Complete genome sequence of a novel secovirid infecting cassava in the Americas.

We report the complete genome sequence of a field isolate of a novel bipartite secovirid infecting cassava in Colombia, provisionally named "cassava torrado-like virus" (CsTLV). The genome sequence was obtained using Oxford Nanopore Technology, and the 5' ends were confirmed by RACE. The RNA1 is 7252 nucleotides (nt) long, encoding a polyprotein of 2336 amino acids (aa) containing the typical "replication block", conserved torradovirus motifs, and a Maf/Ham1 domain, which is not commonly found in viral genomes. The RNA2 is 4469 nt long and contains two overlapping ORFs encoding proteins of 226 and 1179 aa, showing the characteristic genome arrangement of members of the genus Torradovirus.

Association of leisure time and occupational physical activity with obesity and cardiovascular risk factors in Chile.

The aim of this study was to investigate the association between physical activity (PA), both occupational (OPA) and during leisure time (LTPA), with obesity and cardiovascular risk factors in Chilean adults. 5,157 participants from the Chilean National Health Survey 2009-2010 were included in this study. OPA and LTPA levels were assessed using the Global Physical Activity Questionnaire. The association between both PA with obesity and cardiovascular risk factors was determined using logistic regression. Our findings showed a significant trend between higher LTPA and lower odds for obesity (OR 0.64 [95% CI: 0.53; 0.76], central obesity 0.52 [0.44; 0.61]) and other cardiovascular risk factors including diabetes (OR: 0.72 [0.55; 0.94]), hypertension (OR: 0.59 [0.50; 0.71]) and metabolic syndrome (OR: 0.62 [0.50; 0.78]). In contrast, OPA was only associated with lower odds of diabetes (OR: 0.79 [0.65; 0.98]) and hypertension (0.85 [0.74; 0.98]). In conclusion, LTPA was associated with a lower risk of all major cardiovascular risk factors, whereas OPA was only associated with a lower risk of diabetes and hypertension.

Joint effect of physical activity and sedentary behaviour on cardiovascular risk factors in Chilean adults.

Background: To investigate the associations between combined categories of moderate-to-vigorous physical activity (MVPA) and sedentary behaviour (SB) with markers of adiposity and cardiovascular risk in adults. Methods: Overall, 5040 participants (mean age 46.4 years and 59.3% women) from the cross-sectional Chilean National Health Survey 2009-2010 were included in this study. MVPA and SB were measured using the Global Physical Activity questionnaire. Four categories were computed using MVPA- and SB-specific cut-offs ('High-SB & Active', 'Low-SB & Active', 'High-SB & Inactive' and 'Low-SB & Inactive'). Results: Compared to the reference group ('High-SB & Inactive'), those in 'High-SB & Active' and 'Low-SB & Active' were less likely to have an obese BMI (OR: 0.67 [0.54; 0.85], P = 0.0001 and 0.74 [0.59; 0.92] P = 0.0007, respectively) and less likely to have metabolic syndrome (OR: 0.63 [0.49; 0.82], P < 0.0001 and 0.72 [0.57; 0.91], P = 0.007), central obesity (OR: 0.79 [0.65; 0.96], P = 0.016 and 0.71 [0.59; 0.84], P < 0.0001), diabetes (OR: 0.45 [0.35; 0.59], P < 0.0001 and 0.44 [0.34; 0.56], P < 0.0001) and hypertension (OR: 0.52 [0.43; 0.63], P < 0.0001 and 0.60 [0.50; 0.72], P < 0.0001), respectively. Conclusions: Being physically active and spending less time in SBs was associated with lower adiposity and improvements in cardiovascular risk factors.

Isolation, genome analysis and tissue localization of Ceratobasidium theobromae, a new encounter pathogen of cassava in Southeast Asia.

In Southeast Asia (SEA) fastidious fungi of the Ceratobasidium genus are associated with proliferation of sprouts and vascular necrosis in cacao and cassava, crops that were introduced from the tropical Americas to this region. Here, we report the isolation and in vitro culture of a Ceratobasidium sp. isolated from cassava with symptoms of witches' broom disease (CWBD), a devastating disease of this crop in SEA. The genome characterization using a hybrid assembly strategy identifies the fungus as an isolate of the species C. theobromae, the causal agent of vascular streak dieback of cacao in SEA. Both fungi have a genome size > 31 Mb (G+C content 49%), share > 98% nucleotide identity of the Internal Transcribed Spacer (ITS) and > 94% in genes used for species-level identification. Using RNAscope® we traced the pathogen and confirmed its irregular distribution in the xylem and epidermis along the cassava stem, which explains the obtention of healthy planting material from symptom-free parts of a diseased plant. These results are essential for understanding the epidemiology of CWBD, as a basis for disease management including measures to prevent further spread and minimize the risk of introducing C. theobromae via long-distance movement of cassava materials to Africa and the Americas.

Ceratobasidium sp. is associated with cassava witches' broom disease, a re-emerging threat to cassava cultivation in Southeast Asia.

