Inferring_pneumococcal_transmission_routes_to_infants_during_a_cluster_randomised_vaccine_trial_in_Nha_Trang__Vietnam. Inferring_pneumococcal_transmission_routes_to_infants_during_a_cluster_randomised_vaccine_trial_in_Nha_Trang__Vietnam

Background and goals A cluster randomised trial in Nha Trang, Vietnam was initiated to assess the potential non-inferiority of a reduced dose schedule of pneumococcal conjugate vaccine (PCV) at a population level. The trial is funded by the Bill and Melinda Gates foundation and is set to conclude in 2021. Co-applicants for the grant were Lay-Myint Yoshida, Kim Mulholland and Stefan Flasche. Also, several trials measuring the efficacy of such reduced dose schedule in comparison to common 3-dose schedules via carriage or immunogenicity endpoints are now underway. A key gap in the understanding of the prospects of such a reduced dose schedule and the ability to extrapolate findings across settings is the understanding of transmission pathways for pneumococcal infections in those infants who will receive less direct protection in a reduced dose schedule. The overarching goal of this study is to establish the transmission pathways for pneumococcal infection in young infants to quantify the risks for a cost saving reduced dose vaccine schedule. This will require addressing a number of scientifically interesting and challenging questions on the way that include eg the inference of transmission events and the direction of transmission from cross-sectional data, as well as the statistically appropriate inclusion of individual-level contact patterns from a nested contact study into the phylogenetic inference. Ultimately the results from the phylogenetic analyses on transmission events will be embedded into a transmission modelling framework to assess risk factors for transmission, account for unobserved carriage and transmission events and the ability to extrapolate results to other settings. #Description of Samples As part of the ongoing vaccine trial in Nha Trang cross-sectional nasopharyngeal carriage samples of 1440 infants, 1440 toddler and their respective caretakers are obtained. The project will deep sequence 2500 samples that are positive for S. pneumoniae. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/