Implications of Viral Sequencing - The Children's Hospital Los Angeles Experience

Dr. Timothy J. Triche MD, PhD, Co-Director of Center for Personalized Medicine at Children’s Hospital Los Angeles​ (CHLA), shares how he and his team used sequencing data generated with the Ion AmpliSeq SARS-CoV-2 Research Panel to analyze phylogenetic relationships among a cluster of six SARS-CoV-2-positive samples. By identifying two distinct lineages between the two sets, the team was able to conclude that the source of transmission wasn’t shared. Comparative analysis showed that, not unexpectedly, the mother and son had nearly identical strains of the virus that originated in Utah, with links to Europe, while the four health care workers had strains only distantly related to each other and to the family. This confirmed that there was no transmission between the patient family and the health care workers. Further, the health care workers acquired the virus from community spread and not from the patient and family member.

The Ion AmpliSeq SARS-CoV-2 Research Panel is a targeted NGS solution that enables interrogation of the complete SARS-CoV-2 genome for epidemiological research. This nucleic acid-to-analysis solution includes the assay and an intuitive and powerful set of analysis tools in the Torrent Suite SARS-CoV-2 Research Plug-in package, enabling hypothesis-neutral analysis and a dramatically simplified workflow.