SARS CoV-2 Surveillance and Exposure in the Perioperative Setting with Universal testing and Personal Protective Equipment (PPE) Policies

DNA amplification tests at universal pre-admission screening with enhanced precaution strategies for asymptomatic patients with COVID-19

Objective

To analyse the effect of hospital pre-admission screening and enhanced precaution strategies on the transmission of severe acute respiratory syndrome coronavirus-2.

Methods

This retrospective cohort study was conducted over 17 months from 11 May 2020 to 30 September 2021 at a large hospital in Tokyo. Universal DNA amplification tests were conducted during pre-admission screening, and enhanced precaution strategies were implemented for all patients with negative admission tests. The primary outcome was the occurrence of symptomatic coronavirus disease 2019 (COVID-19) in patients after admission. The secondary outcomes were time-series analyses of monthly positive admission test numbers, positive rates, clinical features in positive cases, and clinically confirmed nosocomial transmission.

Results

In total, 32,081 patients were screened pre-admission (29,556 asymptomatic patients and 2525 symptomatic patients). Of the asymptomatic patients, 0.11% (n=32) tested positive and were admitted to a designated COVID-19 ward or were not admitted. Among the five inpatients who developed symptomatic COVID-19 during hospitalization, only two cases were related to a single nosocomial transmission.

Conclusion

Pre-admission test screening was effective in identifying asymptomatic cases of COVID-19. This allowed administrators to quarantine patients or delay hospital admission. The combination of testing and enhanced precaution strategies for asymptomatic cases of COVID-19 may minimize nosocomial transmission.

Temporal Series Analysis of Population Cycle Threshold Counts as a Predictor of Surge in Cases and Hospitalizations during the SARS-CoV-2 Pandemic

Tools to predict surges in cases and hospitalizations during the COVID-19 pandemic may help guide public health decisions. Low cycle threshold (CT) counts may indicate greater SARS-CoV-2 concentrations in the respiratory tract, and thereby may be used as a surrogate marker of enhanced viral transmission. Several population studies have found an association between the oscillations in the mean CT over time and the evolution of the pandemic. For the first time, we applied temporal series analysis (Granger-type causality) to validate the CT counts as an epidemiological marker of forthcoming pandemic waves using samples and analyzing cases and hospital admissions during the third pandemic wave (October 2020 to May 2021) in Madrid. A total of 22,906 SARS-CoV-2 RT-PCR-positive nasopharyngeal swabs were evaluated; the mean CT value was 27.4 (SD: 2.1) (22.2% below 20 cycles). During this period, 422,110 cases and 36,727 hospital admissions were also recorded. A temporal association was found between the CT counts and the cases of COVID-19 with a lag of 9-10 days (p ≤ 0.01) and hospital admissions by COVID-19 (p < 0.04) with a lag of 2-6 days. According to a validated method to prove associations between variables that change over time, the short-term evolution of average CT counts in the population may forecast the evolution of the COVID-19 pandemic.

Asymptomatic screening for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) as an infection prevention measure in healthcare facilities: Challenges and considerations

Testing of asymptomatic patients for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) (ie, "asymptomatic screening) to attempt to reduce the risk of nosocomial transmission has been extensive and resource intensive, and such testing is of unclear benefit when added to other layers of infection prevention mitigation controls. In addition, the logistic challenges and costs related to screening program implementation, data noting the lack of substantial aerosol generation with elective controlled intubation, extubation, and other procedures, and the adverse patient and facility consequences of asymptomatic screening call into question the utility of this infection prevention intervention. Consequently, the Society for Healthcare Epidemiology of America (SHEA) recommends against routine universal use of asymptomatic screening for SARS-CoV-2 in healthcare facilities. Specifically, preprocedure asymptomatic screening is unlikely to provide incremental benefit in preventing SARS-CoV-2 transmission in the procedural and perioperative environment when other infection prevention strategies are in place, and it should not be considered a requirement for all patients. Admission screening may be beneficial during times of increased virus transmission in some settings where other layers of controls are limited (eg, behavioral health, congregate care, or shared patient rooms), but widespread routine use of admission asymptomatic screening is not recommended over strengthening other infection prevention controls. In this commentary, we outline the challenges surrounding the use of asymptomatic screening, including logistics and costs of implementing a screening program, and adverse patient and facility consequences. We review data pertaining to the lack of substantial aerosol generation during elective controlled intubation, extubation, and other procedures, and we provide guidance for when asymptomatic screening for SARS-CoV-2 may be considered in a limited scope.

