bluuebunny/crossref_metadata_2025 huggingface dataset:
405. Trend in blood culture results in Washington DC during and prior to Pandemic COVID-19
Authors: Klein Adam , Liappis Angelike P
Published: January 2021

Background

The rate of bacterial and/or fungal infections among COVID-19 cases is reportedly low. Antimicrobial Stewardship Programs (ASPs) provide continuous surveillance of blood cultures to secure appropriate choice and duration of therapy. Comparing to historic data, we characterize our ASP experience in bacteremic surveillance during the COVID-19 pandemic.

Methods

Consecutive blood cultures at the Washington DC VA Medical Center were captured in an ASP-driven decision support software system (TheraDoc, Premier/DSS Inc) between Jan 1st 2018-May 31st 2020. In the setting of an established ASP, the organism positive cultures were reviewed over the first five months (Jan-May) of each of the three years collected. Results of cultures were characterized as either pathogenic gram positive (MSSA/MRSA/Enterococci/PSSP/PRSP/Strep sp.), pathogenic aerobic and anaerobic gram negative organisms and a skin contaminant-category (GPRs/skin flora/CNS).

Results

Over 3 yrs, 528 patients had 1464 positive cultures from among 8727 admissions, 83638 inpatient-days. The proportion of pathogenic GP bacteria and pathogenic GN bacteria were not statistically significantly different 38% (2018) vs 37% (2019) vs 39% (2020) and 33%, 31%, 27% respectively. There was slight trend in the increase of pathogenic GP 9.6 vs 9.5 vs 11.7 per 1,000 inpatient days and skin contaminant-category with 12.0 vs 11.0 vs. 14.1 per 1,000 patient days from 2019 to 2020. We noted a dramatic shift in culture surveillance report during the peak COVID-infection rates (March-April), notable for several weeks of few to no culture positive results. When broken down by month, variability was noted (data not shown). COVID-19 infected patients represented 9.0% (7/78) of positive blood culture results in 2020 Jan-May, only 5.1% (4/78) were treated as non-contaminants and were related to indwelling catheters or urosepsis.

Conclusion

Overall and adjusted rates of the blood cultures sent during the pandemic months in 2020 were comparable to the comparative years. Surveillance revealed short term changes in patterns which may have reflected the pandemic induced changes to admissions. COVID-19 infected patients rarely experienced line and hospital acquired bactermia/fungemia, most during the recovery period.

Disclosures

All Authors: No reported disclosures
406. Utility of Tracheal Aspirates in Guiding Antibiotic Use in Mechanically Ventilated Patients with COVID-19
Authors: Shihadeh Katherine C , Hussain Cory , Deida Axel Vazquez , Neumeier Anna , Jenkins Timothy C
Published: January 2021

Background

In critically ill patients with COVID-19 it is difficult to determine the presence of bacterial co-infection. Many patients receive antibiotics until a bacterial infection can be ruled out. To minimize aerosolization of SARS-CoV-2, non-invasive sampling, such as endotracheal aspiration (ETA), is preferred over invasive techniques. The purpose of this study is to determine the diagnostic yield of ETA and effect of ETA on antibiotic management in patients with COVID-19.

Methods

This retrospective analysis included patients admitted to the intensive care unit (ICU) from March 1 to May 31, 2020 who tested positive for SARS-CoV-2. Patients who did not receive mechanical ventilation were excluded. Data were extracted from electronic medical records. When ETA was performed, records were manually reviewed to determine diagnostic yield and effect on antibiotic management. Diagnostic yield was defined as ETA result with a plausible respiratory pathogen in a quantity of moderate or many. Plausible respiratory pathogens exclude normal flora, yeast, coagulase-negative Staphylococcus sp and Enterococcus sp. The primary outcome is the frequency of initiation, change, no change, or discontinuation of antibiotics based on ETA results.

Results

124 patients with COVID-19 were admitted to the ICU; 76 met inclusion criteria. The average age was 58 years and 75% were male. Hispanic or Latino ethnicity made up the majority of the patient population (63%). Antibiotics were administered to 97% of patients for a median of 11 days of therapy (IQR 7, 21). There were 100 ETAs performed on 55 patients for a diagnostic yield of 21%. ETA led to a change in antibiotic management 47% of the time it was performed. Antibiotic changes include de-escalation (29), discontinuation (7), escalation (6), and initiation (5).

Conclusion

The diagnostic yield of ETA in mechanically ventilated patients with COVID-19 was low. Furthermore, ETA results led to a change in antibiotics less than half of the time. The use of ETA to diagnose bacterial co-infection and guide antibiotic therapy in patients with COVID-19 should be weighed against the risk of using a more invasive sampling technique vs the benefit of potential for increased diagnostic yield. Another conclusion may be to forgo ETA if the result is unlikely to change management.

Disclosures

All Authors: No reported disclosures
408. Evaluation of the negative predictive value of the SARS-CoV-2 PCR respiratory assays in asymptomatic children undergoing surgery
Authors: Rao Suchitra , Ambroggio Lilliam , Asturias Edwin J , Bajaj Lalit , Corrado Michelle , Inge Thomas , Jung Sarah , Morrissey Tyler , Osborne Christina M , Searns Justin B , Whitney Gina , Dominguez Samuel
Published: January 2021

Background

Universal pre-operative screening with SARS-CoV-2 PCR has been adopted by institutions to mitigate risk to healthcare workers (HCW) during aerosol-generating procedures such as intubation. However, there remains uncertainty regarding rates of false negative results and optimal sampling type. The objective was to determine the reliability of single, pre-operative SARS-CoV-2 testing from the nasopharynx in children undergoing general anesthesia.

