A comparison of the nucleotide sequence homologies between isolates of the Andean and ordinary strains of potato virus S and their relationship to other carlaviruses (original) (raw)
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Complete nucleotide sequence and molecular probing of potato virus S genome
Acta virologica, 2005
Complete genomes of three isolates of Potato virus S (PVS) were cloned and sequenced. The PVS ORF-1 was characterized for the first time. It encodes a putative replication protein (RPT) that shares the highest homology (about 52%) with that of Blueberry scorch virus (BlScV). ORF-1 motifs, characteristic for carlaviruses were found for methyltransferase (MTR), helicase (HEL) and RNA-dependent RNA polymerase (RdRp). The complete sequence of PVS genome enabled to develop an immunocapture RT-PCR probing of the PVS genome. Using this system, the sequence variability of 11 genome zones was examined for 34 PVS isolates including 15 PVS-CS variants that caused a systemic infection in Chenopodium quinoa. A broad variability between PVS isolates and diverse sequence variants was found. cDNA fragments covering the coat protein (CP) leader and CP-coding region (approx. 420 bp) were pooled for PVS-O and Chenopodium-systemic PVS isolates (PVS-CS) and corresponding cDNA libraries were screened for...
Archives of Virology, 2010
The complete coat protein (CP) nucleotide sequences of 13 Potato virus S (PVS) isolates from Australia and three from Europe were compared to those of 37 others. On phylogenetic analysis, the Australian sequences were in PVS O sub-clades III and IV, and the European isolates were in sub-clades I and VII. The European isolates invaded Chenopodium spp. systemically, but eight Australian isolates did not. Amino acid sequence differences at the N-terminal ends of the CPs were unrelated to the ability to invade Chenopodium spp. systemically. The acronym PVS O-CS is suggested for isolates that invade Chenopodium spp. systemically but are not within clade PVS A .
Eurasian Journal of Applied Biotechnology
Potato virus S (PVS) belongs to the genus Carlavirus of family Betaflexiviridae with a positive-sense single-stranded RNA genome of 8.5 Kb. PVS is one of the most prevalent viruses of cultivated potatoes in Kazakhstan. Here we report phylogenetic analysis of complete genome sequences of Kazakh isolates of PVS from potato cultivars Fortuna and Ushkonyr, design of PVS strain-specific diagnostic PCR and construction of expression cassettes for conserved viral proteins from both isolates. The Fortuna and Ushkonyr isolates were found to share 79.9% nucleotide identity with each other and belong respectively to previously-defined ordinary and Andean strains of PVS. Based on analysis of conserved and variable regions of available PVS isolates, we designed primers for reverse transcription (RT)-duplex PCR to detect both strains in single and mixed infections and established their prevalence in Almaty region of Kazakhstan. Coding sequences of triple gene block proteins (25K, 12K, 7K), coat p...
The Genome Organization of Potato Virus M RNA
Journal of General Virology, 1991
The 8534 nucleotide sequence of the genome of the carlavirus, potato virus M (PVM), has been determined. The sequence contains six large open reading frames (ORFs) and non-coding regions consisting of 75 nucleotides at the 5' end, 70 nucleotides followed by a poly(A) tail at the 3' end and 38 and 21 nucleotides between three large blocks of coding sequences. The ORF beginning at the first initiation codon at nucleotide 76 encodes a polypeptide of 223K which, accord-ing to its primary sequence analysis, seems to be a virus RNA replicase. The next coding block consists of three ORFs encoding polypeptides of 25K, 12K and 7K. The third block consists of two ORFs encoding polypeptides of 34K (PVM coat protein) and llK. The llK polypeptide contains a pattern resembling the consensus for a metal-binding nucleic acid-binding 'finger'. The nucleotide sequence EMBL accession number is X53062.
Archives of Virology, 2012
An isolate of the Andean strain of potato virus S (PVS), named BB-AND, was detected for the first time in a Brazilian potato crop, fully sequenced and analyzed. A comparison of BB-AND with other PVS isolates (Andean and Ordinary) showed that BB-AND is quite distinct. The lowest amino acid sequence identity to the only other fully sequenced Andean isolate was found in ORF 1 (82%) and ORF 6 (87%). Recombination analysis showed that the isolate Vltava (AJ863510), from Germany, is a recombinant between PVS O and PVS A isolates, with the recombination event located between nucleotides 6125 and 8324.
Complete cDNA sequence of a South American isolate of potato virus X
Virus Research, 1990
The complete cDNA sequence corresponding to the genomic RNA of a South American strain of potato virus X (PVXc) is reported. The sequence (6432 nucleotides) contains five open reading frames coding for polypeptides with molecular weights of 165.3, 24.3, 12.3, 7.6 and 25.0 and displays an overall homology of 77.4% with those previously reported for two European isolates. Comparison of amino acid sequences shows an average homology of 87%. Two major domains of variability, located between amino acids 476-615 of ORF 1 and 64-100 of ORF 5, are identified. Sequence similarities between RNA stretches lying upstream of ORFs 2, 4 and 5, and at the 3'-non coding regions of PVX and other plus-strand RNA viruses are described.
Diagnosis of Potato Viruses in Kazakhstan: Molecular Characterisation of Isolates
Eurasian Journal of Applied Biotechnology, 2019
Virus infection is one of the reasons for the low potato yield in Kazakhstan. The combination of modern methods of germplasm improvement and effective virus diagnosis are the most successful measures to overcome potato viruses. Using ELISA and multiplex RT-PCR methods, potato leaf samples from the Almaty and Kostanay regions of Kazakhstan were analysed for the presence of the carlaviruses potato virus M and potato virus S, the potyvirus potato virus Y, the potexvirus potato virus X, and the polerovirus potato leaf roll virus (PVM, PVS, PVY, PVX, and PLRV, respectively). The potato virus spectrum has changed over the last twenty years, and presently carlavirusеs represent the most widespread genus. Of the leaf samples tested, 84.3% and 46.6% were infected by PVM and PVS, respectively, and co-infection by both viruses occurred. Multiplex RT-PCR assays were developed to detect the five potato viruses, and for two strains of PVS. Based on sequence analyses of the central region of the ...
The complete nucleotide sequence of potato virus T
Archives of Virology, 2009
Potato virus T (PVT), a member of an unassigned species in the family Flexiviridae, has a genome 6,539 nt in size with three ORFs coding for replication-associated proteins (185 kDa, ORF 1), movement protein (40 kDa, ORF 2) and coat protein (24 kDa, ORF 3), respectively. PVT differs from the type members of all genera of the family Flexiviridae with a 30K-type movement protein and is phylogenetically distant from all of these viruses, least so from grapevine virus A (GVA, genus Vitivirus), with which it groups in all trees. The viral genome resembles that of trichoviruses but is smaller and does not contain the 3' terminal fourth ORF found in some members of this genus. PTV may represent a new genus of plant viruses for which the provisional name of Andesvirus is proposed.