Nanopore-based complete genome sequence of a Sri Lankan cassava mosaic virus (Geminivirus) strain from Thailand

Sri Lankan cassava mosaic virus is an emerging pathogen in Southeast Asia. Here, we report the complete genome of a Thai isolate obtained using Nanopore technology. The isolate was collected in 2019 from the northeastern province of Surin, soon after disease eradication was reported in the country

Genome sequence of SARS-CoV-2 isolate Cali-01, from Colombia, obtained using Oxford Nanopore MinION Sequencing

We report the genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate obtained from a patient with symptoms of coronavirus disease 2019 (COVID-19) who was infected in Cali, Colombia. The patient had no recent travel record and did not require hospitalization. The virus genome was obtained using Oxford Nanopore MinION sequencing

Cassava torrado-like virus encodes a gene that facilitates the mechanical transmission to Nicotiana benthamiana of Cassava virus X

Cassava-torrado-like virus (CsTLV) is a bipartite single-stranded RNA virus belonging to the family Secoviridae. The virus has been reported in Brazil and Colombia, and is usually found in mixed infections, and in plants affected by Cassava Frogskin Disease (CFSD), an endemic cassava disease in the Americas. Genome analysis of CsTLV identifies a gene in RNA2 implicated in pathogen movement in other torradoviruses. This gene (RNA2-ORF1) and another one no related to virus movement (Maf/Ham1) were amplified by PCR and cloned into constructs under the 35S promoter of cauliflower mosaic virus (CaMV), which then were transfered to agrobacterium binary vectors. When agro-infiltrated in Nicotiana benthamiana plants, only RNA2-ORF1 had a positive effect on the mechanical inoculation of cassava virus X (CsVX), a potexvirus that has a low rate of mechanical infection in N. benthamiana. Efficiency of CsVX mechanical transmission was measured by the number of infected plants, presence of symptoms, and titers of CsVX as measured by ELISA, two weeks after infection. On average, CsVX could infect 2.3 times more plants when these were previously agro-infiltrated with A. tumefaciens binary vector encoding CsTLV RNA2-ORF1. We conclude that the novel secovirid CsTLV associated with leaf spot symptoms in cassava, encodes a gene that could enhance other viral infections in N. benthamiana. Further studies are required to elucidate this effect and its role in mixed infections, often observed in cassava plants affected by CFSD

Natural co-infection of solanum tuberosum crops by the potato yellow vein virus and potyvirus in colombia

The Potato yellow vein virus (PYVV), a Crinivirus with an RNA tripartite genome, is the causal agent of the potato yellow vein disease, reported in Colombian since 1950, with yield reductions of up to 50%. Co-infection of two or more viruses is common in nature and can be associated with differences in virus accumulation and symptom expression. No evidence of mixed infection between PYVV and other viruses has been reported. In this study, eight plants showing yellowing PYVV symptoms: four Solanum tuberosum Group Phureja (P) and four Group Andigena (A), were collected in Cundinamarca, Colombia to detect mixed infection in the isolates using next generation sequencing (NGS). The Potato virus Y (PVY) complete genome (similar to N strain) and the Potato virus V (PVV) partial genomes were detected using NGS and re-confirmed by RT-PCR. Preliminary field screening in a large sample showed that PYVV and PVY co-infect potato plants with a prevalence of 21% within the P group and 23% within the A group. This is the first report of co-infection of PYVV and potyvirus in Colombia and with the use of NGS. Considering that potyviruses enhance symptom severity and/or yield reductions in mixed infections, our results may be relevant for disease diagnosis, breeding programs and tuber certification

Gut-expressed vitellogenin facilitates the movement of a plant virus across the midgut wall in its insect vector

