Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru

Santiago Justo Arevalo (), Carmen Sofia Uribe Calampa, Cinthy Jimenez Silva, Mauro Quiñones Aguilar, Remco Bouckaert and Joao Renato Rebello Pinho
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Santiago Justo Arevalo: Universidad Ricardo Palma
Carmen Sofia Uribe Calampa: Universidad Ricardo Palma
Cinthy Jimenez Silva: University of Auckland
Mauro Quiñones Aguilar: Universidad Ricardo Palma
Remco Bouckaert: University of Auckland
Joao Renato Rebello Pinho: Laboratório Clínico do Hospital Israelita Albert Einstein

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: Abstract At over 0.6% of the population, Peru has one of the highest SARS-CoV-2 mortality rate in the world. Much effort to sequence genomes has been done in this country since mid-2020. However, an adequate analysis of the dynamics of the variants of concern and interest (VOCIs) is missing. We investigated the dynamics of the COVID-19 pandemic in Peru with a focus on the second wave, which had the greatest case fatality rate. The second wave in Peru was dominated by Lambda and Gamma. Analysis of the origin of Lambda shows that it most likely emerged in Peru before the second wave (June–November, 2020). After its emergence it reached Argentina and Chile from Peru where it was locally transmitted. During the second wave in Peru, we identify the coexistence of two Lambda and three Gamma sublineages. Lambda sublineages emerged in the center of Peru whereas the Gamma sublineages more likely originated in the north-east and mid-east. Importantly, it is observed that the center of Peru played a prominent role in transmitting SARS-CoV-2 to other regions within Peru.

Date: 2023
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DOI: 10.1038/s41467-023-39216-8

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