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Rapid Shift from SARS-CoV-2 Delta to Omicron Sub-Variants within a Dynamic Southern U.S. Borderplex
Elisa Robles-Escajeda1,2, Jonathon E Mohl2,3, Lisett Contreras1,2
1The Department of Biological Sciences, The University of Texas at El Paso, 500 W. University Ave, El Paso, TX 79968, USA.
Viruses
|March 30, 2023
Summary
The Omicron variant rapidly replaced the Delta variant in El Paso, Texas, leading to increased COVID-19 cases and hospitalizations. Omicron subvariants BA.1, BA.4, and BA.5 showed S-gene dropout, aiding variant identification.
Area of Science:
- Virology
- Epidemiology
- Public Health
Background:
- COVID-19, caused by SARS-CoV-2, continues to be a global health concern.
- Viral variants significantly impact transmission dynamics and public health responses.
- Border communities face unique challenges due to cross-border movement.
Purpose of the Study:
- To analyze SARS-CoV-2 variant prevalence in a binational border community.
- To investigate the epidemiological impact of variant replacement, specifically Delta by Omicron.
- To identify molecular characteristics of circulating variants.
Main Methods:
- Analysis of 3641 SARS-CoV-2 positive samples over 48 weeks (Fall 2021-Summer 2022).
- Real-time quantitative PCR (qRT-PCR) for variant detection, including S-gene dropout analysis.
- Monitoring of COVID-19 positivity rates, hospitalizations, and case reports.
Main Results:
- The Delta variant (B.1.617.2) was dominant from Sept 2021 to Jan 2022.
- Omicron (B.1.1.529) rapidly replaced Delta, detected from late Dec 2021 onwards.
- Omicron BA.1, BA.4, and BA.5 variants were associated with S-gene dropout, distinguishing them from Delta and BA.2.
Conclusions:
- Highly transmissible variants like Omicron can quickly displace dominant strains in dynamic populations.
- S-gene dropout is a useful marker for identifying specific Omicron subvariants.
- Enhanced surveillance and rapid response are crucial for managing variant-driven COVID-19 surges in border cities.
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