Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

Abstract

Background: Between November 2021 and February 2022, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events.

Methods: We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant.

Findings: We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5' end of the viral genome was from the Delta genome and the 3' end from Omicron, including the majority of the spike protein gene, though the breakpoints were different.

Conclusions: Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared with the circulating Omicron lineages.

Funding: This research was supported by the NIH RADx initiative and by the Centers for Disease Control Contract 75D30121C12730 (Helix).

Keywords: BA.1; Delta; Omicron; RNA virus; SARS-CoV-2; Translation to patients; alternative allele fraction; breakpoint; co-infection; recombination; sequencing.

Graphical abstract

Figure 1

Co-circulation of Delta and Omicron variants in the United States Fraction of lineages sequenced per week in the United States. Delta includes B.1.617.2 and all lineages starting with AY. Delta: orange. Omicron: light blue (BA.1), blue (BA.1.1), and navy blue (BA.2). The week of collection of the sample is on the x axis. See also Tables S1 and S2.

Figure 2

Co-infection with Delta and Omicron variants (A) Schematic of a co-infection and the impact on the sequencing output. (B) Three example graphs representing the alternative allele fraction for each mutation. Forty-seven mutations are plotted in order of their position on the SARS-CoV-2 genome from 5′ to 3′. Genes are separated by dashed vertical lines. Sixteen mutations specific to Delta are represented in orange. Nineteen mutations specific to Omicron and shared by its BA.1 and BA.2 sublineages are represented in blue. Five mutations specific to BA.1 (and BA.1.1) are in light blue. The defining BA.1.1 mutation is in black, and 6 mutations specific to BA.2 are in magenta. The graphs for all 18 co-infections are in Figure S1. (C) The difference of Delta fraction and Omicron fraction is plotted for the initial sample and the replicate sequenced after a new RNA extraction. Dashed lines connect identical samples. Orange dots represent samples with a majority of Delta. Blue dots represent samples with a majority of Omicron. (D) The difference of Delta fraction and Omicron fraction for the initial sample is plotted against the collection week of the sample. Orange dots represent samples with a majority of Delta. Blue dots represent samples with a majority of Omicron. See also Figure S2 and Tables S3, S4, and S5.

Figure 3

Evidence of Delta, Omicron, and recombinant read pairs in HMIX16 (A) Graph representing the alternative allele fraction for each mutation of sample HMIX16. Forty-seven mutations are plotted in order of their position on the SARS-CoV-2 genome from 5′ to 3′. Genes are separated by dashed vertical lines. Sixteen mutations specific to Delta are represented in orange. Nineteen mutations specific to Omicron and shared by its sublineages BA.1 and BA.2 are represented in blue. Five mutations specific to BA.1 (and BA.1.1) are in light blue. One BA.1.1 mutation is in black, and 6 mutations specific to BA.2 are in magenta. The gray box represents the region where the alternative allele fraction changes. (B) An IGV view of the alignments for HMIX16, subsampled to only include read pairs where the first in pair covers the S:156/157del position and the second in pair covers the S:212del position. Read pairs representing three mutation profiles are present: (1) supporting Delta mutations only (7 read pairs), (2) supporting Omicron mutations only (10 read pairs), and (3) supporting a Delta-Omicron recombinant (4 read pairs) marked with a green arrow. Mutations specific to Delta are represented in orange. Mutations specific to Omicron are represented in blue. Read pairs that do not span these mutations are not shown.

Figure 4

Infection with clonal Delta-Omicron recombinants (A) Schematic of the impact of an infection from a virus resulting from the recombination of Delta and Omicron on the sequencing output. (B) Graphs representing the alternative allele fraction for each mutation. Forty-seven mutations are plotted in order of their position on the SARS-CoV-2 genome from 5′ to 3′. Genes are separated by dashed vertical lines. Sixteen mutations specific to Delta are represented in orange. Nineteen mutations specific to Omicron and shared by its sublineages BA.1 and BA.2 are represented in blue. Five mutations specific to BA.1 (and BA.1.1) are in light blue. One BA.1.1 mutation is in black, and 6 mutations specific to BA.2 are in magenta. The gray box represents the homologous region where the breakpoint of the recombination is. See also Figure S3 and Tables S6 and S7.