IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-39216-8.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-39216-8
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-39216-8?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Thomas Hale & Noam Angrist & Rafael Goldszmidt & Beatriz Kira & Anna Petherick & Toby Phillips & Samuel Webster & Emily Cameron-Blake & Laura Hallas & Saptarshi Majumdar & Helen Tatlow, 2021. "A global panel database of pandemic policies (Oxford COVID-19 Government Response Tracker)," Nature Human Behaviour, Nature, vol. 5(4), pages 529-538, April.
    2. Egon A. Ozer & Lacy M. Simons & Olubusuyi M. Adewumi & Adeola A. Fowotade & Ewean C. Omoruyi & Johnson A. Adeniji & Oluseyi A. Olayinka & Taylor J. Dean & Janet Zayas & Pavan P. Bhimalli & Michelle K., 2022. "Multiple expansions of globally uncommon SARS-CoV-2 lineages in Nigeria," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    3. Erik Volz & Swapnil Mishra & Meera Chand & Jeffrey C. Barrett & Robert Johnson & Lily Geidelberg & Wes R. Hinsley & Daniel J. Laydon & Gavin Dabrera & Áine O’Toole & Robert Amato & Manon Ragonnet-Cron, 2021. "Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England," Nature, Nature, vol. 593(7858), pages 266-269, May.
    4. Edouard Mathieu & Hannah Ritchie & Esteban Ortiz-Ospina & Max Roser & Joe Hasell & Cameron Appel & Charlie Giattino & Lucas Rodés-Guirao, 2021. "A global database of COVID-19 vaccinations," Nature Human Behaviour, Nature, vol. 5(7), pages 947-953, July.
    5. Petra Mlcochova & Steven A. Kemp & Mahesh Shanker Dhar & Guido Papa & Bo Meng & Isabella A. T. M. Ferreira & Rawlings Datir & Dami A. Collier & Anna Albecka & Sujeet Singh & Rajesh Pandey & Jonathan B, 2021. "SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion," Nature, Nature, vol. 599(7883), pages 114-119, November.
    6. Philippe Lemey & Samuel L. Hong & Verity Hill & Guy Baele & Chiara Poletto & Vittoria Colizza & Áine O’Toole & John T. McCrone & Kristian G. Andersen & Michael Worobey & Martha I. Nelson & Andrew Ramb, 2020. "Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    7. Antanas Kalkauskas & Umberto Perron & Yuxuan Sun & Nick Goldman & Guy Baele & Stephane Guindon & Nicola De Maio, 2021. "Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk," PLOS Computational Biology, Public Library of Science, vol. 17(1), pages 1-27, January.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    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.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Ilias Chronopoulos & Katerina Chrysikou & George Kapetanios & James Mitchell & Aristeidis Raftapostolos, 2023. "Deep Neural Network Estimation in Panel Data Models," Working Papers 23-15, Federal Reserve Bank of Cleveland.
    2. Emily Cameron-Blake & Helen Tatlow & Bernardo Andretti & Thomas Boby & Kaitlyn Green & Thomas Hale & Anna Petherick & Toby Phillips & Annalena Pott & Adam Wade & Hao Zha, 2023. "A panel dataset of COVID-19 vaccination policies in 185 countries," Nature Human Behaviour, Nature, vol. 7(8), pages 1402-1413, August.
    3. John Gibson, 2023. "Jabbing the economy back to life?," Applied Economics Letters, Taylor & Francis Journals, vol. 30(21), pages 2999-3005, December.
    4. Gillitzer, Christian & Prasad, Nalini, 2024. "The effect of school closures on standardized test scores: Evidence under zero-COVID policies," Economics of Education Review, Elsevier, vol. 102(C).
    5. Caixia Wang & Huijie Li, 2023. "Variation in Global Policy Responses to COVID-19: A Bidirectional Analysis," IJERPH, MDPI, vol. 20(5), pages 1-13, February.
