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Additionally, only a subset of the cases, 10-50% depending on sample size, need to have detailed genetic data for our method to perform well. We show how these probabilities can be used to estimate the average effective reproductive number and apply our method to a tuberculosis outbreak in Hamburg, Germany. CONCLUSIONS Our method is a novel way to infer transmission dynamics in any dataset when only a subset of cases has rich contact investigation and/or genetic data. © The Author(s) 2020; all rights reserved. Published by Oxford Univer