Table 1. Primers and probes designed and validated in this study.

Serotype		Sequence*	Target region	Accession No.	Position	Size (bp)	Limit of detection (fg)	Concentration (nM)
6CD	Forward	CAATCAGGCAGTTCTTTTCTCG	wciNbeta	EF538714	7319–7340	133	5	500
	Reverse	ACCTGACTCACCATCAATAACC			7430–7451			500
	Probe	AAATGGGAGGGCTTTGGATTGGC			7341–7363			200
7BC/40	Forward	TCCAGATATAGTCATTCCCAATCAG	wcxU	CR931641	10720–10744	147	50	400
	Reverse	AAAGAAGGTAAATCCCATGATGAATT			10841–10866			400
	Probe	TGGTGGGTCAGTAATCGATAATGAGGGA			10798–10825			200
7C	Forward	AGTTTGAGCATAACGGAGCG	wchF	CR931642	7010–7029	132	5	200
	Reverse	GAGCTTCATCCTTATTTTCCTTAGC			7117–7141			200
	Probe	CTCGAGCTGGACCAATATTCGGAACAT			7046–7072			200
9LN	Forward	CGTGGAATTTTCTATACTGCAATAGG	wzx	CR931646	11762–11787	115	5	500
	Reverse	CTACTGCTACGATACCATATTCTACAG			11850–11876			500
	Probe	CAGCAATTCTTAGCCGGATTCTCTCACC			11823–11850			200
10A	Forward	AGAGGCCCTAAGAAAAGATTCG	wcrD	CR931649	10268–10289	137	5	400
	Reverse	CCCAGTCATCCCCATCAATAAC			10383–10404			400
	Probe	TGTTGAGCCATGACCTCCATTTTCCT			10315–10340			200
10B	Forward	AAATATGAGATTGGTAAGGAATATTCTGG	wcrD	CR931650	10237–10265	116	5	400
	Reverse	GTCTTTTCACTTAAACGAATTCCATTC			10326–10352			400
	Probe	AACGGATTCCAATGCACTCGGTAACT			10277–10302			200
11F	Forward	TGGTCCAGCTACTTTTATGGC	wchK	CR931657	7485–7505	93	5	400
	Reverse	TGATCATTCACATGCTCCCC			7558–7577			400
	Probe	ACTCCAATAGTTGTTCCGAGGCAAAAGA			7525–7552			200
12B	Forward	TTGGTTGCTGATCAAAAGGTC	wzx	CR931659	13259–13279	228	5	600
	Reverse	CATTTTTGGAAGTGGAGCTATC			13465–13486			600
	Probe	TCACTTTGATGATTTGGAAAGATTTT			13338–13363			400
13	Forward	AGACTACCATTTTTTGATCAGTTAGATT	wzy	CR931661	13163–13190	136	5	500
	Reverse	CAGAAAACATATTTTGTTCATAAATCCATC			13269–13298			500
	Probe	AAGCAGCACTTCCAAGTCGTAATCTACC			13202–13229			300
19“F”	Forward	GTCCTTAGTTCTGGTTATTCGGG	wzy	FJ829071	364–386	106	5	400
	Reverse	GGATGAGGAACCGAATCGAAG			449–469			400
	Probe	CCAGTTATGAAGGTGAGCTAACAGTGCG			419–446			300
24A	Forward	CTTGGAGTTGCTAATTATGGGAAG	wzx	CR931686	15526–15549	120	5	300
	Reverse	ATCTCTTACACGTGCACACTC			15625–15645			300
	Probe	CTGCGGGTATTTTACGATATGCTGTGCG			15596–15623			200
25AF	Forward	ATACCAACTAGAATCAGCAGGAC	wcyE	CR931689	16881–16903	128	5	400
	Reverse	AAATGGAATATCTTTTGATAATTTACTCGC			16979–17008			400
	Probe	CCCGCTGGACTTACTGCAATACTCG			16949–16973			200
27	Forward	AGCGATTTAGCGACTGATATCC	whaK	CR931691	7805–7826	79	50	400
	Reverse	TCTCAAAATCGATCTCGCGTG			7863–7883			400
	Probe	TGTGGAAGGCGTTTGAAGGTGACT			7839–7862			200
31	Forward	GCAGAAGTTTTAAGTCACGGAC	wzy	CR931695	9303–9324	146	5	500