Methods

Children < 18 years of age who underwent intubation for a procedure received pre-operative testing 24–48 hours prior with a nasopharyngeal (NP) swab or wash, in conjunction with intra-operative nasal wash (NW) and tracheal aspirate (TA) sampling. All paired samples underwent testing using the Simplexa DiaSorin platform or a modified Centers for Disease Control assay. Cohen’s Kappa was used for interrater reliability of each sample result. McNemar’s Test was used to compare result proportions by sample type. Positive and negative predictive values (PPV, NPV) were calculated based on the intraoperative NW as the reference standard. Analyses were conducted using SAS (v 9.4).

Results

We collected full sample sets from 364 children from April 14 to May 15; 66% of pre-operative samples were NP swabs. The median age was 6 years (IQR 2,13), 55% were male, 68% were white and 41% of children had a high-risk comorbidity. Most surgeries were conducted by general surgery (23%), followed by orthopedics (19%). Only 2.5% of children had respiratory symptoms, and 4.8% had a documented fever within a week of the procedure. SARS-CoV-2 positive samples occurred in 4/364 (1%) of pre-operative samples, 8/363 (2.2%) of intra-operative samples, and 8/348 (2.3%) of TA samples. The pre-operative test had 100% PPV and 99% NPV, and the TA had 100% PPV and 98.6% NPV (Table 1). There was very good agreement (Figure) between pre- and intraoperative upper respiratory sampling, with a Kappa of 0.66, (95% CI 0.35–0.97). There was no statistical difference in results by sample type.

Table 1. Comparison of intra-operative and pre-operative nasopharyngeal sample results, test characteristics and test concordance

Table 2. Comparison of intra-operative nasopharyngeal and tracheal aspirate sample results, test characteristics and test concordance

Figure 1 Percent agreement between pre-operative and intra-operative samples

Conclusion

There is a high PPV and NPV of pre-operative SARS-CoV-2 PCR testing among children undergoing anesthesia. These data can help inform guidelines regarding appropriate precautions for HCW performing high risk procedures in asymptomatic pediatric patients.

Disclosures

Suchitra Rao, MD, BioFire (Grant/Research Support) Samuel Dominguez, MD, PhD, BioFire (Consultant, Research Grant or Support)
411. Application of a SARS-CoV-2-specific serologic assay for translational research and surveillance
Authors: Sherman Amy C , Smith Teresa C , Espinoza Daniel , Zhu Yerun , Howard-Anderson Jessica , Taibl Kaitlin R , Fairley Jessica K , Wu Henry M , Edupuganti Sri , Rouphael Nadine , Rouphael Nadine , Rodriguez-Morales Alfonso J , Ospina Jaime Cardona , Arias Juan Carlos Sepúlveda , Fridkin Scott , Collins Matthew H
Published: January 2021

Background

Sensitive and specific SARS-CoV-2 antibody diagnostics are urgently needed to estimate the seroprevalence of SARS-CoV-2 infection in both the general population and special risk groups. Moreover, validated serologic assays are critical to understanding immunity to SARS-CoV-2 infection over time and identifying correlates of protection.

Methods

An enzyme-linked immunosorbent assay (ELISA) protocol to detect antibodies (IgG) that bind the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was validated and ROC curve analysis performed by testing a large panel of pre-pandemic sera (n=162) and convalescent sera from RT-PCR-confirmed COVID-19 cases (n=60). We then applied this test in two cohorts: 1) Healthcare personnel (HCP) that were enrolled in a longitudinal surveillance cohort just after peak local transmission and 2) Mildly ill patients being tested for SARS-CoV-2 infection by RT-PCR from NP swabs in an ambulatory testing clinic.

Demographics of mildly symptomatic patients tested for SARS-CoV-2 with RT-PCR

Results

ROC curve analysis yielded an AUC of 0.9953, with a sensitivity and specificity at 91.67% and 99.38% at the optimal OD normalization threshold of 0.20. In 240 HCP surveilled at enrollment, 5.83% had positive IgG results. Of 19 symptomatic patients who presented to the ambulatory clinic, 5/19 had a positive PCR. In convalescence (13–74 days post symptom onset), 3 of those 5 were positive for IgG.

Validation of the SARS-CoV-2 RBD ELISA

ROC Curve Analysis

Conclusion

We demonstrated high sensitivity and specificity of the SARS-CoV-2 RBD ELISA. This simple assay is an efficient way to track seroconversion and duration of antibody responses to SARS-CoV-2 for different populations, particularly since RBD-binding antibodies have been shown to correlate with neutralization activity and may be useful to determine protective immunity following natural infection or vaccination. Ongoing work will assess variation in magnitude, character and duration of antibody responses in key populations and seek to maximize deployability of large-scale SARS-CoV-2 serology.