Routine pre-operative Covid testing in elective surgeries: Is it worth it?

BACKGROUND

Pre-procedural COVID-19 testing in patients scheduled for elective cases have become routine to reduce the risk of COVID-19 exposure and pulmonary complications related to perioperative COVID-19 infection, and to reduce the use of specific hospital resources among other reasons. This study evaluates the efficacy of universal COVID-19 testing for elective procedures.

METHODS

Single institution retrospective observational study from July 2020 through August 2021.

RESULTS

There were a total of 499 unique patients who were scheduled for 581 surgeries or procedures. A total of 569 anterior nares reverse transcriptase polymerase chain reaction (RT-PCR) tests were completed before scheduled procedure. There were 2 (0.35%) positive COVID tests, both of whom were asymptomatic and unvaccinated at time of testing, and 13 (2.2%) cancelled cases overall. The total cost for labor and materials during this period was $19,738, with each RT-PCR test costing $34.69 and each true positive test costing $9,869.

CONCLUSIONS

Given the low COVID-19 positivity in the elective procedural patient population, testing protocols for elective procedures should be re-evaluated as the pandemic evolves.

Effectiveness of MRNA booster vaccine among healthcare workers in New York City during the Omicron surge, December 2021 to January 2022

OBJECTIVE

To describe effectiveness of mRNA vaccines by comparing 2-dose (2D) and 3-dose (3D) healthcare worker (HCW) recipients in the setting of Omicron variant dominance. Performance of 2D and 3D vaccine series against SARS-CoV-2 variants and the clinical outcomes of HCWs may inform return-to-work guidance.

METHODS

In a retrospective study from December 15, 2020 to January 15, 2022, SARS-CoV-2 infections among HCWs at a large tertiary cancer centre in New York City were examined to estimate infection rates (aggregated positive tests / person-days) and 95% CIs over the Omicron period in 3D and 2D mRNA vaccinated HCWs and were compared using rate ratios. We described the clinical features of post-vaccine infections and impact of prior (pre-Omicron) COVID infection on vaccine effectiveness.

RESULTS

Among the 20857 HCWs in our cohort, 20,660 completed the 2D series with an mRNA vaccine during our study period and 12461 had received a third dose by January 15, 2022. The infection rate ratio for 3D versus 2D vaccinated HCWs was 0.667 (95% CI 0.623, 0.713) for an estimated 3D vaccine effectiveness of 33.3% compared to two doses only during the Omicron dominant period from December 15, 2021 to January 15, 2022. Breakthrough Omicron infections after 3D + 14 days occurred in 1,315 HCWs. Omicron infections were mild, with 16% of 3D and 11% 2D HCWs being asymptomatic.

DISCUSSION

Study demonstrates improved vaccine-derived protection against COVID-19 infection in 3D versus 2D mRNA vaccinees during the Omicron surge. The advantage of 3D vaccination was maintained irrespective of prior COVID-19 infection status.

The spike gene target failure (SGTF) genomic signature is highly accurate for the identification of Alpha and Omicron SARS-CoV-2 variants

The Alpha (B.1.1.7) and Omicron (B.1.1.529, BA.1, BA.4 and BA.5) variants of concern (VOC) share several mutations in their spike gene, including mutations resulting in the deletion of two amino acids at position 69 and 70 (del 69-70) in the Spike protein. Del 69-70 causes failure to detect the S gene target on a widely used, commercial test, the TaqPath SARS-CoV-2 RT-PCR (Thermo Fisher). The S gene target failure (SGTF) signature has been used to preliminarily infer the presence of Alpha and Omicron VOC. We evaluated the accuracy of the SGTF signature in identifying these two variants through analysis of all positive SARS-CoV-2 samples tested on the TaqPath RT-PCR and sequenced by next generation sequencing between December 2020 to July 2022. 2324 samples were successfully sequenced including 914 SGTF positive samples. The sensitivity and specificity of the SGTF signature was 99.6% (95% CI 96.1-99.9%) and 98.6% (95% CI 99.2-99.8%) for the Alpha variant and 99.6% (95% CI 98.9-99.9%) and 99.8% (95% CI 99.4-99.9%) for the Omicron variant. At the peak of their corresponding wave, the positive predictive value of the SGTF was 98% for Alpha and 100% for Omicron. The accuracy of the SGTF signature was high, making this genomic signature a rapid and accurate proxy for identification of these variants in real-world laboratory settings.

