Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections

The aims of Estée's research was to examine the utility of rapid sequencing of SARS-CoV-2 combined with a detailed epidemiological analysis, to investigate healthcare-associated COVID-19 infections, and to inform infection control measures.

• For nanopore sequencing, those PCR-positive samples with Ct ≤33 were sequenced using a multiplex PCR-based amplicon tiling approach (ARTIC v2 protocol and v3 primer set).
• In total there were 374 patients in their prospective study, with mean age of 67 years, and ~62% were male.
• Estée: in their prospective study ~70% of infections were community-associated, and 10.7% were suspected to be healthcare-associated.
• Estée showed the epidemic curve pattern; ‘what you can see is a typical epidemic curve pattern’. She also showed the SARS-CoV-2 lineage plots, and stated how the majority of samples were from the same lineage (B1).
• Demonstrating the benefit of combined genomic/epidemiological analysis, Estée shared a scenario where findings led to a review of the unit’s infection control procedures.