Rhesus macaques self-curing from a schistosome infection can display complete immunity to challenge

The rhesus macaque provides a unique model of acquired immunity against schistosomes, which afflict >200 million people worldwide. By monitoring bloodstream levels of parasite-gut-derived antigen, we show that from week 10 onwards an established infection with Schistosoma mansoni is cleared in an exponential manner, eliciting resistance to reinfection. Secondary challenge at week 42 demonstrates that protection is strong in all animals and complete in some. Antibody profiles suggest that antigens mediating protection are the released products of developing schistosomula. In culture they are killed by addition of rhesus plasma, collected from week 8 post-infection onwards, and even more efficiently with post-challenge plasma. Furthermore, cultured schistosomula lose chromatin activating marks at the transcription start site of genes related to worm development and show decreased expression of genes related to lysosomes and lytic vacuoles involved with autophagy. Overall, our results indicate that enhanced antibody responses against the challenge migrating larvae mediate the naturally acquired protective immunity and will inform the route to an effective vaccine.

In vitro schistosomula treatment: we performed three biological replicates for the ATP assays, each containing schistosomula obtained from cercariae from different batches of infected snails, and each biological replicate included two technical replicates, each processed separately but in parallel. For the PI/FDA staining and ChIP-Seq assays, two biological replicates were performed. For the RNA-Seq assays, three biological replicates were performed.This information is described in the methods, the text and figure captions. Experimental findings were reliably reproduced by technical and biological replicates.CAA quantitation: one technical replicate. EPG: three technical replicates. Anti-SEA and anti-SCAP quantitation: two technical replicates. Anti-SWAP and anti-SPP quantitation: two technical replicates. Haematology, IP-10 and SAA quantitation, confocal microscopy: one technical replicate.
Randomization was not performed in the rhesus macaque population, since this study assessed changes after infection and after challenge in all individuals within the same experimental group.
Blinding was not performed since all study rhesus macaques belonged to one experimental group.
Briefly describe the study type including whether data are quantitative, qualitative, or mixed-methods (e.g. qualitative cross-sectional, quantitative experimental, mixed-methods case study).
State the research sample (e.g. Harvard university undergraduates, villagers in rural India) and provide relevant demographic information (e.g. age, sex) and indicate whether the sample is representative. Provide a rationale for the study sample chosen. For studies involving existing datasets, please describe the dataset and source.
Describe the sampling procedure (e.g. random, snowball, stratified, convenience). Describe the statistical methods that were used to predetermine sample size OR if no sample-size calculation was performed, describe how sample sizes were chosen and provide a rationale for why these sample sizes are sufficient. For qualitative data, please indicate whether data saturation was considered, and what criteria were used to decide that no further sampling was needed.
Provide details about the data collection procedure, including the instruments or devices used to record the data (e.g. pen and paper, computer, eye tracker, video or audio equipment) whether anyone was present besides the participant(s) and the researcher, and whether the researcher was blind to experimental condition and/or the study hypothesis during data collection. We require information from authors about some types of materials, experimental systems and methods used in many studies. Here, indicate whether each material, system or method listed is relevant to your study. If you are not sure if a list item applies to your research, read the appropriate section before selecting a response.
Indicate the start and stop dates of data collection. If there is a gap between collection periods, state the dates for each sample cohort.
If no data were excluded from the analyses, state so OR if data were excluded, provide the exact number of exclusions and the rationale behind them, indicating whether exclusion criteria were pre-established.
State how many participants dropped out/declined participation and the reason(s) given OR provide response rate OR state that no participants dropped out/declined participation.
If participants were not allocated into experimental groups, state so OR describe how participants were allocated to groups, and if allocation was not random, describe how covariates were controlled.
Briefly describe the study. For quantitative data include treatment factors and interactions, design structure (e.g. factorial, nested, hierarchical), nature and number of experimental units and replicates.
Describe the research sample (e.g. a group of tagged Passer domesticus, all Stenocereus thurberi within Organ Pipe Cactus National Monument), and provide a rationale for the sample choice. When relevant, describe the organism taxa, source, sex, age range and any manipulations. State what population the sample is meant to represent when applicable. For studies involving existing datasets, describe the data and its source.
Note the sampling procedure. Describe the statistical methods that were used to predetermine sample size OR if no sample-size calculation was performed, describe how sample sizes were chosen and provide a rationale for why these sample sizes are sufficient.
Describe the data collection procedure, including who recorded the data and how.
Indicate the start and stop dates of data collection, noting the frequency and periodicity of sampling and providing a rationale for these choices. If there is a gap between collection periods, state the dates for each sample cohort. Specify the spatial scale from which the data are taken If no data were excluded from the analyses, state so OR if data were excluded, describe the exclusions and the rationale behind them, indicating whether exclusion criteria were pre-established.
Describe the measures taken to verify the reproducibility of experimental findings. For each experiment, note whether any attempts to repeat the experiment failed OR state that all attempts to repeat the experiment were successful.
Describe how samples/organisms/participants were allocated into groups. If allocation was not random, describe how covariates were controlled. If this is not relevant to your study, explain why.
Describe the extent of blinding used during data acquisition and analysis. If blinding was not possible, describe why OR explain why blinding was not relevant to your study.
Describe the study conditions for field work, providing relevant parameters (e.g. temperature, rainfall).
State the location of the sampling or experiment, providing relevant parameters (e.g. latitude and longitude, elevation, water depth).
Describe the efforts you have made to access habitats and to collect and import/export your samples in a responsible manner and in compliance with local, national and international laws, noting any permits that were obtained (give the name of the issuing authority, the date of issue, and any identifying information).
Describe any disturbance caused by the study and how it was minimized. Tick this box to confirm that the raw and calibrated dates are available in the paper or in Supplementary Information.

