Real-world utilization of SARS-CoV-2 serological testing in RNA positive patients across the United States.

BACKGROUND: As diagnostic tests for COVID-19 were broadly deployed under Emergency Use Authorization, there emerged a need to understand the real-world utilization and performance of serological testing across the United States. METHODS: Six health systems contributed electronic health records and/or claims data, jointly developed a master protocol, and used it to execute the analysis in parallel. We used descriptive statistics to examine demographic, clinical, and geographic characteristics of serology testing among patients with RNA positive for SARS-CoV-2. RESULTS: Across datasets, we observed 930,669 individuals with positive RNA for SARS-CoV-2. Of these, 35,806 (4%) were serotested within 90 days; 15% of which occurred <14 days from the RNA positive test. The proportion of people with a history of cardiovascular disease, obesity, chronic lung, or kidney disease; or presenting with shortness of breath or pneumonia appeared higher among those serotested compared to those who were not. Even in a population of people with active infection, race/ethnicity data were largely missing (>30%) in some datasets-limiting our ability to examine differences in serological testing by race. In datasets where race/ethnicity information was available, we observed a greater distribution of White individuals among those serotested; however, the time between RNA and serology tests appeared shorter in Black compared to White individuals. Test manufacturer data was available in half of the datasets contributing to the analysis. CONCLUSION: Our results inform the underlying context of serotesting during the first year of the COVID-19 pandemic and differences observed between claims and EHR data sources-a critical first step to understanding the real-world accuracy of serological tests. Incomplete reporting of race/ethnicity data and a limited ability to link test manufacturer data, lab results, and clinical data challenge the ability to assess the real-world performance of SARS-CoV-2 tests in different contexts and the overall U.S. response to current and future disease pandemics.

Real-world performance of SARS-Cov-2 serology tests in the United States, 2020.

BACKGROUND: Real-world performance of COVID-19 diagnostic tests under Emergency Use Authorization (EUA) must be assessed. We describe overall trends in the performance of serology tests in the context of real-world implementation. METHODS: Six health systems estimated the odds of seropositivity and positive percent agreement (PPA) of serology test among people with confirmed SARS-CoV-2 infection by molecular test. In each dataset, we present the odds ratio and PPA, overall and by key clinical, demographic, and practice parameters. RESULTS: A total of 15,615 people were observed to have at least one serology test 14-90 days after a positive molecular test for SARS-CoV-2. We observed higher PPA in Hispanic (PPA range: 79-96%) compared to non-Hispanic (60-89%) patients; in those presenting with at least one COVID-19 related symptom (69-93%) as compared to no such symptoms (63-91%); and in inpatient (70-97%) and emergency department (93-99%) compared to outpatient (63-92%) settings across datasets. PPA was highest in those with diabetes (75-94%) and kidney disease (83-95%); and lowest in those with auto-immune conditions or who are immunocompromised (56-93%). The odds ratios (OR) for seropositivity were higher in Hispanics compared to non-Hispanics (OR range: 2.59-3.86), patients with diabetes (1.49-1.56), and obesity (1.63-2.23); and lower in those with immunocompromised or autoimmune conditions (0.25-0.70), as compared to those without those comorbidities. In a subset of three datasets with robust information on serology test name, seven tests were used, two of which were used in multiple settings and met the EUA requirement of PPA ≥87%. Tests performed similarly across datasets. CONCLUSION: Although the EUA requirement was not consistently met, more investigation is needed to understand how serology and molecular tests are used, including indication and protocol fidelity. Improved data interoperability of test and clinical/demographic data are needed to enable rapid assessment of the real-world performance of in vitro diagnostic tests.

On variants and vaccines: The effectiveness of Covid-19 monoclonal antibody therapy during two distinct periods in the pandemic.

BACKGROUND: While Covid-19 monoclonal antibody therapies (Mab) have been available in the outpatient setting for over a year and a half, little is known about the impact of emerging variants and vaccinations on the effectiveness of Mab therapies. We sought to determine the effectiveness of Covid-19 Mab therapies during the first two waves of the pandemic in Los Angeles County and assess the impact of vaccines, variants, and other confounding factors. METHODS AND FINDINGS: We retrospectively examined records for 2209 patients of with confirmed positive molecular SARS-CoV2 test either referred for outpatient Mab therapy or receiving Mab treatment in the emergency department (ED) between December 2020 and 2021. Our primary outcome was the combined 30-day incidence of ED visit, hospitalization, or death following the date of referral. Additionally, SARS-CoV2 isolates of hospitalized patients receiving Mabs were sequenced. The primary outcome was significantly reduced with combination therapy compared to bamlanivimab or no treatment (aHR 0·60; 95% CI ·37, ·99), with greater benefit in unvaccinated, moderate-to-high-risk patients (aHR ·39; 95% CI ·20, ·77). Significant associations with the primary outcome included history of lung disease (HR 7·13; 95% CI 5·12, 9·95), immunocompromised state (HR 6·59; 95% CI 2·91-14·94), and high social vulnerability (HR 2·29, 95% CI 1·56-3·36). Two predominant variants were noted during the period of observation: the Epsilon variant and the Delta variant. CONCLUSIONS: Only select monoclonal antibody therapies significantly reduced ED visits, hospitalizations, and death due to COVID-19 during. Vaccination diminished effectiveness of Mabs. Variant data and vaccination status should be considered when assessing the benefit of novel COVID-19 treatments.

Clinical and genomic characterization of hypervirulent Klebsiella pneumoniae (hvKp) infections via passive surveillance in Southern California, 2020-2022.

