Life & Health Sciences
Infectious disease epidemiology research
Infectious disease epidemiology research tracks how pathogens spread and change, and its practice depends on surveillance data and openly shared genomes. Case and trend data come from national and international systems: CDC WONDER for notifiable conditions, tuberculosis and sexually transmitted disease, the ECDC Surveillance Atlas built from Member State reports to TESSy, the WHO data portal, and the WHO Global Influenza Surveillance and Response System, running since 1952. Pathogen sequences go to GenBank, part of the International Nucleotide Sequence Database Collaboration, or to GISAID, whose registered-access model expects users to acknowledge the sources of the data. NCBI Pathogen Detection clusters bacterial and fungal genomes to flag possible transmission chains, and Nextstrain tracks pathogen evolution in near real time. Laboratory work follows the CDC and NIH Biosafety in Microbiological and Biomedical Laboratories (BMBL), an advisory document rather than a regulation, while possession, use and transfer of listed agents and toxins falls under the Federal Select Agent Program run by CDC and APHIS. Research during epidemics raises its own ethics questions, covered in WHO guidance and training material on outbreaks and emergencies. NIAID is the main US funder, and the WHO R&D Blueprint plans the rapid activation of research during epidemics. Findings often appear first on medRxiv, which warns that preprints should not guide clinical practice, then in Emerging Infectious Diseases, Eurosurveillance or the American Journal of Epidemiology.
New to the field? What is Infectious Disease & Epidemiology? →
Reviewed 5 November 2026 by CASRAI Editorial Board
- CDC WONDER(read 5 November 2026)
- ECDC Surveillance Atlas of Infectious Diseases(read 5 November 2026)
- WHO data portal(read 5 November 2026)
- WHO GISRS(read 5 November 2026)
- NCBI GenBank(read 5 November 2026)
- GISAID(read 5 November 2026)
- NCBI Pathogen Detection(read 5 November 2026)
- Nextstrain(read 5 November 2026)
- CDC: BMBL(read 5 November 2026)
- Federal Select Agent Program(read 5 November 2026)
- WHO: Guidance for managing ethical issues in infectious disease outbreaks(read 5 November 2026)
- WHO: Ethics in epidemics, emergencies and disasters(read 5 November 2026)
- Wikipedia: NIAID(read 5 November 2026)
- WHO R&D Blueprint(read 5 November 2026)
- medRxiv: about(read 5 November 2026)
- Emerging Infectious Diseases(read 5 November 2026)
- Eurosurveillance: about(read 5 November 2026)
- American Journal of Epidemiology(read 5 November 2026)
Field at a glance
Archives, facilities and data
- GISAID
- Registered-access sharing mechanism for influenza, SARS-CoV-2, RSV, mpox and arbovirus genomes that expects users to acknowledge data sources.Website ↗ · Our guide →
- GenBank
- The NIH genetic sequence database, part of the INSDC with DDBJ and ENA, which exchange data daily.Website ↗ · Our guide →
- NCBI Pathogen Detection
- Integrates bacterial and fungal pathogen genomes, clusters related isolates to flag transmission chains and screens for resistance genes with AMRFinderPlus.Website ↗
- Nextstrain
- Open-source project for real-time tracking of pathogen evolution from genome data, with tools for custom analyses.Website ↗
- ECDC Surveillance Atlas of Infectious Diseases
- Interactive tables and maps of European surveillance data compiled from Member State submissions to TESSy.Website ↗
- WHO data portal (data.who.int)
- WHO's home for health data, linking the COVID-19 dashboard, the Global Health Observatory and World Health Statistics.Website ↗
- WHO Global Influenza Surveillance and Response System (GISRS)
- Surveillance network for seasonal, pandemic and zoonotic influenza, established 1952, with 166 institutions in 136 Member States.Website ↗
- CDC WONDER
- CDC query system that includes tuberculosis, sexually transmitted disease and National Notifiable Conditions data.Website ↗
Standards and formats
- Biosafety in Microbiological and Biomedical Laboratories (BMBL), 6th edition
- CDC and NIH biosafety guidance, described in its foreword as advisory and not a regulatory document.Website ↗ · Our guide →
- Federal Select Agent Program
