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

Author

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  • Santiago Justo Arevalo

    (Universidad Ricardo Palma
    Laboratório Clínico do Hospital Israelita Albert Einstein
    Universidade de São Paulo)

  • 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
    University of São Paulo School of Medicine)

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.

Suggested Citation

  • Santiago Justo Arevalo & Carmen Sofia Uribe Calampa & Cinthy Jimenez Silva & Mauro Quiñones Aguilar & Remco Bouckaert & Joao Renato Rebello Pinho, 2023. "Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39216-8
    DOI: 10.1038/s41467-023-39216-8
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    1. Tiago Gräf & Alexander A. Martinez & Gonzalo Bello & Simon Dellicour & Philippe Lemey & Vittoria Colizza & Mattia Mazzoli & Chiara Poletto & Vanessa Leiko Oikawa Cardoso & Alexandre Freitas Silva & Fe, 2024. "Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean," Nature Communications, Nature, vol. 15(1), pages 1-11, December.

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