Excel File Contains: Data from paper entitled: Comparison of loop-mediated isothermal amplification (LAMP) and PCR for the diagnosis of infection with Trypanosoma brucei spp. in equids in The Gambia. Authors Lauren Gummery1, Saloum Jallow2, Alexandra G. Raftery1, Euan Bennet1, Jean Rodgers3, David G.M. Sutton1 Affiliations 1.Weipers Equine Centre, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom, GH61 1QH. 2.Gambia Horse and Donkey Trust, Sambel Kunda, Central River District, The Gambia 3.Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom, GH61 1QH Funding: This work was supported by The Royal Society of Tropical Medicine and Hygiene (Grant no. GR000850), The Donkey Sanctuary (grant awarded to DGMS); and The University of Glasgow Small Grants Fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Ethics: Animal use (infected mouse blood) was authorized in the United Kingdom under the Animals (Scientific Procedures) Act 1986 and approved by the University of Glasgow Ethical Review Committee. Ethical approval was provided by University of Glasgow School of Veterinary Medicine Research Ethics Committee (Reference 39a/17), and the Gambian Ministry of Agriculture. Procedures were performed by trained veterinarians or local veterinary technicians and were of direct benefit to the animals (categorised under Veterinary Surgeons Act 1966). Abstract: Infection of equids with Trypanosoma 23 brucei (T. brucei) species is of socioeconomic importance across sub-Saharan Africa as the disease often progresses to cause fatal meningoencephalitis. Loop-mediated isothermal amplification (LAMP) has been developed as a cost effective molecular diagnostic test is potentially applicable to use in field-based laboratories. Part I: Threshold levels for T. brucei spp. detection by LAMP were determined using whole equine blood specimens spiked with known concentrations of parasites. Results were compared to OIE antemortem gold standard of T. brucei-PCR (TBR-PCR). Results 1: Threshold for detection of T. brucei spp. on extracted DNA from whole blood was 1 parasites/ml blood for LAMP and TBR-PCR, and there was excellent agreement (14/15) between tests at high (1 x 103/ml) concentrations of parasites. Detection threshold was 100 parasites/ml using LAMP on whole blood (LWB). Threshold for LWB improved to 10 parasites/ml with detergent included. Performance was excellent for LAMP at high (1 x 103/ml) concentrations of parasites (15/15, 100%) but was variable at lower concentrations. Agreement between tests was weak to moderate, with the highest for TBR42 PCR and LAMP on DNA extracted from whole blood (Cohen’s kappa 0.95, 95% CI 0.64-1.00). Part II: A prospective cross-sectional study of 44 working equids meeting clinical criteria for trypanosomiasis was undertaken in The Gambia. LAMP was evaluated against subsequent TBR-PCR. Results 2: Whole blood samples from 321 equines in The Gambia were processed under field conditions. There was weak agreement between LWB and TBR-PCR (Cohen’s kappa 0.34, 95% CI 0.19-0.49) but excellent agreement when testing CSF (100% agreement on 6 samples). Conclusions: Findings support that LAMP is comparable to PCR when used on CSF samples in the field, an important tool for clinical decision making. Results suggest repeatability is low in animals with low parasitaemia. Negative samples should be interpreted in the context of clinical presentation. Data Summary: Excel document: FinaldataPaper1submission Sheet 1: Raw data ser.dilution Positive and negative results for threshold serial dilution study. Samples were created at each packed cell volume (PCV) by serial dilution (10x) starting at 1 x 10^3 parasites/ml until 1 x 10^-3 parasites/ml. Each sample was then tested in triplicate to give a total of 21 samples at each PCV, and 15 at each parasite concentration. Restuls are also available for negative controls. Samples ar concentrations under which 3 negative results were obtained were not analysed. Sheet2: Codes for data All codes on remaining sheets are clarified. Sheet 3: Above 10^1 summary positives Threshold serial dilution study All results tested above 10^1 x parasites/ml are summarised for each PCV from 10-50% (triplicate results combined). Codes for different test methods are clarified on sheet 2. Sheet 4: Descriptive data Field based study Data for all individual animals sampled in the field is included. Each animal has a code (Column C) to preserve anonimity. Codes are as clarified on Sheet 2. Weight is in kg as estimated on a species specifc nomogram. Age is estimated from dentition Repeat examinations are included and clarified in Column M as months from initial examination. Where FTA cards were used for extraction (rather than whole blood) this is confirmed in Column L. Sheet 5: Final positives Field based study All animals (as described on Sheet 4) minus excluded individuals with missing data are included to report positive resuts, repeats are included All tests are as described on sheet 2. Results from PCR or LAMP from either DNA extracted from FTA cards or DNA extracted from whole blood are combined (Columns D and E) Column F denotes whether an individual had a positive result on more than 1 independent test. Column G denotes whether an individual had a positive result on any one or more tests.