Dauda Nathaniel

The family Geminiviridae comprises 15 genera and over 500 species of diverse plant-infecting viruses. Previous studies on this virus’s diversity primarily focused on the members’ selection without considering the entire genomic divergence. This study presents comprehensive comparative genomic analyses and a global distribution map using 17,718 complete genomes and 28,185 geminivirus-associated metadata records. Intergeneric pairwise identity among monopartite and Begomovirus DNA-A is ≥ 40%, while interspecies identity among Begomovirus DNA-B is ≥ 41%, corresponding to genetic variations of ≤60% and ≤59%, respectively. Begomovirus and Mastrevirus are the only genera detected across all continents, with Asia exhibiting the highest genus diversity (11 genera). However, in Africa, geminiviruses from six genera are more broadly distributed across individual countries. To our knowledge, this is the first geographical map constructed using all genera from the Geminiviridae family. Phylogenetic reconstructions of complete genomes, coat proteins, and replication-associated proteins (Rep) underscored distinct clustering patterns consistent with genus-level classification but revealed exceptions, including misclassified viral species and potential new taxa. Notably, French bean severe leaf curl viru s with accession KC699544 was reclassified from Capulavirus to Begomovirus with the proposed name Corchorus yellow vein mosaic virus. Additionally, two unclassified begomovirus-like viruses, named “begomovirus spathoglottis 1” and “2,” are proposed for reclassification within Maldovirus under the tentative names “maldovirus spathoglottis 1” and “2.” The Begomovirus Rep showed phylogenetic affinity with Rep from Maldovirus, Curtovirus, Turncurtovirus, and Topocuvirus, supporting potential evolutionary relationships among these genera. Recombination analyses confirmed high-frequency interspecies and intergeneric recombination events, predominantly involving Begomovirus , underscoring its pivotal role in geminivirus evolution. Furthermore, we hypothesized specific vector transmission: Opunvirus , Welwivirus , and Topilevirus are transmitted via treehopper species, whereas Citlodavirus and Eragrovirus are transmitted via leafhopper species. Accurate identification and classification of plant viruses and their transmission vectors are essential for developing effective surveillance and management strategies to safeguard global agriculture.

Previous studies on the genetic diversity of Lassa virus (LASV) have often relied on sequences containing undetermined nucleotides. In this study, we analyzed open reading frame (ORF) sequences free of undetermined nucleotides to assess LASV diversity with improved accuracy. The calculated pairwise identity was ≥ 68% for the polymerase, ≥ 74% for the nucleoprotein (NP), and ≥ 75% for the glycoprotein (GP) genes. LASV strains were classified into seven established lineages. Notably, lineage VI (represented by strain KT992435.1_KAK-428) exhibited phylogenetic relatedness to all other lineages, suggesting that it may retain ancestral traits. This observation underscores the potential evolutionary significance of its rodent host, Hylomyscus pamfi. A multiple sequence alignment of the GP gene revealed a unique codon insertion present only in lineages IV and V. The GP from these two lineages showed a predicted antigenicity score of 0.66, which is lower than the maximum scores observed in other lineages. Nonetheless, all lineage representatives were predicted to be non-allergenic and non-toxic and possessed a moderate density of B- and T-cell epitopes with ≥ 90% conservation. Considering the observed genetic divergence, antigenic variation, and epitope conservation, lineage VI (KAK-428) is proposed as a potential target for the development of a broadly protective LASV vaccine.

