bioRxiv preprint doi: https://doi.org/10.1101/2020.09.14.296814; this version posted September 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru Eduardo Juscamayta-López1,2*, David Tarazona1,2, Faviola Valdivia1, Nancy Rojas1, Dennis Carhuaricra2, Lenin Maturrano2, Ronnie Gavilán1 Affiliations: 1Instituto Nacional de Salud, Lima, Peru 2Universidad Nacional Mayor de San Marcos, Lima, Peru *Corresponding author Correspondence: Email:
[email protected],
[email protected] ABSTRACT Peru has become one of the countries with the highest mortality rate from the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. To investigate early transmission event and genomic diversity of SARS-CoV-2 isolates circulating in Peru, we analyzed a total of 3472 SARS-CoV-2 genomes, from which 149 ones were from Peru. Phylogenomic analysis revealed multiple and independent introductions of the virus mainly from Europe and Asia. 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 Peru regions. INTRODUCTION Severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2) is an emerging betacoronavirus responsible for the coronavirus disease 2019 (COVID-19) originated in December 2019 in Wuhan, China (1). Since then, the virus rapidly spread across the globe and was declared a pandemic on 11 March 2020 (2).