Phylogenetic Analysis of Iris yellow spot virus Isolates from Onion (Allium cepa) in Georgia (USA) and Peru

Abstract

Iris yellow spot virus (IYSV) was first observed in sweet onions in Georgia (USA) in 2003 in the Vidalia region. The virus had been reported in the onion‐growing regions in western USA several years before being detected in Georgia in the east. Although symptoms were observed on onions in Peru several years earlier, the presence of IYSV was not confirmed in Peru until after the virus was detected in Georgia. We characterized nine isolates of IYSV recovered from sweet onions in both Georgia (four isolates) and Peru (five isolates) by sequencing the nucleocapsid (N) gene and compared those sequences with sequences available in GenBank. Sequence divergence between IYSV isolates from Georgia and Peru was low with 1.1%, and comparisons with IYSV isolates from other regions showed divergence of up to 11.4%. Bootstrap analysis indicated with a high degree of confidence that the Georgia and Peruvian isolates fell into the same clade and were different from known isolates from western USA that fell into sister clades. The high degree of similarity between Georgia and Peruvian isolates suggests that gene flow occurred from Peru into Georgia.

98% identical, 100% wrong: per cent nucleotide identity can lead plant virus epidemiology astray

“…However, infected plant material and disease vectors are inadvertently traded around the world and phylogenies of genes or genomes of individual species of plant viruses often reveal that viruses from distant geographical areas are closely related to one another. For example, outbreaks of iris yellow spot virus in onions from the American state of Georgia are very closely related to strains circulating in Peru (Nischwitz et al 2007). Some pathogens move frequently and are repeatedly re-introduced to certain geographical areas.…”

First report of Iris yellow spot virus in Costa Rica

“…1a-d). These symptoms were similar to those described for IYSV infection in Georgia (USA) and Peru (Nischwitz et al 2007); however, diamond-shaped lesions with a green center, a diagnosis-value symptom ( P a p p u e t a l . 2 0 0 8 ) , w e r e o b s e r v e d s e l d o m .…”

“…Moreover, the distribution of IYSV throughout an infected plant is uneven (Kritzman et al 2001;Smith et al 2006) and thus the pieces of tissue used for ELISA and RT-PCR may contain differential virus titer, even when extracted from the same plant. The low frequency of diamond-shaped lesions (diagnosis-value symptom) may be due to different onion varieties and/or weather conditions (Nischwitz et al 2006(Nischwitz et al , 2007.…”

“…These results confirmed the detection of IYSV in onion samples from Costa Rica. Moreover, the IYSV partial N sequences (accession numbers KY569524 to KY569538) were aligned against a selection of IYSV sequences worldwide (Nischwitz et al 2007;Krauthausen et al 2012;Iftikhar et al 2014) with MEGA7 (Kumar et al 2016) using MUSCLE (Edgar 2004). Phylogeny was inferred in MrBayes v.3.2.6 (Ronquist et al 2012) with a mixed substitution model (lset = mixed) and gamma-shaped rate variation with a proportion of invariable sites (lset rate = invgamma).…”

Detección de Iris yellow spot virus en cebolla cultivada en Tepalcingo, Morelos, México

“…Its presence has been detected since 1981 in Brazil and the United States (Cortês et al, 1998.). IYSV has exteded to important onion-producing regions worldwide (Bulajić et al, 2009;Córdoba et al, 2005;Du Toit et al, 2004;Gent et al, 2006;Gera et al, 2004;Nischwitz et al, 2007;Pozzer et al, 1999;Schwartz et al, 2002;Smith et al, 2006).…”