Pathogen Sequencing Protocols

The Pathogen Genomics Centers of Excellence (PGCoE) Network is currently conducting a viral respiratory benchmarking study, which aims to compare the results of pathogen whole genome sequencing protocols used across the United States. When complete, the protocols listed below will be annotated according to their applicability for different sequencing platforms and effectiveness for specific pathogens.

Further information on this benchmarking study, including details about the tool we are using to evaluate sequencing results, are available in our benchmarking repository.

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Sample Collection Protocols

Sample Collection for Genomic Endpoints

The PGCoE network is developing a document that contains guidance for sample collection and storage with genomic endpoints in mind. This sample collection protocol will be linked here when available.

Sequencing Primers and Probes

Primal Scheme Amplicon Sequencing Primers

Primer sets for amplicon-based sequencing of many different pathogens (including RSV, SARS-CoV-2, measles, mpox, and others) are available on the labs.primalscheme site, to which NE PGCoE partners regularly contribute.

Viral Sequencing Protocols

H5N1-specific Molecular Inversion Probes

Protocol for sequencing H5N1 viral genomes from animal specimens at Washington Animal Disease Diagnostic Laboratory using hybrid capture with Molecular Inversion Probes. This protocol will be linked here when available.

Automated Viral Amplicon Sequencing on Liquid Handlers

This repository contains protocols for automated viral sequencing on Hamilton Microlab STAR liquid handlers. These protocols have been validated by the DAMP Lab at Boston University.