show a different transmissibility or severity.

Privacy

Sequence data must comply with applicable confidentiality rules.

Decision

Authorities combine genomics, epidemiology, clinical and laboratory before recommending a measure.

LandPutting into context

Situations to be considered

Sequencing adds information on the agent; it must be reconciled with the cases and methods of sampling.

New lineage announced

Check its frequency, evolution and clinical data before deducing a different severity or transmissibility.

Two samples are similar

Genetic proximity can help an investigation, without alone proving direct contact between two people.

Few samples are sequenced

Interpret proportions with caution: selection of samples may differ depending on the location and timing.

QuestionsClarifications

Frequently Asked Questions

Do two close sequences prove direct transmission?

No. They may indicate genetic kinship; it is also necessary to examine dates, possible contacts and other transmission chains.

Is a new lineage necessarily more dangerous?

No. Its detection justifies observation, and possibly further studies on its circulation and properties.

Is a new variant necessarily more dangerous?

No. Its genetic appearance does not show an increase in severity or a change in transmission; further observations are needed.

Does sequencing replace clinical surveillance?

No. The symptoms, hospitalizations, exposures and laboratory data answer additional questions.

Institutional sources

External sources can evolve. Check their date and instructions for your territory.

PratiqueCheck before deciding

Trois niveaux d’interprétation

Reading guidance and interpretation limits
Concept or situationWhat it describesPoint to watch
SéquenceInformation génétique obtenue à partir d’un prélèvement.Qualité, couverture et date sont essentielles.
Groupe génétiqueRegroupement selon des ressemblances de séquences.Une proximité génétique ne prouve pas à elle seule un contact direct.
Décision sanitaireInterpretation alongside clinical and epidemiological data.Représentativité des prélèvements et biais de sélection.