- Joint CDC and APHIS programme that oversees possession, use and transfer of agents and toxins that could endanger people, animals or plants.Website ↗ · Our guide →
- WHO Guidance for managing ethical issues in infectious disease outbreaks (2016)
- WHO guideline for policy makers, providers and researchers preparing for the ethical problems outbreaks raise.Website ↗
- WHO Ethics in epidemics, emergencies and disasters (2015)
- WHO training manual on ethical issues in research, surveillance and patient care during epidemics and emergencies.Website ↗
- STROBE Statement
- Reporting checklist for cohort, case-control and cross-sectional studies, the core designs of epidemiology.Website ↗ · Our guide →
Funders and programmes
- National Institute of Allergy and Infectious Diseases (NIAID)
- One of the 27 NIH institutes and centers; conducts and funds research on infectious, immunologic and allergic diseases.Website ↗ · Our guide →
- WHO R&D Blueprint
- Global strategy and preparedness plan for rapid activation of research and development during epidemics.Website ↗
Journals
- Emerging Infectious Diseases
- Journal hosted on the CDC website (ISSN 1080-6059) carrying research, dispatches and research letters.Website ↗
- Eurosurveillance
- Peer-reviewed open access journal on communicable disease epidemiology, published by ECDC, free for readers and authors.Website ↗
- American Journal of Epidemiology
- Peer-reviewed journal on Oxford Academic and the official journal of the Society for Epidemiologic Research.Website ↗
Societies
- Infectious Diseases Society of America (IDSA)
- Membership society of more than 13,000 members; members receive The Journal of Infectious Diseases and Clinical Infectious Diseases.Website ↗
- Society for Epidemiologic Research (SER)
- Professional organisation for epidemiologic science with over 2,500 members and an annual meeting.Website ↗
Preprints and indexes
- medRxiv
- Health sciences preprint server that screens for health-risk and dual-use content and warns preprints should not guide clinical practice.Website ↗ · Our guide →
- ProMED
- Round-the-clock outbreak alert service with expert-verified reports and an archive of more than three decades of outbreak data.Website ↗
47 pages across 8 topic areas
Patient Safety & Infection Prevention
- Enhanced Barrier Precautions (EBP): What It Requires That Standard and Contact Precautions Do Not
Enhanced Barrier Precautions require gown and gloves during eight high-contact resident care activities in nursing homes, without the room restriction…
- Epidemic Curve: Choosing the Interval, Onset vs Specimen Date, and Bounding the Exposure Window
The construction decisions behind a hospital epidemic curve: choosing the x-axis interval from the incubation period, why symptom onset and specimen c…
- Healthcare-Associated Infection Definitions: NHSN's CLABSI, CAUTI, SSI, and VAE Criteria Compared
How NHSN defines a healthcare-associated infection: the date-of-event and infection-window-period concepts, the admission day-3 attribution rule, and…
- Navigating the NHSN Patient Safety Component Manual: A Chapter Map
A practical map of the NHSN Patient Safety Component manual's chapter structure — why chapters 8 and 13 are missing, where numerator vs. denominator r…
- NHSN Reporting Requirements for Hospitals: Mandatory Measures, Deadlines, and the CMS IQR Link
Which NHSN HAI modules CMS actually requires for the Hospital IQR Program, how the monthly reporting plan works, the quarterly deadline cadence, and h…
- Outbreak Investigation Steps in a Hospital: The Full Sequence
The CDC field-epidemiology sequence — verify diagnosis, case definition, line list, descriptive epidemiology, hypotheses, control measures, communicat…
- PPE Donning and Doffing: The Sequence, the Trained Observer, and the Competency Record
Isolation PPE donning and doffing for infection preventionists: the ordering logic, the OSHA clauses that make competency enforceable, the trained-obs…
- SEP-1: The 3-Hour and 6-Hour Bundle Elements as the Measure Actually Scores Them
SEP-1 is an all-or-nothing, chart-abstracted composite: a hospital can deliver excellent sepsis care and still fail on abstraction technicalities. How…
- Standardized Antimicrobial Administration Ratio (SAAR)
