title: Quantifying transmission by stage of infection in the field: the example of SIV-1 and STLV-1 infecting mandrills.
abstract: The early stage of viral infection is often followed by an important increase of viral load and is generally considered to be the most at risk for pathogen transmission. Most methods quantifying the relative importance of the different stages of infection were developed for studies aimed at measuring HIV transmission in Humans. However, they cannot be transposed to animal populations in which less information is available. Here we propose a general method to quantify the importance of the early and late stages of the infection on micro-organism transmission from field studies. The method is based on a state space dynamical model parameterized using Bayesian inference. It is illustrated by a 28 years dataset in mandrills infected by Simian Immunodeficiency Virus type-1 (SIV-1) and the Simian T-Cell Lymphotropic Virus type-1 (STLV-1). For both viruses we show that transmission is predominant during the early stage of the infection (transmission ratio for SIV-1: 1.16 [0.0009; 18.15] and 9.92 [0.03; 83.8] for STLV-1). However, in terms of basic reproductive number (R0 ), which quantifies the weight of both stages in the spread of the virus, the results suggest that the epidemics of SIV-1 and STLV-1 are mainly driven by late transmissions in this population.
authors.affiliation: Université de Lyon, F-69000, Lyon ; Université Lyon 1 ; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France; LabEx ECOFECT - Ecoevolutionary Dynamics of Infectious Diseases, Université de Lyon, Lyon, France.
authors.forename: Marion
authors.initials: M
authors.lastname: Roussel
authors.forename: Dominique
authors.initials: D
authors.lastname: Pontier
authors.forename: Mirdad
authors.initials: M
authors.lastname: Kazanji
authors.forename: Barthélémy
authors.initials: B
authors.lastname: Ngoubangoye
authors.forename: Renaud
authors.initials: R
authors.lastname: Mahieux
authors.forename: Delphine
authors.initials: D
authors.lastname: Verrier
authors.forename: David
authors.initials: D
authors.lastname: Fouchet
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D006800:Deltaretrovirus Infections / Q000453:epidemiology / Q000635:transmission* / Q000662:veterinary / Q000821:virology; D018562:Disease Transmission, Infectious; D005260:Female; D008297:Male; D048528:Mandrillus; D015233:Models, Statistical; D016097:Simian Acquired Immunodeficiency Syndrome / Q000453:epidemiology / Q000635:transmission* / Q000821:virology; D015302:Simian Immunodeficiency Virus; D015303:Simian T-lymphotropic virus 1; D019562:Viral Load
keywords: Bayesian inference; epidemic stochastic modeling; non-human primates natural population; state space model