Evaluation of Screening Program and Phylogenetic Analysis of SARS-CoV-2 Infections among Hospital Healthcare Workers in Liège, Belgium

Abstract

Healthcare workers (HCWs) are known to be at higher risk of developing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections although whether these risks are equal across all occupational roles is uncertain. Identifying these risk factors and understand SARS-CoV-2 transmission pathways in healthcare settings are of high importance to achieve optimal protection measures. We aimed to investigate the implementation of a voluntary screening program for SARS-CoV-2 infections among hospital HCWs and to elucidate potential transmission pathways though phylogenetic analysis before the vaccination era. HCWs of the University Hospital of Liège, Belgium, were invited to participate in voluntary reverse transcriptase-polymerase chain reaction (RT-PCR) assays performed every week from April to December 2020. Phylogenetic analysis of SARS-CoV-2 genomes were performed for a subgroup of 45 HCWs. 5095 samples were collected from 703 HCWs. 212 test results were positive, 15 were indeterminate, and 4868 returned negative. 156 HCWs (22.2%) tested positive at least once during the study period. All SARS-CoV-2 test results returned negative for 547 HCWs (77.8%). Nurses (p < 0.05), paramedics (p < 0.05), and laboratory staff handling respiratory samples (p < 0.01) were at higher risk for being infected compared to the control non-patient facing group. Our phylogenetic analysis revealed that most positive samples corresponded to independent introduction events into the hospital. Our findings add to the growing evidence of differential risks of being infected among HCWs and support the need to implement appropriate protection measures based on each individual’s risk profile to guarantee the protection of both HCWs and patients. Furthermore, our phylogenetic investigations highlight that most positive samples correspond to distinct introduction events into the hospital.

Keywords: COVID-19; SARS-CoV-2; healthcare workers; healthcare-associated transmission; infection prevention and control; occupational exposure; phylogenetic analysis.

Figure 1

Study design. Among 846 consenting healthcare workers (HCWs) participants, 143 subjects were excluded from the study because they did not complete the requested questionnaire. Between April and December 2020, 5411 tests were performed in the 703 individuals included in the study. Among these tests, 316 were excluded for one of the following reasons: no results available (37 samples), duplicate tests (223 samples), ineligible sampling method (14 saliva samples), and two samples performed the same week for the same patient (42 samples). 212 SARS-CoV-2 reverse transcriptase-polymerase chain reaction (RT-PCR) assays were positive, 15 were indeterminate and 4868 returned negative. Of the 703 included subjects, 156 presented with at least one positive or indeterminate test result during the study period. For the remaining 547 participants, all SARS-CoV-2 tests were negative. Reprinted with permission from ref. [54].

Figure 2

(a) Evolution of the number of reverse transcriptase-polymerase chain reaction (RT-PCR) assays performed and their results over time; (b) SARS-CoV-2 RT-PCR positive results rates (%) over time.

Figure 3

Impact of the healthcare workers (HCWs) staff role on the risk of developing SARS-CoV-2 infection (at least one RT-PCR positive result). Odds ratio and 95% confidence intervals calculated by logistic regression when compared to control non-patients facing group (administrative staff and research scientists).

Figure 4

Time-scaled phylogeny in which we identified phylogenetic clades introduced in the University Hospital of Liège (Belgium) and delineated through a discrete phylogeographic reconstruction along the tree (while only considering two potential ancestral locations: “hospital” and “other location”). We identified a minimum of 35 introduction events into the hospital (95% highest posterior density interval = [36–38]) for 45 sequences sampled among healthcare workers (HCWs) from the hospital. On the phylogeny, large red nodes correspond to the most ancestral node of each clade resulting from an introduction event into the hospital. Most of these clades consist of only one sampled sequence: 30 (95% highest posterior density interval = [27–32]) out of 45 sequenced positive cases corresponded to independent introduction events into the hospital. In the figure, small red nodes correspond to sampled sequences that would not result from a distinct introduction event into the hospital. In other words, smaller red nodes are tip nodes belonging to clades gathering at least two sequences sampled among HCWs from the hospital. In the figure, smaller red nodes are tip nodes corresponding to sequences sampled among HCWs but that do not result from a distinct introduction event into the hospital. In other words, smaller red nodes correspond to clades gathering at least two sequences sampled among HCWs, and the phylogenetic branches of these clades are also highlighted in red. See Figure S1 for an alternative circular visualization of this annotated phylogenetic tree.