Severe acute respiratory syndrome coronavirus 2 with intra-host recombination during superinfection with Alpha and Epsilon variants

We detected an instance of SARS-CoV-2 superinfection, whereby an individual was simultaneously infected with two distinct viral variants, Alpha (B.1.1.7) and Epsilon (B.1.429). Full genome sequencing from independent extracts indicate that the Alpha variant alleles comprised between 70-80% of the sample, whereas the Epsilon variant alleles comprised between 20-30% of the sample. Analysis of the genome assemblies as well as cloned sequences revealed the presence of numerous recombinant haplotypes spanning the genome, particularly in spike, N, and ORF8 regions. Here we provide the raw reads for the extracts as well as the cloned sequences.