Survey and molecular detection of Sri Lankan cassava mosaic virus in Thailand

Abstract

Cassava plantations in an area of 458 hectares spanning five provinces along the Thailand-Cambodia border were surveyed from October 2018 to July 2019 to determine the prevalence of cassava mosaic disease (CMD) caused by Sri Lankan cassava mosaic virus (SLCMV) in the region. CMD prevalence was 40% in the whole area and 80% in Prachinburi, 43% in Sakaeo, 37% in Burium, 25% in Surin, and 19% in Sisaket provinces. Disease incidence of CMD was highest 43.08% in Sakaeo, followed by 26.78% in Prachinburi, 7% in Burium, 2.58% in Surin, and 1.25% in Sisaket provinces. Disease severity of CMD symptoms was mild chlorosis to moderate mosaic (2-3). The greatest disease severity was recorded in Prachinburi and Sakaeo provinces. Asymptomatic plants were identified in Surin (12%), Prachinburi (5%), Sakaeo (0.2%), and Buriram (0.1%) by PCR analysis. Cassava cultivars CMR-89 and Huai Bong 80 were susceptible to CMD. In 95% of cases, the infection was transmitted by whiteflies (Bemisia tabaci), which were abundant in Sakaeo, Buriram, and Prachinburi but were sparse in Surin; their densities were highest in May and June 2019. Nucleotide sequencing of the mitochondrial cytochrome oxidase 1 (mtCO1) gene of whiteflies in Thailand revealed that it was similar to the mtCO1 gene of Asia II 1 whitefly. Furthermore, the AV1 gene of SLCMV-which encodes the capsid protein-showed 90% nucleotide identity with SLCMV. Phylogenetic analysis of completed nucleotide sequences of DNA-A and DNA-B components of the SLCMV genome determined by rolling circle amplification (RCA) indicated that they were similar to the nucleotide sequence of SLCMV isolates from Thailand, Vietnam, and Cambodia. These results provide important insights into the distribution, impact, and spread of CMD and SLCMV in Thailand.

Fig 1. Location of sampling sites of Sri Lankan cassava mosaic virus (SLCMV) in Thailand.

The survey was conducted from October 2018 to July 2019 on 201 cassava fields in Sisaket, Surin, Buriram, Sakaeo, and Prachinburi provinces.

Fig 2. Phylogenetic analysis of the nucleotide sequences of the mtCOI gene (length = 867 bp) of whitefly (Bemisia tabaci) collected from Surin (LC579572), Sakaeo (LC579573), and Buriram provinces (LC579574) in Thailand and that of other whitefly species.

Vertical distances are arbitrary. Horizontal distances are proportional to the calculated mutation distances. Numbers at nodes represent percent bootstrap confidence scores (1,000 replicates). The mtCOI gene of B. tabaci collected in this study clustered with that of Middle East Asia Minor 1 (MEAM1), Mediterranean (MED), New World, Asia 1, China 1, Asia II 7, Asia II 1, Asia II 3, and New World 2 species available in GenBank.

Fig 3. Phylogenetic analysis of the nucleotide sequences of the DNA-A component of the Sri Lankan cassava mosaic virus (SLCMV) isolate collected from Buriram province (LC586845) and that of other CMV species.

Vertical distances are arbitrary. Horizontal distances are proportional to the calculated mutation distances. Numbers at nodes represent percent bootstrap confidence scores (1,000 replicates). ICMV, Indian cassava mosaic virus; CMMGV, Cassava mosaic Madagascar virus; SACMV, South African cassava mosaic virus; EACMZV, East African cassava mosaic Zanzibar virus; EACMKV, East African cassava mosaic Kenya virus; EACMCV, East African cassava mosaic Cameroon virus; EACMV, East African cassava mosaic virus; EACMMV, East African cassava mosaic Malawi virus.

Fig 4. Phylogenetic analysis of the nucleotide sequences of the DNA-B component of the SLCMV isolate collected from Buriram province (LC588395) and that of other CMV species.

Vertical distances are arbitrary. Horizontal distances are proportional to the calculated mutation distances. Numbers at nodes represent percent bootstrap confidence scores (1,000 replicates). ICMV, Indian cassava mosaic virus; ACMV, African cassava mosaic virus; ACMBFV, African cassava mosaic Burkina Faso virus; EACMCV, East African cassava mosaic Cameroon virus; CMMGV, Cassava mosaic Madagascar virus; EACMZV, East African cassava mosaic Zanzibar virus; EACMMV, East African cassava mosaic Malawi virus; SACMV, South African cassava mosaic virus; EACMV, East African cassava mosaic virus; EACMKV, East African cassava mosaic Kenya virus.