Squares indicate the extent to which an individual-to-individual transmission event is consistent with the data collected, when considered on a pairwise level. Our analysis highlighted multiple …
Assessment of pairwise transmission events.
Circles represent individuals and arrows show transmission events. White circles represent patients while grey circles represent health care workers. Individuals for which no transmission events …
Statistics were calculated across maximum likelihood network reconstructions. The great majority of patient infections were inferred to arise from other patients, while HCWs were infected roughly …
Data were compiled over sets of plausible reconstructions, weighted by likelihood. The width of each arrow is proportional to the probability that a specific transmission event occurred. Arrows are …
Posterior probabilities of transmission between individuals on each ward.
Circles represent individuals and arrows show transmission events. White circles represent patients while grey circles represent health care workers. Individuals for which no transmission events …
(A) Fit of the output of the Poisson model (black dots) to the ensemble data (yellow bars). The weighted number of transmissions per individual reflects the uncertainty in the network reconstruction …
Distributions of number of individuals infected by each individual and fits to these data using Poisson and Negative Binomial models.
(A) Fit of the output of a Poisson model (black dots) to the ensemble data (yellow bars). The weighted number of transmissions per individual reflects the uncertainty in the network reconstruction …
Distributions of number of individuals on green wards infected by each individual and fits to these data using Poisson and Negative Binomial models.
Distributions of known Ct values collected from all samples from the wards studied (yellow) and from individuals identified as superspreaders (grey). Samples from superspreaders were not …
(A) Maximum likelihood network of transmission events. (B) Maximum likelihood spread of infection given this network. (C) Distributions of the times at when transmission occurred were calculated …
Distributions of timings of transmission events on ward A.
(A) Maximum likelihood network of transmission events. (B) Maximum likelihood spread of infection given this network. Timings are shown relative to the first transmission event. Infection of the …
Distributions of timings of transmission events on ward B.
(A) Maximum likelihood network of transmission events. (B) Maximum likelihood spread of infection given this network. Timings are shown relative to the first transmission event. Infection of the …
Distributions of timings of transmission events on ward D.
Blue squares show days on which individuals became symptomatic, while green squares show inferred days of individuals becoming symptomatic when these dates were unknown or not applicable. Red …
Data were compiled over sets of plausible reconstructions, weighted by likelihood. The width of each arrow is proportional to the probability that a specific transmission event occurred. Arrows are …
Posterior probabilities of transmission between individuals on each ward inferred under a model in which no padding for HCW locations was included.
Data are shown only for wards in which the inference was different from the original.
(A) Fit of the output of a Poisson model (black dots) to the ensemble data (yellow bars). (B) Fit of the output of the negative binomial model (black dots) to the ensemble data (yellow bars). (C) …
Distributions of number of individuals on all wards infected by each individual, as inferred under a model in which no padding for HCW locations was included, alongside fits to these data using Poisson and Negative Binomial models.
(A) Case of the last transmission event. Transmission occurs from A to B at time tAB. Viral sequence data is collected from A at time DA and from B at time DB. Grey markers show points which may be …
Here sequences collected from the individuals B and C (i.e. in the set Ia) have the variant a, but no other sequences have this variant. Data from individual i was collected at time Di. We assume …
Comparisons of the number of infections per individual and the probabilities of specific edges being found in the transmission network for a ‘partial’ set of networks and for a more complete, ‘full’ …
Probabilities of transmission events between individuals inferred from data describing ward A calculated across partial and fuller sets of networks.
The values reported here show convergence in the model with the addition of further networks.
‘Total cases before network analysis’ were derived by adding patients with potential hospital-acquired COVID-19 infections and HCW cases from each ward. The five wards with the largest combined …
Ward name | Ward type | Total cases before network analysis | HAI cases before network analysis | HCW cases before network analysis | Cases after network analysis | Cases after network analysis with genomic data |
---|---|---|---|---|---|---|
A | Green | 14 | 12 | 2 | 16 | 15 |
B | Green | 11 | 2 | 9 | 15 | 12 |
C | Green | 12 | 5 | 7 | 20 | 19 |
D | Green | 14 | 4 | 10 | 16 | 16 |
E | Red | 13 | 3 | 10 | 47 | 39 |
GISAID sequence identifiers for the genomes used in this study.
COG-UK sequence identifiers for the genomes used in this study.