Fig 2 - uploaded by Titus Kathurima
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Phylogenetic relationship of the 6KI gene sequences of CBSV and UCBSV obtained from de novo assembly of the Illumina deep sequencing. The sequences represented Coast, Western, and Nyanza regions. Additional sequences from Genebank (accession no. HG965221, FN434109, FN433930, FN433931, FN433932FN433933, FJ185044, FJ039620, GU563327, HG965221, FN434436, FN434437 and GQ329864) were included for analysis. Numbers at nodes indicate percent bootstrap values of 1000 replicates
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Cassava brown streak disease is caused by cassava brown streak virus (CBSV) and Uganda cassava brown streak virus (UCBSV). Many of the CBSV and UCBSV diversity studies utilize partial coat protein sequences due to the unavailability of representative full genome sequences. Hence, there is little information on the diversity of cassava brown streak...
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Context 1
... consisted of UCBSV sequences which had two sub-clusters. Sub-cluster I had a majority of sequences from Coast, Western, and Nyanza and sub-cluster II had FJ039520. Cluster B and cluster C consisted of CBSV sequences which grouped into two subclusters. Sub-cluster I had Nyanza and Western sequences while sub-cluster II had sequences from genebank (Fig. ...
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Background
In December 2019, the COVID-19 disease started in Wuhan, China. WHO declared a pandemic on March 12, 2020, and the disease started in Myanmar on March 23, 2020. December brought variants around the world, threatening the healthcare systems. To counter those threats, Myanmar started the COVID-19 variant surveillance program in late 2020....
In December 2019, the COVID‐19 disease started in Wuhan, China. The WHO declared a pandemic on 12 March 2020, and the disease started in Myanmar on 23 March 2020. In December 2020, different variants were brought worldwide, threatening global health. To counter those threats, Myanmar started the COVID‐19 variant surveillance program in late 2020. W...
Citations
... For UCBSV, the analyses were mainly carried out on a few partial coat protein sequences. They reported a country-wide nucleotide divergence from under 1 per cent in Mayotte (n = 8 sequences) and Kenya (n = 9) (Roux-Cuvelier et al. 2014;Kathurima and Ateka 2019) to 12 per cent in Rwanda (n = 24) (Munganyinka et al. 2017). The first complete genome sequences of viruses were obtained by Sanger sequencing of PCR amplicons (Mbanzibwa et al. 2011a). ...
Cassava Brown Streak Disease (CBSD), which is caused by cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), represents one of the most devastating threats to cassava production in Africa, including in Rwanda where a dramatic epidemic in 2014 dropped cassava yield from 3.3 million to 900,000 tonnes (1). Studying viral genetic diversity at the genome level is essential in disease management, as it can provide valuable information on the origin and dynamics of epidemic events. To fill the current lack of genome-based diversity studies of UCBSV, we performed a nationwide survey of cassava ipomovirus genomic sequences in Rwanda by high-throughput sequencing (HTS) of pools of plants sampled from 130 cassava fields in 13 cassava-producing districts, spanning seven agro-ecological zones with contrasting climatic conditions and different cassava cultivars. HTS allowed the assembly of a nearly complete consensus genome of UCBSV in 12 districts. The phylogenetic analysis revealed high homology between UCBSV genome sequences, with a maximum of 0.8 % divergence between genomes at the nucleotide level. An in-depth investigation based on Single Nucleotide Polymorphisms (SNP) was conducted to explore the genome diversity beyond the consensus sequences. First, to ensure the validity of the result, a panel of SNPs was confirmed by independent RT-PCR and Sanger sequencing.
Furthermore, the combination of fixation index (FST) calculation and Principal Component Analysis (PCA) based on SNPs patterns identified three different UCBSV haplotypes geographically clustered. The haplotype 2 (H2) was restricted to the central regions, where the NAROCAS 1 cultivar is predominantly farmed. RT-PCR and Sanger sequencing of individual NAROCAS1 plants confirmed their association with H2. Haplotype 1 was widely spread, with a 100% occurrence in the Eastern region, while Haplotype 3 was only found in the Western region. These haplotypes’ associations with specific cultivars or regions would need further confirmation. Our results prove that a much more complex picture of genetic diversity can be deciphered beyond the consensus sequences, with practical implications on virus epidemiology, evolution, and disease management. Our methodology proposes a high-resolution analysis of genome diversity beyond the consensus between and within samples. It can be used at various scales, from individual plants to pooled samples of virus-infected plants. Our findings also showed how subtle genetic differences could be informative on the potential impact of agricultural practices, as the presence and frequency of a virus haplotype could be correlated with the dissemination and adoption of improved cultivars.
... The study revealed that cassava brown streak virus (CBSV) was the most predominant virus at incidence of 59% and was detected in all the three Counties (Kilifi, Kwale, and Taita-Taveta) followed by UCBSV at 54.2%. These findings are consistent with previous studies by Kathurima and Ateka (2019), who reported CBSV to be the predominant virus in the coastal region of Kenya. However, the incidence of CBSV was significantly lower compared with our study. ...
... Co-infection of the two viruses was recorded in all the surveyed areas in Kilifi and Kwale Counties except in Taita-Taveta County. However, our findings reported a lower incidence of coinfection than previously reported by Kathurima and Ateka (2019). These findings are contrary to previous studies that had associated CBSV as restricted to coastal lowlands and UCBSV regarded a highland epidemic virus (Alicai et al., 2007;Monger et al., 2010;Winter et al., 2010). ...
Cassava productivity is threatened by viral diseases which have become the main phytosanitary problems in cassava farmers. Cassava brown streak disease (CBSD) is a devastating viral disease caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) which are transmitted by whitefly vectors and mainly disseminated through the use of infected stem cuttings as planting materials. The aim of the current study was to: (1) assess farmers' knowledge, perceptions on spread, causes and current management practices of CBSD; (2) determine the factors associated with farmers' satisfaction with cassava planting material; and (3) determine the distribution, incidence, and severity of CBSD and association of factors influencing the disease epidemics in smallholder cassava cropping systems in coastal Kenya. Information was collected using semi-structured questionnaire administered to 250 smallholder farmers through face-to-face interviews coupled with field visits to assess the incidence, severity and distribution of CBSD. Symptomatic and asymptomatic cassava leaf samples were collected for reverse transcription-polymerase chain reaction (RT-PCR) analysis of the causal viruses of CBSD. The results revealed that majority of the farmers (96.6%) could recognize CBSD symptoms on the roots, and only 11.5% could recognize the foliar symptoms of the disease. The cause of the disease was unknown to the farmers, with no effective management methods available to them. Majority of farmers (82.5%) recycled own cassava cuttings from previous season's crop as planting material followed by exchanging/borrowing from neighbors (67.5%). The field incidence of CBSD was highest in Kilifi (27.9%) followed by Kwale (24.7%) and Taita Taveta (10.8%), with severities ranging from 2 to 3 in the three Counties. RT-PCR analysis indicated that 91% of the symptomatic samples tested positive for either of the two viruses occurring either singly or as dual infection. Approximately 3.2% of the asymptomatic samples tested positive for only CBSV. Findings from this study demonstrates the need for awareness creation of farmers on the causes, spread and management practices to control CBSD and the importance of strengthening certified cassava seed systems to reduce the impact of the disease. The study provides base-line information imperative for development of management strategies of CBSD.
... The impending catastrophe is due to the highly vulnerable varieties, though CMD resistant, currently in fields (Taylor et al., 2012). It is conveyed through white flies within plantation and contaminated stem cutting for long distance (Kathurima and Ateka, 2019). ...