Disclosures

Jessica Howard-Anderson, MD, MSc, Antibacterial Resistance Leadership Group (ARLG) (Other Financial or Material Support, The ARLG fellowship provides salary support for ID fellowship and mentored research training) Nadine Rouphael, MD, Lilly (Grant/Research Support)Merck (Grant/Research Support)Pfizer (Grant/Research Support)Quidel (Grant/Research Support)Sanofi Pasteur (Grant/Research Support)
415. Clinical Impact of Molecular Point-of-Care Testing for COVID-19 in Adults Presenting to Hospital: A Prospective, Interventional, Non-Randomised, Controlled Study
Authors: Brendish Nathan J , Poole Stephen , Naidu Vasanth V , Mansbridge Christopher , Norton Nicholas , Wheeler Helen , Presland Laura , Ewings Sean , Kidd Stephen P , Cortes Nick , Clark Tristan William
Published: January 2021

Background

The management of the COVID-19 pandemic is hampered by the long delays associated with laboratory PCR testing. In hospitals this leads to poor patient flow and nosocomial transmission and so rapid, accurate diagnostic tests are urgently required. The aim of this study was to evaluate the clinical impact and real-world diagnostic accuracy of molecular point-of-care testing (mPOCT) for COVID-19 in hospital.

Methods

We performed a prospective, interventional, non-randomised, controlled study of mPOCT for COVID-19 in adults presenting to hospital with suspected COVID-19. Patients were tested using the QIAstat-Dx SARS-CoV-2 at the point-of-care with results delivered to clinical and infection control teams. Control patients were tested using the PHE Rdrp reference assay. The Primary outcome measure was time to result and secondary outcome measures included infection control outcomes and measures of diagnostic accuracy.

Results

Between 20th March and 29th April 2020 500 patients were tested by POCT and 555 controls, who were tested with laboratory PCR, were identified. Overall 33% were positive for SARS-CoV-2. Median time to results with POCT was 1.7 (1.6 to 1.9) hours versus 21.3 (16.0 to 27.9) hours in the control group (difference of 19.6 hours, 95%CI 19.0 to 20.3; p< 0.0001). Median time to arrival in definitive clinical area (COVID-19 positive or negative ward) was 8.0 (6.0 to 15.0) hours in the POCT group versus 28.8 (23.5 to 38.9) hours in the control group, p< 0.0001. Median time to enrolment into other COVID-19 clinical trials was 1.5 (1 to 3) days in the POCT versus 3.0 (2 to 5) days in the control group, p< 0.0001. Sensitivity of the POCT was 99.4% and specificity was 98.3%. The sensitivity of the laboratory PHE reference RdRp assay was 87.2% and specificity was 98.9%.

Conclusion

mPOCT was associated with a large reduction in time to results and improvements in infection control measures and patient flow, compared with laboratory PCR. In addition, patients were recruited onto other clinical trials more rapidly with POCT. The QIAstat-Dx SARS-CoV-2 panel had high diagnostic accuracy for the detection of COVID-19 compared to laboratory PCR. Resources should be urgently made available to support the widespread implementation of mPOCT in hospitals, in preparation for the second wave.

Disclosures

Tristan William. Clark, BM MRCP DTM&H MD, BioFire Diagnostics (Other Financial or Material Support, Equiptment and consumables for the purposes of research)BioMerieux (Other Financial or Material Support, Equipment and consumables for the purposes of research)Qiagen (Other Financial or Material Support, Discounted Equipment and consumables for the purposes of research)
416. Comparative Analytical Assessment of PCR Mastermixes for Detection of SARS-CoV-2 using the CDC Diagnostic Test and the LightMix Modular Test on the cobas® z 480 Analyzer
Authors: Cagas Steven , McCune Stephen , Rodriguez Pedro , Hein Ray , Osiecki John , Robinson Nicole , McGowin Chris L
Published: January 2021

Background

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a betacoronavirus responsible for the ongoing global pandemic and associated respiratory disease. Rapid development and implementation of molecular diagnostic testing solutions has been imperative to meet the enormous and urgent public health needs, and remains a key component of the US emergency response. Nucleic acid amplification tests (NAATs), with emergency use authorization (EUA) by the FDA, have been subject to significant supply chain shortages. This study aims to comparatively assess several commercially available substitutive mastermix reagents for the CDC SARS-CoV-2 EUA test and the TIB Mol Biol LightMix Modular (RUO) test.

Methods

Positive control material included with each testing kit was used directly as DNA template for all manually assembled reactions and comparative evaluation. Additionally, these tests were evaluated similarly using the cobas omni Optimization kit, the first step in assessing suitability on the cobas® omni Utility Channel for high-volume user-defined molecular testing on the fully automated cobas® 6800/8800 Systems. All PCR was performed per the manufacturer’s instructions using the User Defined Workflow (UDF; open channel) on the cobas® z 480 analyzer.

Results

Robust amplification of the commercial control material was observed with each mastermix for all gene targets within the CDC and LightMix tests. Modest but significant (ANOVA, p< 0.05) target-specific Ct-value impacts were observed among the mastermixes assessed in this study. Using the cobas® omni optimization kit, Ct values for each target within the CDC and LightMix tests were consistently and significantly lower (ANOVA, p< 0.05) than the comparator mastermixes.

Conclusion

Each mastermix may be a useful alternative to the recommended mastermix for SARS-CoV-2 detection. Additionally, these findings suggest the CDC and LightMix tests may be adapted for fully-automated, high-throughput testing on the 6800/8800 Systems.