	Reverse	AGCATTACAGATGTCACTAAGGG			9426–9448			500
	Probe	CCCCCACGTAAAACCGCAAGG			9395–9415			200
33B	Forward	CCTGTTAGTGCACCTGTATTTAAC	wciN	CR931699	7069–7092	146	5	500
	Reverse	GCATTCAAAACTCCTTCATCTCC			7192–7214			500
	Probe	TCCTCGATTCGTTGTTCACGCCA			7123–7145			200
33D	Forward	CGTATAGTCTTGCGACATTTCA	wciN	CR931701	7325–7346	81	5	400
	Reverse	TTCCACATGCGTTACCTCAC			7386–7405			400
	Probe	TCAAAAAGACCTTGGCAAGAAAGT			7361–7384			200
34	Forward	CGGTGGAGTAGGTCAAGATG	wzy	CR931703	8096–8115	144	5	300
	Reverse	GTCTGTTCTCCCCAATATACTGAG			8216–8239			300
	Probe	ACGGAGCGCCAATGTACTTGAATAGTT			8140–8166			200
35AC/42	Forward	GCTTCCCCTTTAGACTATTCGG	wcrK	CR931704	11012–11033	108	5	400
	Reverse	AAATGAAATCAAAGTATCACGTATCGA			11093–11119			400
	Probe	TTCAAAATACCCAGGACACCCGTTCA			11062–11087			200
35F/47F	Forward	GTGGTCGTATATACTTGATGAATAAATCG	wzy	CR931707	7694–7722	145	5	400
	Reverse	ACATACAAATTATCAACATACAGATAGGTC			7809–7838			400
	Probe	TCCATTCAACTGGTCGTCCGAATAATCC			7741–7768			200
36	Forward	CTTGTCTATTCAGCCCTTCTGG	wzy	CR931708	13287–13308	148	5	500
	Reverse	CGCGATTATATTGTAAATTGGGAACT			13409–13434			500
	Probe	TGCCCGCTACAATGAGATACGTTTTCAA			13341–13368			200
39	Forward	CAAAAAAATGAACTAACTCAAATAGTAACG	wcrG	CR931711	12614–12643	143	5	300
	Reverse	ATACTGTAATTTTCTTGTTTATTTGCGG			12729–12756			300
	Probe	AAGTCAGGCGTATTCTTCACAAGGGAAA			12644–12671			200
41A	Forward	GCAAATAGATGTATCCCAGTTAACAC	wciB	CR931713	7130–7155	114	50	300
	Reverse	GGTAGCTCTTTTGGTTTAATGTCC			7220–7243			300
	Probe	CACGACCGAATAGTCTAGCTTCAAAGGG			7155–7182			200
41F	Forward	TTTTTGGGAGGAAGTGCTTTT	wzx	CR931714	14008–14028	134	5	500
	Reverse	AAAACCGCTTTCTCATGATTC			14121–14141			500
	Probe	TTTCTTCTGTGCTAACAGTGGAGA			14030–14053			200
43	Forward	AGAGGCTACATCAAATAGTTGGC	wzx	CR931716	16435–16457	150	5	400
	Reverse	GAATCACACCGTAACTTCCAAAG			16562–16584			400
	Probe	TCCAATAGTACTCACCCCTACCGAGC			16471–16496			200
45	Forward	TCTAGCTACTTGACTAAAATATTTGAACTG	wzy	CR931718	13743–13772	88	50	400
	Reverse	GACGAGTCGATTTCGCTGTAT			13810–13830			400
	Probe	TAGGGAGCGAGGTCACTAAAAGTCGT			13774–13799			200
46	Forward	CGAAGTTTTTATATCTCTATTGGTTTG	wzy	CR931719	9232–9258	133	50	1000
	Reverse	TATCCCAGGAACTGGACGAA			9345–9364			1000
	Probe	TCATTCTTTCTTCAATTCCTTTCTGA			9319–9344			500
47AF	Forward	AGGAATTGGTAGAGAGTTTGTGG	whaI	CR931721	8235–8257	121	50	400
	Reverse	GAAAGTTGAACCATCATCCGTC			8334–8355			400
	Probe	CACTTGATGGAATGCCTGCTGCC			8271–8293			200

*Probes were labeled at 5’ with FAM (6-carboxyfluorescein) and at 3’ with BHQ1 (Black Hole Quencher-1).