Diagnostic yield and costs associated with a routine pre-operative COVID-19 testing algorithm for asymptomatic patients prior to elective surgery

OBJECTIVES

Infection with COVID-19 presents known and unknown perioperative risks to the patient and operative staff. Pre-operative testing protocols have become widespread, yet little is known about the utility of this practice in asymptomatic patients undergoing elective surgery. We describe the impact and cost of a routine testing protocol on elective surgical procedures in a retrospective series at a single institution.

METHODS

Standardized pre-operative COVID-19 testing in all surgical patients was implemented in May 2020. Health system protocol required testing 3 to 5 days before all elective surgery. Data stratified by surgical specialty were collected over the initial 90-day period and disposition over a period of 6-months was assessed for all positive and indeterminate results.

RESULTS

Thirty-one (0.41%) positive results amongst 7579 pre-procedural tests, including 3 of 792 (0.38%) for urologic procedures, were noted in asymptomatic patients. Following a positive test, 20 procedures (62.5%) were delayed an average of 49 days, 8 were not performed and 3 proceeded without delay. All 3 urologic procedures were delayed a mean of 59 days. Institutional cost per test ranged from $34-$54. The number needed to test for one positive result was 244 with a cost of $11,573 for each positive result.

CONCLUSIONS

Institution of a universal pre-operative COVID-19 screening protocol for asymptomatic, unvaccinated patients undergoing elective surgery identified clinically silent infection in 0.4% of cases with a significant associated cost. Risk and symptom-based testing is likely a better strategy for triaging resources.

Implementation of Pre-Admission Caregiver Testing for COVID-19

BACKGROUND

Caregivers are often at the bedside of hospitalized children posing an additional risk for coronavirus disease 2019 (COVID-19) transmission. We describe the implementation of caregiver COVID-19 testing before inpatient pediatric admissions and the effect on patient cohorting and bed capacity.

METHODS

We implemented an ordering pathway to facilitate COVID-19 testing of caregivers of patients admitted to the inpatient units from the pediatric emergency department, elective procedural admissions, or direct admissions at a tertiary children's hospital in the Northeastern United States in August 2021. Testing was expedited by the clinical laboratory, and caregiver results were used to inform cohorting, infection prevention, and bed management decisions.

RESULTS

From August 2021 to January 2022, 2558 caregiver tests were ordered through this pathway, and 83 (3.2%) were positive. Of the positive tests, 72 (86.7%) occurred after December 18, 2021, coinciding with the local Omicron variant wave. Among positives, 67 caregiver or child pairs were identified, and 36 positive caregivers had a COVID-19 negative child leading to use of isolation precautions. Reintroduction of patient cohorting increased overall bed capacity from 74% to 100% of available beds.

CONCLUSIONS

The overall incidence of COVID-19 among caregivers before admission correlated well with rates of COVID-19 positivity among asymptomatic adults in the community during the study period. Implementation of caregiver testing increased bed capacity by reintroducing cohorting of patients and identified patients needing isolation that would have been missed by patient testing alone. More research is necessary to determine the extent that routine caregiver testing mitigates the risk of nosocomial severe acute respiratory syndrome coronavirus 2 transmission.

Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1

Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here, we describe partial ORF1ab gene target failure (pOGTF) on the cobas SARS-CoV-2 assays, defined by a ≥2-thermocycle delay in detection of the ORF1ab gene compared to that of the E-gene. We demonstrate that pOGTF is 98.6% sensitive and 99.9% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may affect transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly, increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.

Occurrence and transmission potential of asymptomatic and presymptomatic SARS-CoV-2 infections: Update of a living systematic review and meta-analysis

BACKGROUND

Debate about the level of asymptomatic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection continues. The amount of evidence is increasing and study designs have changed over time. We updated a living systematic review to address 3 questions: (1) Among people who become infected with SARS-CoV-2, what proportion does not experience symptoms at all during their infection? (2) What is the infectiousness of asymptomatic and presymptomatic, compared with symptomatic, SARS-CoV-2 infection? (3) What proportion of SARS-CoV-2 transmission in a population is accounted for by people who are asymptomatic or presymptomatic?

