Table 2.

Sequencing and bioinformatics methods used in the long-term care facilities genomic epidemiology studies

	Location	Sample preparation method	Sequencing	Method of genome construction strategy	Software used to infer phylogenetic trees	Data availability*
Dautzenberg et al (2020)16	Southeast Netherlands	Amplicon	Nanopore	Consensus	NR	Not available
van den Besselaar et al (2021)17	South Holland	Amplicon	Nanopore	Consensus	IQ-TREE	Not available
Hamilton et al (2021)18	East of England, UK	Amplicon†	Nanopore or Illumina	Consensus	IQ-TREE and PhyML	Available but not linked
Page et al (2021)19	Norfolk, UK	Amplicon†	Illumina	Consensus	IQ-TREE	Available
Graham et al (2020)20	London	Amplicon†	Illumina	Reference-guided assembly	IQ-TREE	Not available
Ladhani et al (2020)21	London	Whole genome sequencing	Illumina	Consensus	IQ-TREE	Available but not linked
Lemieux et al (2020)23	Boston, MA, USA	Metagenomic	Illumina	Reference-guided assembly	IQ-TREE and Bayesian Evolutionary Analysis Sampling Trees	Available
Zhang et al (2020)24	CA, USA	Metagenomic	Illumina	Consensus	IQ-TREE	Available
Gallichote et al (2020)25	CO, USA	Amplicon†	Illumina	Consensus gap filled with reference	Geneious	Not available
Taylor et al (2020)26	MN, USA	Amplicon†	NR	NR	IQ-TREE	Available but not linked
Arons et al (2020)27	WA, USA	NR	Nanopore	Consensus	Geneious	Available

NR=not reported. The companies for the sequencing methods are: Nanopore, Oxford Nanopore Technologies, Oxford, UK, and Illumina, San Diego, CA, USA.

^*If data are present in the Global Initiative on Sharing Avian Influenza Data or the International Nucleotide Sequence Database Collaboration database they are labelled as available, and when there is no linkage information between the samples used in the article and the data in the public archives, they are labelled as not linked.

^†Amplicon sequencing uses the ARTIC protocol.²⁹