The displacement of the SARS-CoV-2 variant Delta with Omicron: An investigation of hospital admissions and upper respiratory viral loads

SARS-CoV-2–specific immune responses in boosted vaccine recipients with breakthrough infections during the Omicron variant surge

“…While we were not able to document infection with the Omicron strain in breakthrough VRs, the participants were infected when this VOC accounted for more than 90% of the SARS-CoV-2 isolates sequenced at the Johns Hopkins Hospital during a 22-day time period in late December 2021 to mid-January 2022 when the VRs became symptomatic (ref. 24 and Figure 1B). In addition, we tested immune responses in individuals prior to receiving booster doses, more than 6 months following their second mRNA vaccine (referred here after as preboost VRs).…”

The circulation of Non-SARS-CoV-2 respiratory viruses and coinfections with SARS-CoV-2 during the surge of the Omicron variant

“…In November 2021, the World Health Organization (WHO) designated the SARS-COV-2 variant, Omicron (B.1.1.529), as a variant of concern (VOC) [ 1 , 2 ]. Omicron rapidly displaced the circulating Delta variant and was associated with a remarkable increase in symptomatic and asymptomatic COVID-19 cases [ 3 , 4 ]. The impact of Omicron on the circulation of other respiratory viruses, particularly influenza, has been an area of major interest.…”

Sequencing during Times of Change: Evaluating SARS-CoV-2 Clinical Samples during the Transition from the Delta to Omicron Wave

“…The Omicron variant and its emerging sublineages, (e.g., BA.1 and BA.2) are characterized by an increased number of mutations in the spike gene (>30 amino acid substitutions) that allow for evasion of vaccine-induced immunity, along with specific changes outside of the spike gene, (e.g., non-structural and nucleocapsid genes) that may play important roles in facilitating viral replication [ 11 , 12 , 13 ]. Omicron VOCs have been associated with reduced pathogenesis in animal model systems [ 14 , 15 , 16 ], but higher rates of transmission compared to the Delta variant [ 17 , 18 , 19 ]. Evaluating SARS-CoV-2 sequencing data along with patient status information may provide insights into drivers of viral evolution in this particularly vulnerable population.…”