Evidence of co-infections during Delta and Omicron SARS-CoV-2 variants co-circulation through prospective screening and sequencing

The Omicron variant of concern: Diversification and convergent evolution in spike protein, and escape from anti-Spike monoclonal antibodies

“…Further complicating the landscape, several Delta-BA.1 ( Combes et al, 2022 ) and BA.1-BA.2 ( Gjorgjievska et al, 2022 , Vatteroni et al, 2022 ) co-infections have been reported.…”

Simultaneous co-infection with Omicron (B.1.1.529) and Delta (21A/478K.V1) SARS-CoV-2 variants confirmed by whole genome sequencing

“…Only one sample with co-infections of three SARS-CoV-2 lineages was firstly noted (Zhou et al, 2021). In France, Delta/Omicron SARS-CoV-2 variants co-infection was detected and confirmed during the fifth wave of COVID-19 pandemics in 7 immunocompetent and epidemiologically unrelated patients (Combes et al, 2022). Another recent study using whole genome sequencing data reported prevalence for Delta/Omicron (BA.1) and Omicron BA.1/BA.2 estimated at 0.18% and 0.26% respectively (Bal et al, 2022).…”

SARS-CoV-2 Variability in Patients and Wastewaters—Potential Immuno-Modulation during the Shift from Delta to Omicron

“…For another limitation, the potential Delta/Omicron co-infections in the 10 patients of the present study could favor recombination events. Even though no possible recombinant was highlighted in our hands, additional methods able to explore longer viral genomic fragments could be informative in the future within the field of variant recombination [ 5 ]. At last, complementary analyses, such as neutralizing antibody testing and cellular immune assays against the various variants harboring different mutational patterns, would be informative.…”

“…In addition, the co-circulation of several mutant strains increases the risk of co-infection, which may modify the viral pathogeny and eventually promote potential inter-strain recombination [ 1 , 2 ], mainly occurring in ORF1a and in the S gene [ 3 ], especially in the 174–2692 nt region of ORF1ab, 21,801–22,281 nt and 24,174–24,648 nt in the S gene in Sarbecoviruses [ 3 , 4 ]. However, the literature on co-infection by different SARS-CoV-2 variants and potential subsequent changes in the biological properties of this pandemic virus remains limited [ 3 , 4 , 5 ]. A recent work in France by P Combes at al showed mutation profiles suggesting that a Delta/Omicron population mixture was observed in 7 nasopharyngeal swabs out of 3831 respiratory samples in a high co-circulation period of the two variants.…”

“…A recent work in France by P Combes at al showed mutation profiles suggesting that a Delta/Omicron population mixture was observed in 7 nasopharyngeal swabs out of 3831 respiratory samples in a high co-circulation period of the two variants. Co-infections can further lead to genetic recombination, observed in 1 of the 3831 samples, the authors suggesting that such chimeric variants with unpredictable epidemic or pathogenic properties might regularly occur [ 5 ].…”