EP333: Tracking the emergence of SARS-CoV-2 variants of concern in vaccinated and unvaccinated patients

Abstract

Emerging infectious organisms, such as SARS-CoV-2, create public health crises that demand real-time tracking and ongoing surveillance of new variants to monitor changes in transmissibility, virulence, and effectiveness of vaccines. Aegis Sciences BioPharma Laboratory has sequenced over 250,000 RT-PCR-confirmed SARS-CoV-2 positive specimens from patients across the United States and Puerto Rico and evaluated the emergence, community spread, and dominance of variants of concern (VOC) in vaccinated and unvaccinated individuals. Through a collaboration with Walgreens, Aegis Sciences BioPharma Laboratory performs COVID-19 testing on patient specimens from all over the United States. Patients schedule appointments via an online portal, submit health data and vaccination status for physician review, and perform socially-distanced, self-collections from the Walgreens pharmacy drive-through while being observed by a trained clinical team member. SARS-CoV-2 positive specimens with an average cycle threshold (Ct) value of <30 were selected for sequencing based on their state’s testing volume and overall population statistics. SARS-CoV-2 genome sequencing and lineage analysis was performed via an optimized workflow using the Illumina COVIDSeq RUO Kits with the NovaSeq 6000 sequencer and the Illumina DRAGEN COVID Lineage Application. The prevalence and spread of variants of concern was evaluated in both vaccinated and unvaccinated patients. Since March 2021, Aegis has submitted over 250,000 sequences from COVID-19 positive patient specimens to the GISAID database, including 437 unique SARS-CoV-2 lineages. Starting in May, the patient’s vaccination status was captured to help monitor vaccine effectiveness and compare variant spread in vaccinated versus unvaccinated individuals. In total, 170,019 patient specimens with a vaccination status have been sequenced. From March to May 2021, Alpha (B.1.1.7) cases increased from 8% to 66%. At Alpha’s peak (May to Mid-June), the average rate of breakthrough cases neared 10% of total sequenced samples. In early June, Delta (B.617.2) cases accounted for only 3% of samples but quickly rose to 60% while Alpha declined from 38% to 6%. From July to November 2021, Delta and its sub-lineages (AY) have dominated and accounted for >90% of all cases with an average breakthrough rate of ∼30% overall. In early August, Delta’s AY sublineages emerged and have since become more prevalent than their B.617.2 parent lineage. Of note, AY.25 (33.54%), AY.44 (37.69%), and AY.39 (36.79%) also have increased vaccine breakthrough rates with the highest breakthrough rate in AY.103 (41.36%). Monitoring viral variant trends and epidemiology through community surveillance programs is critical during a public health crisis. The data generated through these collaborations is vital to tracking viral evolution and understanding changes in transmissibility, virulence, and vaccine effectiveness. Aegis’ sequencing and analysis of >250,000 SARS CoV-2 specimens will continue to contribute to our understanding of COVID-19 for years to come.