Value of SARS-COV-2 genomic characterization in elucidating within-hospital transmission

Introduction: Identifying probable transmission routes of SARS-CoV-2 in the hospital setting is needed to direct implementation of infection prevention measures to stop transmission. Objectives: We investigated probable transmission routes of clusters of SARS-CoV-2 using both epidemiological data and Next generation sequencing (NGS), and assessed congruence. Methods: All positive SARS-CoV-2 PCR test performed in our hospital from both patients and healthcare workers (HCW) between September and December 2020 were evaluated. When more than two HCW or patients from the same ward tested positive within 14 days (a potential cluster), the ward was contacted to identify transmission routes. Suspected transmission was categorized based on epidemiological data (e.g. attendance, contacts in and outside the hospital). All available samples within clusters with sufficient viral load (CT value < 30) were analysed using NGS. A team of molecular biologists, infection prevention specialists and virologists discussed the NGS results and called possible, probable or unlikely clusters based on phylogenetic reconstruction, background prevalence and the epidemiological data. Results: From 14 possible clusters NGS was performed on 98 samples (Table 1). Congruence between epidemiological data and expert conclusion was high for probable transmission (89%) and unlikely transmission (76%). In case of possible transmission NGS guided the definite conclusion in 85% towards probable. Four of the five cases in which no transmission was suspected based on epidemiological data, but were identical in NGS analysis, occurred in one cluster. Other disconcordances were dispersed in different clusters. Conclusion: In 33% NGS changed the conclusion on transmission events. NGS analysis enables confirmation that transmission has ended and thereby helps evaluate outbreak management(OM). Besides, concerns of HCW can be managed by definite results on specific transmission events. One of fourteen clusters was only detected by NGS. Epidemiological data alone can give direction to OM, however NGS analysis gives essential feedback on OM and specific transmission events. (Figure Presented). (Figure Presented).