By: Modjadji, WARN-ID, SEARCH
This is a framework document describing molecular (ddPCR/qPCR) and sequencing-based assays for the detection, (clade/sub-clade/lineage) typing, and focused genomic characterization of monkeypox virus (MPXV) from wastewater/environmental and clinical samples.
By: Allison Steedman, Alana Weiss, Christina Mac, Kelly Nguyen, Mark Zeller
This protocol is adapted from our PrimalSeq-LibAmp Illumina Sequencing protocol. The general approach is to amplify SARS-CoV-2 genomes in small (~250 bp) overlapping fragments using two separate, highly multiplexed PCR reactions.
By: Ezra Kurzban, Sarah Perkins, Catie Anderson, Madison Schwab, Mark Zeller
Protocol for sequencing SARS-CoV-2 using a long amplicon scheme for PrimalSeq. The average length of amplicons in this protocol is ~1200 nt, making this well-suited to sequencing on Oxford Nanopore platforms.
By: Catie Anderson, Mark Zeller
Updated protocol for sequencing SARS-CoV-2 using a shorter amplicon scheme for PrimalSeq. The average length of amplicons in this protocol is ~250 nt, making this well-suited to sequencing on NovaSeq, iSeq, and NextSeq platforms.
By: Catie Anderson, Mark Zeller
Protocol for sequencing SARS-CoV-2 using ARTIC PrimalSeq. The average length of amplicons in this protocol is ~400 nt, making this well-suited to sequencing on the MiSeq.
By: Nate Matteson, Nate Grubaugh, Karthik Gangavarapu, Josh Quick, Nick Loman, Kristian Andersen
This is an easy-to-follow protocol (“PrimalSeq”) that uses “PrimalScheme”-based amplicon sequencing of virus genomes directly on the Illumina platform. In this updated version, we use spike-ins to control for cross-sample contamination.
By: Catie Anderson, Mark Zeller
Protocol for COVID-19 screening using CDC and WHO primers.
By: Glenn Oliveira
This is an easy-to-follow protocol for creating a plaque assay for Zika virus using crystal violet for easy counting.
By: Matthias Pauthner
This is an easy-to-follow protocol for high-coverage sequencing of Lassa virus S Segments.
By: Josh Quick, Nick Loman, Team ZiBRA
This is an easy-to-follow protocol that uses “PrimalScheme”-based amplicon sequencing of Zika virus genomes directly on the MinION platform.