Sequence alignment of the primer and probe binding sites. Primer pairs JV12/JV13 and SR33/SR46 are A) endpoint RT-PCR assays; B) real-time RT-PCR. Mismatches between the primer/probe sequences are indicated by a shaded font and are underlined. Genbank accession numbers are as follows: GI.1 (2011), KF039733.1; GI.3 (2008), JN603244.1; GI.4 (2008), JN603245.1; GI.6 (2010), JQ388274.1; GII.1 (2011), KC597150.1; GII.3 (2006), GU980585.1; GII.7 (2010), JQ750988.1; GII.13 (2010), JX439807.1; GII.4 (2004), JQ798158.1; GII.4 (2006b), AB447442.1; GII.4 (2009), GU445325.2; GII.4 (2012), JX459908.1. Abbreviations: B = C, G, or T; R = A or G; Y = C or T; I = A, C, G, or T.