Nosocomial Outbreak of SARS-CoV-2 in a "Non-COVID-19" Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission

Abstract

Dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions affects both patients and health-care workers (HCW), as well as the institutional capacity to provide essential health services. Here, we investigated an outbreak of SARS-CoV-2 in a "non-COVID-19" hospital ward unveiled by massive testing, which challenged the reconstruction of transmission chains. The contacts network during the 15-day period before the screening was investigated, and positive SARS-CoV-2 RNA samples were subjected to virus genome sequencing. Of the 245 tested individuals, 48 (21 patients and 27 HCWs) tested positive for SARS-CoV-2. HCWs were mostly asymptomatic, but the mortality among patients reached 57.1% (12/21). Phylogenetic reconstruction revealed that all cases were part of the same transmission chain. By combining contact tracing and genomic data, including analysis of emerging minor variants, we unveiled a scenario of silent SARS-CoV-2 dissemination, mostly driven by the close contact within the HCWs group and between HCWs and patients. This investigation triggered enhanced prevention and control measures, leading to more timely detection and containment of novel outbreaks. This study shows the benefit of combining genomic and epidemiological data for disclosing complex nosocomial outbreaks, and provides valuable data to prevent transmission of COVID-19 in healthcare facilities.

Keywords: COVID-19; SARS-CoV-2; contact tracing; genome sequencing; healthcare institution; nosocomial outbreak.

Figure 1

Timeline of events during the SARS-CoV-2 nosocomial outbreak. The figure summarizes the main events occurring during the study period, in which day 1 corresponds to the first day of the 15-day period before the large screening. It depicts the day of hospital admission (●), rooms transfer, sample collection for the last negative SARS-CoV-2 test (green), sample collection for the first positive test (pink), transfer to the COVID-19 ward (dark blue) and clinical outcome (death (black), hospital discharge (orange)) for each of the 21 infected patients. The patient numbers are colored according to the phylogenetic reconstruction (as in Figure 2A), where numbers colored in grey indicate samples for which virus genome data could not be obtained. To facilitate the identification of patient-to-patient contact, patient timelines (rows in the figure) are grouped by room (identified by capital letters, see Figure S1). The hospitalization days are highlighted in light blue and the room numbers are indicated on the day a given patient was transferred to that room (the room stay extends until a new transfer appears on the timeline). With the exception of patient 35 (Ward A), all patients and room numbers are relative to Ward B. The presence in other hospital areas is also indicated when relevant (Hemodialysis (Ꚛ), Emergency department (‡)). The date of sample collection for healthcare workers (HCWs) testing positive is also presented at the bottom. The timeline presented starts two weeks before the large test screening and extends until the date of sample collection of the last outbreak-related positive case. Light grey fields (on both sides of the timeline) are included to show events occurring outside the study timeline. (†) List of HCWs with a positive test on large screening: 1,2,4,5,11,13,14,17,18,22,24,27,28,29,31,33 and 40 (no sequencing data). (*), Patient admission before study period; (**), Patient admission and last negative test before the study period.

Figure 2

Combined genomic and epidemiological investigation of a SARS-CoV-2 nosocomial outbreak. (A) Maximum likelihood phylogenetic tree of SARS-CoV-2 genome sequences analyzed during the investigation of SARS-CoV-2 positive cases detected in a hospital ward in August 2020, Portugal. The tree includes viral consensus sequences obtained from 22 out of the 27 infected health-care workers (HCWs) and 17 out of 21 infected patients (colored nodes). To provide better phylogenetic context, the two closest sequences of the outbreak SARS-CoV-2 variant detected in Portugal (Portugal/PT1550/2020, collected in 21 June 2020, and Portugal/PT1614/2020, collected on 8 July 2020; https://insaflu.insa.pt/covid19/; as of 9 November 2020) and the SARS-CoV-2 reference genome sequence (used as root; Wuhan-Hu-1/2019; MN908947.3) were also included. Bar graphs next to the tree depict the within-patient frequency fluctuation of three SNP phylogenetic markers (also highlighted in the respective branch) that were detected either as minor variants (<50% in frequency) or as (nearly-)fixed variants in viral populations collected from distinct infected individuals (bars are colored according to the phylogenetic placement of the respective SARS-CoV-2 consensus sequences). The SNP profile of the outbreak-related SARS-CoV-2 is provided in Supplementary Table S2. (B) HCW-patient contacts occurring during the 15-day period before the large screening. HCW and patient codes are colored according to the phylogenetic placement of the respective SARS-CoV-2 consensus sequences (panel A), with exception of those without SARS-CoV-2 genome data (gray numbers in white fields). The “contact tracing matrix” summarizes the visits of infected HCWs to patient’s rooms (more details about the timeline of the visits is provided in Figure S1) (colored fields). Fields are colored according to virus sequence similarity between HCW and patients, as follows: (i) if a given HCW visited a room with a patient with the identical viral consensus sequence (i.e., same genetic profile), the field is colored according to the genetic profile (as in panel A) (high likelihood of direct transmission); (ii) if the contact involved ascendent/descendent genetic profiles (plausible transmission) and there was no other contact with an individual with an identical virus genetic profile, the field is colored in black with a colored arrow indicating the potential direction of transmission; (iii) if the contact HCW-patient is not supported by viral genetic evidence (implausible transmission), the fields are colored in gray. HD, hemodialysis. N, patients testing negative for SARS-CoV-2; Underlined patient number means that the patient stayed in different rooms during the study period.