Lessons learned: use of WGS in real-time investigation of suspected intrahospital SARS-CoV-2 outbreaks

Abstract

Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been a continuing source of hospital-acquired infection and outbreaks. At Akershus University Hospital in Norway, traditional contact tracing has been combined with whole-genome sequencing (WGS) surveillance in real-time to investigate potential hospital outbreaks.

Aim: To describe the advantages and challenges encountered when using WGS as a real-time tool in hospital outbreak investigation and surveillance during the SARS-CoV-2 pandemic.

Methods: Routine contact tracing in the hospital was performed for all healthcare workers (HCWs) who tested positive for SARS-CoV-2. Viral RNA from all positive patient and HCW samples was sequenced in real-time using nanopore sequencing and the ARTIC Network protocol. Suspected outbreaks involving five or more individuals with viral sequences were described.

Findings: Nine outbreaks were suspected based on contact tracing, and one outbreak was suspected based on WGS results. Five outbreaks were confirmed; of these, two outbreaks were supported but could not be confirmed by WGS with high confidence, one outbreak was found to consist of two different lineages, and two outbreaks were refuted.

Conclusions: WGS is a valuable tool in hospital outbreak investigations when combined with traditional contact tracing. Inclusion of WGS data improved outbreak demarcation, identified unknown transmission chains, and highlighted weaknesses in existing infection control measures.

Keywords: COVID-19; Genomic epidemiology; Healthcare-associated; SARS-CoV-2; Surveillance; Whole-genome sequencing.

Figure 1

Phylogenetic tree of whole-genome-sequenced severe acute respiratory syndrome coronavirus-2 from Akershus University Hospital and a selection of viral genomes from the local area (Viken County, Norway), collected from January to April 2021. The three suspected outbreaks are highlighted. HCW, healthcare worker.

Figure 2

Phylogenetic tree of whole-genome-sequenced severe acute respiratory syndrome coronavirus-2 from Akershus University Hospital collected from September to December 2021. The seven suspected outbreaks are highlighted. HCW, healthcare worker.