METHODS AND FINDINGS

The protocol was first published on 1 April 2020 and last updated on 18 June 2021. We searched PubMed, Embase, bioRxiv, and medRxiv, aggregated in a database of SARS-CoV-2 literature, most recently on 6 July 2021. Studies of people with PCR-diagnosed SARS-CoV-2, which documented symptom status at the beginning and end of follow-up, or mathematical modelling studies were included. Studies restricted to people already diagnosed, of single individuals or families, or without sufficient follow-up were excluded. One reviewer extracted data and a second verified the extraction, with disagreement resolved by discussion or a third reviewer. Risk of bias in empirical studies was assessed with a bespoke checklist and modelling studies with a published checklist. All data syntheses were done using random effects models. Review question (1): We included 130 studies. Heterogeneity was high so we did not estimate a mean proportion of asymptomatic infections overall (interquartile range (IQR) 14% to 50%, prediction interval 2% to 90%), or in 84 studies based on screening of defined populations (IQR 20% to 65%, prediction interval 4% to 94%). In 46 studies based on contact or outbreak investigations, the summary proportion asymptomatic was 19% (95% confidence interval (CI) 15% to 25%, prediction interval 2% to 70%). (2) The secondary attack rate in contacts of people with asymptomatic infection compared with symptomatic infection was 0.32 (95% CI 0.16 to 0.64, prediction interval 0.11 to 0.95, 8 studies). (3) In 13 modelling studies fit to data, the proportion of all SARS-CoV-2 transmission from presymptomatic individuals was higher than from asymptomatic individuals. Limitations of the evidence include high heterogeneity and high risks of selection and information bias in studies that were not designed to measure persistently asymptomatic infection, and limited information about variants of concern or in people who have been vaccinated.

CONCLUSIONS

Based on studies published up to July 2021, most SARS-CoV-2 infections were not persistently asymptomatic, and asymptomatic infections were less infectious than symptomatic infections. Summary estimates from meta-analysis may be misleading when variability between studies is extreme and prediction intervals should be presented. Future studies should determine the asymptomatic proportion of SARS-CoV-2 infections caused by variants of concern and in people with immunity following vaccination or previous infection. Without prospective longitudinal studies with methods that minimise selection and measurement biases, further updates with the study types included in this living systematic review are unlikely to be able to provide a reliable summary estimate of the proportion of asymptomatic infections caused by SARS-CoV-2.

REVIEW PROTOCOL

Open Science Framework (https://osf.io/9ewys/).

Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1

Mutations in the viral genome of SARS-CoV-2 can impact the performance of molecular diagnostic assays. In some cases, such as S gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here we describe partial ORF1ab gene target failure (pOGTF) on the cobas ^® SARS-CoV-2 assays, defined by a ≥2 thermocycles delay in detection of the ORF1ab gene compared to the E gene. We demonstrate that pOGTF is 97% sensitive and 99% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may impact transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.

SARS-CoV-2 testing in patients with low COVID-19 suspicion at admission to a tertiary care hospital, Stockholm, Sweden, March to September 2020

Background

Universal SARS-CoV-2 testing at hospital admission has been proposed to prevent nosocomial transmission.

Aim

To investigate SARS-CoV-2 positivity in patients tested with low clinical COVID-19 suspicion at hospital admission.

Methods

We characterised a retrospective cohort of patients admitted to Karolinska University Hospital tested for SARS-CoV-2 by PCR from March to September 2020, supplemented with an in-depth chart review (16 March–12 April). We compared positivity rates in patients with and without clinical COVID-19 suspicion with Spearman’s rank correlation coefficient. We used multivariable logistic regression to identify factors associated with test positivity.

Results

From March to September 2020, 66.9% (24,245/36,249) admitted patient episodes were tested; of those, 61.2% (14,830/24,245) showed no clinical COVID-19 suspicion, and the positivity rate was 3.2% (469/14,830). There was a strong correlation of SARS-CoV-2 positivity in patients with low vs high COVID-19 suspicion (rho = 0.92; p < 0.001).

From 16 March to 12 April, the positivity rate was 3.9% (58/1,482) in individuals with low COVID-19 suspicion, and 3.1% (35/1,114) in asymptomatic patients. Rates were higher in women (5.0%; 45/893) vs men (2.0%; 12/589; p = 0.003), but not significantly different if pregnant women were excluded (3.7% (21/566) vs 2.2% (12/589); p = 0.09). Factors associated with SARS-CoV-2 positivity were testing of pregnant women before delivery (odds ratio (OR): 2.6; 95% confidence interval (CI): 1.3–5.4) and isolated symptoms in adults (OR: 3.3; 95% CI: 1.8–6.3).

Conclusions

This study shows a relatively high SARS-CoV-2 positivity rate in patients with low COVID-19 suspicion upon hospital admission. Universal SARS-CoV-2 testing of pregnant women before delivery should be considered.

