Pandemic Demand for SARS-CoV-2 Testing Led to Critical Supply and Workforce Shortages in U.S. Clinical and Public Health Laboratories.

COVID-19 has brought unprecedented challenges to clinical and public health laboratories. While U.S. laboratories have continued striving to provide quality test results during the pandemic, the uncertainty and lack of supplies became a significant hurdle, hindering day-to-day laboratory operations and the ability to increase testing capacity for both SARS-CoV-2 and non-COVID-19 testing. In addition, long-standing laboratory workforce shortages became apparent, hindering the ability of clinical and public health laboratories to rapidly increase testing. The American Society for Microbiology, the College of American Pathologists, the National Coalition of STD Directors, and the Emerging Infections Network independently conducted surveys in 2020 and early 2021 to assess the capacity of the nation's clinical laboratories to respond to the increase in demand for testing during the COVID-19 pandemic. The results of these surveys highlighted the shortages of crucial supplies for SARS-CoV-2 testing and supplies for other routine laboratory diagnostics, as well as a shortage of trained personnel to perform testing. The conclusions are based on communications, observations, and the survey results of the clinical laboratory, public health, and professional organizations represented here. While the results of each survey considered separately may not be representative of the entire community, when considered together they provide remarkably similar results, further validating the findings and highlighting the importance of laboratory supply chains and the personnel capable of performing these tests for any response to a large-scale public health emergency.

Principles of diagnostic stewardship: A practical guide from the Society for Healthcare Epidemiology of America Diagnostic Stewardship Task Force.

We provide an overview of diagnostic stewardship with key concepts that include the diagnostic pathway and the multiple points where interventions can be implemented, strategies for interventions, the importance of multidisciplinary collaboration, and key microbiologic diagnostic tests that should be considered for diagnostic stewardship. The document focuses on microbiologic laboratory testing for adult and pediatric patients and is intended for a target audience of healthcare workers involved in diagnostic stewardship interventions and all workers affected by any step of the diagnostic pathway (ie, ordering, collecting, processing, reporting, and interpreting results of a diagnostic test). This document was developed by the Society for Healthcare Epidemiology of America Diagnostic Stewardship Taskforce.

Association between job role and coronavirus disease 2019 (COVID-19) among healthcare personnel, Iowa, 2021.

We describe the association between job roles and coronavirus disease 2019 (COVID-19) among healthcare personnel. A wide range of hazard ratios were observed across job roles. Medical assistants had higher hazard ratios than nurses, while attending physicians, food service workers, laboratory technicians, pharmacists, residents and fellows, and temporary workers had lower hazard ratios.

Coronavirus disease 2019 (COVID-19) among nonphysician healthcare personnel by work location at a tertiary-care center, Iowa, 2020-2021.

We describe COVID-19 cases among nonphysician healthcare personnel (HCP) by work location. The proportion of HCP with coronavirus disease 2019 (COVID-19) was highest in the emergency department and lowest among those working remotely. COVID-19 and non-COVID-19 units had similar proportions of HCP with COVID-19 (13%). Cases decreased across all work locations following COVID-19 vaccination.

The long-term effectiveness of coronavirus disease 2019 (COVID-19) vaccines: A systematic literature review and meta-analysis.

Background: Although multiple studies revealed high vaccine effectiveness of coronavirus disease 2019 (COVID-19) vaccines within 3 months after the completion of vaccines, long-term vaccine effectiveness has not been well established, especially after the δ (delta) variant became prominent. We performed a systematic literature review and meta-analysis of long-term vaccine effectiveness. Methods: We searched PubMed, CINAHL, EMBASE, Cochrane Central Register of Controlled Trials, Scopus, and Web of Science from December 2019 to November 15, 2021, for studies evaluating the long-term vaccine effectiveness against laboratory-confirmed COVID-19 or COVID-19 hospitalization among individuals who received 2 doses of Pfizer/BioNTech, Moderna, or AstraZeneca vaccines, or 1 dose of the Janssen vaccine. Long-term was defined as >5 months after the last dose. We calculated the pooled diagnostic odds ratio (DOR) with 95% confidence interval for COVID-19 between vaccinated and unvaccinated individuals. Vaccine effectiveness was estimated as 100% × (1 - DOR). Results: In total, 16 studies including 17,939,172 individuals evaluated long-term vaccine effectiveness and were included in the meta-analysis. The pooled DOR for COVID-19 was 0.158 (95% CI: 0.157-0.160) with an estimated vaccine effectiveness of 84.2% (95% CI, 84.0- 84.3%). Estimated vaccine effectiveness against COVID-19 hospitalization was 88.7% (95% CI, 55.8%-97.1%). Vaccine effectiveness against COVID-19 during the δ variant period was 61.2% (95% CI, 59.0%-63.3%). Conclusions: COVID-19 vaccines are effective in preventing COVID-19 and COVID-19 hospitalization across a long-term period for the circulating variants during the study period. More observational studies are needed to evaluate the vaccine effectiveness of third dose of a COVID-19 vaccine, the vaccine effectiveness of mixing COVID-19 vaccines, COVID-19 breakthrough infection, and vaccine effectiveness against newly emerging variants.