The Standardized Antimicrobial Administration Ratio (SAAR) is NHSN's observed-to-predicted metric for hospital antimicrobial use, distinct from the St…
- Syndromic Surveillance Reporting for Hospitals: The ED Feed, NSSP Onboarding, and the CMS Measure
A hospital syndromic surveillance feed carries near-real-time ED registration and triage data to a public health agency. This guide covers the NSSP Pr…
- Terminal Cleaning Protocol and Audit: The Discharge Sequence, the High-Touch Checklist, and What Each Audit Method Measures
A guide for EVS and infection prevention: the terminal-cleaning discharge sequence, the CDC high-touch surface checklist, disinfectant contact-time (w…
Research Methods & Statistics
- Biostatistics vs Epidemiology: What Is the Difference?Comparison
Epidemiology studies how disease is distributed in populations and what determines it; biostatistics develops and applies the statistical methods that…
- Epidemiology vs Public Health: What Is the Difference?Comparison
Epidemiology is the science of disease patterns and causes in populations; public health is the broader practice of acting on that evidence. Here is h…
- How to Read a Phylogenetic Tree: Nodes, Branch Lengths and Bootstrap Values
Nodes, branch lengths, tip order and the numbers on the branches (bootstrap values vs Bayesian posterior probabilities) explained with a worked interp…
- MMWR Weeks: CDC Epidemiological Calendar and Rules
A comprehensive reference for CDC MMWR weeks: official business rules, date hierarchy, full 2025–2026 lookup tables, calculation algorithms, and code.…
- Sentinel Surveillance: Definition, Types and Methods
An authoritative guide to sentinel surveillance: architectural design, site selection criteria, comparison of the 5 surveillance types, and diagnostic…
- Seroprevalence
A methodological guide to seroprevalence in epidemiological research, examining population-based study designs, assay sensitivity adjustments, and ser…
- Vaccine Efficacy: Formula, Worked Example and Interpretation
Vaccine efficacy is 1 minus the risk ratio. Formula, two worked examples, a reading table, and Excel, R and Python code.…
- What Is Epidemiology? Research Areas, Funding, and Career Paths
A complete guide to epidemiology: its core definition and methods, major subfields, the real funding landscape (NIH institutes, CDC, NSF, private foun…
- What Is Parasitology? A Guide to the Field
Parasitology is the study of parasites and their hosts. Learn its subfields, methods, societies, journals, NIH/NIAID funding and training paths.…
- What Is Tropical Medicine and Global Health Research?
Tropical medicine and global health research study diseases of poverty and the health of populations worldwide. Learn the subfields, methods, societie…
Scholarly Publishing
- CSTE
An overview of the Council of State and Territorial Epidemiologists (CSTE), examining position statements, surveillance case definitions, and fellowsh…
- Emerging Infectious Diseases Journal (CDC EID)
Comprehensive overview of Emerging Infectious Diseases (EID), CDC's diamond open-access journal covering emerging pathogens, global surveillance, and…
- ESCMID
A comprehensive researcher guide to ESCMID: clinical practice guidelines, Study Groups, EUCAST breakpoints, ESCMID Global, and CMI journal publishing.…
- IDWeek
A comprehensive guide to IDWeek for researchers, covering partner societies, abstract submissions, the OFID supplement, and conference scheduling.…
- Infectious Diseases Society of America (IDSA)
Overview of the Infectious Diseases Society of America (IDSA), covering its clinical guidelines methodology, GRADE framework, peer-reviewed journals,…
- NCBI Pathogen Detection: Isolate Surveillance Guide
A guide to the NCBI Pathogen Detection system, detailing how whole-genome sequencing data are clustered into SNP groups to trace disease outbreaks and…
- PLOS Neglected Tropical Diseases (PLOS NTD): Scope, Fees and Indexing
PLOS NTD scope, ISSNs, editors, indexing, the $2,670 fee and Research4Life terms, from the journal and PLOS pages read 2026-11-08.…
- Society for Epidemiologic Research
A complete guide to the Society for Epidemiologic Research (SER): AJE journal publishing, annual meetings, causal inference workshops, and member awar…
Laboratory Operations & Safety
- Biosafety Level 2 (BSL-2) Requirements: Facility and Equipment Buying Guide
