Developing a Large-Scale Covid-19 Surveillance System to Reopen Campuses

Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 and Variants Using Digital Droplet Polymerase Chain Reaction at a Large University and Healthcare System in California

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with different infectivity, transmission potential, and morbidity change the characteristics of local epidemics and affect vaccine effectiveness. As part of the University of Southern California COVID-19 Pandemic Research Center's efforts to understand, control, and inform local community on coronavirus disease 2019 (COVID-19), we implemented a SARS-CoV-2 surveillance program among students, employees, and USC Keck Medical Center patients. We present the epidemiology and distribution of SARS-CoV-2 and its variants among the population.

Methods

We used digital droplet reverse-transcriptase polymerase chain reaction (PCR) to analyze in real-time remnant SARS-CoV-2 PCR-positive saliva specimens stored at the USC Keck Medicine laboratory between September 2020 and April 2022. Samples were tested for the original strain (A20) and 9 SARS-CoV-2 variants: α(B.1.1.7, Q.1-Q.8), β(B.1.351, B.1.351.2, B.1.351.3), γ(P.1, P.1.1, P.1.2), δ(B.1.617.2), δ+(or δ417N), ε(B.1.427 and B.1.429), η(B.1.525), λ(C.37) and ο(B.1.1.529, ΒΑ.1, BA.2). We reviewed deidentified health information from positive cases including demographics, history of COVID-19 (eg, symptoms, hospitalizations, and repeat infections), and COVID-19 vaccination status.

Results

We reviewed 1169 cases and determined the variant type of 482 specimens: 77 specimens were original strain, 119 "Delta", 165 "Omicron". The original strain was detected during the third and fourth quarters of 2020. The Delta variant appeared during the second quarter of 2021, whereas Omicron appeared in the fourth quarter of 2021.

Conclusions

Prospectively tracking SARS-CoV-2 variants in a university population and a hospital system, utilizing a low-cost, high-throughput PCR assay, was feasible. Local variant monitoring remains important to inform prevention and control efforts among university and clinical settings.

Design, Implementation, and Outcomes of a Volunteer-Staffed Case Investigation and Contact Tracing Initiative at an Urban Academic Medical Center

IMPORTANCE

The COVID-19 pandemic has claimed nearly 6 million lives globally as of February 2022. While pandemic control efforts, including contact tracing, have traditionally been the purview of state and local health departments, the COVID-19 pandemic outpaced health department capacity, necessitating actions by private health systems to investigate and control outbreaks, mitigate transmission, and support patients and communities.

OBJECTIVE

To investigate the process of designing and implementing a volunteer-staffed contact tracing program at a large academic health system from April 2020 to May 2021, including program structure, lessons learned through implementation, results of case investigation and contact tracing efforts, and reflections on how constrained resources may be best allocated in the current pandemic or future public health emergencies.

DESIGN, SETTING, AND PARTICIPANTS

This case series study was conducted among patients at the University of Pennsylvania Health System and in partnership with the Philadelphia Department of Public Health. Patients who tested positive for COVID-19 were contacted to counsel them regarding safe isolation practices, identify and support quarantine of their close contacts, and provide resources, such as food and medicine, needed during isolation or quarantine.

RESULTS

Of 5470 individuals who tested positive for COVID-19 and received calls from a volunteer, 2982 individuals (54.5%; median [range] age, 42 [18-97] years; 1628 [59.4%] women among 2741 cases with sex data) were interviewed; among 2683 cases with race data, there were 110 Asian individuals (3.9%), 1476 Black individuals (52.7%), and 817 White individuals (29.2%), and among 2667 cases with ethnicity data, there were 366 Hispanic individuals (13.1%) and 2301 individuals who were not Hispanic (82.6%). Most individuals lived in a household with 2 to 5 people (2125 of 2904 individuals with household data [71.6%]). Of 3222 unique contacts, 1780 close contacts (55.2%; median [range] age, 40 [18-97] years; 866 [55.3%] women among 1565 contacts with sex data) were interviewed; among 1523 contacts with race data, there were 69 Asian individuals (4.2%), 705 Black individuals (43.2%), and 573 White individuals (35.1%), and among 1514 contacts with ethnicity data, there were 202 Hispanic individuals (12.8%) and 1312 individuals (83.4%) who were not Hispanic. Most contacts lived in a household with 2 to 5 people (1123 of 1418 individuals with household data [79.2%]). Of 3324 cases and contacts who completed a questionnaire on unmet social needs, 907 (27.3%) experienced material hardships that would make it difficult for them to isolate or quarantine safely. Such hardship was significantly less common among White compared with Black participants (odds ratio, 0.20; 95% CI, 0.16-0.25).

CONCLUSIONS AND RELEVANCE

These findings demonstrate the feasibility and challenges of implementing a case investigation and contact tracing program at an academic health system. In addition to successfully engaging most assigned COVID-19 cases and close contacts, contact tracers shared health information and material resources to support isolation and quarantine, thus filling local public health system gaps and supporting local pandemic control.

Durability of Severe Acute Respiratory Syndrome Coronavirus 2 Messenger RNA Booster Vaccine Protection Against Omicron Among Healthcare Workers With a Vaccine Mandate

BACKGROUND

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has spread rapidly throughout the world since being identified in South Africa in November 2021. Few studies have assessed primary series and booster vaccine effectiveness against Omicron among US healthcare workers.

METHODS

We conducted a test-negative case-control design to estimate BNT162b2 and mRNA1273 primary vaccination and booster effectiveness against SARS-CoV-2 infection and symptomatic coronavirus disease 2019 during an Omicron surge among employees of the University of Pennsylvania Health System. The study period was between 1 July 2021 and 5 April 2022. We defined the Delta period as 1 July to 12 December 2021 and the Omicron period as beginning 12 December 21.

RESULTS

Our sample included 14 520 tests (2776 [19%] positive)-7422 (506 [7%] positive) during Delta and 7098 (2270 [32%] positive) during Omicron. Benchmarked against Delta, the vaccine effectiveness of 2 vaccine doses was lower during Omicron, with no significant protection against infection. Booster doses added significant protection, although they also showed reduced effectiveness during Omicron. Compared with findings in employees who had received 2 vaccine doses, 3 doses of BNT162b2 had a relative effectiveness of 50% (95% confidence interval, 42%-56%) during Omicron, relative to 78% (63%-87%) during Delta; 3 doses of mRNA1273 had a relative effectiveness of 56% (45%-65%) during Omicron, relative to 96% (82%-99%) during Delta. Restricting the sample to symptomatic tests yielded similar results to our primary analysis. After initial waning in BNT162b2 booster protection against infection, it remained largely stable for ≥16 weeks after vaccination.

CONCLUSIONS

Our findings provide a strong rationale for boosters among healthcare workers in the Omicron era.