Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands

Abstract

Cassava is one of the most important staple crops in Africa and its production is seriously damaged by viral diseases. In this study, we identify for the first time and characterize the genome organization of novel ampeloviruses infecting cassava plants in diverse geographical locations using three high-throughput sequencing protocols [Virion-Associated Nucleotide Acid (VANA), dsRNA and total RNA], and we provide a first analysis of the diversity of these agents and of the evolutionary forces acting on them. Thirteen new Closteroviridae isolates were characterized in field-grown cassava plants from the Democratic Republic of Congo (DR Congo), Madagascar, Mayotte, and Reunion islands. The analysis of the sequences of the corresponding contigs (ranging between 10,417 and 13,752 nucleotides in length) revealed seven open reading frames. The replication-associated polyproteins have three expected functional domains: methyltransferase , helicase, and RNA-dependent RNA polymerase (RdRp). Additional open reading frames code for a small transmembrane protein, a heat-shock protein 70 homolog (HSP70h), a heat shock protein 90 homolog (HSP90h), and a major and a minor coat protein (CP and CPd respectively). Defective genomic variants were also identified in some cassava accessions originating from Madagascar and Reunion. The isolates were found to belong to two species tentatively named Manihot esculenta-associated virus 1 and 2 (MEaV-1 and MEaV-2). Phylogenetic analyses showed that MEaV-1 and MEaV-2 belong to the genus Ampelovirus, in particular to its subgroup II. MEaV-1 was found in all of the countries of study, while MEaV-2 was only detected in Madagascar and Mayotte. Recombination analysis provided evidence of intraspecies recombination occurring between the isolates from Madagascar and Mayotte. No clear association with visual symptoms in the cassava host could be identified.

Survey of cassava brown streak disease and association of factors influencing its epidemics in smallholder cassava cropping systems of coastal Kenya

“…Similarly, papaya mealybugs (Paracoccus marginatus Williams) has been reported along the coastal belts of Kenya especially in Kwale, Kilifi, Mombasa, and Taita-Taveta counties on papaya, cassava, chili pepper, amaranth, coconut, and other fruits, ornamental plants and weeds (Macharia et al, 2017). Mealy bugs have been reported as vectors of many species of viruses (Selvarajan et al, 2016) including the recently identified novel amplelovirus infecting cassava in Central Africa and South West Ocean islands (Kwibuka et al, 2021). Future studies therefore recommend investigative studies on the possible role played by the mealybug species observed on cassava in the coastal region of Kenya in the spread of CBSD during their feeding patterns on cassava.…”

Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis

“…For instance, viruses from the genus Tenuivirus have almost complementary 3′ and 5′ genome ends ( Gaafar et al, 2021 ), which can provide an indication on genome completeness. Similarly, if the novel genome contains a 3′ poly-A tail or the assembled genome length is very similar to that of closely related viruses, it provides an indication that the UTRs are likely complete or only missing a few nucleotides ( Kwibuka et al, 2021 ). However, if an incomplete genome assembly is obtained, it is a good practice to carry out additional analyses to complete the genome, such as iterative mapping of unassembled reads ( Olmedo-Velarde et al, 2022 ).…”

“…Collecting this information at the time of sampling can facilitate and minimize efforts later on. Additionally, the documentation could include the economic importance and geographical distribution of the crop species affected, globally or domestically ( Kwibuka et al, 2021 ). Optionally, plants that are taxonomically related to the infected hosts, including other crops and wild plants that could potentially be threatened by the virus or be a reservoir or alternate host, could also be documented.…”

“…Communication between stakeholders and the scientific community is essential for a quick decision-making process. Pre-publication data sharing between research groups that independently detected the novel virus is highly encouraged, because it can provide valuable information on the presence, distribution, host range, and impact of the novel virus ( Koloniuk et al, 2018 ; Sõmera et al, 2019 ; Kwibuka et al, 2021 ; Temple et al, 2022 ). For example, actinidia virus X (AVX) was first reported as a novel virus infecting kiwifruit and blackcurrant, although it was later found to be synonymous with plantain virus X (PlVX) ( Hammond et al, 2021 ); or potato virus V (PVV), which was confused with potato virus Y (PVY) since it caused similar symptoms when inoculated to PVY-sensitive cultivars ( Fuentes et al, 2022 ).…”

Persistent, and Asymptomatic Viral Infections and Whitefly-Transmitted Viruses Impacting Cantaloupe and Watermelon in Georgia, USA

“…This technique employs the use of RNA interference (RNAi), a natural antivirus defense mechanism present in the host cell, to generate small RNAs that are 21-24 nt long for the analysis of the viral population present in a tested plant sample [10]. The technique has become an important tool and has been used widely in the diagnosis, identification, and characterization of viruses in recent years [5,[11][12][13][14][15][16][17][18][19].…”