Disclosures

Steven Cagas, PhD, Roche Diagnostics Corp (Employee) Stephen McCune, BS, Roche Diagnostics Corp (Employee) Pedro Rodriguez, Ph.D, Roche Diagnostics Corp (Employee) Ray Hein, PhD, Roche Diagnostics Corp (Employee) John Osiecki, PhD, Roche Diagnostics Corp (Employee) Nicole Robinson, Ph.D, Roche Diagnostics Corp (Employee) Chris L. McGowin, PhD, Roche Diagnostics Corp (Employee)
417. Comparative Assessment of Multiple SARS-CoV-2 Antibody and Neutralization Assays from Blood Samples in COVID-19 Infected Patients
Authors: Dewar Robin L , Trevino Christina , Lallemand Perrine , Highbarger Helene , Elbeik Tarek A , Rehman Tauseef , Holbrook Michael , Schmaljohn Connie , Lane Cliff , Chary Aarthi , Holodniy Mark
Published: January 2021

Background

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) has caused a world-wide pandemic. Diagnosis is usually made by an RT-PCR test from a respiratory sample. A number of tests are available for antibody detection or assessment, including rapid, enzyme immunoassays (EIA) and neutralization. However, characterization of the antibody immune response is not well documented and the clinical significance of COVID antibodies remains largely unknown. In addition, comparison of results across different assay formats using identical samples has not been rigorously studied, making clinical interpretation of serologic tests difficult.

Assessment of multiple SARS-CoV-2 antibody and neutralization assays from blood samples in COVID-19 infected patients

Methods

1–5 serial (total 33) serum or plasma samples from 14 patients who were positive for SARS-CoV-2 by EUA authorized RT-PCR assays from nasopharyngeal specimens where tested with the following COVID-19 antibody tests: LFA rapid tests (Chembio DPP IgM/IgG, SD Biosensor Standard IgM/IgG, BTNX Rapid Response IgM/IgG), and EIA tests (BioRad Platelia SARS-CoV-2 Total antibody-IgG/IgM/IgA, EuroImmun SARS-CoV-2 IgG, and EuroImmun SARS-CoV-2 IgA). See Table 1 for results and EUA. Results were recorded as positive, negative, or equivocal. Additionally, antibody neutralization was assessed on matched samples.

Results

Mean age of SARS-CoV-2 positive patients was 73 years (range 65–89), 11/14 had symptoms, all were male and hospitalized (6 ICU), and 3 died. Average number of days serum was collected after RT-PCR positivity was 13.5 days (range -3 to 46 d). BTNX assay was only tested on 16 samples. Among all assays, total concordance of results was 91%. When only IgG/IgM or total antibody assays were considered, concordance of results was 96% (Table). IgA specific results were discordant in 9/33 (27%) of samples compared to other assays. Two patients were negative in all assays in serial samples collected within one week of PCR positivity. Antibody neutralization was detected, but not from all samples.

Conclusion

In general, there was good agreement among antibody detection assays. Neutralization may reflect disease outcome. The study was limited by the number of positive samples and patient number, and at the time specificity was not addressed for all the assays.

Disclosures

All Authors: No reported disclosures
418. Comparison of the Abbott SARS-CoV-2 IgG and DiaSorin LIASON SARS-CoV-2 S1/S2 IgG Antibody Assays
Authors: Schaack Grace A , Chen Derrick
Published: January 2021

Background

The Abbott Laboratories SARS-CoV-2 IgG assay and the DiaSorin LIASON SARS-CoV-2 S1/S2 IgG assay are both chemiluminescent immunoassays that qualitatively detect IgG antibodies against SARS-CoV-2 antigens. The Abbott assay detects IgG against the viral nucleocapsid (N) protein, while the DiaSorin assay uses antigen derived from the viral spike (S) protein. Here we evaluate the performance of these two assays at our institution.

Methods

45 patient samples (serum or plasma) were tested for anti-SARS-CoV-2 IgG by both the Abbott and DiaSorin assays. The samples were previously characterized at a national reference laboratory using the Abbott assay or by an in-house PCR-based test for SARS-CoV-2 RNA. Samples yielding discordant results across platforms were further tested using the EUROIMMUN Anti-SARS-CoV-2 ELISA (IgG) assay at the reference laboratory.

Results

22 samples tested negative for SARS-CoV-2 by the reference lab Abbott assay, and 23 tested positive by the same reference lab test (n = 13) or by an in-house PCR-based test (n = 10). The 22 samples characterized as negative again tested negative by both the Abbott (in-house) and DiaSorin assays (100% NPA). Among the 23 samples characterized as positive, all 23 tested positive by the Abbott assay (100% PPA), while only 15 tested positive by the DiaSorin assay (65% PPA). For each of the 8 discordant cases, samples were further tested by EUROIMMUN assay, which targets the S protein; 7 of the 8 samples tested negative by this assay, in agreement with the DiaSorin test results. Thus, for the discordant cases, testing for IgG against N (in-house and reference lab Abbott assays) gave positive results, while testing for IgG against S (DiaSorin and EUROIMMUN assays) mostly gave negative results.

Conclusion

These findings highlight the importance of the differences between various SARS-CoV-2 antibody tests, and providers should be aware of the specific antigenic target(s) in each test. Selection of a specific assay may depend on the need to assess past exposure to SARS-CoV-2 (for which a nucleocapsid target may be more sensitive) or to detect neutralizing antibodies (for which a spike target may be more relevant). This also has implications for disease surveillance as reliance on anti-spike antibodies alone may underestimate infection prevalence.

Disclosures

All Authors: No reported disclosures
424. Sensitivity Results for the Abbott m2000 PCR Assay of SARS-CoV-2 at a Denver, Colorado Medical Center
Authors: Aragon Deborah , Young Heather , Wilson Michael L , Knepper Bryan C , Triplett Laura , Bacon Tim
Published: January 2021

Background

The Abbott RealTime SARS-CoV-2 assay (Abbott Laboratories, Chicago, Illinois) is an RT-PCR test for qualitative detection of SARS-CoV-2 nucleic acid in NP and OP specimens performed on the Abbott m2000 System. Currently, no published data exists on the performance characteristics of the assay.

