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

The dataset presented here was collected during field surveys conducted in 2015 and 2017, to determine the distribution of African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV) across 12 Nigerian states and the Federal Capital Territory (FCT), Abuja. In each state, cassava farms were systematically sampled at 10 km intervals except in locations with sparse distribution of cassava farms. In each farm, 30 cassava plants were visually assessed for presence or absence of cassava mosaic disease (CMD) foliar symptoms along two diagonals. Whitefly population was assessed by counting the number of whiteflies on the top five leaves of each sampled plant. Then an average of 4 cassava leaf samples were collected from each farm, and screened for ACMV and EACMV infections using polymerase chain reaction. The dataset includes CMD incidence, symptom severity and the relative abundance of whiteflies in each field as well as laboratory results that show the distribution of ACMV and EACMV across the regions surveyed.


a b s t r a c t
The dataset presented here was collected during field surveys conducted in 2015 and 2017, to determine the distribution of African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV) across 12 Nigerian states and the Federal Capital Territory (FCT), Abuja. In each state, cassava farms were systematically sampled at 10 km intervals except in locations with sparse distribution of cassava farms. In each farm, 30 cassava plants were visually assessed for presence or absence of cassava mosaic disease (CMD) foliar symptoms along two diagonals. Whitefly population was assessed by counting the number of whiteflies on the top five leaves of each sampled plant. Then an average of 4 cassava leaf samples were collected from each farm, and screened for ACMV and EACMV infections using polymerase chain reaction. The dataset includes CMD incidence, symptom severity and the relative abundance of whiteflies in each field as well as laboratory results that show the distribution of ACMV and EACMV across the regions surveyed.

Value of the Data
• The two years field survey data presented here provides an update on the distribution of cassava begomoviruses in Nigeria since the last surveys conducted over ten years ago. • The data presented here is useful to governments and agricultural stakeholders who need to plan and implement interventions towards the management of cassava begomoviruses in Nigeria. • The data presented here could serve as baseline for future endeavours at mapping the distribution of cassava mosaic begomoviruses. • Data could be used to model disease spread pattern.

Data Description
The dataset provided with this submission contains field and laboratory results of samples collected during surveys conducted in 2015 and 2017 across the South West and North Central regions of Nigeria ( Fig. 1 ). A total of 184 and 328 cassava farms were surveyed in 2015 and 2017, respectively from which 613 and 704 cassava leaf samples were collected and analysed ( Table 1 ).

Dataset documentation
The dataset is provided as long form tables in an excel file with three worksheets as contained in Table 2 . Variable information for each worksheet is provided in Table 3 .

Table 2
Details of worksheets in the provided dataset.

Sheet Name Info
Field Contains data collected on the field such as location, CMD symptom severity and CMD incidence Lab Contains data for each sample analysed Field_Lab Contains laboratory data aggregated by field

Result
Aggregated laboratory results by field. There are 5 possible outcomes here ACMV -A field in which only ACMV is found to be infecting plants EACMV -A field in which only EACMV is found to be infecting plants EACMV + ACMV -A field in which both EACMV and ACMV occur but not as a mixed infection. i.e both viruses singly infecting plants in one field Mixed -A field in which ACMV and EACMV are found to be infecting the sample plant.

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.

a. 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 .

b. Origin of infection and whitefly abundance
Summary plot showing the proportion of infections originating from whitefly vector transmission versus infections as a result of the propagation of infected cuttings is presented in Fig. 2 . Summary plots for whitefly abundance across the states surveyed is presented in Fig. 3 .

Survey
We conducted surveys of cassava farms across the South West and North Central regions of Nigeria in 2015 and 2017.

Sampling
Sampling was performed following previously described methods with slight modifications [1] . 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 [2] . 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.

DNA extraction
Extraction of DNA was carried out following the methods of Dellaporta et al. [6] . The concentrations of the extracted DNA were assessed using Nano Drop 20 0 0 spectrophotometer (Thermo Fisher Scientific, Waltham, Massachusetts, USA) and adjusted to 50 ng/μl for PCR.

PCR
The isolated DNA were screened for ACMV and EACMV by polymerase chain reaction according to the methods of Fondong et al. [7] . 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, Madisson 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).

Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships which have, or could be perceived to have, influenced the work reported in this article.