Ethics oversight
Note that full information on the approval of the study protocol must also be provided in the manuscript. State the source of each cell line used.
Describe the authentication procedures for each cell line used OR declare that none of the cell lines used were authenticated.
Confirm that all cell lines tested negative for mycoplasma contamination OR describe the results of the testing for mycoplasma contamination OR declare that the cell lines were not tested for mycoplasma contamination.
Name any commonly misidentified cell lines used in the study and provide a rationale for their use.
Provide provenance information for specimens and describe permits that were obtained for the work (including the name of the issuing authority, the date of issue, and any identifying information).
Indicate where the specimens have been deposited to permit free access by other researchers.
If new dates are provided, describe how they were obtained (e.g. collection, storage, sample pretreatment and measurement), where they were obtained (i.e. lab name), the calibration program and the protocol for quality assurance OR state that no new dates are provided.
Identify the organization(s) that approved or provided guidance on the study protocol, OR state that no ethical approval or guidance was required and explain why not.

Policy information about studies involving animals; ARRIVE guidelines recommended for reporting animal research
Laboratory animals

Wild animals
Field-collected samples

Ethics oversight
Note that full information on the approval of the study protocol must also be provided in the manuscript.

Human research participants
Policy information about studies involving human research participants Population characteristics

Recruitment
Ethics oversight Note that full information on the approval of the study protocol must also be provided in the manuscript.

Clinical data Policy information about clinical studies
All manuscripts should comply with the ICMJEguidelines for publication of clinical research and a completedCONSORT checklist must be included with all submissions.

Clinical trial registration
Study protocol

Data collection
Outcomes Dual use research of concern Policy information about dual use research of concern

Hazards
Could the accidental, deliberate or reckless misuse of agents or technologies generated in the work, or the application of information presented in the manuscript, pose a threat to: This study did not involve wild animals This study did not involve samples collected from the field -Housing conditions of the rhesus macaques and experimental protocols used in the study were in strict accordance with the Ethical Principles in Animal Research adopted by the Conselho Nacional de Controle de Experimentação Animal (CONCEA) and were approved by the Institutional Animal Care and Use Committee of Instituto Butantan (CEUAIB 1388/ 15). The study was carried out in compliance with the ARRIVE guidelines. Design and execution of the study complied with the recommendations of the Weatherall report (2006) and with principles set out in the UK NC3Rs Guidelines "Primate accommodation, care and use (revised version, October 2017)" (http://www.nc3rs.org.uk/primatesguidelines).
-Housing conditions of the hamsters and experimental procedures used in this study were also in strict accordance with the Ethical Principles in Animal Research adopted by the CONCEA and the experimental protocol was approved by the Ethics Committee for Animal Experimentation of Butantan Institute (CEUAIB n! 6748040515).
-Housing conditions and experimentation with mice followed the recommendations from the Biology Department Ethics Committee, University of York, and experiments were performed on personal (PIL 50/592) and project licences (PPL 60/4340) issued to RAW.
Describe the covariate-relevant population characteristics of the human research participants (e.g. age, gender, genotypic information, past and current diagnosis and treatment categories). If you filled out the behavioural & social sciences study design questions and have nothing to add here, write "See above." Describe how participants were recruited. Outline any potential self-selection bias or other biases that may be present and how these are likely to impact results.
Identify the organization(s) that approved the study protocol.
Provide the trial registration number from ClinicalTrials.gov or an equivalent agency.
Note where the full trial protocol can be accessed OR if not available, explain why.
Describe the settings and locales of data collection, noting the time periods of recruitment and data collection.
Describe how you pre-defined primary and secondary outcome measures and how you assessed these measures.

April 2020
No Yes

Experiments of concern
Does the work involve any of these experiments of concern: No Yes Confirm that both raw and final processed data have been deposited in a public database such as GEO.
Confirm that you have deposited or provided access to graph files (e.g. BED files) for the called peaks.

Data access links
May remain private before publication. Flow Cytometry Plots Confirm that:

Files in database submission
The axis labels state the marker and fluorochrome used (e.g. CD4-FITC).
The axis scales are clearly visible. Include numbers along axes only for bottom left plot of group (a 'group' is an analysis of identical markers).
All plots are contour plots with outliers or pseudocolor plots.
A numerical value for number of cells or percentage (with statistics) is provided.