Use of Ampliseq™ panels to study SARS-CoV-2 and the host response to infection

Use of Ampliseq™ panels to study SARS-CoV-2and the host response to infection

Soren Alexandersen^1,2,3

¹ Geelong Centre for Emerging Infectious Diseases, Geelong, VIC 3220, Australia;

² Deakin University, Geelong, VIC 3220, Australia;

³ Barwon Health, University Hospital Geelong, Geelong, VIC 3220 Australia

Ampliseq™ panels and next generation sequencing (NGS) on the Ion Torrent platform of diagnostic samples from infected individuals were used to study severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and to look at the host response to infection. We present selected results of near-full length SARS-CoV-2 virus genomic sequences assembled from such samples as well as show preliminary data on analysis of the expression of inflammatory genes. Future studies are planned to look even closer at the host immune response by using additional panels including the available Ampliseq™ Oncomine Immune Response, BCR and TCR panels. We also very briefly present very recent and exciting data on analysis of SARS-CoV-2 subgenomic RNAs by close analysis of NGS reads.