Methods

Denver Health Medical Center (DHMC) is a 550-bed hospital that is Denver County’s safety net institution. The Department of Pathology and Laboratory Services at DHMC provides testing for both inpatient and outpatient populations. In March 2020, we validated the Abbott RealTime SARS-CoV-2 assay. Beginning March 19, inpatients and outpatients with SARS-CoV-2 symptoms were tested. On April 22, universal testing began on admitted patients, regardless of symptoms, and on May 2, testing began on asymptomatic outpatients prior to time-sensitive procedures. We evaluated the sensitivity and negative predictive value (NPV) for tests done March 19 through June 16 using a surrogate method. False negative (FN) results: patients with an initial negative test then a positive test within 7 or 14 days. True negative (TN) results: patients with two initial consecutive negative tests within 7 or 14 days. True positive (TP) results: patients with an initial positive test.

Results

There were 16,152 tests done for 13,673 patients. Test results are shown in Table 1. Sensitivity for 7 and 14 days was 99.1% and 97.6%, respectively. The NPV for 7 and 14 days was 94.7% and 91.4%, respectively.

Table 1

Conclusion

There are limitations to our analysis. First, our assumption of no false positives may be incorrect. Although PCR assays are known to have a low false positive rate, the rate likely is not zero, but in the absence of a true gold standard comparator, we could not calculate test specificity. Second, testing asymptomatic patients may artificially inflate the TN results and the NPV. Third, results depend on the quality of specimen collection, preservation, transport, and handling. We believe accounting for repeat testing in a short timeframe lends credibility to the sensitivity and NPV results. Without published gold standard data on SARS-CoV-2 testing, infection can be reliably ruled both in and out using this assay. Providers can confidently use the results to make clinical and infection prevention management decisions.

Disclosures

All Authors: No reported disclosures
428. Very High Clinical Likelihood (VHCL) Of COVID-19 Infection: Peering Beyond A Negative Nasopharyngeal Swab
Authors: Khatri Akshay M , Flannery Sarah , Singh Vansha , Khameraj Aradhana , Malhotra Prashant , Farber Bruce , Kast Charles L , Gitman Michael , Foley Mathew , Hirschwerk David
Published: January 2021

Background

Diagnosis of COVID-19 relies upon RT-PCR assays for SARS-CoV-2 from a nasopharyngeal swab (NPS). However, results depend upon duration of illness at the time of testing and operator performance. False negatives occur 10–30% of the time. In our center we formulated & applied a clinical prediction tool for diagnosis of COVID-19 infection. Patients who satisfied criteria were designated as having COVID-19 regardless of NPS results. Herein, we describe the set of patients who fulfilled full and strict clinical criteria (VHCL) (Table 1) and had at least 2 negative NPSs on hospital admission.

Table 1: Clinical criteria for Very High Clinical Likelihood of COVID-19 Infection (VHCL COVID-19)

Methods

A retrospective descriptive study was conducted from March 4th to April 11th, 2020. We evaluated patients with ≥ 2 consecutive negative NPS COVID-19 results admitted to our hospital. Of these, we identified patients fitting all 5 criteria for Very High Clinical Likelihood (VHCL) of COVID-19 infection (Table 1). We analyzed symptoms & lab data (including results of repeat NPS testing if performed) in those patients.

Results

1855 patients were diagnosed with COVID-19 in the study period. Of these, 23 had ≥ 2 negative COVID-19 NPS results but met criteria for VHCL (Table 2). Of these 23, 7 had a subsequent 3rd NPS that was positive-proving infection. Similar to other reports, patients had low lymphocytes and elevated procalcitonin, ferritin, C-reactive protein levels. And consistent with proven cases, our cohort presented after a median of 5 days of symptoms (Table 3).

Table 2: Clinical and laboratory characteristics of VHCL COVID-19 patients [Rows Bolded include those patients who had a 3rd NPS swab that was positive].

Table 3: Demographic and Median Lab Data of VHCL COVID-19 patients

Conclusion

It is critical to be mindful of the imperfection of laboratory testing & to integrate clinical criteria to diagnostic algorithms. This is especially true in the COVID-19 pandemic, which is marked by high morbidity & mortality. In our study, we demonstrated how a set of clinical parameters (which we termed VHCL) can aid in widening the net of patients diagnosed with COVID-19 despite negative laboratory tests. While 16 patients in our cohort did not have a confirmatory result, the strict criteria for VHCL & the close match of other study variables with those of proven cases supports the value of VHCL designation. Applying VHCL can optimize infection control, identify patients for emerging therapeutics & aid in contact tracing to reduce nosocomial & community transmission of COVID-19.

Disclosures

All Authors: No reported disclosures
429. County-level predictors of COVID-19 testing across the 62 counties in New York State: A comparison across machine learning algorithms
Authors: Zeng Chengbo , Xiao Yunyu
Published: January 2021

Background

More than 360,000 people infected with COVID-19 in New York State (NYS) by the end of May 2020. Although expanded testing could effectively control statewide COVID-19 outbreak, the county-level factors predicting the number of testing are unknown. Accurately identifying the county-level predictors of testing may contribute to more effective testing allocation across counties in NYS. This study leveraged multiple public datasets and machine learning algorithms to construct and compare county-level prediction models of COVID-19 testing in NYS.

