Phylogenomics reveals multiple introductions and early spread of SARS‐CoV‐2 into Peru

Juscamayta‐López, Eduardo; Carhuaricra, Dennis; Tarazona, David; Valdivia, Faviola; Rojas, Nancy; Maturrano, Lenin; Gavilán, Ronnie

Peru has become one of the countries with the highest mortality rates from the current coronavirus disease 2019 (COVID‐19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). To investigate early transmission events and the genomic diversity of SARS‐CoV‐2 isolates circulating in Peru in the early COVID‐19 pandemic, we analyzed 3472 viral genomes, of which 149 were from Peru. Phylogenomic analysis revealed multiple and independent introductions of the virus likely from Europe and Asia and a high diversity of genetic lineages circulating in Peru. In addition, we found evidence for community‐driven transmission of SARS‐CoV‐2 as suggested by clusters of related viruses found in patients living in different regions of Peru.