    6. Mary M. Barker & Kadri Kõiv & Ingibjörg Magnúsdóttir & Hannah Milbourn & Bin Wang & Xinkai Du & Gillian Murphy & Eva Herweijer & Elísabet U. Gísladóttir & Huiqi Li & Anikó Lovik & Anna K. Kähler & Arc, 2024. "Mental illness and COVID-19 vaccination: a multinational investigation of observational & register-based data," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    7. Joel O. Wertheim & Jade C. Wang & Mindy Leelawong & Darren P. Martin & Jennifer L. Havens & Moinuddin A. Chowdhury & Jonathan E. Pekar & Helly Amin & Anthony Arroyo & Gordon A. Awandare & Hoi Yan Chow, 2022. "Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    8. Galdikiene, Laura & Jaraite, Jurate & Kajackaite, Agne, 2024. "Effects of cooperative and uncooperative narratives on trust during the COVID-19 pandemic: Experimental evidence," Journal of Behavioral and Experimental Economics (formerly The Journal of Socio-Economics), Elsevier, vol. 112(C).
    9. Salvatore F. Pileggi, 2022. "Holistic Resilience Index: measuring the expected country resilience to pandemic," Quality & Quantity: International Journal of Methodology, Springer, vol. 56(6), pages 4107-4127, December.
    10. Edyth Parker & Catelyn Anderson & Mark Zeller & Ahmad Tibi & Jennifer L. Havens & Geneviève Laroche & Mehdi Benlarbi & Ardeshir Ariana & Refugio Robles-Sikisaka & Alaa Abdel Latif & Alexander Watts & , 2022. "Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    11. Reyna-Lara, Adriana & Soriano-Paños, David & Arenas, Alex & Gómez-Gardeñes, Jesús, 2022. "The interconnection between independent reactive control policies drives the stringency of local containment," Chaos, Solitons & Fractals, Elsevier, vol. 158(C).
    12. Aizenman, Joshua & Cukierman, Alex & Jinjarak, Yothin & Nair-Desai, Sameer & Xin, Weining, 2022. "Gaps between official and excess Covid-19 mortality measures: The effects of institutional quality and vaccinations," Economic Modelling, Elsevier, vol. 116(C).
    13. Polyzos, Efstathios & Fotiadis, Anestis & Huan, Tzung-Cheng, 2023. "From Heroes to Scoundrels: Exploring the effects of online campaigns celebrating frontline workers on COVID-19 outcomes," Technology in Society, Elsevier, vol. 72(C).
    14. Hannah Carver & Tracey Price & Danilo Falzon & Peter McCulloch & Tessa Parkes, 2022. "Stress and Wellbeing during the COVID-19 Pandemic: A Mixed-Methods Exploration of Frontline Homelessness Services Staff Experiences in Scotland," IJERPH, MDPI, vol. 19(6), pages 1-20, March.
    15. Xiao Chen & Hanwei Huang & Jiandong Ju & Ruoyan Sun & Jialiang Zhang, 2022. "Endogenous cross-region human mobility and pandemics," CEP Discussion Papers dp1860, Centre for Economic Performance, LSE.
    16. Yekaterina Chzhen & Jennifer Symonds & Dympna Devine & Júlia Mikolai & Susan Harkness & Seaneen Sloan & Gabriela Martinez Sainz, 2022. "Learning in a Pandemic: Primary School children’s Emotional Engagement with Remote Schooling during the spring 2020 Covid-19 Lockdown in Ireland," Child Indicators Research, Springer;The International Society of Child Indicators (ISCI), vol. 15(4), pages 1517-1538, August.
    17. Mirko Licchetta & Giovanni Mattozzi & Rafal Raciborski & Rupert Willis, 2022. "Economic Adjustment in the Euro Area and the United States during the COVID-19 Crisis," European Economy - Discussion Papers 160, Directorate General Economic and Financial Affairs (DG ECFIN), European Commission.
    18. S. D. Sreeganga & Ajay Chandra & Arkalgud Ramaprasad, 2021. "Ontological Analysis of COVID-19 Vaccine Roll out Strategies: A Comparison of India and the United States of America," IJERPH, MDPI, vol. 18(14), pages 1-18, July.
    19. Lucia Freira & Marco Sartorio & Cynthia Boruchowicz & Florencia Lopez Boo & Joaquin Navajas, 2021. "The interplay between partisanship, forecasted COVID-19 deaths, and support for preventive policies," Palgrave Communications, Palgrave Macmillan, vol. 8(1), pages 1-10, December.
    20. Galil, Koresh & Varon, Eva, 2024. "National culture and banks stock volatility," Journal of International Financial Markets, Institutions and Money, Elsevier, vol. 91(C).

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39216-8. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.