Methods

Testing data by May 15th was extracted from the Department of Health in NYS. A total of 28 county-level predictors derived from multiple public datasets (e.g., American Community Survey and US Health Data) were used to construct the prediction models. Three machine learning algorithms, including generalized linear regression with the least absolute shrinkage and selection operator(LASSO), ridge regression, and regression tree, were used to identify the most important county-level predictors, adjusting for prevalence and incidence. Model performances were assessed using the mean square error (MSE), with smaller MSE indicating a better model performance.

Results

The testing rate was 70.3 per 1,000 people in NYS. Counties (Rockland and Westchester) closed to the epicenter had high testing rates while counties (Chautauqua and Clinton) located at the boundary of NYS and were far away from the epicenter had low testing rates. The MSEs of linear regression with the LASSO penalty, ridge regression, and regression tree was 123.60, 40.59, and 298.0, respectively. Ridge regression was selected as the final model and revealed that the mental health provider rate was positively associated with testing (β=5.11, p=.04) while the proportion of religious adherents (β=-3.91, p=.05) was inversely related to the variation of testing rate across counties.

Conclusion

This study identified healthcare resources and religious environment as the strongest predictor of spatial variations of COVID-19 testing across NYS. Structural or policy efforts should address the spatial variations and target the relevant county-level predictors to promote statewide testing.

Disclosures

All Authors: No reported disclosures
431. Geospatial prediction model of COVID-19 outbreak in New York State
Authors: Zeng Chengbo , Xiao Yunyu
Published: January 2021

Background

More than 360,000 people infected with COVID-19 in New York State (NYS) by the end of May 2020.The spatial variations of prevalence across the counties in NYS suggested that variations in county-level factors might contribute to the statewide COVID-19 outbreak. However, no study to date investigates such variations and the relevant predictors. We leveraged multiple public datasets and machine learning approaches to construct the county-level spatial-temporal prediction model of COVID-19 in NYS. Findings generating from this study help identify counties with high prevalence, county-level predictors, and promising next steps for policy efforts to control the second wave of statewide COVID-19 transmission.

Methods

Cumulative confirmed case rates (CCCR) of COVID-19 by county in NYS were extracted from the US Health Data system at four critical time points including March 17th (state of emergency, 4.40 per 100,000 people), April 18th (coronavirus peak, 310.10 per 100,000 people), April 25th (expand testing, 393.90 per 100,000 people), and May 11th (daily increased rate back to the level in March, 505.30 per 100,000 people. A total of 28 county-level predictors were used to construct the prediction model, and the generalized linear mixed effect least absolute shrinkage and selection operator (LASSO) regression was employed to select the predictors of COVID-19 outbreak across the counties in NYS with adjusting for time effect.

Results

The CCCR by the final timepoint was 1,850.3 per 100,000 people. Rockland County had the highest CCCR than any other counties, with a rate of 3,856.82 per 100,000 people, while Chautauqua and Franklin counties had the lowest CCCR (0.03 per 100,000 people). LASSO regression revealed counties with a larger proportion of non-citizen (β=9537.97, p=0.02) had a higher CCCR of COVID-19 across the time. In contrast, counties with a lower proportion of people with at least high school education (β=-6157.89, p=0.025) and a larger proportion of houses with less than 3 people (β=-5995.79471, p=0.01) had lower CCCR.

Conclusion

We identified immigrant status, education level and household type influenced the spatial variations of COVID-19 outbreak in NYS. Future interventions shall target on areas with greater density of non-citizens to prevent transmission.

Disclosures

All Authors: No reported disclosures
436. Assessing SARS-CoV-2 Infection among Persons Experiencing Homelessness — Atlanta, GA, 2020
Authors: Yoon Jane C , Morris Sapna , Schmit Kristine , Hernandez Alfonso , Montgomery Martha , Ko Jean , Boyd Andrew T , Buff Ann , Flowers Nicole , Jamison Calla , Mosites Emily , Paulin Heather , Ajoku Sophia , Swancutt Mark , Holland David , Turner Kim , Andrews Tom , Shah Sarita , Prieto Juliana , Smith Sasha , Gaffga Nicholas , Cavanaugh Joseph , Marchman Cathryn
Published: January 2021

Background

Persons experiencing homelessness (PEH) often do not have sufficient resources to practice public health interventions. PEH may reside at overcrowded shelters, have poor access to health care, and often suffer from significant co-morbid conditions. In this study, we describe prevalence of COVID-19 amongst PEH and homeless service staff in Atlanta, Georgia, as well as demographic data, underlying conditions, and symptoms.

Methods

In response to the COVID-19 pandemic in Atlanta, PEH and homeless service providers were offered PCR testing for SARS-CoV-2 via nasopharyngeal, nasal mid-turbinate, and oropharyngeal swabs. Shelters identified as having a higher number of COVID-19 infections underwent re-testing 3–4 weeks after initial testing. Demographic information was collected, and individuals were screened for symptoms and underlying conditions.

