Molecular characterization and complete genome of a novel nepovirus from red clover

Abstract

During high throughput sequencing (HTS) of leaves from a symptomatic red clover plant, a new RNA virus, tentatively named red clover nepovirus A (RCNVA), was discovered. The complete genomic sequence was determined and characterized. Particularly noteworthy was that RCNVA shares high sequence identities in RNA1 with a group of phylogenetically related nepoviruses while homologies in the RNA2 segments are markedly lower. Based on the genomic organization and phylogenetic attributes, RCNVA should be classified as a novel virus of the genus Nepovirus (subfamily Comovirinae, family Secoviridae, order Picornavirales).

Investigating the Pea Virome in Germany—Old Friends and New Players in the Field(s)

“…) recently identified the genome of RCCV1 and found that its capsid protein sequence is closely related to its homolog from RCVMV but the RdRp sequence differs significantly. RCNVA is a new virus that was identified in red clover (Trifolium pratense L.) in the Czech Republic (Koloniuk et al, 2018). It was detected only once in 2018 in the sL pool of Landkreis Rostock.…”

Molecular and biological properties of two putative new cytorhabdoviruses infecting Trifolium pratense

“…A considerable disadvantage of growing clover is its limited persistence, due in large measure to its susceptibility to viral and phytoplasma diseases (Edwardson & Christie, ; Taylor & Quesenberry, ; Fránová et al , ; Jones, ). More than 30 viruses are known to infect red clover (Edwardson & Christie, ), and this list could certainly be extended with further discoveries (Fránová et al , ; Fránová & Jakešová, ; Koloniuk & Fránová, ; Lenz et al , ; Koloniuk et al , ,).…”

An Annotated List of Legume-Infecting Viruses in the Light of Metagenomics

“…( Table 1 ) [ 14 , 26 , 27 , 28 , 29 , 30 ]. Red clover nepovirus A (RCNVA, genus Nepovirus ), red clover-associated varicosavirus ( Rhabdoviridae family), and phasey bean mild yellows virus (PBMYV, genus Polerovirus ) are suggested as new clover pathogens still pending official classification [ 31 , 32 , 33 ].…”

“…PSbMV, CMV, PEMV, PeSV, and BYMV cause mosaic and mottling, which is often confused with abiotic diseases (e.g., nutrient deficiencies, physiological disorders, herbicide damage, and waterlogging stress) [ 2 , 5 , 7 , 82 , 84 ]. The new but not officially approved polerovirus PBMYV [ 32 ] may also infect lentil.…”