Evaluation of a comprehensive pre-procedural screening protocol for COVID-19 in times of a high SARS CoV-2 prevalence: a prospective cross-sectional study

BACKGROUND

To minimise the risk of COVID-19 transmission, an ambulant screening protocol for COVID-19 in patients before admission to the hospital was implemented, combining the SARS CoV-2 reverse-transcriptase polymerase chain reaction (RT-PCR) on a nasopharyngeal swab, a chest computed tomography (CT) and assessment of clinical symptoms. The aim of this study was to evaluatethe diagnostic yield and the proportionality of this pre-procedural screeningprotocol.

METHODS

In this mono-centre, prospective, cross-sectional study, all patients admitted to the hospital between 22nd April 2020 until 14th May 2020 for semi-urgent surgery, haematological or oncological treatment, or electrophysiological investigationunderwent a COVID-19 screening 2 days before their procedure. At a 2-week follow-up, the presence of clinical symptoms was evaluated by telephone as a post-hoc evaluation of the screening approach.Combined positive RT-PCR assay and/or positive chest CT was used as gold standard. Post-procedural outcomes of all patients diagnosed positive for COVID-19 were assessed.

RESULTS

In total,528 patients were included of which 20 (3.8%) were diagnosed as COVID-19 positive and 508 (96.2%) as COVID-19 negative. 11 (55.0%) of COVID-19 positive patients had only a positive RT-PCR assay, 3 (15.0%) had only a positive chest CT and 6 (30%) had both a positive RT-PCR assay and chest CT. 10 out of 20 (50.0%) COVID-19 positive patients reported no single clinical symptom at the screening. At 2 week follow-up, 50% of these patients were still asymptomatic. 37.5% of all COVID-19 negative patients were symptomatic at screening. In the COVID-19 negative group without symptoms at screening, 78 (29.3%) patients developed clinical symptoms at a 2-week follow-up.

CONCLUSION

This study suggests that routine chest CT and assessment of self-reported symptoms have limited value in the preprocedural COVID-19 screening due to low sensitivity and/or specificity.

Global Percentage of Asymptomatic SARS-CoV-2 Infections Among the Tested Population and Individuals With Confirmed COVID-19 Diagnosis: A Systematic Review and Meta-analysis

IMPORTANCE

Asymptomatic infections are potential sources of transmission for COVID-19.

OBJECTIVE

To evaluate the percentage of asymptomatic infections among individuals undergoing testing (tested population) and those with confirmed COVID-19 (confirmed population).

DATA SOURCES

PubMed, EMBASE, and ScienceDirect were searched on February 4, 2021.

STUDY SELECTION

Cross-sectional studies, cohort studies, case series studies, and case series on transmission reporting the number of asymptomatic infections among the tested and confirmed COVID-19 populations that were published in Chinese or English were included.

DATA EXTRACTION AND SYNTHESIS

This meta-analysis was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. Random-effects models were used to estimate the pooled percentage and its 95% CI. Three researchers performed the data extraction independently.

MAIN OUTCOMES AND MEASURES

The percentage of asymptomatic infections among the tested and confirmed populations.

RESULTS

Ninety-five unique eligible studies were included, covering 29 776 306 individuals undergoing testing. The pooled percentage of asymptomatic infections among the tested population was 0.25% (95% CI, 0.23%-0.27%), which was higher in nursing home residents or staff (4.52% [95% CI, 4.15%-4.89%]), air or cruise travelers (2.02% [95% CI, 1.66%-2.38%]), and pregnant women (2.34% [95% CI, 1.89%-2.78%]). The pooled percentage of asymptomatic infections among the confirmed population was 40.50% (95% CI, 33.50%-47.50%), which was higher in pregnant women (54.11% [95% CI, 39.16%-69.05%]), air or cruise travelers (52.91% [95% CI, 36.08%-69.73%]), and nursing home residents or staff (47.53% [95% CI, 36.36%-58.70%]).

CONCLUSIONS AND RELEVANCE

In this meta-analysis of the percentage of asymptomatic SARS-CoV-2 infections among populations tested for and with confirmed COVID-19, the pooled percentage of asymptomatic infections was 0.25% among the tested population and 40.50% among the confirmed population. The high percentage of asymptomatic infections highlights the potential transmission risk of asymptomatic infections in communities.

Host methylation predicts SARS-CoV-2 infection and clinical outcome

BACKGROUND

Since the onset of the SARS-CoV-2 pandemic, most clinical testing has focused on RT-PCR1. Host epigenome manipulation post coronavirus infection2-4 suggests that DNA methylation signatures may differentiate patients with SARS-CoV-2 infection from uninfected individuals, and help predict COVID-19 disease severity, even at initial presentation.

