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Nosocomial outbreak of SARS-CoV-2 in a ‘non-COVID-19’ hospital ward: virus genome sequencing as a key tool to understand cryptic transmission

Our take —

This study, available as a preprint and thus not yet peer-reviewed, investigated a COVID-19 outbreak in two wards in a large hospital in Portugal. Large scale testing was initiated after a recently discharged patient presented to the emergency department and tested positive for COVID-19. This individual was also a close contact of a current inpatient in the hospital within a non-COVID-19 ward. In total, 27 out of 102 staff (26.4%) and 21 out of 92 (22.8%) inpatients in the single non-COVID-19 ward of interest tested positive. Whole-genome sequencing and bioinformatics analysis determined that cases were part of a single origin SARS-CoV-2 variant, belonging to the COG-UK lineage B.1.1 and Nextstrain clade 20B. Most individuals were asymptomatic during the time of testing, suggesting likely silent transmission. The findings highlight the importance of periodic testing of staff and patients in healthcare settings for earlier detection of cases, and prevention and control of outbreaks.

Study design


Study population and setting

This study investigated a COVID-19 outbreak in a large hospital in Portugal, which provides care to about 250,000 people and has about 1,500 employees. An outbreak took place in a non-COVID-19 ward (Ward B) in Summer 2020. The investigation was triggered following presentation to the emergency department by an individual who had concluded a hospital stay three days prior in another ward (Ward A). This individual was a close contact of a current inpatient in the non-COVID-19 ward (Ward B). The inpatient and a clinician (from Ward B) presented with COVID-19 like symptoms and subsequently tested positive, triggering further testing of close contacts, or persons presenting with symptoms in both wards in the 15 days prior. In total, 245 staff and patients were tested for SARS-CoV-2. Nasal and oropharyngeal swabs were collected, and RT-PCR was performed. RNA samples that were positive for SARS-CoV-2 were sent for whole-genome sequencing and bioinformatics analysis.

Summary of Main Findings

No cases were detected among 51 persons tested in Ward A. However, in Ward B, 27 out of 102 staff (26.4%) and 21 out of 92 (22.8%) inpatients tested positive. Most staff were asymptomatic at testing and all recovered. While inpatients were mostly asymptomatic at testing, mortality rate was high, 12 out of 21 died (57.1%). Results of high-quality SARS-CoV-2 genome sequences from 39 positive samples (22 staff and 17 patients) showed that all cases were part of a single origin, belonging to the COG-UK lineage B.1.1 and Nextstrain clade 20B, with spike amino acid changes D614G and L176F. The investigators hypothesized that the virus was likely introduced to the ward a few weeks before the large screening, then spread through interactions among health care workers, and interactions between health care workers and patients. Patient-to-patient transmission was very limited. Following the investigation, the hospital put in place and reinforced stricter infection prevention and control measures.

Study Strengths

Use of reverse-transcription PCR testing to confirm COVID-19 diagnosis. Genome sequences associated with the outbreak had >88% of the genome covered by at least 10-fold.


While investigators hypothesized about which health care workers and patients could have been the index case given the epidemiologic and phylogenetic data, this could not be definitively determined.

Value added

This study highlights the usefulness of combining epidemiologic and genomic data in improving understanding about transmission of SARS-CoV-2.

This review was posted on: 23 April 2021