China CDC Sentinel Hospital Surveillance Data

Automated weekly extraction of respiratory disease surveillance data from China CDC sentinel hospitals — curated for epidemiological research and forecasting.

Latest Snapshot

SARS-CoV-2 weekly ILI positivity rate at sentinel hospitals — 5-week moving average (CDC sentinel convention). Latest week: 2026-09-21.

Data Pipeline

flowchart LR
    A([China CDC<br/>Website]) -->|crawl links| B[New URL<br/>Discovery]
    B -->|render page| C[PDF<br/>Snapshot]
    C -->|MinerU OCR| D[Markdown<br/>Document]
    D -->|LLM extract| E[Structured<br/>CSV Records]
    E -->|dedup + merge| F[(Main<br/>Datasets)]
    F -->|chart refresh| H[ILI Chart<br/>PNG]
    F -->|auto commit| G([GitHub<br/>Release])
    H --> G

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Orchestrated by Apache Airflow — runs every Friday at 00:00 (Asia/Shanghai) and only commits when new reports are detected.

Datasets

data/cncdc_surveillance_covid19.csv

Weekly SARS-CoV-2 positivity rates, formatted for the China-COVID-19-Forecast-Hub project.

Column	Type	Description
reference_date	date	Surveillance week start (Monday)
target_end_date	date	Surveillance week end (Sunday)
report_week	int	ISO week number
pathogen	string	Pathogen name (新型冠状病毒 / SARS-CoV-2)
ili_percent	float	Outpatient ILI positive rate (%)
sari_percent	float	Inpatient SARI positive rate (%)

data/cncdc_surveillance_all.csv

Full multi-pathogen surveillance panel with the same schema, covering all 11 monitored respiratory pathogens.

data/cncdc_suverillance_2025_14_22.csv

COVID-19-only records reconstructed from monthly China CDC reports for 2025 weeks 14–22, when weekly bulletins were temporarily replaced by monthly summaries.

Pathogens Monitored

Chinese name	English / Scientific name
新型冠状病毒	SARS-CoV-2
流感病毒	Influenza virus (A & B)
呼吸道合胞病毒	Respiratory Syncytial Virus (RSV)
人偏肺病毒	Human Metapneumovirus (hMPV)
副流感病毒	Parainfluenza virus (PIV)
普通冠状病毒	Common human coronaviruses (HCoV)
腺病毒	Adenovirus
博卡病毒	Bocavirus
鼻病毒	Rhinovirus
肠道病毒	Enterovirus
肺炎支原体	Mycoplasma pneumoniae

Repository Layout

cn_cdc_data/
├── data/
│   ├── cncdc_surveillance_covid19.csv      # COVID-19 weekly series
│   ├── cncdc_surveillance_all.csv          # All 11 pathogens
│   └── cncdc_suverillance_2025_14_22.csv   # Historical gap (W14–W22 2025)
└── update/
    └── YYYY-MM-DD/                         # One folder per weekly report
        ├── pdf/                            # Original page snapshot
        ├── md/                             # OCR'd markdown
        └── csv/                            # Extracted weekly records

Quick Start

Load directly from GitHub:

import pandas as pd

URL = "https://raw.githubusercontent.com/dailypartita/cn_cdc_crawl/main/data/cncdc_surveillance_covid19.csv"
df = pd.read_csv(URL)

Notes

• 2025 Weeks 14–22 gap — China CDC published only monthly aggregated reports during this period. Recovered COVID-19 data is provided separately in data/cncdc_suverillance_2025_14_22.csv; other pathogens are not available for these weeks.
• Reporting basis — Rates reflect positivity among sampled patients at sentinel hospitals, not population incidence.
• Late revisions — China CDC occasionally revises prior weeks retroactively; the pipeline deduplicates by (reference_date, pathogen) and keeps the most recent value.

Data Source

Official surveillance bulletins from the Chinese Center for Disease Control and Prevention (China CDC): https://www.chinacdc.cn/jksj/jksj04_14275/

Contact

Kaixin Yang — yang_kaixin@gzlab.ac.cn Guangzhou Laboratory · Computational Epidemiology Group

Disclaimer

This dataset is redistributed for non-commercial research and analytical purposes. All original data remains the intellectual property of the Chinese Center for Disease Control and Prevention. Users are responsible for verifying data fitness for their specific use case and for citing the original source.