Discovery and Characterization of a Novel Carlavirus Infecting Potatoes in China

Abstract

A new carlavirus, tentatively named Potato virus H (PVH), was found on potato plants with mild symptoms in Hohhot, Inner Mongolia Autonomous Region, China. PVH was confirmed by genome sequencing, serological reactions, electron microscopy, and host index assays. The PVH particles were filamentous and slightly curved, with a modal length of 570 nm. Complete RNA genomic sequences of two isolates of PVH were determined using reverse transcription-PCR (RT-PCR) and the 5′ rapid amplification of cDNA ends (5' RACE) method. Sequence analysis revealed that PVH had the typical genomic organization of members of the genus Carlavirus, with a positive-sense single-stranded genome of 8410 nt. It shared coat protein (CP) and replicase amino acid sequence identities of 17.9–56.7% with those of reported carlaviruses. Phylogenetic analyses based on the protein-coding sequences of replicase and CP showed that PVH formed a distinct branch, which was related only distantly to other carlaviruses. Western blotting assays showed that PVH was not related serologically to other potato carlaviruses (Potato virus S, Potato virus M, and Potato latent virus). PVH systemically infected Nicotiana glutinosa but not Nicotiana tabacum, Nicotiana benthamiana , or Chenopodium quinoa , which is in contrast with the other potato carlaviruses. These results support the classification of PVH as a novel species in the genus Carlavirus. Preliminary results also indicated that a cysteine-rich protein encoded by the smallest ORF located in the 3' proximal region of the genome suppressed local RNA silencing and enhanced the pathogenicity of the recombinant PVX.

Molecular variability in the cysteine rich protein of potato virus M

“…The lack of association of isolate variation with geographic location highlights the world-wide movement of potato germplasm. Similar results have been reported for PVS [2,16], PVM [18,21], PVP [6] and Hop mosaic virus (HpMV) [15].…”

“…To date, Potato virus S (PVS), Potato virus H (PVH), Potato latent virus (PotLV), Potato virus P (PVP) and PVM are known carlaviruses reported to infect potato plants naturally worldwide [4,6,10,14].…”

“…The maximum likelihood tree was constructed using MEGA 6.06 with Jones-Taylor-Thornton (JTT) model as the best fitted model with 1000 bootstrap replicates and the pairwise deletion. Viruses names, acronyms and GenBank accession numbers are in Table 1 Table [4,6,10,14]. Maximum likelihood based phylogenetic trees constructed using nucleotide or amino acid sequences of the p11 gene resembled identical topology.…”

Pest categorisation of non‐EU viruses and viroids of potato

“…PYMV is considered rare in potato (Geraud-Pouey et al, 2016) and reported to incidentally infect potato plants that grow in the vicinity of infected tomato crops . Might cause symptoms under specific conditions (particular varieties, mixed infections) PVH Yes Not evaluated Yes Two reports in potato, one indicating mild leaf symptoms (Li et al, 2013). Therefore, no impact is expected on potato or other hosts in the EU territory.…”

“…: IIIA 10,11,12; IVAI 25.Additional experimental Solanaceous hosts are reported(Li et al, 2013). Data regarding natural hosts were retrieved from the EPPO global database and CABI crop protection compendium (CABI cpc) up to 30-4-2019 and if different source used specified in the table Narrow host range reported, additional natural hosts may exist Nicotiana sp.…”