Genomic epidemiology of COVID-19 in care homes in the east of England

Abstract

COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, 1167 residents from 337 care homes were identified from a dataset of 6600 COVID-19 cases from the East of England. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data, 409 viral clusters within the 292 homes were identified, indicating two different patterns – outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission within care homes should be a key target for infection control to reduce COVID-19 mortality in this population.

SciScore for 10.1101/2020.08.26.20182279: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Software and Algorithms
Sentences	Resources
Samples were either sequenced on site using Oxford Nanopore Technologies or transported to the Wellcome Sanger Institute for Illumina sequencing.	Oxford Nanopore suggested: (Oxford Nanopore Technologies, RRID:SCR_003756)
Genomes were generated for each library’s sequencing data using bwa mem (Li, 2013) for alignment with MN908947.3 (Wu et al., 2020) as reference, samtools (Li et al., 2009) for pileup and ivar (Grubaugh et al., 2019) for trimming and consensus generation, all orchestrated by the ncov2019-artic-nf pipeline (Bull, 2020).	samtools suggested: (SAMTOOLS, RRID:SCR_002105)
21/23 of …

SciScore for 10.1101/2020.08.26.20182279: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

NIH rigor criteria are not applicable to paper type.

Table 2: Resources

Software and Algorithms
Sentences	Resources
Samples were either sequenced on site using Oxford Nanopore Technologies or transported to the Wellcome Sanger Institute for Illumina sequencing.	Oxford Nanopore suggested: (Oxford Nanopore Technologies, RRID:SCR_003756)
Genomes were generated for each library’s sequencing data using bwa mem (Li, 2013) for alignment with MN908947.3 (Wu et al., 2020) as reference, samtools (Li et al., 2009) for pileup and ivar (Grubaugh et al., 2019) for trimming and consensus generation, all orchestrated by the ncov2019-artic-nf pipeline (Bull, 2020).	samtools suggested: (SAMTOOLS, RRID:SCR_002105)
21/23 of these were tested on the SAMBA platform at CUH (Collier et al., 2020), which is not PCR-based; sequencing was not possible for these samples owing to rapid RNA degradation.	SAMBA suggested: (Samba, RRID:SCR_006557)
The 700 de-duplicated viral genomes from care home residents passing QC were aligned using MAFFT (v 7.458) (Katoh and Standley, 2013) with default settings.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
Phylogenetic trees were generated using IQ-TREE (v 1.6.12 built Aug 15 2019).	IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254)
A multiple sequence alignment was produced in MAFFT and phylogenetic tree produced using IQTREE, command line: iqtree -s alignment_all.aln -m GTR+F -nt AUTO -ntmax 16 -mem 16G -bb 1000 The tree was manipulated in FigTree (v 1.4.4) and Figure 6 supplement 1 was produced in R using the ggtree package as with Figure 6.	FigTree suggested: (FigTree, RRID:SCR_008515)
The resulting pairwise transmission probabilities were used to generate a pairwise distance matrix and clustering was performed using single linkage hierarchical clustering with the R hclust function.	hclust suggested: (HCLUST, RRID:SCR_009154)

Results from OddPub: Thank you for sharing your code and data.

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

There are several limitations to this study. First, not all of the COVID-19 cases from the East of England have been included. Serology data suggest that 10.5% of all residents in care homes for people aged 65 and older in England had been infected with SARS-CoV-2 by early June, the majority of whom were asymptomatic (UK government, 2020c). The Cambridge CMPHL did not receive all of the samples tested from the region; national data indicate around half of the COVID-19 cases reported from EoE during the study were included. Viral sequence data were not available for 40% of care home residents, as a result of missing samples, mismatches between sequences and metadata, genomes not passing quality control filtering using a stringent threshold (<10% missing calls), or sequences being unavailable at the time of data extraction. Viral cluster sizes may therefore be underestimated. Second, the nature of diagnostic testing sites changed during the study period as regional hospitals developed their own in-house testing capacity and community testing laboratories were set up. “Pillar 2” testing in the UK was outsourced to high-throughput laboratories during April 2020 and performed an increasing proportion of community testing. It is possible that some care home residents from the same care home could have been tested through different routes, with symptomatic cases more likely to be tested in “Pillar 1” via the CMPHL (and included in this dataset), and asymptomatic screening occurring ...

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from rtransparent:

Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
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No protocol registration statement was detected.

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Genomic epidemiology of COVID-19 in care homes in the east of England

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