Cassava witches' broom disease (CWBD) is a devastating disease of cassava in Southeast Asia (SEA), of unknown etiology. Affected plants show reduced internodal length, proliferation of leaves and weakening of stems. This results in poor germination of infected stem cuttings (i.e., planting material) and significant reductions in fresh root yields and starch content, causing economic losses for farmers and processors. Using a metagenomic approach, we identified a fungus belonging to the Ceratobasidium genus, sharing more than 98.3-99.7% nucleotide identity at the Internal Transcribed Spacer (ITS), with Ceratobasidium theobromae a pathogen causing similar symptoms in cacao. Microscopy analysis confirmed the identity of the fungus and specific designed PCR tests readily showed (1) Ceratobasidium sp. of cassava is strongly associated with CWBD symptoms, (2) the fungus is present in diseased samples collected since the first recorded CWBD outbreaks in SEA and (3) the fungus is transmissible by grafting. No phytoplasma sequences were detected in diseased plants. Current disease management efforts include adjustment of quarantine protocols and guarantee the production and distribution of Ceratobasidium-free planting material. Implications of related Ceratobasidium fungi, infecting cassava, and cacao in SEA and in other potential risk areas are discussed.

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.

Complete Genome Sequence of the Plant Pathogen Ralstonia solanacearum Strain CIAT-078, Isolated in Colombia, Obtained Using Oxford Nanopore Technology.

Moko is one of the main diseases affecting banana and plantain in Colombia. Here, we report the genome sequence of the causal agent, the bacterium Ralstonia solanacearum (Smith) strain CIAT-078, collected in 2004 from affected plantains in central-west Colombia. The assembled genome was obtained using Oxford Nanopore Technology.

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.

Surveillance and diagnostics of the emergent Sri Lankan cassava mosaic virus (Fam. Geminiviridae) in Southeast Asia.

Emergent agricultural pathogens cause severe damage worldwide and their invasive potential is significantly increased by global trade, crop intensification and climate change. Standard surveillance and diagnostic protocols need to be evaluated and implemented, particularly with diseases caused by a wide range of pathogens that induce similar symptoms. Such is the case with Cassava Mosaic Disease (CMD) present in Africa and Asia, and associated with mixed virus infections and recombinant and re-assorted virus strains. CMD has been recently reported in Southeast Asia (SEA) and is already widely spread throughout this region. This communication offers an update on protocols and tools used to track the distribution of CMD and to characterize the pathogen associated with it in SEA.

Resolution of cassava-infecting alphaflexiviruses: Molecular and biological characterization of a novel group of potexviruses lacking the TGB3 gene.

Several potexviruses (Family Alphaflexiviridae) have been reported infecting cassava (Manihot esculenta Crantz) in the Americas. They were isolated from severely diseased plants during the last 30-40 years and include: Cassava common mosaic virus (CsCMV), Cassava Caribbean mosaic virus (CsCaMV), Cassava Colombian symptomless virus (CsCSV) and Cassava virus X (CsVX). However, their definitive classification as distinct species remains unresolved for several reasons, including the lack of sequence data and unavailability of samples from original isolates. This complicates disease diagnostics, cassava germplasm exchange certification, evaluation of virus cleaning protocols and epidemiological studies. Furthermore, a recently detected novel alphaflexivirus, indicates that cassava-infecting potexviruses may be more diverse. To solve the identity of these viruses, we started indexing samples from different parts of Colombia using different sets of PCR primers, antisera available and inoculation to indicator plants. Results show that there are three major phylogenetic groups of potexviruses infecting cassava, and they correspond to CsCMV, CsVX and the newly identified Cassava new alphaflexivirus (CsNAV). Bioassays and sequence analysis established that isolates of CsNAV and CsVX cause latent infections in different cassava landraces, they are not efficiently transmitted to the indicator plant Nicotiana benthamiana and they lack the gene 3 of the conserved potexviral 'triple gene block' (TGB). In contrast, all isolates of CsCMV (which have a characteristic potexvirus genome arrangement) caused Cassava Common Mosaic Disease (CCMD) in single infections and were efficiently transmitted to N. benthamiana. Although phylogenetic analysis of the replicase sequence placed CsNAV and CsVX as members of the Potexvirus genus, their distinct genome arrangement and biological characteristics suggest they can be considered as members of a separate taxonomic group.

Excited-State Electron Transfer in a Chromophore-Quencher Complex. Spectroscopic Identification of a Redox-Separated State.

In the chromophore-quencher complex fac-[Re(Aqphen)(CO)(3)(py-PTZ)](+) (Aqphen is 12,17-dihydronaphtho[2,3-h]dipyrido[3,2-a:2',3'-c]-phenazine-12,17-dione; py-PTZ is 10-(4-picolyl)phenothiazine), Aqphen is a dppz derivative, containing a pendant quinone acceptor at the terminus of a rigid ligand framework. This introduces a third, low-lying, ligand-based pi acceptor level localized largely on the quinone fragment. Laser flash excitation of fac-[Re(Aqphen)(CO)(3)(py-PTZ)](+) (354.7 nm; in 1,2-dichloroethane) results in the appearance of a relatively long-lived transient that decays with tau(298K) = 300 ns (k = 3.3 x 10(6) s(-)(1)). Application of transient absorption, time-resolved resonance Raman, and time-resolved infrared spectroscopies proves that this transient is the redox-separated state fac-[Re(I)(Aqphen(*)(-)())(CO)(3)(py-PTZ(*)(+)())](+) in which the excited electron is localized largely on the quinone portion of the Aqphen ligand.