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

2022; Frontiers Media; Volume: 10; Linguagem: Inglês

10.3389/fpubh.2022.849978

2296-2565

Ronaldo da Silva Francisco, Luiz Gonzaga Paula de Almeida, Alessandra P. Lamarca, Liliane Cavalcante, Yasmmin Martins, Alexandra Lehmkuhl Gerber, Ana Paula de Campos Guimarães, Ricardo Barbosa Salviano, Fernanda Leitão dos Santos, Thiago Henrique de Oliveira, Isabelle Vasconcellos de Souza, Erika Martins de Carvalho, Mário Sérgio Ribeiro, Silvia Carvalho, Flávio Dias da Silva, Márcio Henrique de Oliveira Garcia, Leandro Magalhães de Souza, Cristiane Gomes da Silva, Caio Luiz Pereira Ribeiro, Andréa Cony Cavalcanti, Claudia Maria Braga de Mello, Amílcar Tanuri, Ana Tereza Ribeiro de Vasconcelos,

Viral gastroenteritis research and epidemiology

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.