Table 1. Primers and probes used in this study.

Name*	Sequence (5’–3’)	Amplicon length, bp	Subgroup	Purpose
ALVAF	GCCACACGGTTCCTCCTTAGA	114	ALV A	Multiplex primer
ALVAR	CGCAGTACTCACTCCCCATGAA	114	ALV A	Multiplex primer
APL	(5R6G)TACGGTGG(dT-BHQ1)GACAGCGGATAG-P		ALV A	Multiplex probe
ALBF1	GGCCGAGGCCTCCCCGAAA	77	ALV B	Multiplex primer
ALVBR	GTCTCATTAATTTCCTTTGATTGA	77	ALV B	Multiplex primer
BPL1G	(Cy5)CCCATGTACC(dT-BHQ2)CCCGTGCCTTG-P		ALV B	Multiplex probe
JFF1F	GCCCTGGGAAGGTGAGCAAGA	139	ALV J	Multiplex primer
JJR	GGAAATAATAACCACGCACACGA	139	ALV J	Multiplex primer
JNP	(ROX)TCCTCTCGA(dT-BHQ2)GGCAGCAAGGGTGTC-P		ALV J	Multiplex probe
JJPLN	(ROX)CAGCA AGGGTG(dT-BHQ2)CTTCTCCG-P		ALV J	Multiplex probe
ALVKF	CGGAGCATTGACAAGCTTTCAGA	72	ALV K	Multiplex primer
ALVKR	GTGATTGCGGCGGAGGAGGA	72	ALV K	Multiplex primer
KPL	(Cy5.5)CCACCTCGTGAG(dT-BHQ2)TGCGGCC-P		ALV K	Multiplex probe
ALV-JNF [9]	TTGCAGGCATTTCTGACTGG	214	ALV J	Published primer
ALV-JNR [9]	ACACGTTTCCTGGTTGTTGC	214	ALV J	Published primer
JCP [9]	(FAM)CCTGGGAAGGTGAGCAAGAAGGA-BHQ1		ALV J	Published probe
H5 [10, 11]	GGATGAGGTGACTAAGAAAG	545	ALV J	Published primer
H7 [10, 11]	CGAACCAAAGGTAACACACG	545	ALV J	Published primer
Probe [10, 11]	(FAM)CTCTTTGCAGGCATTTCTGACTGGGC(TAMRA)		ALV J	Published probe
SEQA-KR	CGCGATCCCCACAAATGAGGAAA	443	ALV A	Sequencing primer
SEQA-KR	CGCGATCCCCACAAATGAGGAAA	253	ALV B	Sequencing primer
SEQJF	CCCTGGGAAGGTGAGCAAGAA	498	ALV J	Sequencing primer
SEQJR	CCTTTATAGCACACCGAACCGAA	498	ALV J	Sequencing primer
SEQA-KR	CGCGATCCCCACAAATGAGGAAA	466	ALV K	Sequencing primer
JEF	CCTATTCAAGTTGCCTCTGTGGA	72	ALV J	LTR primer
JER	GCTTGCTCTATTTGGCCGTCAGA	72	ALV J	LTR primer
JEP	(Cy5)CCATCCGAGC(dT-BHQ2)GCCTCCAGTCC-P		ALV J	LTR probe

*References provided for previously published primers