Frontiers in Public Health (Feb 2022)

Emergence of Within-Host SARS-CoV-2 Recombinant Genome After Coinfection by Gamma and Delta Variants: A Case Report

  • Ronaldo da Silva Francisco Junior,
  • Luiz G. P. de Almeida,
  • Alessandra P. Lamarca,
  • Liliane Cavalcante,
  • Yasmmin Martins,
  • Alexandra L. Gerber,
  • Ana Paula de C. Guimarães,
  • Ricardo Barbosa Salviano,
  • Fernanda Leitão dos Santos,
  • Thiago Henrique de Oliveira,
  • Isabelle Vasconcellos de Souza,
  • Erika Martins de Carvalho,
  • Mario Sergio Ribeiro,
  • Silvia Carvalho,
  • Flávio Dias da Silva,
  • Marcio Henrique de Oliveira Garcia,
  • Leandro Magalhães de Souza,
  • Cristiane Gomes da Silva,
  • Caio Luiz Pereira Ribeiro,
  • Andréa Cony Cavalcanti,
  • Claudia Maria Braga de Mello,
  • Amilcar Tanuri,
  • Ana Tereza R. Vasconcelos

DOI
https://doi.org/10.3389/fpubh.2022.849978
Journal volume & issue
Vol. 10

Abstract

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In this study, we report the first case of intra-host SARS-CoV-2 recombination during a coinfection by the variants of concern (VOC) AY.33 (Delta) and P.1 (Gamma) supported by sequencing reads harboring a mosaic of lineage-defining mutations. By using next-generation sequencing reads intersecting regions that simultaneously overlap lineage-defining mutations from Gamma and Delta, we were able to identify a total of six recombinant regions across the SARS-CoV-2 genome within a sample. Four of them mapped in the spike gene and two in the nucleocapsid gene. We detected mosaic reads harboring a combination of lineage-defining mutations from each VOC. To our knowledge, this is the first report of intra-host RNA-RNA recombination between two lineages of SARS-CoV-2, which can represent a threat to public health management during the COVID-19 pandemic due to the possibility of the emergence of viruses with recombinant phenotypes.

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