Table 3.

Differentially expressed miRNAs and common differentially expressed genes (predicted) to be targeted. Differentially expressed miRNAs were determined by adjusting the p-value < 0.05 and log 2 fold change >|1|. “Upregulated” refers to miRNAs upregulated during viremia compared to pre-challenge infection and “downregulated” refers to miRNAs downregulated during viremia compared to pre-challenge infection. Predicted genes to be targeted by miRNAs during viremia include only genes to be found significantly differentially regulated in our gene expression analysis (see also Table A1). A significant upregulation during viremia of those genes is indicated by ↑ and a significant downregulation is indicated by ↓.

ID	Log2 Fold	Padj	MirBase ID	Human Ortholog	Mature Sequence	Precursor Sequence	Differentially Expressed Gene Targets
	Upregulated miRNAs
Equine_chr11_2567	1.2	3.5 × 10−8	eca-miR-9104		CTGACCTGAGGCCTCTGCTGCA	GAGTGGCTGGGCTCAGCAGGGCGGAGGGTCAGGAGGTGAGCTTGGCTCTGCTGACCTGAGGCCTCTGCTGCA
Equine_chrX_44985	1.1	1.3 × 10−17	eca-miR-652	hsa-miR-652-3p	AATGGCGCCACTAGGGTTG	CAACCCTAGGAGAGGGTGCCATTCACATAGACTATAATTGAATGGCGCCACTAGGGTTG	TNRC6A↓, NPTN↑, KPNA1↓, TP53↑
Equine_chrX_45803	1.1	2.0 × 10−3	eca-miR-2483		TCTGTCAACCATCCAGCTGTTT	TCTGTCAACCATCCAGCTGTTTGGGGTGATGCAAACAAACATCTAGTTGGTTGAGAGAAT
	Downregulated miRNAs
Equine_chr15_10631	−1	1.4 × 10−2	-	hsa-miR-6852-5p	ACCTGGGGATCTGAGGAG	ACCTGGGGATCTGAGGAGGCCCTTCCAGCCCCAAGGCTGGGAATGCTCCTGGTCCCCTTTCTTGC	IFIT5↑, Mx2↑, OAS3↑, OAS2↑, CCL8↑, BCL2LI4↑, MPZ↑, TGM2↑, HSDIIB1↑ FN1↓, DEFB1↓
EHV-2_38	−1	1.0 × 10−2	-		TATGATAGTCCATACCCTTAAGT	TATGATAGTCCATACCCTTAAGTTTGATAAGTAAAAAATTTAAGTACGTGGACTGTCAACA