Molecular and Clinical Epidemiology of SARS-CoV-2 Infection among Vaccinated and Unvaccinated Individuals in a Large Healthcare Organization from New Jersey

Abstract

New Jersey was among the first states impacted by the COVID-19 pandemic, with one of the highest overall death rates in the nation. Nevertheless, relatively few reports have been published focusing specifically on New Jersey. Here we report on molecular, clinical, and epidemiologic observations, from the largest healthcare network in the state, in a cohort of vaccinated and unvaccinated individuals with laboratory-confirmed SARS-CoV-2 infection. We conducted molecular surveillance of SARS-CoV-2-positive nasopharyngeal swabs collected in nine hospitals from December 2020 through June 2022, using both whole genome sequencing (WGS) and a real-time RT-PCR screening assay targeting spike protein mutations found in variants of concern (VOCs) within our region. De-identified clinical data were obtained retrospectively, including demographics, COVID-19 vaccination status, ICU admission, ventilator support, mortality, and medical history. Statistical analyses were performed to identify associations between SARS-CoV-2 variants, vaccination status, clinical outcomes, and medical risk factors. A total of 5007 SARS-CoV-2-positive nasopharyngeal swabs were successfully screened and/or sequenced. Variant screening identified three predominant VOCs, including Alpha (n = 714), Delta (n = 1877), and Omicron (n = 1802). Omicron isolates were further sub-typed as BA.1 (n = 899), BA.2 (n = 853), or BA.4/BA.5 (n = 50); the remaining 614 isolates were classified as “Other”. Approximately 31.5% (1577/5007) of the samples were associated with vaccine breakthrough infections, which increased in frequency following the emergence of Delta and Omicron. Severe clinical outcomes included ICU admission (336/5007 = 6.7%), ventilator support (236/5007 = 4.7%), and mortality (430/5007 = 8.6%), with increasing age being the most significant contributor to each (p < 0.001). Unvaccinated individuals accounted for 79.7% (268/336) of ICU admissions, 78.3% (185/236) of ventilator cases, and 74.4% (320/430) of deaths. Highly significant (p < 0.001) increases in mortality were observed in individuals with cardiovascular disease, hypertension, cancer, diabetes, and hyperlipidemia, but not with obesity, thyroid disease, or respiratory disease. Significant differences (p < 0.001) in clinical outcomes were also noted between SARS-CoV-2 variants, including Delta, Omicron BA.1, and Omicron BA.2. Vaccination was associated with significantly improved clinical outcomes in our study, despite an increase in breakthrough infections associated with waning immunity, greater antigenic variability, or both. Underlying comorbidities contributed significantly to mortality in both vaccinated and unvaccinated individuals, with increasing risk based on the total number of comorbidities. Real-time RT-PCR-based screening facilitated timely identification of predominant variants using a minimal number of spike protein mutations, with faster turnaround time and reduced cost compared to WGS. Continued evolution of SARS-CoV-2 variants will likely require ongoing surveillance for new VOCs, with real-time assessment of clinical impact.

Genomic Surveillance Reveals the Rapid Expansion of the XBB Lineage among Circulating SARS-CoV-2 Omicron Lineages in Southeastern Wisconsin, USA

“…Each of the ten HHS regions directly serves a range of 4–10 states/islands and local organizations within their jurisdictions. While these reports delineate circulating SARS-CoV-2 lineages broadly, genomic surveillance reports within HHS, specifically at the individual states, regions within states or local populations, would benefit tracking the regional prevalence, emerging VOCs and guiding public health action within their jurisdictions [ 3 , 15 , 16 , 17 , 18 , 19 , 20 ]. HHS Region 5 consists of six states, including Wisconsin.…”

Characteristics and Presentations of Hospitalized Children Due to 3 Predominate COVID-19 Variants Within a Health Care Network

“…Only 2 pediatric patients had infection with the gamma variant and were not included in this study. 8 During each separate wave of infection, children and young adults hospitalized had varying presentations and severities of illness. The objectives of this study are to describe differences in the demographic and clinical characteristics, severity of illness, and outcomes in pediatric patients during the different SARS-CoV-2 waves in our hospital network.…”

Placental Infection Associated with SARS-CoV-2 Wildtype Variant and Variants of Concern

“…Then, the original SARS-CoV-2 lineages have been replaced by successive variants of concern (VOCs) (Alpha, Beta, Gamma, Delta, Omicron) over time [ 4 ]. These variants exhibit higher transmissibility and cause COVID-19 disease of lower severity (with associated lower mortality rates) compared to SARS-CoV-2 wildtype [ 5 , 6 ].…”