Prolonged replication of BA.1 and BA.2 Omicron lineages compared to Delta variant in nasopharyngeal samples from COVID-19 patients - 02/12/22

Doi : 10.1016/j.idnow.2022.10.001

Elisa Teyssou ^a,^⁎ , Stéphane Marot ^a, Théophile Cocherie ^a, Antoine Fauchois ^a, Basma Abdi ^a, Eve Todesco ^a, Sepideh Akhavan ^a, Valérie Pourcher ^b, Vincent Calvez ^a, Anne-Geneviève Marcelin ^a, Cathia Soulie ^a,^⁎
^a Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F-75013 Paris, France
^b Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, Service des maladies infectieuse, F-75013 Paris, France

^⁎Corresponding authors at: Department of Virology, Pitié-Salpêtrière Hospital, 83 Boulevard de l'Hôpital, 75013 Paris, France.Department of VirologyPitié-Salpêtrière Hospital83 Boulevard de l'Hôpital75013 ParisFrance

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Highlights

•	No significant difference in viral load between the Delta variant and the two Omicron lineages at the time of diagnosis.
•	BA.2 Omicron lineage presents a higher viral load than BA.1 Omicron lineage.
•	BA.1 and BA.2 Omicron lineages have prolonged replication compared to the Delta variant.

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Abstract

Objectives

We aimed to characterize and compare the viral loads (VL) of the Omicron BA.1 and BA.2 lineages and the Delta variant in nasopharyngeal samples from newly diagnosed COVID-19 patients and their kinetics over time.

Patients and methods

The kinetics of the VL were measured on the CT data from 215 SARS-CoV-2 positive patients who presented at least two positive PCRs a day apart and were screened for SARS-CoV-2 viral lineages.

Results

We observed no significant difference in median CT value during the first diagnostic test between the Delta variant and the two Omicron lineages. However, the kinetics of CT decreases for the BA.1 and BA.2 lineage were significantly lengthier in time than the kinetics for the Delta variant. The BA.2 lineage presented lower median CT value (-2 CT) (inversely proportional to the VL) than the BA.1 lineage.

Conclusions

BA.2 Omicron lineage presented higher VL than BA.1 Omicron lineage at diagnostic. Omicron BA.1 and BA.2 lineages have more prolonged replication than the Delta variant.

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Keywords : SARS-CoV-2, BA.1, BA.2, Viral load, Kinetic