Survey dataset on the epidemiological assessment of cassava mosaic disease in South West and North Central regions of Nigeria reveals predominance of single viral infection.
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ABSTRACT:
SUBMITTER: Eni AO
PROVIDER: S-EPMC8385170 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Cassava mosaic disease (CMD) is one of the most economically important viral diseases of cassava, an important staple food for over 800 million people in the tropics. Although several Cassava mosaic virus species associated with CMD have been isolated and characterized over the years, several new super virulent strains of these viruses have evolved due to genetic recombination between diverse species. In this data article, field survey data collected from 184 cassava farms in 12 South Western and North Central States of Nigeria in 2015 are presented and extensively explored. In each State, one cassava farm was randomly selected as the first farm and subsequent farms were selected at 10 km intervals, except in locations were cassava farms are sporadically located. In each selected farm, 30 cassava plants were sampled along two diagonals and all selected plant was scored for the presence or absence of CMD symptoms. Cassava mosaic disease incidence and associated whitefly vectors in South West and North Central Nigeria are explored using relevant descriptive statistics, box plots, bar charts, line graphs, and pie charts. In addition, correlation analysis, Analysis of Variance (ANOVA), and multiple comparison post-hoc tests are performed to understand the relationship between the numbers of whiteflies counted, uninfected farms, infected farms, and the mean of symptom severity in and across the States under investigation. The data exploration provided in this data article is considered adequate for objective assessment of the incidence and symptom severity of cassava mosaic disease and associated whitefly vectors in farmers' fields in these parts of Nigeria where cassava is heavily cultivated.
| S-EPMC5993015 | biostudies-literature
Project description:Surveys were conducted in 2016 and 2017 across the main cassava-growing regions of Burkina Faso to assess the status of cassava mosaic disease (CMD) and to determine the virus strains causing the disease, using field observation and phylogenetic analysis. CMD incidence varied between regions and across years but was lowest in Hauts-Bassins (6.0%, 2016 and 5.4%, 2017) and highest in Centre-Sud (18.5%, 2016) and in Boucle du Mouhoun (51.7%, 2017). The lowest CMD severity was found in Est region (2.0) for both years and the highest in Sud-Ouest region (3.3, 2016) and Centre-Sud region (2.8, 2017). The CMD infection was primarily associated with contaminated cuttings in all regions except in Hauts-Bassins, where whitefly-borne infection was higher than cuttings-borne infection in 2016. PCR screening of 687 samples coupled with sequence analysis revealed the presence of African cassava mosaic-like (ACMV-like) viruses and East African cassava mosaic-like (EACMV-like) viruses as single infections at 79.5% and 1.1%, respectively. Co-infections of ACMV-like and EACMV-like viruses were detected in 19.4% of the tested samples. In addition, 86.7% of the samples positive for EACMV-like virus were found to be positive for East African cassava mosaic Cameroon virus (EACMCMV). Phylogenetic analysis revealed the segregation of cassava mosaic geminiviruses (CMGs) from Burkina Faso into three clades specific to ACMV, African cassava mosaic Burkina Faso virus (ACMBFV), and EACMCMV, confirming the presence of these viruses. The results of this study show that EACMCMV occurrence may be more prevalent in Burkina Faso than previously thought.
| S-EPMC9291739 | biostudies-literature
Project description:BackgroundCassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species. This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexist within the same environment. The genetic and spatial structure of CMG populations in Madagascar was studied and Bayesian phylogeographic modelling was applied to infer the origins of Madagascan CMG populations within the epidemiological context of related populations situated on mainland Africa and other south western Indian Ocean (SWIO) islands.ResultsThe isolation and analysis of 279 DNA-A and 117 DNA-B sequences revealed the presence in Madagascar of four prevalent CMG species (South African cassava mosaic virus, SACMV; African cassava mosaic virus, ACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV), and of numerous CMG recombinants that have, to date, only ever been detected on this island. SACMV and ACMV, the two most prevalent viruses, displayed low degrees of genetic diversity and have most likely been introduced to the island only once. By contrast, EACMV-like CMG populations (consisting of East African cassava mosaic virus, EAMCKV, EACMCV and complex recombinants of these) were more diverse, more spatially structured, and displayed evidence of at least three independent introductions from mainland Africa. Although there were no statistically supported virus movement events between Madagascar and the other SWIO islands, at least one mainland African ACMV variant likely originated in Madagascar.ConclusionsOur study highlights both the complexity of CMD in Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. Given that more distinct CMG species and recombinants have been found in Madagascar than any other similarly sized region of the world, the risks of recombinant CMG variants emerging on this island are likely to be higher than elsewhere. Evidence of an epidemiological link between Madagascan and mainland African CMGs suggests that the consequences of such emergence events could reach far beyond the shores of this island.
