  Genomic surveillance of SARS-CoV-2 has been instrumental in tracking the
spread and evolution of the virus during the pandemic. The availability of
SARS-CoV-2 molecular sequences isolated from infected individuals, coupled with
phylodynamic methods, have provided insights into the origin of the virus, its
evolutionary rate, the timing of introductions, the patterns of transmission,
and the rise of novel variants that have spread through populations. Despite
enormous global efforts of governments, laboratories, and researchers to
collect and sequence molecular data, many challenges remain in analyzing and
interpreting the data collected. Here, we describe the models and methods
currently used to monitor the spread of SARS-CoV-2, discuss long-standing and
new statistical challenges, and propose a method for tracking the rise of novel
variants during the epidemic.