Many viral pathogens of global importance to plant and animal health are persistently transmitted by insect vectors. Midgut of insects forms the first major barrier that these viruses encounter during their entry into the vectors. However, the vector ligand(s) involved in the movement of plant viruses across the midgut barrier remains largely uncharacterized. Begomoviruses, many of which are disease agents of some major crops worldwide, are persistently transmitted by whiteflies (Bemisia tabaci). Here, in order to identify whitefly midgut proteins that interact with a devastating begomovirus, tomato yellow leaf curl virus (TYLCV), we performed midgut-specific TYLCV coat protein (CP) immunoprecipitation followed by high-throughput mass spectrometry proteomic analysis. We find that vitellogenin (Vg), a critical insect reproductive protein that has been considered to be synthesized by the fat body, is also synthesized by and interacts with TYLCV CP in the whitefly midgut. TYLCV appears to be internalized into midgut epithelial cells as a complex with Vg through endocytosis. Virus-containing vesicles then deliver the virus-Vg complexes to early endosomes for intracellular transport. Systematic silencing of Vg or midgut-specific immune blocking of Vg inhibited virus movement across the midgut wall and decreased viral acquisition and transmission by whitefly. Our findings show that a functional Vg protein is synthesized in the midgut of an insect and suggest a novel Vg mechanism that facilitates virus movement across the midgut barrier of its insect vector

Genoma completo, diagnóstico y resistencia a Ralstonia solanacearum en hibridos de plátano

La marchitez vascular del banano y el plátano, también conocida como enfermedad de Moko, es causada por Ralstonia solanacearum (Rs) filotipo II y es la principal enfermedad bacteriana que afecta a estos cultivos en Colombia. Tras obtener el genoma completo de un aislado colombiano (CIAT-078) y el análisis de secuencia comparativo con otros 44 genomas de Rs, desarrollamos un protocolo de PCR mejorado. Esto se basa en la secuencia de nucleótidos de un gen que codifica una proteína hipotética del dominio DUF3313, que se encontró que estaba presente solo en el filotipo II de Rs y además es conservada y polimórfica. El protocolo se probó con dos métodos de inoculación de Rs (con herida y sin herida), para validar la resistencia de campo reportado en el genotipo híbrido de plátano FHIA-21, previamente reportado como susceptible a la enfermedad de Moko en condiciones de invernadero. Mediante el uso de un método de inoculación sin herida en las raíces, confirmamos la resistencia en FHIA-21 a la enfermedad de Moko (no se detectó Rs por PCR en plantas inoculadas). En contraste, el genotipo Dominico Hartón susceptible al campo desarrolló síntomas severos independientemente de que las raíces tuvieran heridas o no. El genotipo FHIA-21 mostró un área bajo la curva de progresión de la enfermedad (AUDPC) cercana a cero, mientras que las plantas de Dominico Hartón mostraron valores de AUDPC que variaron de 65,8 a 88,4

Draft Genome Sequence of Fusarium oxysporum f. sp. cubense Tropical Race 4 from Peru, obtained by nanopore and illumina hybrid assembly

Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is the causal agent of Fusarium wilt, a major threat to the banana industry worldwide. Here, we report the genome of a Foc TR4 strain from Peru, sequenced using a combination of Illumina and Oxford Nanopore Technologies

Mitochondrial genetic diversity of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) associated with cassava in Lao PDR

Cassava Mosaic Disease (CMD) caused by Sri Lankan cassava mosaic virus (SLCMV), has rapidly spread in Southeast Asia (SEA) since 2016. Recently it has been documented in Lao PDR. Previous reports have identified whitefly species of B. tabaci as potential vectors of CMD in SEA, but their occurrence and distribution in cassava fields is not well known. We conducted a countrywide survey in Lao PDR for adult whiteflies in cassava fields, and determined the abundance and genetic diversity of the B. tabaci species complex using mitochondrial cytochrome oxidase I (mtCOI) sequencing. In order to expedite the process, PCR amplifications were performed directly on whitefly adults without DNA extraction, and mtCOI sequences obtained using nanopore portable-sequencing technology. Low whitefly abundances and two cryptic species of the B. tabaci complex, Asia II 1 and Asia II 6, were identified. This is the first work on abundance and genetic identification of whiteflies associated with cassava in Lao PDR. This study indicates currently only a secondary role for Asia II in spreading CMD or as a pest. Routine monitoring and transmission studies on Asia II 6 should be carried out to establish its potential role as a vector of SLCMV in this region