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Project description:This study was conducted to assess the impact of the eye care programme on cataract blindness and cataract surgical services in Sokoto, Nigeria over a 12 year period 2005-2016.Data from the 2005 population based cross-sectional study of blindness in Sokoto state was re-analysed to obtain baseline estimates of the prevalence of cataract blindness and cataract surgical coverage for persons 50 years and over in Wurno health zone. A population based survey of a representative sample of persons 50 years and over in Wurno health zone was conducted in July 2016. Data on eye health workforce, infrastructure and cataract surgical services between 2005 and 2016 were analysed from relevant documents.In 2005 the unadjusted prevalence of bilateral cataract blindness (<3/60) in people 50 years and over in Wurno health zone was 5.6% (95% CI: 3.1, 10.1). By 2016 this had fallen to 2.1% (95% CI 1.5%, 2.7%), with the age-sex adjusted prevalence being 1.9% (95% CI 1.3%, 2.5%). The CSC for persons with visual acuity <3/60, <6/60, <6/18 for Wurno health zone was 9.1%, 7.1% and 5.5% respectively in 2005 and this had increased to 67.3%, 62.1% and 34.7% respectively in 2016. The CSR in Sokoto state increased from 272 (1005 operations) in 2006, to 596 (2799 operations) in 2014. In the 2005 survey, couching (a procedure used by traditional practitioners to dislocate the lens into the vitreous cavity) accounted for 87.5% of all cataract interventions, compared to 45.8% in the 2016 survey participants. In 2016 18% of eyes having a cataract operation with IOL implantation had a presenting visual acuity of <6/60 (poor outcome) with the main causes being postoperative complications (53%) and uncorrected refractive error (29%).Between 2005 and 2016 there was a doubling in cataract surgical rate, a 7 times increase in cataract surgical coverage (<3/60), and a decrease in cataract blindness and the proportion of eyes being couched. However, there remains a high prevalence of un-operated cataract in 2016 indicating a need to further improve access to affordable and good quality cataract surgical services.
| S-EPMC5560675 | biostudies-other
Project description:Leptospira was detected in 48.9% of blood samples from 182 febrile patients in north-central Bangladesh in 2019. Most Leptospira were classified as L. wolffii (93%) on the basis of phylogenetic analysis of 16S ribosomal RNA genes, while others were assigned to L. borgpetersenii and L. meyeri.
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Project description:The Brazilian AIDS epidemic has been characterized by an increasing rate of BF1 recombinants and so far eight circulating recombinant forms/CRFs_BF1 have been described countrywide. In this study, pol sequences (protease/PR, reverse transcriptase/RT) of 87 BF1 mosaic isolates identified among 828 patients living in six Brazilian States from three geographic regions (Central West, North, Northeast) were analyzed. Phylogenetic and bootscan analyses were performed to investigate the evolutionary relationship and mosaic structure of BF1 isolates. Those analyses showed that 20.7% of mosaics (18 out of 87) were CRFs-like isolates, mostly represented by CRF28/CRF29_BF-like viruses (14 out of 18). We also identified five highly supported clusters that together comprise 42 out of 87 (48.3%) BF1 sequences, each cluster containing at least five sequences sharing a similar mosaic structure, suggesting possible new unidentified CRFs_BF1. The divergence time of these five potential new CRFs_BF1 clusters was estimated using a Bayesian approach and indicate that they probably originated between the middle 1980s and the middle 1990s. DNA was extracted from whole blood and four overlapping fragments were amplified by PCR providing full/near full length genomes (FLG/NFLG) and partial genomes. Eleven HIV-1 isolates from Cluster # 5 identified in epidemiologically unlinked individuals living in Central West and North regions provided FLG/NFLG/partial genome sequences with identical mosaic structure. These viruses differ from any known CRF_BF1 reported to date and were named CRF90_BF1 by the Los Alamos National Laboratory. This is the 9th CRF_BF1 described in Brazil and the first one identified in Central West and North regions. Our results highlight the importance of continued molecular screening and surveillance studies, especially of full genome sequences to understand the evolutionary dynamics of the HIV-1 epidemic in a country of continental dimensions as Brazil.
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Project description: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.
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Project description:The West African forest-savanna mosaic, an important habitat for biodiversity and humans, is severely degraded, fragmented and modified by human activities. However, few studies have quantified the land cover changes observed over time and/or analysed the drivers of change. This study focused on Fazao-Malfakassa National Park, the largest in Togo, uses a combination of remote sensing, ground surveys and questionnaires to: (i) quantify vegetation changes, (ii) determine the drivers of change, (iii) compare results with findings elsewhere in the region and (iv) suggest management interventions. The images used were Landsat 5 TM, Landsat 7 ETM and Sentinel-2. Different vegetation indices were computed including: number of fragments, index of dominance, mean area of a vegetation type and mean annual expansion rate. In total, 300 people (including park staff and local populations) were interviewed using a semi-structured questionnaire. Results indicate that between 1987 and 2015 closed-canopy forest and tree-savanna became severely degraded and fragmented, following trends in other parts of the West African forest-savanna mosaic. The main drivers of change were agricultural expansion, bush fires and timber extraction. Observed changes and drivers altered with time: e.g. agricultural expansion was greatest during 1987-2001 (linked with political instability) while illegal timber extraction augmented during 2001-2015 (following increased timber value). Park staff and local populations' perceptions on drivers of change did not differ. Our study highlights that action is urgently needed if we are to preserve this important habitat, the biodiversity it hosts and the services it provides to humans. We suggest several management interventions, learning from successful interventions elsewhere in the region.
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