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

Li, Kathy K.; Woo, Yeonhee; Stirrup, Oliver; Hughes, Joseph; Ho, Antonia; Filipe, Ana da Silva; Johnson, Natasha; Smollett, Katherine; Mair, Daniel; Carmichael, Stephen; Tong, L.; Nichols, Jenna; Aranday-Cortés, Elihú; Brunker, Kirstyn; Parr, Yasmin A.; Nomikou, Kyriaki; McDonald, Sarah E.; Niebel, Marc; Asamaphan, Patawee; Sreenu, Vattipally B; Robertson, David L.; Taggart, Aislynn; Jesudason, Natasha; Shah, Rajiv; Shepherd, James G.; Singer, Josh; Taylor, Alison; Cousland, Zoe; Price, Jonathan; Lees, Jennifer S; Jones, Timothy Peter; Lopez, Carlos Varon; Maclean, Alasdair; Starinskij, Igor; Gunson, Rory; Morris, Scott; Thomson, Peter; Geddes, Colin C.; Traynor, Jamie P.; Breuer, Judith; Thomson, Emma C.; Mark, Patrick B.

doi:10.1016/j.jinf.2021.04.020

Cited by 12 publications

(9 citation statements)

References 34 publications

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“…[ 7 , 11 ]), been used to support contact tracing and outbreak control (e.g. [ 3 , 9 ]), and enabled the discovery and surveillance of variants of concern (e.g. [ 2 , 13 , 17 ]) or other lineages of virological or epidemiological interest.…”

Section: Introductionmentioning

confidence: 99%

Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences

et al. 2022

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Background More than 2 million SARS-CoV-2 genome sequences have been generated and shared since the start of the COVID-19 pandemic and constitute a vital information source that informs outbreak control, disease surveillance, and public health policy. The Pango dynamic nomenclature is a popular system for classifying and naming genetically-distinct lineages of SARS-CoV-2, including variants of concern, and is based on the analysis of complete or near-complete virus genomes. However, for several reasons, nucleotide sequences may be generated that cover only the spike gene of SARS-CoV-2. It is therefore important to understand how much information about Pango lineage status is contained in spike-only nucleotide sequences. Here we explore how Pango lineages might be reliably designated and assigned to spike-only nucleotide sequences. We survey the genetic diversity of such sequences, and investigate the information they contain about Pango lineage status. Results Although many lineages, including the main variants of concern, can be identified clearly using spike-only sequences, some spike-only sequences are shared among tens or hundreds of Pango lineages. To facilitate the classification of SARS-CoV-2 lineages using subgenomic sequences we introduce the notion of designating such sequences to a “lineage set”, which represents the range of Pango lineages that are consistent with the observed mutations in a given spike sequence. Conclusions We find that many lineages, including the main variants-of-concern, can be reliably identified by spike alone and we define lineage-sets to represent the lineage precision that can be achieved using spike-only nucleotide sequences. These data provide a foundation for the development of software tools that can assign newly-generated spike nucleotide sequences to Pango lineage sets.

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Section: Introductionmentioning

confidence: 99%

Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences

et al. 2022

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“…The COVID-19 pandemic has posed a major challenge to the safety of patients undergoing in-centre haemodialysis (ICHD) treatment, as well as to the organization of services provided by renal centres. Although regarded as clinically extremely vulnerable, patients on ICHD were not able to shield during the pandemic, because of their 470 DOI: 10.1159/000523731 need to visit hospital regularly for their life-sustaining treatment [1,2].…”

Section: Introductionmentioning

confidence: 99%

Comparison of Outcomes of In-Centre Haemodialysis Patients between the 1st and 2nd COVID-19 Outbreak in England, Wales, and Northern Ireland: A UK Renal Registry Analysis

Savino

Santhakumaran

Currie

et al. 2022

Nephron

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Introduction: This retrospective cohort study compares in-centre haemodialysis (ICHD) patients’ outcomes between the 1st and 2nd waves of the COVID-19 pandemic in England, Wales, and Northern Ireland. Methods: All people aged ≥18 years receiving ICHD at 31 December 2019, who were still alive and not in receipt of a kidney transplant at 1 March and who had a positive polymerase chain reaction test for SARS-CoV-2 between 1 March 2020 and 31 January 2021, were included. The COVID-19 infections were split into two “waves”: wave 1 from March to August 2020 and wave 2 from September 2020 to January 2021. Cumulative incidence of COVID-19, multivariable Cox models for risk of positivity, median, and 95% credible interval of reproduction number in dialysis units were calculated separately for wave 1 and wave 2. Survival and hazard ratios for mortality were described with age- and sex-adjusted Kaplan-Meier plots and multivariable Cox proportional models. Results: 4,408 ICHD patients had COVID-19 during the study period. Unadjusted survival at 28 days was similar in both waves (wave 1 75.6% [95% confidence interval [CI]: 73.7–77.5], wave 2 76.3% [95% CI 74.3–78.2]), but death occurred more rapidly after detected infection in wave 1. Long vintage treatment and not being on the transplant waiting list were associated with higher mortality in both waves. Conclusions: Risk of death of patients on ICHD treatment with COVID-19 remained unchanged between the first and second outbreaks. This highlights that this vulnerable patient group needs to be prioritized for interventions to prevent severe COVID-19, including vaccination, and the implementation of measures to reduce the risk of transmission alone is not sufficient.

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“…The battle against coronavirus disease 2019 (COVID-19) remains the biggest challenge in controlling the spread of the disease globally. In this Journal, the report by Li and colleagues highlighted the danger to renal dialysis patients in the COVID-19 pandemic ( 1 ). Using the whole-genome sequencing and epidemiological data, the author demonstrated that the risk of SARS-CoV-2 transmission was present in the community and the hospital setting.…”

mentioning

confidence: 99%

SARS-CoV2 antibody response after a third dose of heterologous ChAdOx1 nCoV-19 and Moderna vaccine in chronic dialysis patients

Cheng

Hsiao

Fang

et al. 2022

Journal of Infection

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

Cited by 12 publications

References 34 publications

Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences

Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences

Comparison of Outcomes of In-Centre Haemodialysis Patients between the 1st and 2nd COVID-19 Outbreak in England, Wales, and Northern Ireland: A UK Renal Registry Analysis

SARS-CoV2 antibody response after a third dose of heterologous ChAdOx1 nCoV-19 and Moderna vaccine in chronic dialysis patients

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