Surface and Air Contamination With Severe Acute Respiratory Syndrome Coronavirus 2 From Hospitalized Coronavirus Disease 2019 Patients in Toronto, Canada, March-May 2020

Abstract

Background: We determined the burden of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in air and on surfaces in rooms of patients hospitalized with coronavirus disease 2019 (COVID-19) and investigated patient characteristics associated with SARS-CoV-2 environmental contamination.

Methods: Nasopharyngeal swabs, surface, and air samples were collected from the rooms of 78 inpatients with COVID-19 at 6 acute care hospitals in Toronto from March to May 2020. Samples were tested for SARS-CoV-2 ribonucleic acid (RNA), cultured to determine potential infectivity, and whole viral genomes were sequenced. Association between patient factors and detection of SARS-CoV-2 RNA in surface samples were investigated.

Results: Severe acute respiratory syndrome coronavirus 2 RNA was detected from surfaces (125 of 474 samples; 42 of 78 patients) and air (3 of 146 samples; 3 of 45 patients); 17% (6 of 36) of surface samples from 3 patients yielded viable virus. Viral sequences from nasopharyngeal and surface samples clustered by patient. Multivariable analysis indicated hypoxia at admission, polymerase chain reaction-positive nasopharyngeal swab (cycle threshold of ≤30) on or after surface sampling date, higher Charlson comorbidity score, and shorter time from onset of illness to sampling date were significantly associated with detection of SARS-CoV-2 RNA in surface samples.

Conclusions: The infrequent recovery of infectious SARS-CoV-2 virus from the environment suggests that the risk to healthcare workers from air and near-patient surfaces in acute care hospital wards is likely limited.

Keywords: COVID-19; SARS-CoV-2; aerosol; contamination; surface.

Figure 1.

Boxplot summary of the cycle threshold values for the untranslated region (UTR) gene (blue) and E gene (orange) targets from the severe acute respiratory syndrome coronavirus 2 polymerase chain reaction analysis for each sample type investigated for 78 coronavirus disease 2019-positive patients in Toronto, Canada. It is notable that air sampling pumps were calibrated to a flow rate of 3.5 L/minutes for 2 hours; each air sample represents 420 liters of air.

Figure 2.

Virus isolation results from 110 nasopharyngeal swabs and 36 surface samples in relation to polymerase chain reaction cycle threshold value and time since symptom onset. CPE, cytopathic effect.

Figure 3.

Phylogenetic tree of 15 severe acute respiratory syndrome coronavirus 2 genomes from inpatients’ nasopharyngeal swabs and environmental surface swabs from 10 patients’ rooms. Augur pipeline from Nextstain was used to build the phylogenetic tree based on the IQTREE method. The root of the tree is obtained with the first isolate from Wuhan-Hu-1 referenced MN908947.3 in National Center for Biotechnology Information. The tree is refined using RAxML.