Campus Epidemiology of SARS-CoV-2 Variant Infections

SARS-CoV-2, also known as COVID-19, has caused significant morbidity and mortality amongst populations globally (1). Contextually, in the United States, COVID-19 has presented a huge burden, totaling over 500,000 deaths. As the pandemic has continued, new variants of SARS-CoV-2 characterized by key mutations in the viral spike protein have been identified globally (2, 3). Recent SARS-CoV-2 cases have cited a presence of variants. The B.1.1.7(United Kingdom), B.1.351(South Africa), and the P.1(Brazil) variants have been associated with increased transmission and prevalence globally. Furthermore, some variants might have increased virulence and be associated with decreased vaccine efficacy (4, 5). Recently in Southern California, a novel SARS-CoV-2 variant (CAL.20C) was identified, different than the 20G clade, the most common clade in North America (6). However, little is known about the epidemiology of those or other variants of SARS-CoV-2 in the United States (7-9). Due to recency of variant exposure in the United States, there is not much literature citing the effects of these variants. The US Centers for Disease Control and Prevention urgently recommends sequencing more SARS-CoV-2 genomes to improve the understanding of circulating SARS-CoV-2 in terms of transmissibility, symptom severity, detection evasion, susceptibility to therapeutics, and evasion of natural or vaccine-induced immunity (10). Although it is unclear what specific variants are present in Los Angeles and what their prevalence or clinical implications might be, this study will aim to address that gap in information.

To further understand how variants impact the current epidemic in Los Angeles, we will study SARS-Co-2variantsin the USC community.  We will (1) Determine the risk factors, epidemiology and clinical outcomes of infections with SARS-CoV-2 variants; (2) Detail how different variants might impact the transmission of infection;(3) Measure how prior infection and vaccination protect against incident infection with select variants, and (4) Inform the safety of continuing work and education at University of Southern California in this dynamic environment. Potentially as part of the larger USC vaccination study proposal, The USC SARS-CoV-2 Vaccination Campaign Research Initiative: Uptake, Markers and Determinants of Effectiveness, Subsequent Behaviors, this study will build upon anticipated behavioral/ clinical data collection to link outcomes related to SARS-CoV-2 virological variation. By using stored remnant positive specimens from routine weekly USC campus SARS-CoV-2 testing, we will link virological data with continually collected meta-data including demographic, behavioral, clinical, and immunological characteristics of infected individuals.

The effectiveness of COVID-19 vaccines against different strains can be inferred in this prospective real-world cohort by comparing the estimated frequency of variants in the populations and the observed frequency of variants among cases of vaccine failure. Currently, we know of no other cohorts studying those questions among SARS-CoV-2 variants in Los Angeles County with paired medical and vaccination history.