Primer Pair p289-p290, Designed To Detect Both Noroviruses and Sapoviruses by Reverse Transcription-PCR, Also Detects Rotaviruses by Cross-Reactivity

Juan E. Ludert; Ana C. Alcalá; Ferdinando Liprandi

doi:10.1128/JCM.42.2.835-836.2004

DOI: 10.1128/JCM.42.2.835-836.2004

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Tables

TABLE 1.

Regions of homology with primer pair p289-p290 of the RNA-dependent RNA polymerase gene of caliciviruses representative of Norovirus genogroups I and II, Sapovirus, and selected rotavirus strains^a

Strain^b	Primer 290 GATTACTCCAAGTGGGACTCCAC	Primer 289 TATGGTGATGATTACATTGTCA	Location	RT-PCR reactivity^c
NORWALK	`-----TA-AGCA--------A--ACAAAA`	`ATTT--------------G-G-----GT`	4568-4886	+
HAWAII	`-----T--TCGA--------A--ACAGCA`	`TTTC--------------G-A-----G-`		+
HOUSTON/86	`-----------A-----------ACAAAA`	`CACACG-----------C-G---GTA--`		+
UK	`ATA---G---G--ATA-TA----CAGTGA`	`CTATCT----------T-ACACGCT-TT`	1314-1547	+
YM	`ATA-------G---TT-TA--T-CAGTAA`	`TTGTCA--------C-T-ACG-GAT-TT`		+
KU	`-TA-------G---TT-T---T-CAGTGA`	`TTATCA--C-------T-ACG-GAT-TT`		NT
SA11	`ATAC--G--TG--ATA-TA----CAGTGA`	`TTGTCA--C--C----TAACGCG-T-TT`		−

↵ a Sequence alignments were made by using the program DNAman, version 5.2.2 (Lynnon, Bio Soft, Quebec, Canada).
↵ b Norwalk, Hu/NV/GI/Norwalk/1968/US, GenBank accession no. M87661 ; Hawaii, Hu/NV/GII/Hawaii/1971/US, GenBank accession no. U07661 ; Houston/86, Hu/SV/Houston/1986/US, GenBank accession no. U65427 ; UK, bovine rotavirus strain, GenBank accession no. X55444 ; YM, porcine rotavirus strain, GenBank accession no. X76486 ; KU, human rotavirus strain, GenBank accession no. AB022765 ; SA11, simian rotavirus strain, GenBank accession no. X16830 . The locations of the primers in the genome are based on the sequence of the full-length Norwalk genome and the complete sequence of UK VP1.
↵ c +, reactive by RT-PCR; −, nonreactive by RT-PCR; NT, not tested.