Sweet potato (Ipomoea batatas (L.) Lam) is critical for food security in developing nations, yet yields are limited by suboptimal propagation practices. Vine cutting is the main method, but interaction between varietal genetics and cutting position on growth and yield is poorly understood. This study investigated vine cutting position and variety effects on sweet potato performance in southeast Nigeria. A 2x2 factorial experiment, conducted in 2024 at University of Nigeria, used a randomized complete block design with three replications. Two varieties (Beauregard and Hannah) were propagated using 30 cm top (apical) and basal cuttings. Beauregard outperformed Hannah across all traits (P < 0.05), yielding 34.17% more roots (32. 55 vs. 24.26 Kg/plot), with larger tubers (13.22 cm vs. 12.40 cm length). Top part cuttings surpassed basal, with 87 % more roots (102.60 vs. 55.00 No./plot) and 72% higher yield (35.89 kg/plot vs 20.92 kg/plot). A significant genotype x cutting position interaction (p < 0.05) revealed Beauregard-Top part of vine cutting combinations as optimal achieving peak yield (44.97 Kg/plot) -123% higher than Beauregard-basal. Hannah showed stability but lower yields. Strong correlations emerged between root yield and both root number (r= +0.93) and stem count (r= +0.92), to establish them as reliable key yield predictors. GGE biplot confirmed revealed Beauregard-Top part of vine cutting as the highest yielding, most stable combination, and driving resources efficient tuber enlargement. In conclusion, top part cuttings of high performing varieties (e.g. Beauregard) synergistically enhance productivity though optimized physiological vigor. This precision propagation strategy offers small holder farmers a low input solution to sustainably intensify sweet potato production, addressing both yield gaps and climate resilience in tropical agroecologies.

Introduction Lassa fever is an acute viral haemorrhagic illness caused by the Lassa virus (LASV), primarily transmitted through contact with the multimammate rat. The disease is endemic to West Africa, where it is estimated to affect approximately two million individuals annually. Previous diversity studies on LASV relied on partial or complete gene sequences containing undetermined nucleotides (“N”), which can compromise the accuracy and reliability of phylogenetic and evolutionary analyses. To enhance the robustness and credibility of genomic investigations, this study aims to comprehensively assess the genetic diversity of LASV using full-length open reading frames (ORFs) encoding the polymerase, nucleoprotein, and glycoprotein, all free from “N.” Methods LASV nucleotide sequences were retrieved from GenBank. Sequences exhibiting ≥90% pairwise identity and originating from the same country were clustered into groups. From each group, representative sequences with no “N” within the polymerase ORF were selected. For each chosen L segment (polymerase), the corresponding S segment (nucleoprotein and glycoprotein) from the same viral isolate was also selected, provided it contained no “N.” Genetic variability among the selected ORFs was assessed using the Sequence Demarcation Tool (SDT). Multiple sequence alignment was conducted using MAFFT (Multiple Alignment using Fast Fourier Transform), and phylogenetic inference was performed with IQ-TREE2. Results The study revealed genetic variability of up to 32%, 26%, and 25% in the polymerase, nucleoprotein, and glycoprotein ORFs, respectively. LASV strains are classified into seven distinct lineages. Notably, lineage VI exhibited a phylogenetic relationship with all other LASV lineages and also showed evolutionary relatedness to other Old World arenaviruses. Conclusion Conclusion: The findings of this study suggest that lineage VI may possess ancestral traits, underscoring the evolutionary importance of Hylomyscus pamfi in the Lassa virus evolution. We recommend considering lineage VI in the vaccine development for possible broad protection.

Introduction The development of a broadly protective Lassa virus (LASV) vaccine is a critical public health priority. Several promising vaccine candidates are currently in various stages of development; however, most are based on the Josiah strain, which belongs to lineage IV. The extent to which the Josiah strain can confer cross-lineage protection remains uncertain. This study aims to compare representative strains from all known lineages using computational approaches to identify potential candidates for broad-spectrum Lassa virus vaccines. Methods A representative strain from each Lassa virus lineage was selected based on glycoprotein (GP) and nucleoprotein (NP) amino acid sequences. These sequences were aligned and analyzed using various comparative genomics and proteomics approaches. Analyses were conducted using the Base-by-Base tool, phylogenetic methods, and the Immune Epitope Database (IEDB). Epitopes with a percentile rank ≤ 0.5% and binding affinity (IC₅₀) ≤ 50 nM were considered to exclude weak-binding ligands. Furthermore, antigenicity, allergenicity, and toxicity of the predicted epitopes were evaluated using VaxiJen 3.0, AllerTOP v2.1, and ToxinPred 3.0, respectively. Results The GP lineage IV (Josiah) and V representatives were 66% immunogenic, which is lower than the 100% observed in other lineages. However, the immunogenicity of the NP is 100% for all the selected strains. Additionally,multiple sequence alignment of the glycoprotein gene revealed a unique codon insertion present only in lineages IV and V. Nonetheless, all lineage representatives were predicted to be non-allergenic and non-toxic and possessed a moderate density of B and T cell epitopes with ≥90% conservancy. Conclusion Considering the observed relationship of the LASV GPs, antigenic variations, and epitope conservation, lineage VI (KAK-428) is proposed as a promising candidate for the development of a broadly protective LASV vaccine.

