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. 2021 Jul;83(1):96-103.
doi: 10.1016/j.jinf.2021.04.020. Epub 2021 Apr 22.

Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - A high risk community-hospital interface

Kathy K Li  1 , Y Mun Woo  2 , Oliver Stirrup  3 , Joseph Hughes  1 , Antonia Ho  1 , Ana Da Silva Filipe  1 , Natasha Johnson  1 , Katherine Smollett  1 , Daniel Mair  1 , Stephen Carmichael  1 , Lily Tong  1 , Jenna Nichols  1 , Elihu Aranday-Cortes  1 , Kirstyn Brunker  1 , Yasmin A Parr  1 , Kyriaki Nomikou  1 , Sarah E McDonald  1 , Marc Niebel  1 , Patawee Asamaphan  1 , Vattipally B Sreenu  1 , David L Robertson  1 , Aislynn Taggart  1 , Natasha Jesudason  1 , Rajiv Shah  1 , James Shepherd  1 , Josh Singer  1 , Alison H M Taylor  4 , Zoe Cousland  4 , Jonathan Price  4 , Jennifer S Lees  5 , Timothy P W Jones  6 , Carlos Varon Lopez  7 , Alasdair MacLean  8 , Igor Starinskij  8 , Rory Gunson  8 , Scott T W Morris  2 , Peter C Thomson  2 , Colin C Geddes  2 , Jamie P Traynor  2 , Judith Breuer  9 , Emma C Thomson  10 , Patrick B Mark  11 ; COVID-19 Genomics UK (COG-UK) consortium  12
Affiliations

Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - A high risk community-hospital interface

Kathy K Li et al. J Infect. 2021 Jul.

Abstract

Objectives: Patients requiring haemodialysis are at increased risk of serious illness with SARS-CoV-2 infection. To improve the understanding of transmission risks in six Scottish renal dialysis units, we utilised the rapid whole-genome sequencing data generated by the COG-UK consortium.

Methods: We combined geographical, temporal and genomic sequence data from the community and hospital to estimate the probability of infection originating from within the dialysis unit, the hospital or the community using Bayesian statistical modelling and compared these results to the details of epidemiological investigations.

Results: Of 671 patients, 60 (8.9%) became infected with SARS-CoV-2, of whom 16 (27%) died. Within-unit and community transmission were both evident and an instance of transmission from the wider hospital setting was also demonstrated.

Conclusions: Near-real-time SARS-CoV-2 sequencing data can facilitate tailored infection prevention and control measures, which can be targeted at reducing risk in these settings.

Keywords: COVID-19; Haemodialysis; Infection control; Nosocomial; Outbreak; Rapid sequencing; Renal dialysis unit; SARS-CoV-2.

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Conflict of interest statement

Declaration of interests The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Cumulative cases of COVID-19 cases (left y-axis) with arrows demonstrating additional infection control measures (narrow arrow - RDU1, wide arrow covers the dates for all other RDUs). Cumulative infection numbers for Scotland are on the right y-axis.
Fig. 2
Fig. 2
Phylogenetic tree showing the relationship of 39 sequences from RDU patients and additional SARS-CoV-2 genomes from Scotland. Sequences are colour-coded by RDU location. Dashed boxes highlight the UK lineage and are shown in more detail in Fig. 3. The numerical suffixes of the CVR identifier indicate the posterior probability (as a percentage) of the patient acquiring SARS-CoV-2 from the RDU (p_RDU) or from the wider hospital where dialysis takes place (p_hRDU). The scale bar indicates substitutions per nucleotide site.
Fig. 3
Fig. 3
Timeline of detection of first SARS-CoV-2 positive results in haemodialysis patients in RDUs with details of dialysis sessions and shared patient transport in relation to the UK lineage. The phylogenetic trees are derived from the dashed boxes in Fig. 2. Circled numbers in the phylogenetic tree represent the number of indistinguishable sequences from Scotland for the given node on the phylogeny. The numerical suffixes of the CVR identifier indicate the posterior probability (as a percentage) of the patient acquiring SARS-CoV2 from the RDU or from another healthcare-related infection (i.e., hospital where dialysis takes place and ward and/or hospital they have been admitted to), respectively. The scale bar indicates substitutions per nucleotide site.
See this image and copyright information in PMC

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