Laboratory
Laboratory protocols, standard operating procedures, and related documentation from the CDC Influenza Division.
Extraction & Purification
Automated RNA Extraction using QIAcube HT
Standard operating procedure for automated RNA extraction using the QIAcube HT instrument for influenza and respiratory virus sample processing.
MRT-PCR Purification using Exonuclease
Procedure for purifying MRT-PCR products using exonuclease treatment to remove residual primers and single-stranded DNA prior to library preparation.
Sequencing & QC
DNA Quantification with Qubit dsDNA High Sensitivity Kit
Procedure for quantifying double-stranded DNA using the Qubit fluorometer and the dsDNA High Sensitivity assay kit for quality control of sequencing libraries.
Performing a MiSeq Next Generation Sequencing Run
Standard operating procedure for setting up and performing a next generation sequencing run on the Illumina MiSeq platform.
QIAxcel Sample Preparation and Quality Control Procedure
Procedure for preparing samples and performing quality control analysis using the QIAxcel capillary electrophoresis system for PCR product verification.
Data Access
Flu Labs Genetic Data Portal
Secure CDC portal where State Public Health Laboratories retrieve the sequencing results for specimens they submitted to their National Influenza Reference C...
Specimen Submission
Influenza Specimen Submission Form
Form for submitting influenza specimens to the CDC Influenza Division, capturing specimen, patient, and submitter information required for laboratory testing...
April 02, 2025PCR & Amplification
MRT-PCR of Influenza A Viruses for Sequencing
Multi-segment reverse transcription PCR protocol for amplifying influenza A virus genome segments for sequencing. Current revision.
Multi-segment Reverse Transcription-PCR (M-RTPCR) of Influenza A and B
Protocol for multi-segment reverse transcription PCR of both influenza A and influenza B viruses, generating full-genome amplicons for sequencing.
RT-PCR of the SARS-CoV-2 S-gene for Sequencing
Reverse transcription PCR protocol targeting the SARS-CoV-2 S-gene to generate amplicons for downstream sequencing applications.
Library Preparation
Manual Procedure Illumina DNA Prep Library SOP
Manual procedure for Illumina DNA Prep library preparation, covering tagmentation, cleanup, and amplification steps for sequencing library construction. Curr...
MiSeq Library Loading Preparation
Standard operating procedure for preparing and loading sequencing libraries onto the Illumina MiSeq platform for influenza virus characterization.
January 15, 2024Native Library Prep & Nanopore Sequencing of InfA Virus & SARS-CoV-2 S-gene Amplicons
Protocol for native library preparation and Oxford Nanopore sequencing of influenza A virus and SARS-CoV-2 S-gene amplicons. Current revision.
Preparation of DNA Libraries and Loading on the MiSeq i100
Standard operating procedure for preparing DNA sequencing libraries and loading them onto the Illumina MiSeq i100 platform for influenza virus characterization.
Preparation of DNA Libraries and Loading on the NextSeq 1000/2000
Standard operating procedure for preparing DNA sequencing libraries and loading them onto the Illumina NextSeq 1000/2000 platform for influenza virus charact...
Other
2026-27 Influenza Season Surveillance Guidance
Surveillance guidance for the 2026-27 influenza season, covering monitoring of seasonal influenza viruses and detection of novel influenza A viruses, includi...