Omicron-Delta mixed Infections

February 19, 2022

In a recent study researchers found that, co-infection of Delta and Omicron variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in two epidemiologically unrelated patients, who were suffering from chronic kidney disease and were requiring hemodialysis.

Key Points

Both the variants of SARS-CoV-2 were co-circulating locally in Sydney at the time of detection.
Co-infection comprising of different SARS-CoV-2 variants was rarely reported during the first wave of COVID-19 pandemic.
Studies suggested that, such co-infections could result in greater disease severity and duration. However, co-infections with variants of concern (VOCs) like Delta or Omicron have not been reported previously, specifically in immunosuppressed hosts.

Key findings of the study

In the recent study, researchers found the first cases of Delta and Omicron co-infection in Sydney, in two immunocompromised individuals, who were at risk of severe COVID-19.
Researchers identified the co-infection, when there was local co-circulation of both the variants of SARS-CoV-2.
Case A was aged between 60 to 70 years and presented it to the Emergency Department (ER) with mild respiratory symptoms. It was later tested positive for SARS-CoV-2 by polymerase chain reaction (PCR).
Case B was aged between 50 to 60 years. He was presented with fever. Later he was diagnosed PCR-positive for SARS-CoV-2.
Samples from both patients were subjected to genome sequencing, under the genomic surveillance program in New South Wales (NSW).
A detailed case review revealed that both cases had chronic kidney disease because of type 2 diabetes, as well as ischemic heart disease and obesity. They were receiving hemodialysis thrice weekly at the dialysis centre.

What researchers observed?

Researchers used amplicon-based and probe-based sequencing with short-read and long-read technologies for identifying and measuring Delta and Omicron subpopulations in respiratory samples of the patients. Relative frequency review of 10 Delta and 17 Omicron variant-defining markers highlighted co-infection with both the variants. All three sequencing methods highlighted the highly similar overall proportion of both the variants. Thus, findings of study highlighted the significance of genomic surveillance of SARS-CoV-2 in vulnerable populations to diagnose the co-infections. These co-infections may trigger saltational evolution.

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