First nosocomial cluster of COVID-19 due to the Delta variant in a major acute care hospital in Singapore: investigations and outbreak response

Abstract

Objectives: The first large nosocomial cluster of coronavirus disease 2019 (COVID-19) in Singapore in April 2021 led to partial closure of a major acute care hospital. This study examined factors associated with infection among patients, staff and visitors; investigated the possible role of aerosol-based transmission; evaluated the effectiveness of BNT162.b2 and mRNA1273 vaccines; and described the successful containment of the cluster.

Methods: Close contacts of patients with COVID-19 and the affected ward were identified and underwent surveillance for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Patient, staff and visitor cohorts were constructed and factors associated with infection were evaluated. Phylogenetic analysis of patient samples was performed. Ward air exhaust filters were tested for SARS-CoV-2.

Results: In total, there were 47 cases, comprising 29 patients, nine staff, six visitors and three household contacts. All infections were of the Delta variant. Ventilation studies showed turbulent air flow and swabs from air exhaust filters were positive for SARS-CoV-2. Vaccine breakthrough infections were seen in both patients and staff. Among patients, vaccination was associated with a 79% lower odds of infection with COVID-19 (adjusted odds ratio 0.21, 95% confidence interval 0.05-0.95).

Conclusions: This cluster occurred despite enhancement of infection control measures that the hospital had undertaken at the onset of the COVID-19 pandemic. It was brought under control rapidly through case isolation, extensive contact tracing and quarantine measures, and led to enhanced use of hospital personal protective equipment, introduction of routine rostered testing of inpatients and staff, and changes in hospital infrastructure to improve ventilation within general wards.

Keywords: COVID-19; COVID-19 vaccines; Infection control; Outbreak; Phylogeny.

Figure 1

Epidemic curve observed in the Ward I cluster.

Figure 2

Phylogenetic relationship of severe acute respiratory syndrome coronavirus-2 sequences, as generated by IQTree with γ-distributed rate differences and 1000 bootstrap validation. All sequences were identified by GISAID accession numbers, with global and Singapore references in magenta and black, respectively. Cases related to Ward I are in blue (Node 18). The scale bar indicates genetic distance between sequences, and bootstrap values are indicated at node branches. Samples from Patient A (index case), Patient B (symptomatic physician), Patient C (primary case) and Patient D (patient from Ward II) are shown.

Figure 3

Bed location of all patient cases of coronavirus disease 2019 in the Ward I cluster, and air exhaust filter swab results. SARS-CoV-2, severe acute respiratory syndrome coronavirus-2; PCR, polymerase chain reaction.

Figure 4

Adjusted odds ratio for stay in Ward I on specific days during the period from 20^th to 28^th April 2021. Note: Each model was adjusted for the following variables: age, gender, co-morbidities (diabetes mellitus, malignancies, leukaemia, lymphoma, connective tissue disease, chronic lung disease, congestive cardiac failure), whether patient had received at least one dose of coronavirus disease 2019 vaccine, and duration on the ward.