Geographic Structuring of the Tomato Brown Rugose Fruit Virus Populations in Morocco

Tomato brown rugose fruit virus (Tobamovirus fructirugosum, ToBRFV) is an emerging virus that affects tomatoes, capsicum, and chili. Since its first detection in Jordan in 2015, the virus has been reported in more than 40 countries across all the continents. In Morocco, the virus was reported for the first time in October 2021. However, its genetic diversity remains unexplored. In this work, we used a collection of 100 tomato fruits from local markets to investigate the virus’s variability. Thirty-eight sequences were recovered and used to study evolutionary pressures acting on the N-terminus of the RNA-dependent RNA polymerase, the movement protein (MP), and the coat protein (CP) genes. The genetic diversity among Moroccan sequences was low, with over 99% nucleotide identity, which is consistent with the global situation, with the CP exhibiting higher diversity followed by the MP. We identified two sites with non-synonymous substitutions in the CP, and one in the MP. We used haplotype network analyses to reveal the population structure within the Moroccan isolates and studied their relationships with sequences from the rest of the world. Sequences from Morocco showed a clear geographic structure, suggesting that geographic factors, potentially combined with agricultural practices, may contribute to shaping the population structure of ToBRFV in Morocco. Our analyses suggest few introduction events, probably from Israel, Jordan, and Italy.