A mixed infection of helenium virus S with two distinct isolates of butterbur mosaic virus, one of which has a major deletion in an essential gene

Authors: Hammond, John; Reinsel, Michael; Grinstead, Sam; LOCKHART, BENHAM - University Of Minnesota; Jordan, Ramon; Mollov, Dimitre

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/27/2020
Publication Date: 12/21/2020
Citation: Hammond, J., Reinsel, M.D., Grinstead, S.C., Lockhart, B., Jordan, R.L., Mollov, D.S. 2020. A mixed infection of helenium virus S with two distinct isolates of butterbur mosaic virus, one of which has a major deletion in an essential gene. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2020.612936.
DOI: https://doi.org/10.3389/fmicb.2020.612936

Interpretive Summary: Many ornamental plants are susceptible to virus infection, and vegetatively-propagated plants are particularly affected due to maintenance of the virus through successive propagations, and the possibility of further introduction of other virus by vectored transmission. Many viruses adversely affect crop yield and quality, so identification of viruses is critical to select or develop plant material free from virus infection. ARS scientist noticed virus symptoms in a commercially grown plant of Veronica, a flowering bedding plant which has rarely been reported to be virus infected. They discovered a mixed infection of two carlaviruses, a group of aphid-transmitted viruses, with two distinct variants of one of these viruses. One of these isolates had a deletion in its genetic material, and could only survive in the plant with complementation from a fully functional isolate. This is the first demonstration of maintenance of a virus isolate with a genetic deletion in a natural infection of a carlavirus. Additional isolates of one virus species were detected in single infections in three additional Veronica cultivars. Neither virus species had previously been reported in Veronica, and one had not previously been reported in the United States. Both species have a very narrow natural host range of one or two plant species, so identification in Veronica represents a significant expansion of their known host ranges. This information will be valuable to producers, plant diagnosticians, regulatory officials, and virologists interested in plant virus variability and evolution.

Technical Abstract: Multiple carlaviruses infect various ornamental plants, often having limited host ranges and causing minor symptoms, yet often reducing yield or quality. A mixed infection of butterbur mosaic virus (ButMV) and helenium virus S (HelVS) was identified from a plant of veronica (Veronica sp.) showing foliar mosaic and distortion. Carlavirus-like particles were observed by transmission electron microscopy (TEM), and RNA from partially purified virions was amplified by random RT-PCR, yielding clones of 439-1385 bp. Two partially overlapping clones including coat protein (CP) sequence, and two of four partial replicase clones, were closely related to ButMV-J (AB517596), previously reported only from butterbur (Petasites japonicus) in Japan. Two other partial replicase clones showed lower identity to multiple carlaviruses. Generic primers which amplify the 3’-terminal region of multiple carlaviruses yielded clones of three distinct sequences: 1) HelVS (98% identity); 2) ButMV-A (82% identity to ButMV-J); and 3) ButMV-B (78% identity to each of ButMV-J and ButMV-A). HelVS was previously reported only from Helenium hybrids and Impatiens holstii. Further amplification of upstream fragments revealed that ButMV-B had an internal deletion in TGB1, confirmed by amplification across the TGB1 region of both ButMV-A and ButMV-B using isolate-specific primers. Essentially the complete genomes of both ButMV-A and ButMV-B were obtained from high throughput sequencing (HTS), confirming the deletion within ButMV-B, which is presumably maintained through complementation by ButMV-A. An essentially complete HelVS genome was obtained by HTS from the same sample. Additional Veronica hybrids infected with HelVS were identified by TEM and RT-PCR, including cv. ‘Sunny Border Blue’ which was also subjected to HTS. This resulted in assembly of an 8,615 nt near complete HelVS genome, with high identity to that from the mixed infection. The predicted CP sequence has 96% amino acid (aa) identity to HelVS from helenium (Q00556). Other ORFs show a maximum of 54% (TGB3) to 68% (NABP) aa identity to the equivalent ORFs of other carlaviruses. These results confirm that HelVS is a distinct species in the genus Carlavirus, and demonstrate for the first time maintenance of a carlavirus isolate with a major deletion in an essential gene by complementation.