Impact of COVID-19 on an infection prevention and control program, Iowa 2020-2021.

BACKGROUND: The COVID-19 pandemic has affected infection prevention and control (IPC) programs worldwide. We evaluated the impact of COVID-19 on the University of Iowa Hospitals & Clinics IPC program by measuring the volume of calls to the program, changes in healthcare-associated infection rates, and team member perceptions. METHODS: We retrieved the IPC call log and healthcare-associated infection trends for 2018-2020. We defined 2 periods: pre-COVID-19 (2018-2019) and COVID-19 (January-December 2020). We also conducted one-on-one interviews and focus group interviews with members of the IPC program and describe changes in their working conditions during the COVID-19 period. RESULTS: A total of 6,564 calls were recorded during 2018-2020. The pre-COVID-19 period had a median of 71 calls and/or month (range: 50-119). During the COVID-19 period, the median call volume increased to 368/month (range: 149-829), and most calls were related to isolation precautions (50%). During the COVID-19 period, the central line-associated bloodstream infection incidence increased significantly. Infection preventionists reported that the ambiguity and conflicting guidance during the pandemic were major challenges. CONCLUSIONS: Our IPC program experienced a 500% increase in consultation requests. Planning for future bio-emergencies should include creative strategies to increase response capacity within IPC programs.

Coronavirus Disease 2019 Serial Testing Among Hospitalized Patients in a Midwest Tertiary Medical Center, July-September 2020.

We implemented serial coronavirus disease 2019 testing for inpatients with a negative test on admission. The conversion rate (negative to positive) on repeat testing was 1%. We identified patients during their incubation period and hospital-onset cases, rapidly isolated them, and potentially reduced exposures. Serial testing and infectiousness determination were resource intensive.

Coronavirus disease 2019 (COVID-19) incidence after exposures in shared patient rooms in a tertiary-care center in Iowa, July 2020-May 2021.

The incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure in shared patient rooms was low at our institution: 1.8 per 1,000 shared-room patient days. However, the secondary attack rate (21.6%) was comparable to that reported in household exposures. Lengthier exposures were associated with SARS-CoV-2 conversion. Hospitals should implement measures to decrease shared-room exposures.

Coronavirus disease 2019 (COVID-19) admission screening and assessment of infectiousness at an academic medical center in Iowa, 2020.

OBJECTIVE: Patients admitted to the hospital may unknowingly carry severe acute respiratory coronavirus virus 2 (SARS-CoV-2), and hospitals have implemented SARS-CoV-2 admission screening. However, because SARS-CoV-2 reverse-transcription polymerase chain reaction (RT-PCR) assays may remain positive for months after infection, positive results may represent active or past infection. We determined the prevalence and infectiousness of patients who were admitted for reasons unrelated to COVID-19 but tested positive for SARS-CoV-2 on admission screening. METHODS: We conducted an observational study at the University of Iowa Hospitals & Clinics from July 7 to October 25, 2020. All patients admitted without suspicion of COVID-19 were included, and medical records of those with a positive admission screening test were reviewed. Infectiousness was determined using patient history, PCR cycle threshold (Ct) value, and serology. RESULTS: In total, 5,913 patients were screened and admitted for reasons unrelated to COVID-19. Of these, 101 had positive admission RT-PCR results; 36 of these patients were excluded because they had respiratory signs/symptoms on admission on chart review. Also, 65 patients (1.1%) did not have respiratory symptoms. Finally, 55 patients had Ct values available and were included in this analysis. The median age of the final cohort was 56 years and 51% were male. Our assessment revealed that 23 patients (42%) were likely infectious. The median duration of in-hospital isolation was 5 days for those likely infectious and 2 days for those deemed noninfectious. CONCLUSIONS: SARS-CoV-2 was infrequent among patients admitted for reasons unrelated to COVID-19. An assessment of the likelihood of infectiousness using clinical history, RT-PCR Ct values, and serology may help in making the determination to discontinue isolation and conserve resources.

Coronavirus disease 2019 (COVID-19) research agenda for healthcare epidemiology.

This SHEA white paper identifies knowledge gaps and challenges in healthcare epidemiology research related to coronavirus disease 2019 (COVID-19) with a focus on core principles of healthcare epidemiology. These gaps, revealed during the worst phases of the COVID-19 pandemic, are described in 10 sections: epidemiology, outbreak investigation, surveillance, isolation precaution practices, personal protective equipment (PPE), environmental contamination and disinfection, drug and supply shortages, antimicrobial stewardship, healthcare personnel (HCP) occupational safety, and return to work policies. Each section highlights three critical healthcare epidemiology research questions with detailed description provided in supplementary materials. This research agenda calls for translational studies from laboratory-based basic science research to well-designed, large-scale studies and health outcomes research. Research gaps and challenges related to nursing homes and social disparities are included. Collaborations across various disciplines, expertise and across diverse geographic locations will be critical.

