First Report of Agapanthus Carlavirus B Infecting African Lily in Germany

African lily (genus Agapanthus, family Amaryllidaceae), also known as Lily of the Nile, is native to Southern Africa and is usually propagated via rhizomes. Six species are described in the literature (Zonneveld and Duncan 2003) and although they are of limited economic importance, the hundreds of cultivars derived from them are very popular ornamental plants worldwide. In summer 2025, suspected virus symptoms in the form of chlorotic streaks were observed on the leaves of a cultivated purple-flowering African lily plant (Figure 1) in a private garden in the Hanover region in Lower Saxony, Germany. Electron microscopy showed the presence of flexuous filaments, resembling those of carlaviruses; however, mechanical inoculation of diseased leaf tissue to a range of herbaceous indicator host plants under greenhouse conditions failed. An attempt with asymptomatic blossom tissue of the same plant used as inoculum was also unsuccessful. In order to identify the suspected virus, total RNA was extracted from diseased leaf tissue using a Spectrum Plant Total RNA Kit (Sigma-Aldrich, USA) including DNase treatment. A cDNA library was prepared with a NEBNext UltraExpress RNA Library Prep Kit (New England Biolabs, USA) and sequenced on an Illumina NextSeq2000 platform (2 × 150 bp paired-end reads). Analysis of the assembled contigs (Geneious Prime, New Zealand) allowed the identification of the complete genome sequence of a carlavirus (GenBank Accession No. PX505953) showing the highest nucleotide sequence identity (96.0%) to Agapanthus carlavirus B (AgCVB; NC_077096). No other viruses were identified in the library. To confirm the presence of the virus, specific primers were designed for detection by RT-PCR (AgCVB-s: 5′-GGACTTTCGATCCCTTGAA-3′, AgCVB-as: 5′-ATCAGGCAAATCGGGAATA-3′), which amplify a 949 bp fragment in the CP gene region. Although all rhizomes of the plant are connected and it can be assumed that the individual plants have a uniform virus status, four additional diseased individual plants from the same pot were sampled and tested positive by RT-PCR. Direct sequencing of one representative amplified product showed 100% identity with the originally obtained HTS sequence, confirming the presence of AgCVB. Very little is known about the worldwide distribution of AgCVB, which has recently been identified in a survey of plants of the family Amaryllidaceae in South Africa (Read et al. 2021); to date, only a single sequence is available in GenBank (NC_077096). In order to gain insight into the spread of the virus, three further African lily plants of unknown varieties (two different blue- and one white-flowering variant) were examined using RT-PCR, of which one blue and the white also proved to be positive, despite being asymptomatic. These samples came from plants in different private gardens in the Hanover region, and were originally purchased in different garden centres in Germany. The results indicate that the spread of AgCVB is not limited to South Africa, and that it occurs latently in various, albeit unknown, African lily cultivars. Its presence in randomly selected plants suggests that it is already widespread, hence, virus testing of vegetative propagation material is advisable to prevent further spread. Reference material of the original specimen is available under accession number PV-1543 in the DSMZ plant virus collection.