AUTHOR=Francisco Junior Ronaldo da Silva , Almeida Luiz G. P. de , Lamarca Alessandra P. , Cavalcante Liliane , Martins Yasmmin , Gerber Alexandra L. , Guimarães Ana Paula de C. , Salviano Ricardo Barbosa , dos Santos Fernanda Leitão , de Oliveira Thiago Henrique , de Souza Isabelle Vasconcellos , de Carvalho Erika Martins , Ribeiro Mario Sergio , Carvalho Silvia , da Silva Flávio Dias , Garcia Marcio Henrique de Oliveira , de Souza Leandro Magalhães , da Silva Cristiane Gomes , Ribeiro Caio Luiz Pereira , Cavalcanti Andréa Cony , de Mello Claudia Maria Braga , Tanuri Amilcar , Vasconcelos Ana Tereza R. TITLE=Emergence of Within-Host SARS-CoV-2 Recombinant Genome After Coinfection by Gamma and Delta Variants: A Case Report JOURNAL=Frontiers in Public Health VOLUME=10 YEAR=2022 URL=https://www.frontiersin.org/journals/public-health/articles/10.3389/fpubh.2022.849978 DOI=10.3389/fpubh.2022.849978 ISSN=2296-2565 ABSTRACT=

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.