Analysis of two sequential SARS-CoV-2 outbreaks on a haematology-oncology ward and the role of infection prevention

Abstract

Two SARS-CoV-2 nosocomial outbreaks occurred on the haematology ward of our hospital. Patients on the ward were at high risk for severe infection because of their immunocompromised status. Whole Genome Sequencing proved transmission of a particular SARS-CoV-2 variant in each outbreak. The first outbreak (20 patients/31 healthcare workers (HCW)) occurred in November 2020 and was caused by a variant belonging to lineage B.1.221. At that time, there were still uncertainties on mode of transmission of SARS-CoV-2, and vaccines nor therapy were available. Despite HCW wearing II-R masks in all patient contacts and FFP-2 masks during aerosol generating procedures (AGP), the outbreak continued. Therefore, extra measures were introduced. Firstly, regular PCR-screening of asymptomatic patients and HCW; positive patients were isolated and positive HCW were excluded from work as a rule and they were only allowed to resume their work if a follow-up PCR CT-value was ≥30 and were asymptomatic or having only mild symptoms. Secondly, the use of FFP-2 masks was expanded to some long-lasting, close-contact, non-AGPs. After implementing these measures, the incidence of new cases declined gradually. Thirty-seven percent of patients died due to COVID-19. The second outbreak (10 patients/2 HCW) was caused by the highly transmissible omicron BA.1 variant and occurred in February 2022, where transmission occurred on shared rooms despite the extra infection control measures. It was controlled much faster, and the clinical impact was low as the majority of patients was vaccinated; no patients died and symptoms were relatively mild in both patients and HCW.

Keywords: Infection control; Outbreak; SARS-CoV2; Screening asymptomatic healthcare workers; Screening asymptomatic patients; Whole Genome Sequencing.

Figure 1

Epidemic curve 2020 and 2022.

Figure 2

Whole Genome Sequencing results 2020. A. Radial phylogenetic tree of all sequenced isolates from outbreak 1. Isolates that clustered were highlighted by a black oval. B. Detailed phylogenetic relationship of the isolates that clustered in this study. Healthcare workers are highlighted in red, while patients were highlighted in blue. The phylogenetic tree was visualized using the auspice tool from Nextstrain (https://auspice.us/). Sample 206/2020 and sample 228/2020 belong to the same patient.

Figure 3

Whole Genome Sequencing results 2022. Radial phylogenetic tree of all sequenced isolates from outbreak 2. Isolates that clustered were highlighted by a black oval. B. Detailed phylogenetic relationship of the isolates that clustered in this study. Healthcare workers are highlighted in red, while patients were highlighted in blue. The phylogenetic tree was visualized using the auspice tool from Nextstrain (https://auspice.us/).