The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks

Area of Science:

• Infectious Diseases
• Genomics
• Public Health

Background:

• Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections significantly impacted hospital capacity and patient flow during the pandemic.
• Effective infection control strategies are crucial for managing healthcare-associated outbreaks.

Purpose of the Study:

• To investigate the utility of whole-genome sequencing (WGS) in identifying and managing SARS-CoV-2 outbreaks within a hospital setting.
• To guide infection control resource allocation and intervention strategies during a major pandemic wave.

Main Methods:

• Whole-genome sequencing (WGS) of SARS-CoV-2 isolates.
• Phylogenetic analysis integrating genomic data with epidemiological information.
• Real-time monitoring of transmission events and outbreak dynamics.

Main Results:

• WGS identified an initial SARS-CoV-2 transmission event linked to an admission ward, with evidence of community-acquired infection in the index case.
• Asymptomatic staff infections with genetically identical viral strains were observed, contributing to outbreak propagation.
• WGS facilitated targeted interventions, including point-of-care testing and HEPA filter implementation, and excluded nosocomial transmission in specific cases, optimizing resource use.

Conclusions:

• Whole-genome sequencing significantly enhances the understanding of SARS-CoV-2 transmission clusters in hospitals.
• WGS enables precise identification of high-risk areas and validation of control measures, supporting sustained clinical services.
• Genomic surveillance is a valuable tool for effective nosocomial infection control and pandemic preparedness.