METHODS

We customized Illumina's Infinium MethylationEPIC array to enhance immune response detection and profiled peripheral blood samples from 164 COVID-19 patients with longitudinal measurements of disease severity and 296 patient controls.

RESULTS

Epigenome-wide association analysis revealed 13,033 genome-wide significant methylation sites for case-vs-control status. Genes and pathways involved in interferon signaling and viral response were significantly enriched among differentially methylated sites. We observe highly significant associations at genes previously reported in genetic association studies (e.g. IRF7, OAS1). Using machine learning techniques, models built using sparse regression yielded highly predictive findings: cross-validated best fit AUC was 93.6% for case-vs-control status, and 79.1%, 80.8%, and 84.4% for hospitalization, ICU admission, and progression to death, respectively.

CONCLUSIONS

In summary, the strong COVID-19-specific epigenetic signature in peripheral blood driven by key immune-related pathways related to infection status, disease severity, and clinical deterioration provides insights useful for diagnosis and prognosis of patients with viral infections.

Behind Every Great Infection Prevention Program is a Great Microbiology Laboratory: Key Components and Strategies for an Effective Partnership

A great clinical microbiology laboratory supporting a great infection prevention program requires focusing on the following services: rapid and accurate identification of pathogens associated with health care-associated infections; asymptomatic surveillance for health care-acquired pathogens before infections arise; routine use of broad and flexible antimicrobial susceptibility testing to direct optimal therapy; implementation of epidemiologic tracking tools to identify outbreaks; development of clear result communication with interpretative comments for clinicians. These goals are best realized in a collaborative relationship with the infection prevention program so that both can benefit from the shared priorities of providing the best patient care.

Asymptomatic SARS-CoV-2 infection: A systematic review and meta-analysis

Quantification of asymptomatic infections is fundamental for effective public health responses to the COVID-19 pandemic. Discrepancies regarding the extent of asymptomaticity have arisen from inconsistent terminology as well as conflation of index and secondary cases which biases toward lower asymptomaticity. We searched PubMed, Embase, Web of Science, and World Health Organization Global Research Database on COVID-19 between January 1, 2020 and April 2, 2021 to identify studies that reported silent infections at the time of testing, whether presymptomatic or asymptomatic. Index cases were removed to minimize representational bias that would result in overestimation of symptomaticity. By analyzing over 350 studies, we estimate that the percentage of infections that never developed clinical symptoms, and thus were truly asymptomatic, was 35.1% (95% CI: 30.7 to 39.9%). At the time of testing, 42.8% (95% prediction interval: 5.2 to 91.1%) of cases exhibited no symptoms, a group comprising both asymptomatic and presymptomatic infections. Asymptomaticity was significantly lower among the elderly, at 19.7% (95% CI: 12.7 to 29.4%) compared with children at 46.7% (95% CI: 32.0 to 62.0%). We also found that cases with comorbidities had significantly lower asymptomaticity compared to cases with no underlying medical conditions. Without proactive policies to detect asymptomatic infections, such as rapid contact tracing, prolonged efforts for pandemic control may be needed even in the presence of vaccination.

First Do No Harm: Moving Beyond Universal Preprocedural Testing for COVID-19

Preprocedural testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was introduced early in the pandemic in an effort to protect health care workers, direct appropriate use of personal protective equipment (PPE), and improve patient outcomes. In light of our appreciation for the efficacy of PPE and the nuances associated with interpretation of polymerase chain reaction testing for SARS-CoV-2, particularly as community transmission decreases, we call for a re-evaluation of universal preprocedural testing. We propose a transition to a patient-centered approach, focusing on testing patients whose outcomes would be improved by a delayed procedure in the event of a positive test and a greater reliance on appropriate PPE rather than preprocedural test results. We recommend that a community infection rate threshold be set at which point preprocedural testing is discontinued, understanding that there is an inflection point at which testing downsides outweigh the benefits.

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.

