Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Abstract

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

Intermolecular base‐pairing interactions, a unique topology and exoribonuclease‐resistant noncoding RNAs drive formation of viral chimeric RNAs in plants

“…Notably, both BNYVV and BSBMV share identical 'coremin' sequences (Flobinus et al, 2016). Moreover, when applied to BNYVV and two newly reported benyviruses BuMV and RSMV (Kondo et al, 2013;Bagayoko et al, 2021), RNAfold algorithms predict and overall topology (intermolecular base-pairing interactions + adjacent SL1) similar to that of BSBMV (Fig. 3), suggesting conservation of these folds at least in the genus Benyvirus.…”

A Review of Vector-Borne Rice Viruses

“…RSNV-causing disease was first described in 1977 as a new virus infecting rice in Côte d’Ivoire [ 33 ] and was subsequently observed in Liberia, Nigeria, and Sierra Leone [ 56 ]. RSNV was initially identified in the Ivory Coast in 1983 and the incidence of disease ranged locally from 37% to 80% in these African countries [ 34 ]. Since then, this virus was nearly undetected in the fields in Africa.…”

“…Since then, this virus was nearly undetected in the fields in Africa. However, it has been episodically reported in several South and Central American countries, including Colombia, Brazil, Ecuador, Panama, and Argentina [ 34 , 56 , 57 , 58 , 59 , 60 ], causing severe epidemics and leading to up to 40% yield losses [ 60 ]. Notably, characteristic symptoms of crinkling yellow color and deformation of rice leaves were recently observed in West African countries, including Burkina Faso [ 61 ], Benin [ 62 ], Mali [ 63 ], and Sierra Leone [ 64 ], suggesting that RSNV is re-emerging in Africa.…”

Discovery of aphid-transmitted Rice tiller inhibition virus from native plants through metagenomic sequencing

“…Surprisingly, although aphid-transmitted viruses such as cucumoviruses and potyviruses are widespread in crops, no sequenced rice virus has been shown to spread by aphid vectors [10,12,13]. Notably, insect-borne viruses emerge and re-emerge to cause devastating rice disease epidemics without clearly defined origins [14][15][16][17][18]. These include rice tungro viruses, rice grassy stunt virus, rice ragged stunt virus and rice gall dwarf virus emerged in 1960's and 1970's as well as Southern rice black-streaked dwarf virus (SRBSDV) that began to circulate over two decades ago [19][20][21][22][23][24].…”