We reconstructed the SARS-CoV-2 epidemic caused by Omicron variant in Puerto Rico by sampling genomes collected during October 2021-May 2022. Our study revealed that Omicron BA.1 emerged and replaced Delta as the predominant variant in December 2021. Increased transmission rates and a dynamic landscape of Omicron sublineage infections followed.
Keywords: COVID-19; Delta; NGS; Omicron; Puerto Rico; SARS-CoV-2; coronavirus disease; genomic surveillance; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses.