Whole genome sequencing of H5N1 from dairy products with tiled 250bp amplicons v1
Year: 2024
Type: preprint
Abstract: Here we present a new short tiled amplicon scheme for the whole-genome sequencing of H5N1 from dairy product samples, and the methods we have used to successfully obtain whole-genome H5N1 sequences from dairy product samples using these primers. The majority of these primers were created using primalscheme with recent H5N1 sequences provided by the Andersen Lab (https://github.com/andersen-lab/avian-influenza/tree/master/alignments) used as a reference.1-2 The primalscheme amplicons left coverage gaps at the very 5' and 3' ends of each gene segment, so we manually added additional primers to supplement these gaps informed by primers developed by the Moncla Lab (https://github.com/moncla-lab/h5-sequencing-protocol-dev/blob/main/RT_and_PCR_protocol.md).3 The attached BED file contains the primer sequences aligned to gene segment sequences from A/Bovine/texas/24-029328-01/2024(H5N1).4 We were inspired by the effectiveness of the QIAseq DIRECT SARS-CoV-2 250bp tiled amplicon scheme at amplifying difficult environmental samples for sequencing, and continue to use QIAseq Direct SARS-CoV-2 reagents and protocols in this workflow for that reason.5 We plan to add our qPCR and sequencing results from commercial dairy samples to our github at https://github.com/dholab/dairy-hpai-monitoring.
Institution: University of Wisconsin–Madison
Language: English
Subfield: Epidemiology
Field: Medicine
Domain: Health Sciences
SDG: Zero hunger
Open Access status: green
OpenAlex ID: W4399370505