Molecular characterization of a Chinese isolate of potato virus A (PVA) and evidence of a genome recombination event between PVA variants at the 3′-proximal end of the genome

Abstract

Potato plants that exhibited mosaic symptoms were collected in Xiangxi, Hunan province, China. Multiplex RT-PCR screening for common viruses revealed the presence of potato virus A (PVA) in these samples. ELISA with virus-specific antibodies confirmed infection by PVA in the plants. Rod-shaped virions of ~750 nm in length and ~13 nm in width were observed by transmission electron microscopy. One virus isolate (designated PVA-Hunan) was subjected to molecular characterization. The viral genome consisted of 9,567 nucleotides, excluding the poly(A) tail, and encoded a polyprotein of 3,059 amino acids. A second characteristic potyvirus open reading frame (ORF), pretty interesting Potyviridae ORF (pipo), was located at nucleotides 2,834-3,139. The isolate shared 84% to 98% and 93% to 99% sequence identity with other PVA isolates at the nucleotide and amino acid level, respectively. Phylogenetic analysis demonstrated that, within the PVA group, PVA-Hunan clustered most closely with the Finnish isolate Her, then with isolates 143, U, Ali, M and B11. The isolate TamMV stood alone at a separate branch. However, scanning of complete genome sequences using SimPlot revealed 99%-sequence identity between PVA-Hunan and TamMV in the 3'-proximal end of the genome (~nt 9,160 to the 3'end) and a 50%-94% (average~83%) identity upstream of nt 9,160. In contrast, 98% identity between PVA-Hunan and isolates M and B11 was detected for nucleotides 1 to ~9,160, but only ~94% for the 3'-proximal region, suggesting a genome recombination event (RE) at nt 9,133. The recombination breakpoint also was identified by the Recombination Detection Program (RDP). The RE was further confirmed by analysis of the CP gene, where the apparent RE was located.

Integrated mRNA and microRNA transcriptome analysis reveals miRNA regulation in response to PVA in potato

“…However, cultivated potatoes, like many other plants, are exposed to diverse abiotic and biotic stresses, especially the host of a broad range of pathogens 1 . As a vegetatively propagated crop, potato is prone to virus infection during propagation, and this is one of the most challenging problems affecting potato production 2 . In China, six viruses, potato virus Y (PVY), potato virus X (PVX), potato virus A (PVA), potato virus S (PVS), potato leafroll virus (PLRV) and potato virus M (PVM), occur with a high incidence 3 , 4 .…”

“…PVA ( Potyvirus genus, Potyviridae family) is one of the most harmful viruses infecting potatoes, reaching 40% of yield losses 2 . PVA can cause various symptoms, ranging from mild mosaic to severe leaf necrosis, depending on the potato cultivar and virus strain 5 .…”

Identificación molecular de Potyvirus infectando cultivos de papa en el oriente de Antioquia (Colombia)

“…En cultivos de papa de todo el mundo, se ha reportado principalmente a las especies de potyvirus PVY, PVV y PVA, como las más prevalentes (Karasev y Gray, 2013;He et al, 2014;Gutiérrez et al, 2016). En este trabajo se evaluó mediante pruebas moleculares de RT-PCR, la presencia de dichos virus en cultivos de papa del oriente de Antioquia, encontrándose la ocurrencia de los virus PVY y PVV, pero no de PVA.…”

“…Rajamäki et al (1998), con base en secuenciación de la región CP, pruebas serológicas y de patogenicidad sobre papa (híbrido A6) confirmaron que el virus del tomate de árbol: tamarillo mosaic virus (TaMV) es realmente una cepa de PVA. A pesar de que la ocurrencia de PVA es definida como esporádica en muchos países, He et al (2014) reportan a este virus como uno de los más incidentes en cultivos de papa de China; mientras que Singh et al (1998) indican que en algunas variedades de papa cultivadas en Norteamérica pueden presentarse niveles de incidencia de PVA de entre 9 y 11 %.…”

Current status of viral diseases of potato and their ecofriendly management -A critical review

“…A successful beginning towards the ecofriendly management of viral diseases of different crops could also be achieved [77,97,[230][231][232][233][234][235]. Immunization by plant products that stimulate the plant's natural disease resistance mechanism may provide a new strategy for crop protection against viruses.…”