PCI Ecology

Direct submissions to PCI Ecology from bioRxiv.org are possible using the B2J service

Title *

Detecting within-host interactions using genotype combination prevalence datause asterix (*) to get italics

Authors *

Samuel Alizon, Carmen Lía Murall, Emma Saulnier, Mircea T SofoneaPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year *

2018

Picture *

Abstract *

<p>Parasite genetic diversity can provide information on disease transmission dynamics but most methods ignore the exact combinations of genotypes in infections. We introduce and validate a new method that combines explicit epidemiological modelling of coinfections and regression Approximate Bayesian Computing (ABC) to detect within-host interactions. Using genital infections by different types of Human Papillomaviruses (HPVs) as a test case, we show that, if sufficiently strong, within-host parasite interactions can be detected from epidemiological data and that this detection is robust even in the face of host heterogeneity in behaviour. These results suggest that the combination of mathematical modelling and sophisticated inference techniques is promising to extract additional epidemiological information from existing datasets.</p>

Indicate the full web address (DOI or URL) giving public access to these data (if you have any problems with the deposit of your data, please contact contact@ecology.peercommunityin.org). In case all raw data are included in the preprint, indicate the DOI or URL of the preprint. *

https://www.biorxiv.org/content/10.1101/256586v3.supplementary-materialYou should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

Indicate the full web address (DOI or URL) giving public access to these scripts (if you have any problems with the deposit of your scripts, please contact contact@ecology.peercommunityin.org). In case all raw scripts are included in the preprint, indicate the DOI or URL of the preprint. *

You should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://

Indicate the full web address (DOI, SWHID or URL) giving public access to these codes (if you have any problems with the deposit of your codes, please contact contact@ecology.peercommunityin.org). In case all raw codes are included in the preprint, indicate the DOI or URL of the preprint. *

You should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://

Keywords (optional)

modelling, virus, multiple infections, Approximate Bayesian Computing, within-host interacvtions

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields *

Eco-immunology & Immunity, Epidemiology, Host-parasite interactions, Statistical ecology

Suggested reviewers - Suggest up to 10 reviewers (provide names and Email addresses). (Optional)

e.g. John Doe john@doe.com

No need for them to be recommenders of PCIEcology. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

Opposed reviewers - Suggest up to 5 people not to invite as reviewers. (Optional)

e.g. John Doe john@doe.com

Submission date

2018-02-01 09:23:26

Recommender

Dustin Brisson

Reviewers

Samuel Díaz Muñoz, Erick Gagne

or Register
Submit a preprint