High-throughput sequencing of three pooled apple leaf samples from different regions of Iran revealed several viruses previously recorded; apple stem pitting virus, apple chlorotic leaf spot virus, and apple stem grooving virus, as well as apple hammerhead viroid. In addition two negative-sense RNA viruses, Coguvirus citri (citrus concave gum-associated virus, CCGaV) and Rubodvirus prosserense (apple rubbery wood virus 2, ARWV-2), together with Luteovirus mali (apple luteovirus 1, ALV-1), none of them had previously been reported from Iran, and they have only been detected in a few other countries. The distribution of the novel viruses was further surveyed by RT-PCR in 103 apple samples collected in the west and northwest of Iran. We found that 6, 5, and 21 samples tested positive for ALV-1, ARWV-2, and CCGaV, respectively. All three viruses were isolated from leaves showing symptoms, but ARWV-2 and CCGaV were sometimes isolated from apparently healthy leaves. The phylogenies of all three viruses showed that the Iranian isolates formed sister basal lineages to all isolates from other parts of the world. The Iranian lineages may have come from the initial ‘centre of emergence’ of these viruses, which could have been the site of domestication of apples in the Tian Shan Mountains of Kazakstan; apple could be the primary host of CCGaV, citrus and pear secondary. The world distribution of these viruses indicates that apple quarantine has been inadequate.