Results

A total of 2,294 PEH and 544 staff underwent SARS-CoV-2 PCR testing from April 8 - May 6, 2020. 24 homeless shelters were included in this study. The majority of individuals were male (66.3% sheltered, 85.5% unsheltered, 55.3% staff), and 2,192 of 2,838 (78.3%) persons identified as black. Approximately half of individuals had no known underlying conditions (51.5% sheltered, 47.7% unsheltered, 55.5% staff). Cardiovascular disease was the most frequently reported condition (32.0%), followed by chronic lung disease (14.8%). In total, 45 of 2,823 (1.6%) individuals had detectable PCR results for SARS-CoV-2, including 35 of 1,666 (2.1%) sheltered clients, 3 of 614 (0.5%) unsheltered clients, and 7 of 543 (1.3%) staff. Among individuals with detectable SARS-CoV-2, 5 of 20 (25%) reported at least one symptom in the last week. Most shelters (16 of 24) had at least one individual with detectable SARS-CoV-2. The prevalence of SARS-CoV-2 in the majority of shelters (19 of 24) was < 3%, with a median prevalence of 0.2% across all shelters. Upon retesting 4 shelters with a higher number of COVID-19 infections, only 3 individuals from 2 shelters tested positive out of 357 total retested (0.8%).

Conclusion

We identified a low prevalence of SARS-CoV-2 infection among PEH in Atlanta, which was influenced by a pre-emptive testing strategy. Continued vigilance is necessary to limit spread in this vulnerable population.

Disclosures

All Authors: No reported disclosures
439. Clinical Characteristics and Mortality of an Initial Cohort of COVID-19 Patients in México City
Authors: Castañeda-Mendez Paulo F , Castillo-Álvarez José Luis , Barragán-Reyes Armando , Bay-Sansores Daniela , Pulido-Enríquez Jessica Isabel , González-Ramírez Luis Humberto , Cabrera-Ruiz Maria Lorena , Aguilar-Zapata Daniel , Reyes-Mar Javier , Soto-Ramírez Luis Enrique
Published: January 2021

Background

As of today, more than 8 million people have been infected and around 440,000 of them have lost their lives due to complications of SARS-CoV-2 infection.

The first confirmed case of COVID-19 in Mexico was on February 28, 2020, and currently, there are more than 150,300 confirmed cases and more than 17,500 deaths have been reported, this work presents the characteristics of the first cases on a tertiary care center with special focus on common comorbidities in Mexicans.

Methods

We conducted a case series of patients with the diagnosis of pneumonia due to SARS-CoV-2 virus admitted to a tertiary care center in Mexico City, between March 14th and May 4th, 2020. Data collected included demographic information, comorbidities, clinical presentation, and outcomes. Regarding clinical outcomes, we measured the need of admission to Intensive Care Unit (ICU), mortality during hospitalization, discharge, and patients that remained hospitalized.

Results

85 patients were included, median age 53.5 years; 69.4% were male. Most common clinical manifestations at admission were fever (61, 71.8%), cough (29, 34.1%), headache (25, 29.4%) and dyspnea (22, 25.9%). Most common comorbidities were overweight (44/82, 53.6%), obesity (25/82, 30.5%), hypertension (18, 21.2%), and diabetes (17, 20%).

31 of 85 (36.5%) patients were diagnosed with critical disease, whereas 54 of 85 (63.5%) were classified as non-critical. In the 31 critically ill patients, the length of invasive mechanical ventilation was 13 days [range {2–45}]; 5 patients (16.1%) required tracheostomy. The mean of mechanical ventilation prior to tracheostomy was 19.8 days [range {14–25}].

In all patients, the total length of hospitalization was 12.1 days [range {2–52}], 14.8 days [range {3–52}] in ICU patients, and 6.7 days [range {2–30}] in floor unit patients. No readmissions were documented.

Global mortality was 4.7% (9.6% in ICU, 1.8% in floor unit). Of the 4 deceased patients, 3 presented comorbidities (75%), while 1 was previously healthy, documenting massive pulmonary embolism as the cause of sudden death.

Conclusion

This study shows that the clinical characteristics in this initial cohort are not different that described elsewhere. Mortality is low but it is mainly related to prevalent comorbidities in the Mexican population.

Disclosures

All Authors: No reported disclosures
442. Common symptoms of outpatient COVID-19 compared to non-COVID-19 Cases: A prospective epidemiologic study in a major US metropolitan area
Authors: Fairley Jessica K , Taibl Kaitlin R , Landay Taylor , Sherman Amy C , Wu Henry M , Collins Matthew H
Published: January 2021

Background

The majority of novel coronavirus 2019 (COVID-19) cases is comprised of non-critically ill adults. However, the medical epidemiology and clinical profile for mild COVID-19 is poorly described in the United States.

Methods

We prospectively recruited 151 mildly symptomatic adults from Emory Healthcare COVID-19 screening clinics in Atlanta, Georgia from March 18 to June 16, 2020. Interview-based questionnaires captured participants’ demographics, epidemiological history, and clinical features. Nasopharyngeal swabs were collected to test for SARS-CoV-2 by RT-PCR. Convalescent serum (13–74 days post symptom onset) from 19 participants was tested by an IgG ELISA. Descriptive and χ 2 analyses were performed to determine the characteristics of COVID-19 cases compared to patients who tested negative.

Results

A total of 151 patients were recruited. The majority were non-Hispanic white (51%), female (60%), middle-aged adults (46.3 y +/-15). Twenty-seven (17.9%) tested positive for SARS-CoV-2 and most frequently reported fever (63%), cough (67%), fatigue (56%), and myalgias (56%). See Table 1. Fever was statistically more common in positive cases vs negative (63% vs 34%, p = 0.005). Cases also experienced loss of taste (22%) and loss of smell (19%) more frequently than non-cases (p=0.01 and p=0.03). Diarrhea (22% vs 23%) and shortness of breath (33% vs 36%) did not differ significantly between groups. None of the 14 PCR-negative participants tested positive for SARS-CoV-2-specific IgG and 3 out of 5 COVID-19 cases tested positive for SARs-CoV-2-specific IgG.