A procurement-focused breakdown of BSL-2 facility, equipment, and documentation requirements, plus how to evaluate biosafety cabinet certifiers and eq…
- Containment Level 3 Laboratory vs. CL2: Canada's Biosafety Standard ComparedComparison
CL2 vs. CL3 containment laboratories under Canada's Biosafety Standard (CBS): facility engineering requirements, PHAC/HPTA licensing, and how the term…
- CROI: Conference on Retroviruses and Opportunistic Infections
CROI explained: who runs it, how abstracts are reviewed, and the prior-publication, preprint and copyright rules to check before submitting.…
- FoodNet: Foodborne Active Surveillance Guide
FoodNet is CDC's collaborative active surveillance network tracking major foodborne pathogens across 10 US sites to determine national burden and tren…
- Nowcasting in Infectious Disease Surveillance: Reporting Delays Explained
Nowcasting estimates current disease trends from incomplete recent data. Learn reporting triangles, delay types and when nowcasts can mislead.…
- WastewaterSCAN: Surveillance & Lab Workflows
Explore WastewaterSCAN methods: wastewater solids analysis, RT-ddPCR quantification, PMMoV normalization, and multi-pathogen surveillance data.…
Laboratory Compliance & Quality
- Animal Biosafety Level 2 (ABSL-2): Requirements and the BSL-2 Deltas
What Animal Biosafety Level 2 actually requires beyond laboratory BSL-2: caging and cage-decontamination specifics, PPE, facility controls, the IACUC-…
- Biosafety Levels BSL-1 to BSL-4: Containment Requirements Compared
A cross-level comparison of BSL-1 through BSL-4 on the four elements BMBL 6th edition actually uses — standard practices, special practices, primary b…
- Bloodborne Pathogens Standard (29 CFR 1910.1030) in Research Laboratories: Paragraph (e) and the Cell Line Question
Clinical bloodborne pathogens guidance stops at Universal Precautions. Paragraph (e) of 29 CFR 1910.1030 adds containment, a separate biosafety manual…
- Exposure Control Plan for Bloodborne Pathogens: The Five Elements 29 CFR 1910.1030(c) Requires
What has to be in a written Exposure Control Plan under 29 CFR 1910.1030(c): exposure determination, methods-of-compliance scheduling, Hepatitis B vac…
Research Integrity & Compliance
- Dual Use Research of Concern (DURC), Select Agents, and Biosafety Oversight
A compliance map for US research-administration offices: what makes research DURC, how the Federal Select Agent Program registration process works, ho…
- The Federal Select Agent Program: Registration and Responsible Official Duties
How FSAP registration, amendment, and renewal actually work, and the specific duties 42 CFR 73.9 assigns to the Responsible Official.…
- What Is an Institutional Biosafety Committee (IBC)?
An Institutional Biosafety Committee (IBC) is the committee institutions must establish under the NIH Guidelines to review recombinant/synthetic nucle…
- What Is Gain-of-Function Research?
Gain-of-function research modifies a pathogen to enhance transmissibility or virulence. Most is routine; a narrow, federally regulated subset (ePPP/da…
Grants Management & Research Funding
- European Centre for Disease Prevention (ECDC)
Comprehensive guide to the European Centre for Disease Prevention and Control (ECDC): governance, EpiPulse portal, Surveillance Atlas, and fellowship…
- KEMRI: Research Centres, Programmes, and How to Get SERU Approval
KEMRI is Kenya’s national medical research institute. Its research centres and programmes, how the Scientific and Ethics Review Unit (SERU) reviews no…
- NNDSS
A complete researcher guide to CDC's NNDSS: nationally notifiable diseases, CSTE case definitions, HL7 case notification data, and MMWR weekly tables.…
Research Data Management
- Submitting Sequence Data to NCBI SRA
A step-by-step guide to depositing sequencing reads in NCBI SRA: how BioProject, BioSample, and SRA run accessions relate, when to route data to dbGaP…
Key terms
- Biosafety and Biosecurity
- Biosafety Level (BSL)
- Biosafety Level 1 (BSL-1)
- Biosafety Level 2 (BSL-2)
- Biosafety Level 3 (BSL-3)
- Biosafety Level 4 (BSL-4)
- Dual-Use Research of Concern (DURC)
- Eurosurveillance
- Institutional Biosafety Committee (IBC)
- Select Agent List
- Sequence Read Archive (SRA)
- Standardized Infection Ratio (SIR)
