Identification and incidence of Iris yellow spot virus in Allium field crops in Southwest Germany

After the first detection of Iris yellow spot virus (IYSV) in Germany in 2007 a 3-year monitoring program was started to determine the occurrence and geographical distribution of IYSV in Allium field crops in southwest Germany (Rhine valley area) and to characterise the German IYSV isolates on the basis of the nucleotide sequence of the nucleocapsid gene. Surveys revealed that IYSV was present in 27 out of 175 onion fields. In most cases disease incidence was low, but in a few fields infection rates of up to 18?% and 50?% were observed for bulb and bunching onions, respectively. In leek, IYSV was found for the first time in 2010. For about 25?% of the tested samples, IYSV-like symptoms were not confirmed by laboratory tests, such as ELISA and/or RT-PCR. This clearly demonstrates the need for reliable diagnostic tools to identify IYSV. New RT-PCR primers were designed as commonly used primers did not yield a PCR product from many clearly ELISA-positive samples. Phylogenetic analyses of 46 isolates revealed a limited degree of diversity among IYSV isolates from southwest Germany. Nearly all German IYSV isolates were closely related to each other, with only four isolates being genetically distinct from the others. IYSV is considered a serious emerging disease in German Allium field crops, especially in bunching onions.