Using multiple sampling strategies to estimate SARS-CoV-2 epidemiological parameters from genomic sequencing data

Using multiple sampling strategies to estimate SARS-CoV-2 epidemiological parameters from genomic sequencing data

Abstract The choice of viral sequences used in genetic and epidemiological analysis is important as it can induce biases that detract from the value of these rich datasets. This raises questions about how a set of sequences should be chosen for analysis. We provide insights on these largely understudied problems using SARS-CoV-2 genomic sequences from Hong Kong, China, and the Amazonas State, Brazil. We consider multiple sampling schemes which were used to estimate Rt and rt as well as related …