Ambient air pollution and low temperature associated with case fatality of COVID-19: A nationwide retrospective cohort study in China

The evidence for the effects of environmental factors on COVID-19 case fatality remains controversial, and it is crucial to understand the role of preventable environmental factors in driving COVID-19 fatality. We thus conducted a nationwide cohort study to estimate the effects of environmental factors (temperature, particulate matter [PM_2.5, PM₁₀], sulfur dioxide [SO₂], nitrogen dioxide [NO₂], and ozone [O₃]) on COVID-19 case fatality. A total of 71,808 confirmed COVID-19 cases were identified and followed up for their vital status through April 25, 2020. Exposures to ambient air pollution and temperature were estimated by linking the city- and county-level monitoring data to the residential community of each participant. For each participant, two windows were defined: the period from symptom onset to diagnosis (exposure window I) and the period from diagnosis date to date of death/recovery or end of the study period (exposure window II). Cox proportional hazards models were used to estimate the associations between these environmental factors and COVID-19 case fatality. COVID-19 case fatality increased in association with environmental factors for the two exposure windows. For example, each 10 μg/m³ increase in PM_2.5, PM₁₀, O₃, and NO₂ in window I was associated with a hazard ratio of 1.11 (95% CI 1.09, 1.13), 1.10 (95% CI 1.08, 1.13), 1.09 (95 CI 1.03, 1.14), and 1.27 (95% CI 1.19, 1.35) for COVID-19 fatality, respectively. A significant effect was also observed for low temperature, with a hazard ratio of 1.03 (95% CI 1.01, 1.04) for COVID-19 case fatality per 1°C decrease. Subgroup analysis indicated that these effects were stronger in the elderly, as well as in those with mild symptoms and living in Wuhan or Hubei. Overall, the sensitivity analyses also yielded consistent estimates. Short-term exposure to ambient air pollution and low temperature during the illness would play a nonnegligible part in causing case fatality due to COVID-19. Reduced exposures to high concentrations of PM_2.5, PM₁₀, O₃, SO₂, and NO₂ and low temperature would help improve the prognosis and reduce public health burden.

Correlation of Population SARS-CoV-2 Cycle Threshold Values to Local Disease Dynamics: Exploratory Observational Study

BACKGROUND

Despite the limitations in the use of cycle threshold (CT) values for individual patient care, population distributions of CT values may be useful indicators of local outbreaks.

OBJECTIVE

We aimed to conduct an exploratory analysis of potential correlations between the population distribution of cycle threshold (CT) values and COVID-19 dynamics, which were operationalized as percent positivity, transmission rate (Rt), and COVID-19 hospitalization count.

METHODS

In total, 148,410 specimens collected between September 15, 2020, and January 11, 2021, from the greater El Paso area were processed in the Dascena COVID-19 Laboratory. The daily median CT value, daily Rt, daily count of COVID-19 hospitalizations, daily change in percent positivity, and rolling averages of these features were plotted over time. Two-way scatterplots and linear regression were used to evaluate possible associations between daily median CT values and outbreak measures. Cross-correlation plots were used to determine whether a time delay existed between changes in daily median CT values and measures of community disease dynamics.

RESULTS

Daily median CT values negatively correlated with the daily Rt values (P<.001), the daily COVID-19 hospitalization counts (with a 33-day time delay; P<.001), and the daily changes in percent positivity among testing samples (P<.001). Despite visual trends suggesting time delays in the plots for median CT values and outbreak measures, a statistically significant delay was only detected between changes in median CT values and COVID-19 hospitalization counts (P<.001).

CONCLUSIONS

This study adds to the literature by analyzing samples collected from an entire geographical area and contextualizing the results with other research investigating population CT values.

Pitfall of Universal Pre-Admission Screening for SARS-CoV-2 in a Low Prevalence Country

It is unclear whether universal PCR screening for SARS-CoV-2 in asymptomatic individuals prior to admission is useful. From April to December 2020, the positive rate of universal pre-admission screening was 0.005% (4/76,521) in a tertiary care hospital in Korea. The positive rates were not different between the periods (period 1 (daily new patients of <1 per million inhabitants) vs. period 2 (1-8.3 per million inhabitants) vs. period 3 (10.3 to 20 per million inhabitants); P = 0.45). Universal pre-admission screening for SARS-CoV-2 had a lower positive rate than that of symptom-based screening (0.005% vs. 0.049% (53/109,257), p < 0.001). In addition, seven patients with negative pre-admission test results had subsequent positive PCR during hospitalization, and four patients had secondary transmission. Universal pre-admission PCR screening may not be practical in settings of low prevalence of COVID-19, and negative PCR results at admission should not serve as a basis for underestimating the risk of nosocomial spread from asymptomatic patients.

Preprocedural SARS-CoV-2 Testing to Sustain Medically Needed Health Care Delivery During the COVID-19 Pandemic: A Prospective Observational Study

BACKGROUND

We implemented a preprocedural severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) screening initiative designed to sustain health care during a time when the extent of SARS-CoV-2 infection was unknown.

