TABLE 2.

Primer combinations targeting the RdRp region for human sapovirus detection

Primer or probe	Sequence (5′ to 3′)	Functiona	Location in sapovirus genome	Strain	Accession no.	Reference
Sapp36	GTT GCT GTT GGC ATT AAC A	Forward	4273–4291	Manchester	X86560	141
Sapp35	GCA GTG GGT TTG AGA CCA AAG	Reverse	4740–4760	BR-DF01	AB614356
4490	ACA CGT GGT GGT CTA CCA TCT GG	Forward	4510–4532	Manchester	X86560	143
4485	CAC ACT GTA CAT GCA RTC ATC ACC	Reverse	4666–4689	Manchester	X86560
p290	GAT TAC TCC AAG TGG GAC TCC AC	Forward	4354–4376	Manchester	X86560	144
p289	TGA CAA TGT AAT CAT CAC CAT A	Reverse	4663–4684	Manchester	X86560
SR80	TGG GAT TCT ACA CAA AAC CC	Forward	4366–4385	Manchester	X86560	147
JV33	GTG TAN ATG CAR TCA TCA CC	Reverse	4666–4685	Manchester	X86560
SV-s1	CCC TGG CAA TAT TGG AGA GAT TTG	Forward	4403–4426	Manchester	X86560	148
SV-s2	AAG GCC TAT GAA CCA CAT GGG GC	Forward	4601–4623	Bristol	AJ249939
SV-s3	GAC ATC AAG TTT GAT ACC AAG GA	Forward	4495–4517	BR-DF01	AB614356
SV-r-c	GCA TTG TAG GTG GCG AGA GCC	Reverse	5079–5099	Manchester	X86560
Sapp128	GAT TAC ACC AAA TGG GAT TCC AC	Forward	4354–4376	Manchester	X86560	149
Sapp129	GCA GTC ATC ACC ATA CGT GTG AA	Reverse	4655–4677	Manchester	X86560
SLV-OFa	ACT SCA AAT GGG ATT CCA CWC AAM ACC	First, forward	4358–4384	Manchester	X86560	150
SLV-OFb	ACW CTA AAT GGG AYT CCA CAC AGA ATC C	First, forward	4358–4385	Manchester	X86560
SLV-ORa	GTG RAA GAT KGA WGC RGT GGC AGG	First, reverse	4693–4716	Manchester	X86560
SLV-ORb	TCA AAG ATG GAA GCG GTT GCC G	First, reverse	4694–4715	Manchester	X86560
SLV-IF	TGG HCT MCC WTC WGG SAT GCC	Second, forward	4518–4538	Manchester	X86560
SLV-IRa	CAC ACR CTG TAS ATG CAG TCA TCA CC	Second, reverse	4666–4691	Manchester	X86560
SLV-IRb	CAC AAG GAG TAT ATG CAA TCA TCA CC	Second, reverse	4666–4691	Manchester	X86560
p290h	GAT TAC TCC AGG TGG GAC TCC AC	Forward	4354–4376	Manchester	X86560	46
p290i	GAT TAC TCC AGG TGG GAC TCA AC	Forward	4354–4376	Manchester	X86560
p290j	GAT TAC TCC AGG TGG GAT TCA AC	Forward	4354–4376	Manchester	X86560
p290k	GAT TAC TCC AGG TGG GAT TCC AC	Forward	4354–4376	Manchester	X86560
p289h	TGA CGA TTT CAT CAT CAC CAT A	Reverse	4663–4684	Manchester	X86560
p289i	TGA CGA TTT CAT CAT CCC CGT A	Reverse	4663–4684	Manchester	X86560
SR80	TGG GAT TCT ACA CAA AAC CC	First, forward	4366–4385	Manchester	X86560	152
JV33	GTG TAN ATG CAR TCA TCA CC	First, reverse	4666–4685	Manchester	X86560
SR80 GI 1–3	CTR KCV GAT ATT GGA RAG ATT T	Second, forward	4404–4425	Manchester	X86560
SR80 GI 2	AGT CTY TCC ATC TTA GAG AGA	Second, forward	4402–4422	BR-DF01	AB614356
SR80 GII 1–2	GCT GCR TCY TTG KCA ATC CT	Second, forward	4400–4419	Bristol	AJ249939
JV33	GTG TAN ATG CAR TCA TCA CC	Second, reverse	4666–4685	Manchester	X86560
SV36	GTT TCT GTT GGC ATT AAC A	First, forward	4273–4291	Manchester	X86560	153
SRGA	CWG TAB ATG CAR TCA TCA CC	First, reverse	4666–4685	Manchester	X86560
SVS1	CCC TGG CAA TAT TGG AGA GAT TTG	Second, forward	4403–4426	Manchester	X86560
SRGE	TAC WGY AAA TGG GAT TCCAC	Second, forward	4357–4376	Manchester	X86560
SRGA	CWG TAB ATG CAR TCA TCA CC	Second, reverse	4666–4685	Manchester	X86560
SRGS2A	CAC ATT ACC AGT GTA AGG TGC CC	Second, reverse	4620–4642	Bristol	AJ249939
Sapp36	GTT GCT GTT GGC ATT AAC A	Forward	4273–4291	Manchester	X86560	100
SV-s1	CCC TGG CAA TAT TGG AGA GAT TTG	Forward	4403–4426	Manchester	X86560
SV-s2	AAG GCC TAT GAA CCA CAT GGG GC	Forward	4601–4623	Bristol	AJ249939
SV-s3	GAC ATC AAG TTT GAT ACC AAG GA	Forward	4495–4517	BR-DF01	AB614356
GV-GLPSGM	GGT CTC CCC TCG GGC ATG	Forward	4560–4577	NongKhai24	AY646856
SaV1245R	CCC TCC ATY TCA AAC ACT A	Reverse	5159–5177	Manchester	X86560

^aPrimers used for nested RT-PCR are designated first and second.