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
6 A.O. Eni, O.P. Efekemo and O.A. Onile-ere et al. /Data in Brief 38 (2021) 107282 1.2. Exploration of dataset
Here we present an exploration of the dataset, all codes used for this exploration are available as a supplementary python script and Jupyter notebook.
- CMD incidence and CMD symptom severity
Summary of CMD incidence and CMD symptom severity in the different regions across 2015 and 2017 is presented in Fig. 1.
- Origin of infection and whitefly abundance
Summary plot showing the proportion of infections originating from whitefly vector trans mission versus infections as a result of the propagation of infected cuttings is presented in Fig. 2.
Fig. 2. Proportion of cutting transmitted and whitefly transmitted CMD infections across States in North Central and South West Nigeria surveyed in 2015 and 2017.
Summary plots for whitefly abundance across the states surveyed is presented in Fig. 3. Fig. 3. Relative whitefly abundance across States in North Central and South West Nigeria surveyed in 2015 and 2017.
- Type of Begomovirus infection
All samples collected were assessed for the presence of ACMV or EACMV by PCR. Samples were either negative, positive for either virus or positive for both viruses in a mixed infection. Summary plots on the proportion of the different viruses in collected samples are presented in Figs. 4–5.
A.O. Eni, O.P. Efekemo and O.A. Onile-ere et al. /Data in Brief 38 (2021) 107282 7
Fig. 4. Proportion of ACMV infected, EACMV infected, mixed ACMV & EACMV infected and uninfected cassava leaf sam ples across North Central and South West Nigeria in 2015 and 2017.
Fig. 5. Proportion of ACMV infected, EACMV infected, mixed ACMV & EACMV infected and uninfected cassava leaf sam ples in the North Central and South West regions in 2015 and 2017.
8 A.O. Eni, O.P. Efekemo and O.A. Onile-ere et al. /Data in Brief 38 (2021) 107282 2. Experimental Design, Materials and Methods
We conducted surveys of cassava farms across the South West and North Central regions of Nigeria in 2015 and 2017.
Sampling was performed following previously described methods with slight modifications . Following a road map of the surveyed regions, cassava farms located at an average of 10 km apart along surveyed routes were sampled. In each farm, 30 cassava plants were randomly selected along two diagonals and observed for the presence or absence of CMD symptoms. For plants exhibiting CMD symptoms, symptom severity was scored following previously described methods . CMD symptom severity was scored on a scale of 1–5 as previously described [3,4]. CMD incidence was calculated as the proportion of sampled plants showing CMD symptoms. For symptomatic plants, the origin of the infection was determined based on the distribution of symptoms on the plant as previously described [2,5]. The relative abundance of whitefly vectors in each farm was determined by counting the number of whiteflies present on the underside of the five topmost leaves of each of the 30 plants sampled within the farm. Then an average of four (4) cassava leaf samples were collected and stored in herbarium presses prior to laboratory analysis.
- Molecular Detection of Cassava Mosaic Begomoviruses
3.1. DNA extraction
Extraction of DNA was carried out following the methods of Dellaporta et al. . The concen trations of the extracted DNA were assessed using Nano Drop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, Massachusetts, USA) and adjusted to 50 ng/μl for PCR.
The isolated DNA were screened for ACMV and EACMV by polymerase chain reaction accord ing to the methods of Fondong et al. . Multiple specific PCR primers were used to ensure that strain variations were adequately captured (Table 4). The PCR mixture contained 1 × PCR reaction buffer [200 mM Tris HCl (pH 8.4) and 500 mM KCl], 10 mM dNTPs (Promega, Madis son Wisconsin USA), 25 mM MgCl2, 20 pmol of each primer and 1 U of Taq DNA Polymerase (Promega). The PCR products were resolved on a 1% agarose gel stained with ethidium bromide (10 mg/ml) alongside a 1 kbp plus DNA ladder (Thermo Fisher Scientific) at 100 V. The gels were analysed under UV light using a gel documentation system (UVP Gel Doc-IT2, LLC Analytik Jena, Germany).
A.O. Eni, O.P. Efekemo and O.A. Onile-ere et al. /Data in Brief 38 (2021) 107282 9
List of Primers used in detecting Cassava mosaic begomoviruses.
Primer Pair Specificity Primer Sequence Reference
JSP 1 & 2 ACMV ATGTCGAAGCGACCAGGAGAT  TGTTTATTAATTGCCAATACT
JSP 1 & 3 EACMV ATGTCGAAGCGACCAGGAGAT  CCTTTATTAATTTGTCACTGC
ACMVB F&R ACMV TCGGGAGTGATACATGCGAAGGC  TCGGGAGTGATACATGCGAAGGC
EACMV 1 & 2 EACMV GTTCGGCTATCACCTTCTAGAACA  CAAGGCTTACATTGAAAAGGGA
EAB555 F & R EACMV TACATCGGCCTTTGAGTCGCATGG  CTTATTAACGCCTATATAAACACC
VNF031/F & VNF032/R EACMCV GGATACAGATAGGGTTCCCAC  GACGAGGACAAGAATTCCAAT
CRediT Author Statement
Angela O. Eni Conceptualisation, Methodology, Funding acquisition, Writing – review & edit ing; Oghenevwairhe P. Efekemo: Investigation; Olabode A. Onile-ere: Original draft prepara tion, Formal analysis; Justin S. Pita: Conceptualisation, Methodology, Funding acquisition.
Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal rela tionships which have, or could be perceived to have, influenced the work reported in this article.
This work was fully funded by the Bill and Melinda Gates Foundation and the Department for International Development (DFID) Grant no. OPP1082413 “West African Virus Epidemiology (WAVE) for root and tuber crops” through a sub-grant from Université Félix Houphouët-Boigny (UFHB).
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