Responding to the COVID‐19 pandemic in real time: coordinating a local hospital response using whole genome sequencing of SARS‐CoV‐2

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No relevant disclosures.

To the Editor:

Molecular diagnostics with whole genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has been well described as a method to monitor the evolving epidemiology of the coronavirus disease 2019 (COVID‐19) pandemic and coordinate public health responses. ¹ , ² WGS allows for the accurate identification of COVID‐19 variants, which, when combined with accessible diagnostic testing with polymerase chain reaction (PCR) and rapid antigen tests, supports contact tracing and public health action. ¹ , ² Since January 2022, by agreement with the Forensic and Scientific Services reference laboratory, it has been our practice at the Prince Charles Hospital — a tertiary cardiothoracic transplant centre in Brisbane — to sequence all SARS‐CoV‐2 samples of patients requiring hospital admission for COVID‐19. The rapid turnaround times, averaging 36 hours, supported decisions on variant‐specific therapeutics and optimised bed management.

The first case of the Omicron BA.2 subvariant detected at our centre was from a sample collected on 4 March 2022 (Box). This was 17 days before public announcements of the dominance of the BA.2 strain by the Queensland Chief Health Officer on 21 March 2022. ³ With the anticipated increase in local BA.2 cases, we were able to tailor our hospital level response in real time. ⁴ Initially, even though case numbers were low, from an infection prevention and control perspective, we cohorted BA.1 and BA.2 patients separately to mitigate the risk of nosocomial co‐infection. We maintained the workforce and resourcing surge capacity with a second COVID‐19 ward that opened within days of the initial BA.2 case being identified. Furthermore, genome sequencing for COVID‐19 therapeutics resistance mutations led to alterations in clinical management as BA.2 became the dominant local strain, given its lack of susceptibility to sotrovimab.

Box 1. Number of patients admitted and sequenced with coronavirus disease 2019 (COVID‐19) at the Prince Charles Hospital from 1 January to 3 April 2022 by genotype*.

*Bubble size range, 1–9; total number of patients, 256.

At the hospital and health service level, access to rapid WGS for identification of emerging variants provides the basis for greater infection prevention and control practices, resource and workforce management, and epidemiological monitoring, and carries implications for clinical management and therapeutics. WGS allows for rapid detection and contact tracing of nosocomial outbreaks, supporting identification of chains of transmission within hospitals. This information augments infection prevention and control by identifying gaps in current practice as well as supporting safer health care environmental design that minimises nosocomial transmission. Furthermore, detection of novel variants at the hospital level can help to predict new waves that require allocation of additional staffing and resources.

The Australian Government has recognised the evolving role of microbial genomics in public health surveillance but has not yet committed to further development to optimise personalised medicine, hospital care, and therapeutic decision making. ⁵ We strongly advocate for the inclusion of funding for sustainable rapid WGS that provides real‐time results under the Medicare Benefits Schedule. This will expedite Australia's transition to living with COVID‐19 and will allow us to better prepare our health system to manage new and emerging pathogens into the future.