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

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Juscamayta-López, E.
Carhuaricra D.
Tarazona, D.
Valdivia, F.
Rojas, N.
Maturrano L.
Gavilán R.
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John Wiley and Sons Inc
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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. © 2021 Wiley Periodicals LLC
We are greatly grateful to all health personnel of Peru, especially to members of the Respiratory Virus Laboratory from NHI-Peru for their dedication in providing continued diagnostic and high-quality care during the pandemic. The authors would like to express our deep gratitude to Dr. Kelly Levano for his critical review of this manuscript. In addition, we wish to thank Guillermo Trujillo and members of the Respiratory Infectious Diseases Laboratory from NHI-Peru, especially Helen Horna and Liza Linares for their support for the Whole-Genome Sequencing. This work was supported by the National Institute of Health of Peru and the CONCYTEC-FONDECYT Program of Proyectos Especiales: Respuesta al COVID-19 2020-01-01 [grant number 034-2020-FONDECYT].
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whole-genome sequencing, evolution, molecular epidemiology, phylogenomics, SARS-CoV-2, transmission