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.
Keywords: COVID-19; SARS-CoV-2; coinfection; iSNVs; recombination.
Copyright © 2022 Francisco Junior, Almeida, Lamarca, Cavalcante, Martins, Gerber, Guimarães, Salviano, dos Santos, de Oliveira, de Souza, de Carvalho, Ribeiro, Carvalho, da Silva, Garcia, de Souza, da Silva, Ribeiro, Cavalcanti, de Mello, Tanuri and Vasconcelos.