Conclusion

Mild COVID-19 cases reported fever, loss of smell and loss of taste significantly more than non-COVID-19 cases. Strong correlations between anosmia and ageusia with COVID-19 have been reported elsewhere, however these symptoms were only present in 19–22% of cases at the time of testing, limiting their utility for clinical diagnosis. Also, none of the PCR-negative participants tested positive for convalescent serology, supporting good sensitivity and negative predictive value of the RT-PCR test used in our clinic. Symptoms alone cannot differentiate COVID-19 from other illnesses, highlighting the critical need for widely available and highly sensitive and specific diagnostic tests.

Disclosures

All Authors: No reported disclosures
443. Comparison of Clinical Characteristics of Endemic vs. SARS-CoV-2 Coronavirus Infection in Patients Admitted to a Community Teaching Hospital
Authors: Politis Paula Ann , Oravec Michael J , Hoisington Lisa , Tan Michael , Agarwal Shanu , Agarwal Shanu , England Matthew , File Thomas M , File Thomas M
Published: January 2021

Background

Endemic coronaviruses [EC] (NL63, 229E, OC43, HKU1) have been identified in humans since the 1960s. Most are associated with mild upper respiratory tract infections (RTIs) but can be associated serious disease. More recently, novel coronaviruses associated with SARS, MERS, and COVID-19 caused by SARS-CoV-2 have emerged and are often associated with serious disease and death. With this report, we compare presenting clinical characteristics and some outcomes of patients hospitalized with RTIs caused by ECs or by SARS-CoV-2 (COVID-19).

Methods

Patients admitted to the Summa Health System with RTIs associated with EC were identified via multiplex PCR method (BioFire™). Patients admitted with COVID-19 were identified by real-time, reverse transcriptase-PCR method using one of several platforms. Patients were selected from two existing quality improvement registries encompassing EC and COVID-19 cases. We compared clinical characteristics and outcomes of EC patients to those of COVID-19 patients using chi-squared tests for proportions and independent samples t-tests for means.

Results

Shown in Table 1. Significant differences in patient characteristics with EC vs. COVID-19 included: older age, primarily Caucasian, smoking history, requiring O2 supplementation on admission, and having chronic heart, lung, or renal disease. Significant differences in patient characteristics with COVID-19 vs. EC included: admission from extended care facility, obesity, presenting with fever, gastrointestinal symptoms and/or myalgia, presence of radiographic infiltrates, abnormal liver tests, and longer length of stay (LOS). A non-significant difference was noted in 30 day mortality rates. Coronavirus OC43 accounted for 54% of EC strains.

Conclusion

There were significant differences in clinical characteristics between the two groups with EC patients more likely to have lung disease (often COPD) and requiring admission for need of O2 supplementation. COVID-19 patients were more likely to present with a febrile illness associated with pneumonia and require longer LOS (often requiring O2 supplementation later in hospitalization). Patients admitted with COVID-19 present with different clinical characteristics than those with EC with numerically higher mortality rate.

Disclosures

All Authors: No reported disclosures
446. COVID 19 Pandemicity: a global situation report as of June 9, 2020
Authors: Sanyaolu Adekunlle , Okorie Chuku , Hosein Zaheeda , Patidar Risha , Desai Priyank , Prakash Stephanie , Jaferi Urooj , Mangat Jasmine , Marinkovic Aleksandra
Published: January 2021

Background

The World Health Organization (WHO) declared severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) a pandemic on March 11, 2020. This report takes a closer look at the cases, fatalities, and recoveries in different regions of the world with details regarding the geographic scale of SARS-CoV-2 spread, risks, and the subsequent impact on the countries affected. Also, this report discusses some effective measures that were carried out by some countries that helped them to mitigate the pandemic and flatten the curve of COVID-19 spread as early as possible.

Methods

Our research was conducted via an electronic literature review on PubMed, Google Scholar, and MedLine Plus. Data were then collected from peer-reviewed articles that included applicable keywords and published between January 1, 2020, and June 9, 2020

Results

The rapid spread of infection has impacted over 200 countries and territories to date. As of June 9, 2020, there were 7,039,918 confirmed cases and 404,396 deaths globally. The USA is the North American country with the highest number of confirmed COVID 19 cases with 1,993,560. In South America, total confirmed cases in Brazil are 691,758. The most affected country in the African region is South Africa with 50,879. In Europe, the Russian Federation top with 485,253 confirmed cases. China with 84,638 is still the Western Pacific country with the most confirmed COVID 19 cases. India had 266,598 total confirmed cases and Australia reported 7,265 confirmed cases. Fatalities recorded similar patterns regionally except in Europe where the UK recorded the highest number of fatalities with 40,597 deaths and Iran had the highest number of fatalities with 5,957 cases in Asia. The goal of the practice “slowing the spread” is to prevent hospital systems from being strained beyond their capacity, thus resulting in less mortality. Countries yet to see the peak would benefit substantially by implementing aggressive social distancing, self-isolation, closure of schools and other institutions, encouraging working from home, and/or placing hard limits on the size of crowds at events.

Confirmed cases of COVID-19 globally, as of June 9, 2020.

Confirmed fatalities due to COVID-19 globally, as of June 9, 2020.

Conclusion

As the number of cases increases, an immediate need to “flatten the curve” is essential to avoid catastrophic overwhelming of hospital systems across the affected countries.

Disclosures

All Authors: No reported disclosures