METHODS

This was a prospective study of patients undergoing procedures at 3 academic hospitals in Pittsburgh, Pennsylvania (April 21-June 11), and 19 community hospitals across Middle/Western Pennsylvania and Southwestern New York (May 1-June 11). Patients at academic hospitals underwent symptom screening ≤7 days preprocedure, then SARS-CoV-2 nasopharyngeal polymerase chain reaction (PCR) testing 1-4 days preprocedure. A subset also underwent day-of-procedure testing. Community hospital patients underwent testing per local protocols. We report SARS-CoV-2 PCR positivity rates, impact, and barriers to testing encountered through June 11. PCR positivity rates of optional preprocedural SARS-CoV-2 testing for 2 consecutive periods following the screening initiative are also reported.

RESULTS

Of 5881 eligible academic hospital patients, 2415 (41.1%) were tested (April 21-June 11). Lack of interest, distance, self-isolation, and nursing home/incarceration status were barriers. There were 11 PCR-positive patients (10 asymptomatic) among 10 539 patients tested (0.10%; 95% CI, 0.05%-0.19%): 3/2415 (0.12%; 95% CI, 0.02%-0.36%) and 8/8124 (0.10%; 95% CI, 0.04%-0.19%) at academic and community hospitals, respectively. Procedures were performed as scheduled in 40% (4/10) of asymptomatic PCR-positive patients. Positivity increased during subsequent coronavirus disease 2019 (COVID-19) surges: 54/34 948 (0.15%; 95% CI, 0.12%-0.20%) and 101/24 741 (0.41%; 95% CI, 0.33%-0.50%) PCR-positive patients from June 12-September 10 and September 11-December 15, respectively (P < .0001).

CONCLUSIONS

Implementing preprocedural PCR testing was complex and revealed low infection rates (0.24% overall), which increased during COVID-19 surges. Additional studies are needed to define the COVID-19 prevalence threshold at which universal preprocedural screening is warranted.

Digital Pathology Operations at an NYC Tertiary Cancer Center During the First 4 Months of COVID-19 Pandemic Response

Implementation of an infrastructure to support digital pathology began in 2006 at Memorial Sloan Kettering Cancer Center. The public health emergency and COVID-19 pandemic regulations in New York City required a novel workflow to sustain existing operations. While regulatory enforcement discretions offered faculty workspace flexibility, a substantial portion of laboratory and digital pathology workflows require on-site presence of staff. Maintaining social distancing and offering staggered work schedules. Due to a decrease in patients seeking health care at the onset of the pandemic, a temporary decrease in patient specimens was observed. Hospital and travel regulations impacted onsite vendor technical support. Digital glass slide scanning activities onsite proceeded without interruption throughout the pandemic, with challenges including staff who required quarantine due to virus exposure, unrelated illness, family support, or lack of public transportation. During the public health emergency, we validated digital pathology systems for a remote pathology operation. Since March 2020, the departmental digital pathology staff were able to maintain scanning volumes of over 100 000 slides per month. The digital scanning team reprioritized archival slide scanning and participated in a remote sign-out validation and successful submission of New York State approval for a laboratory developed test. Digital pathology offers a health care delivery model where pathologists can perform their sign out duties at remote location and prevent disruptions to critical pathology services for patients seeking care at our institution during emergencies. Development of standard operating procedures to support digital workflows will maintain turnaround times and enable clinical operations during emergency or otherwise unanticipated events.

Evaluation of rapid antigen detection kit from the WHO Emergency Use List for detecting SARS-CoV-2

BACKGROUND

Currently, there are two rapid antigen detection (RAD) kits from the WHO Emergency Use List for detecting SARS-CoV-2.

OBJECTIVE

The Panbio COVID-19 Ag Rapid Test Device was selected to evaluate the performance for detecting SARS-CoV-2.

STUDY DESIGN

Analytical sensitivity for the detection of SARS-CoV-2 virus was determined by limit of detection (LOD) using RT-PCR as a reference method. Clinical sensitivity was evaluated by using respiratory specimens collected from confirmed COVID-19 patients.

RESULTS

The LOD results showed that the RAD kit was 100 fold less sensitive than RT-PCR. Clinical sensitivity of the RAD kit was 68.6 % for detecting specimens from COVID-19 patients.

CONCLUSIONS

The RAD kit evaluated in the present study shared similar performance with another kit from the WHO Emergency Use List, the Standard Q COVID-19 Ag. Understanding the clinical characteristics of RAD kits can guide us to decide different testing strategies in different settings.