Identification of Omicron-Delta Coinfections Using PCR-Based Genotyping

SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in Argentina

“…In this context of co-circulation of variants, 3 samples with Delta/Omicron SARS-CoV-2 co-infection were identified, all of them detected the last 2 weeks of December, when co-circulation of Delta and Omicron was registered (13). Co-infection events between dominant SARS-CoV-2 lineages have been previously reported, also in a very low proportion of the tested samples (3,(6)(7)(8). Although these events are rare, they are believed to be quite common during periods of high viral prevalence (15) and are believed to be underreported (6), as they are not easy to identify.…”

“…Although these events are rare, they are believed to be quite common during periods of high viral prevalence (15) and are believed to be underreported (6), as they are not easy to identify. Generally, one of the lineages is present in a greater proportion (3), which sometimes causes only one lineage to be detected, which has been registered for Delta/Omicron mixed infection (8). In addition, specialized personnel are required for the interpretation of variant-specific real-time PCR, which is not always capable of detecting subtleties in the reaction results.…”

“…Molecular SARS-CoV-2 surveillance has allowed the identification of the simultaneous infection (co-infection) of a single individual by two distinct SARS-CoV-2 lineages, an event that has been sporadically reported (3,(6)(7)(8). These cases constitute an opportunity for viral genetic recombination and the emergence of new lineages with different phenotypes (6), which may cause more severe clinical symptoms (7).…”

Rapid and accurate identification of SARS-CoV-2 Omicron variants using droplet digital PCR (RT-ddPCR)

“…For example, use of this assay in March and August of 2021 allowed us to rapidly select Alpha, Epsilon, and Delta variant samples [11] , enabling a comparison of variant growth in culture that would have been much more tenuous if the specimens needed to be held for sequencing (either subjected to lengthy storage at 4°C or to additional freeze-thaw cycles) before selection. It also allowed us to identify two specimens as Delta-Omicron coinfections, rather than novel variants [51] .…”

SARS-CoV-2 dual infection with Delta and Omicron variants in an immunocompetent host: a case report

“…Dual infections (those caused by two different virus variants) have been described with RNA viruses but are rare among respiratory viral infections ( Calistri et al, 2011 ; Myers et al, 2011 ). For COVID-19, a few cases of dual infection have been reported despite of an extremely high number of infected people worldwide ( Francisco et al, 2021 ; Pedro et al, 2021 ; Roychoudhury et al, 2022 ; Samoilov et al, 2021 ; Vankeerberghen et al, 2021 ). However, pinning down these cases is complicated and can be identified with higher probability during the transition from dominance of one SARS-CoV-2 variant of concern to another among the population.…”