The study examined the effect of weed control practices and different fertilizer sources for the optimum growth and yield of bell pepper. The study was conducted at the teaching farm of the Department of Crop Science, University of Nigeria, Nsukka. The sample for the study were weed control practices comprising black polyethylene mulch, un-weeded plot, and manual weeding with hoe at 2-week intervals and different fertilizer types comprising cow dung, pig dung, and poultry manure at 20 t/ha, respectively; NPK fertilizer at 150 kg/ha; and no fertilizer (control). There were 15 treatment combinations arranged in a randomized complete block design (RCBD) replicated three times. The study revealed that the plots mulched with black polyethylene and poultry manure recorded a significantly higher number of leaves per plant (82.0), plant height (16.47 cm), a lower number of broadleaved weeds (1.45/0.5m2), grasses (1.50/0.5 m2), and sedges (0.70/0.5m2), weed dry weight (0.81 g), and higher weed control efficiency (86.48%). It concluded that applying black polyethylene mulch with the application of NPK or poultry manure provided positive results for growth as well as weed control and therefore should be recommended to the extension agents and farmers for efficient and profitable production of bell pepper.

The rapid increase in publicly available genomic sequences alongside the need for constant updates poses challenges for representative sampling in diversity studies. This protocol describes a systematic method for representative sampling of geminiviruses, a highly diverse group of plant-infecting viruses. By using specific identity thresholds for each genus, this protocol makes sure to select a wide and representative range of genomes that are appropriate for studying diversity and phylogeny-based evolutionary relationships. Additionally, it includes procedures for constructing a geographical distribution map using genome metadata.

Research Journal of Agricultural Science

Ocimum sanctum is a leaf‐vegetable and spice crop with several nutritional, therapeutic, and curative properties. Economic losses due to weeds have posed a major challenge to farmers, who have adopted different techniques to manage weeds without regard to its effect on the crop's nutritional qualities. The objective of this study was to investigate the effect of weed control techniques on weed eradication, leaf yield, and nutritional qualities of O. sanctum. Nine weed control techniques comprising black, red, and transparent polyethylene mulches, rice husk and sawdust mulches, daily removal of weed (DROW), hoe‐weeded, application of Haloxyfop post‐emergence herbicide spray (PEHS), and un‐weeded were investigated in a randomized complete block design with three replications. Significant variations in leaf‐yield and nutritional qualities among the different weed control techniques were recorded. Leaf yield was higher in plots treated with rice husk and black polyethylene mulches. Haloxyfop PEHS and transparent polyethylene mulch were superior in enhancing the proximate and vitamin contents of O. sanctum while black polyethylene and DROW were more efficient in weed control compared with the other weed control techniques. The use of polyethylene mulch as an effective weed management option offers numerous benefits for agriculture and gardening. Its ability to conserve moisture, suppress weed growth, and improve the crop microclimate, makes it a sustainable and cost‐effective option for farmers globally. Additionally, the use of herbicide to exploit plant biosynthetic pathways could lead to the unearthing of chemical innovations that could in addition to eradicating weed, also improve the nutritional qualities of crop.