17d9ca0e37
RKI AMELAG wastewater surveillance data with CSV exports and bun fetch script. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
107 lines
4.2 KiB
Markdown
107 lines
4.2 KiB
Markdown
# DE Wastewater Surveillance (AMELAG)
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---
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## 🎯 BEST ESTIMATE
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| Metric | Value | Confidence | Last Updated |
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|--------|-------|------------|--------------|
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| **SARS-CoV-2 viral load (national)** | **~1,554 gc/L** | 90% | 2026-04-15 |
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| **SARS-CoV-2 4-week trend** | **-52.8% (↓↓)** | 85% | 2026-04-15 |
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| **SARS-CoV-2 % of all-time peak** | **0.3%** | 90% | 2026-04-15 |
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| **Influenza A 4-week trend** | **-39.3% (↓↓)** | 85% | 2026-04-15 |
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| **RSV B 4-week trend** | **-27.0% (↓↓)** | 85% | 2026-04-15 |
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**One-liner:** All five tracked respiratory pathogens declining in German wastewater, SARS-CoV-2 at 0.3% of peak.
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**Caveat:** Wastewater surveillance detects population-level viral shedding, not clinical severity; seasonal declines are expected in spring.
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---
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## Quick Context
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Germany's AMELAG network (Abwassersurveillance für die epidemiologische Lagebewertung) monitors respiratory viruses in wastewater from ~67–75 treatment plants covering ~25% of the population. Wastewater data provides an unbiased signal of community infection levels because it captures all shedding individuals regardless of testing behavior. The system tracks SARS-CoV-2, Influenza A/B, and RSV A/B with weekly population-weighted national aggregates.
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---
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## Datasets
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### wastewater-latest.csv
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Full time series for all pathogen types (SARS-CoV-2, Influenza A/B, RSV A/B, and combined variants).
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- **datum**: Week date (Wednesday of reporting week)
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- **typ**: Pathogen type
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- **n_sites**: Number of reporting wastewater treatment plants
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- **pop_coverage_pct**: Population coverage percentage
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- **viruslast_gc_per_l**: Viral load in gene copies per liter
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- **viruslast_normalisiert**: Flow-normalized viral load
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- **vorhersage_gam**: GAM-smoothed prediction value
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- **obere_schranke / untere_schranke**: 95% confidence intervals
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### wastewater-summary.csv
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Current status summary per primary pathogen with trend analysis.
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---
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## Methodology Summary
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**Approach:** Population-weighted aggregation of wastewater treatment plant viral load measurements, smoothed with Generalized Additive Models (GAM).
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**Sources:**
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- [AMELAG — RKI / Umweltbundesamt (GitHub)](https://github.com/robert-koch-institut/Abwassersurveillance_AMELAG)
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- [Infektionsradar (Dashboard)](https://infektionsradar.rki.de/de/covid/abwasser)
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- [Umweltbundesamt PiA-Monitor](https://www.umweltbundesamt.de/amelag)
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**Definition Used:** Gene copies per liter (gc/L) of treated wastewater influent, population-weighted national aggregate across reporting sites.
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---
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## Source Analysis
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### Why These Sources?
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| Source | Strengths | Weaknesses | Weight Given |
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|--------|-----------|------------|--------------|
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| **AMELAG GitHub (RKI/UBA)** | Official open data, CC-BY 4.0, machine-readable TSV, weekly updates | ~25% population coverage, 1-2 week lag | High |
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| **Infektionsradar Dashboard** | Visual context, additional metrics | No public API, frontend-only | Reference |
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### Key Limitations
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1. Population coverage is ~25% — not all German cities/regions are equally represented.
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2. Lab changes at individual sites can cause discontinuities (flagged in individual site data).
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3. Wastewater measures viral shedding, not infections or severity — the relationship between gc/L and clinical burden is non-linear.
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---
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## Substrate Connection
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- **Problems:** PR-00003 (Performance Society Exhaustion — pandemic impact on work/health)
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- **Related Datasets:** Bay-Area-COVID-Wastewater (US equivalent)
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- **Cross-reference:** DE-Mental-Health (pandemic impact on mental health indicators)
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---
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## Research Metadata
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| Attribute | Value |
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|-----------|-------|
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| **Research Date** | 2026-04-22 |
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| **Researcher** | Sven / PAI |
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| **Method** | Automated fetch from AMELAG GitHub TSV |
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| **Confidence Level** | 90% |
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| **Known Gaps** | Individual site data not included in summary; variant-level data not available in wastewater |
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---
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## Changelog
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| Date | Change | Reason |
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|------|--------|--------|
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| 2026-04-22 | Initial dataset creation | Implement DE wastewater surveillance from AMELAG |
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---
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## Full Data
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See `wastewater-latest.csv` for the complete time series (905 data points across all pathogen types).
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Fetch script: `bun get-de-wastewater` from Substrate root.
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