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Francisco Junior, Ronaldo da Silva; de Almeida, Luiz G P; 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
Frontiers in public health, 02/2022, Volume: 10Journal Article
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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