Rapid repeat infection of SARS-CoV-2 by two highly distinct delta-lineage viruses

Abstract

An instance of sequential infection of an individual with, firstly, the Delta variant and secondly a Delta-sub-lineage has been identified. The individual was found positive for the AY.26 lineage 22 days after being found positive for the Delta [B.1.617.2] variant. The viruses associated with the cases showed dramatic genomic difference, including 31 changes that resulted in deletions or amino acid substitutions. Seven of these differences were observed in the Spike protein. The patient in question was between 30 and 35 years old and had no underlying health conditions. Though singular, this case illustrates the possibility that infection with the Delta variant may not itself be fully protective against a population of SARS-CoV-2 variants that are becoming increasingly diverse.

Keywords: SARS-CoV-2; delta; mutations; reinfection.

Fig. 1

A phylogenetic tree describing the genomic relationships of Case A and Case B relative to other cases, either from the same County as the patient, or elicited from contact tracing and investigation. C = co-community member; * = co-worker; X = direct contact to patient.

Fig. 2

Alignment generated from the FASTQ files of sequences from Case A and B using CLC Genomic Workbench. Mutations [SNV and MNV] in reference to MN908947.3, are presented by red bars in the associated variant track panels of each specimen. Unique mutations in Case A and B, with respect to each other, are marked with asterisks [Red = Case A specific mutations, Green = Case B specific mutations]. Synonymous mutations and mutations in the non-coding region are highlighted with green shadow. C. Frequency [percent] of Case B specific mutations in the sequences from Case A specimen. D. Frequency [percent] of Case A specific mutations in the sequences from Case B specimen. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.) MNV = Multi-nucleotide variant; SNV = single nucleotide variant.