Experience With Pretravel Testing for SARS-CoV-2 at an Academic Medical Center.

International travel has been a significant factor in the coronavirus disease 2019 pandemic. Many countries and airlines have implemented travel restrictions to limit the spread of the causative agent, severe acute respiratory syndrome coronavirus-2. A common requirement has been a negative reverse-transcriptase polymerase chain reaction performed by a clinical laboratory within 48 to 72 hours of departure. A more recent travel mandate for severe acute respiratory syndrome coronavirus-2 immunoglobulin M serology testing was instituted by the Chinese government on October 29, 2020. Pretravel testing for severe acute respiratory syndrome coronavirus-2 raises complications in terms of cost, turnaround time, and follow-up of positive results. In this report, we describe the experience of a multidisciplinary collaboration to develop a workflow for pretravel severe acute respiratory syndrome coronavirus-2 reverse-transcriptase polymerase chain reaction and immunoglobulin M serology testing at an academic medical center. The workflow primarily involved self-payment by patients and preferred retrieval of results by the patient through the electronic health record patient portal (Epic MyChart). A total of 556 unique patients underwent pretravel reverse-transcriptase polymerase chain reaction testing, with 13 (2.4%) having one or more positive results, a rate similar to that for reverse-transcriptase polymerase chain reaction testing performed for other protocol-driven asymptomatic screening (eg, inpatient admissions, preprocedural) at our medical center. For 5 of 13 reverse-transcriptase polymerase chain reaction positive samples, the traveler had clinical history, prior reverse-transcriptase polymerase chain reaction positive, and high cycle thresholds values on pretravel testing consistent with remote infection and minimal transmission risk. Severe acute respiratory syndrome coronavirus-2 immunoglobulin M was performed on only 24 patients but resulted in 2 likely false positives. Overall, our experience at an academic medical center shows the challenge with pretravel severe acute respiratory syndrome coronavirus-2 testing.

Practical Considerations for Implementation of SARS-CoV-2 Serological Testing in the Clinical Laboratory: Experience at an Academic Medical Center.

Molecular techniques, especially reverse transcriptase polymerase chain reaction (RT-PCR), have been the gold standard for the diagnosis of acute severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Serological tests for SARS-CoV-2 have been widely used for serosurveys, epidemiology, and identification of potential convalescent plasma donors. However, the clinical role of serologic testing is still limited and evolving. In this report, we describe the experience of selecting, validating, and implementing SARS-CoV-2 serologic testing for clinical purposes at an academic medical center in a rural state. Successful implementation involved close collaboration between pathology, infectious diseases, and outpatient clinics. The most common clinician concerns were appropriateness/utility of testing, patient charges/insurance coverage, and assay specificity. In analyzing test utilization, serologic testing in the first month after go-live was almost entirely outpatient and appeared to be strongly driven by patient interest (including health care workers and others in high-risk occupations for exposure to SARS-CoV-2), with little evidence that the results impacted clinical decision-making. Test volumes for serology declined steadily through October 31, 2020, with inpatient ordering assuming a steadily higher percentage of the total. In a 5-month period, SARS-CoV-2 serology test volumes amounted to only 1.3% of that of reverse transcriptase polymerase chain reaction. Unlike reverse transcriptase polymerase chain reaction, supply chain challenges and reagent availability were not major issues for serology testing. We also discuss the most recent challenge of requirements for SARS-CoV-2 testing in international travel protocols. Overall, our experience at an academic medical center shows that SARS-CoV-2 serology testing assumed a limited clinical role.

Negative pressure face shield for flexible laryngoscopy in the COVID-19 era.

OBJECTIVE: Introduce novel methods and materials to limit microdroplet spread when performing transnasal aerosol generating procedures in the COVID-19 era. METHODS: Prototypes of a negative pressure face shield (NPFS) were tested then used clinically to create a suction-clearing negative pressure microenvironment with controlled access to the nose and mouth. Air pressure measurements within prototypes were followed by prospective evaluation of 30 consecutive patients treated with the device assessed through questionnaires and monitoring oximetry. RESULTS: The NPFS is a transparent acrylic barrier with two anterior instrumentation ports and a side port to which continuous suction is applied. It is positioned on a stand and employs a disposable antimicrobial wrap to secure an enclosure around the head. This assembly was successfully used to complete transnasal laryngoscopy in all 30 patients studied. Tolerance of the design was excellent, with postprocedure questionnaire identifying no shortness of breath (27/30), no claustrophobia (27/30), no pain (29/30), and no significant changes in pulse oximetry. CONCLUSION: Diagnostic laryngoscopy was successfully performed in a negative pressure microenvironment created to limit dispersion of aerosols. Further application of the NPFS device is targeted for use with transnasal laryngeal laser and biopsy procedures to be followed by additional modification to enable intranasal and intraoral procedures in a similar protected environment. LEVEL OF EVIDENCE: Level 2b (Cohort Study).