Plum pox virus evolution and adaptation: multiple strains on the same host?

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New highly divergent Plum pox virus isolates infecting sour cherry in Russia

Text by Sergei Chirkov and Peter Ivanov

Plum pox virus (PPV) is the causal agent of sharka, the most important viral disease of stone fruit crops (plum, peach, apricot etc.). It causes the premature fruit drop, makes fruits unmarketable and can depress the annual tree growth. The global economic losses are estimated at hundreds of millions of euros annually, and the millions of PPV-infected trees have been destroyed to prevent the spread of the infection.

Our previous investigations have shown the existence of an extensive and unique PPV population in European Russia. The plantings in the middle Volga river region that we studied in 2015 (Fig. 1) were established soon after the Second World War by introduction of a multitude of sour cherry cultivars from all over the country. Typical PPV symptoms (Fig. 2) were observed on plants growing in the existing and abandoned collections and neighbor cultivar test plots as well. Among nine recognized PPV strains only two, C and CR, have been proven able to infect sour cherry and these strains were never detected or only sporadically identified outside Russia until now. Old plant collections can serve as source of rare and atypical isolates.

Indeed, we identified numerous PPV-C samples (and no PPV-CR). To our surprise, some cherry-adapted isolates were not recognized by RT-PCR using commonly employed PPV-C or PPV-CR-specific primers as well as primers, specific to the strains M and W. Another surprise – some of them could be successfully detected using the PPV-D-specific primers (the most common strain). In addition, no correlation between the serological and molecular strain typing tests was observed. It became apparent that we were dealing with some entirely new isolates of this virus. They were named Tat isolates, according to geographic location (Fig. 1).

The sequencing and phylogenetic analysis assigned Tat isolates into the cluster of cherry-adapted strains. However, they grouped separately from the C and CR strains. An extra surprise: they didn’t form a separate cluster, but represented distinct lineages derived from a common ancestor; the divergence between them was comparable to the differences between PPV strains.  Thus, it turned out that new cherry-adapted PPV isolates do not seem to belong to any known strain of the virus.

PPV is one of the most investigated viruses belonging to the “top ten” plant viruses. Nevertheless, study of its natural population in poorly explored areas (e.g. in Russia), using simply a number of routine techniques, can lead to the exciting discoveries.

Our finding can shed more light on the PPV origin, diversity and evolution. In particular, it is a substantial argument in favor of the hypothesis about the Russian origin of the cherry strains. Comparison of the complete genomes of known and newly discovered cherry-adapted PPV isolates can facilitate the search for the amino acid positions responsible for host range determination.

Fig. 1

Fig. 1. Geographic location of new sour cherry-adapted isolates.

 

Fig. 2_small

Fig. 2. Symptoms on the sour cherry root offshoot infected with the Plum pox virus isolate Tat-3 .

Introducing the authors

55389 virology-authors

Pictured from left to right: Sergei Chirkov, Peter Ivanov, Anna Sheveleva: Research virologists, Department of Virology, Lomonosov Moscow State University, Moscow, Russia; Alexander Zakubanskiy: Post-graduated student, Department of Virology, Lomonosov Moscow State University, Moscow, Russia; and Gennady Osipov: Head, Laboratory of fruit crops breeding, Tatar Research Institute of Agriculture, Kazan, Republic of Tatarstan, Russia.

About the research

New highly divergent Plum pox virus isolates infecting sour cherry in Russia
Sergei Chirkov, Peter Ivanov, Anna Sheveleva, Alexander Zakubanskiy, Gennady Osipov
Virology, Volume 502, February 2017, Pages 56–62