TABLE 1.

List of clinical samples containing more than one PRRSV strain (coinfection) and of strains that are classified differently by WGS than the ORF5 method

Sample ID no.	Type of sample	Virus whole-genome sequencing characteristic	Effect on PRRSV classification
1898026	Serum	Coinfectiona	Both strains clustered in different lineages
1952821	Pool of tissues	Coinfection	Both strains clustered differently in the same lineage
1968868	Serum	Coinfection	Both strains clustered differently in the same lineage
2153073	Serum	Coinfection	Both strains clustered in different lineages
1425619	Lung	Recombinantb	Strain clustered differently in the same lineage, unlike ORF5 method
1890826 #2c	Serum	Recombinant	Strain clustered in a different lineage, unlike ORF5 method
1927781	Serum	Recombinant	Strain clustered differently in the same lineage, unlike ORF5 method
1952821 #1	Pool of tissues	Recombinant	Strain clustered in a different lineage than that of ORF5 method
2072533	Serum	Recombinant	Strain clustered in a different lineage than that of ORF5 method
2087409	Lung	Recombinant	Strain clustered differently in the same lineage compared to ORF5 method

^aAt least two PRRSV different strains were identified in the same clinical sample and possessed a nucleotide identity of <96%.

^bPRRSV recombinant status was assigned when a strain clustered more than two nodes away in phylogenetic trees based on PRRSV whole-genome analysis compared to the ORF5 classification method.

^cThe number after the sample identification (ID) number represents one of the two PRRSV strains that was identified within the same clinical sample.