> ## Documentation Index
> Fetch the complete documentation index at: https://docs.ospribrain.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Assay Surveillance

> Monitor assay performance against emerging variants with geographic tracking.

## Overview

Assay Surveillance monitors your assays against emerging pathogen variants to detect potential mismatches in primer/probe binding regions before they affect clinical performance.

## Monitored Assays

Each monitored assay shows:

| Field                 | Description                          |
| --------------------- | ------------------------------------ |
| **Name**              | Assay name                           |
| **Organism**          | Target organism                      |
| **Target Gene**       | Gene being targeted                  |
| **Primers**           | Forward and reverse primer sequences |
| **Probes**            | Probe sequence(s)                    |
| **Binding Positions** | Genomic coordinates                  |

## Mismatch Alerts

When a variant is detected in a primer/probe binding region:

| Field                 | Description                             |
| --------------------- | --------------------------------------- |
| **Variant Accession** | NCBI accession of the variant           |
| **Severity**          | Impact level (critical, warning, info)  |
| **Fwd Mismatches**    | Mismatches in the forward primer region |
| **Rev Mismatches**    | Mismatches in the reverse primer region |
| **Probe Mismatches**  | Mismatches in the probe region          |
| **AI Interpretation** | AI assessment of the clinical impact    |

<Note>
  **Alex's screenshot note:** Take a screenshot of the Surveillance page showing an assay with 1-2 mismatch alerts of different severity levels.
</Note>

## Geographic Tracking

* Filter alerts by geographic region
* View variant prevalence by location
* Monitor threat levels across different areas

## Charts & Analytics

| Chart              | Description                  |
| ------------------ | ---------------------------- |
| **Area chart**     | Variant prevalence over time |
| **Bar chart**      | Distribution by region       |
| **Pie chart**      | Severity breakdown           |
| **Radar chart**    | Multi-axis threat assessment |
| **Threat history** | Week-by-week trend line      |

## Check Now

Click **Check Now** on any assay to trigger an immediate variant scan against the latest NCBI/GISAID data.