Hypervirulent Klebsiella pneumoniae (hvKp) is more invasive and virulent than classical K. pneumoniae, and requires specialized treatment. To raise clinical awareness, this study determined the prevalence, clinical characteristics, and genomic epidemiology of hvKp infections in Southern California (SoCal) by conducting a passive surveillance in a single large academic medical center. We report here that hvKp infections were more common than expected, accounting for 2.6% of invasive K. pneumoniae infections, and presented with a wide disease spectrum, occasionally mimicking tumors, even co-infecting a COVID-19 patient. Most infections were community acquired with no recent international travel, suggesting hvKp strains are circulating in the community. Genomic analysis revealed genetic diversity, with the K1-ST23 lineage predominating but not clonal, and multiple sequence types of K2 including a SoCal unique K2-ST66 sublineage that had been unrecognized. Our findings highlight the urgency of heightened awareness of hvKp infection in the US, the need for rapid diagnosis of hvKp, and the necessity of implementing robust surveillance programs for hvKp at the institutional or local level.

Prevalence and Factors Associated With Antigen Test Positivity Following SARS-CoV-2 Infection Among Health Care Workers in Los Angeles.

Surges of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections among health care workers (HCWs) have led to critical staffing shortages. From January 4 to February 4, 2022, we implemented a return-to-work antigen testing program for HCWs, and 870 HCWs participated. Antigen test positivity was 60.5% for those ≤5 days from symptom onset or positive polymerase chain reaction (PCR), and 47.4% were positive at day 7. Antigen positivity was associated with receiving a booster vaccination and being ≤6 days from symptom onset or PCR test, but not age or a symptomatic infection. Rapid antigen testing can be a useful tool to guide return-to-work and isolation precautions for HCWs following infection.

Clinical, microbiological, and genomic characteristics of clade-III Candida auris colonization and infection in southern California, 2019-2022.

BACKGROUND: Candida auris is an emerging fungal pathogen causing outbreaks in healthcare facilities. Five distinctive genomic clades exhibit clade-unique characteristics, highlighting the importance of real-time genomic surveillance and incorporating genotypic information to inform infection prevention practices and treatment algorithms. METHODS: Both active and passive surveillance were used to screen hospitalized patients. C. auris polymerase chain reaction (PCR) assay on inguinal-axillary swabs was performed on high-risk patients upon admission. All clinical yeast isolates were identified to the species level. C. auris isolates were characterized by both phenotypic antifungal susceptibility tests and whole-genome sequencing. RESULTS: From late 2019 to early 2022, we identified 45 patients with C. auris. Most had a tracheostomy or were from a facility with a known outbreak. Moreover, 7 patients (15%) were only identified through passive surveillance. Also, 8 (18%) of the patients had a history of severe COVID-19. The overall mortality was 18%. Invasive C. auris infections were identified in 13 patients (29%), 9 (69%) of whom had bloodstream infections. Patients with invasive infection were more likely to have a central line. All C. auris isolates were resistant to fluconazole but susceptible to echinocandins. Genomic analysis showed that 1 dominant clade-III lineage is circulating in Los Angeles, with very limited intrahost and interhost genetic diversity. CONCLUSIONS: We have demonstrated that a robust C. auris surveillance program can be established using both active and passive surveillance, with multidisciplinary efforts involving the microbiology laboratory and the hospital epidemiology team. In Los Angeles County, C. auris strains are highly related and echinocandins should be used for empiric therapy.

Clinical and epidemiological characteristics of SARS-CoV-2 Infection in Los Angeles County youth during the first year of the pandemic.

OBJECTIVES: The aim of this study was to characterize SARS-CoV-2 infection patterns in Los Angeles (LA) County youth followed at our institution during the first pandemic year. DESIGN: A prospective cohort of patients aged < 25 years who tested positive for SARS-CoV-2 using reverse-transcriptase polymerase chain reaction (RT-PCR) assays between March 13, 2020, and March 31, 2021, was evaluated at a large LA County health network. Demographics, age distribution, and disease severity were analyzed. RESULTS: There were 28,088 youth aged < 25 years tested for SARS-CoV-2 using RT-PCR, with 1849 positive results identified (7%). Among the positive results, 475 of 11,922 (4%) were identified at the pandemic onset (March-September 2020) (Cohort 1) and 1374 of 16,166 (9%) between October 2020 and March 2021 (Cohort 2), P < 0.001. When disease severity was compared across cohorts, Cohort 2 had a greater proportion of asymptomatic and mild/moderate disease categories than Cohort 1 (98% vs 80%, respectively); conversely, Cohort 1 had a near-10-fold higher proportion of severe disease than Cohort 2 (17% vs 1.8%). Cohort 2 comprised younger patients with a mean age of 13.7 years vs 17.3 years in Cohort 1. Older age was associated with a higher percentage of infection, with 63% of all confirmed cases found in participants aged 19 to 25 years in Cohort 1, compared with 38% of confirmed cases in Cohort 2. Age increase was also associated with greater disease severity by linear regression modeling (P< 0.001). CONCLUSION: Coronavirus disease 2019 (COVID-19) disease severity in youth decreased over time in LA County during the first pandemic year, likely a reflection of changing demographics, with younger children infected. A higher infection rate in youth did not lead to higher disease severity over time.

Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA.

BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global disruption of human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality can inform public health measures and provide insights to contain or prevent viral transmission. Investigation of the transmission history requires efficient sequencing methods and analytic strategies, which can be generally useful in the study of viral outbreaks. METHODS: The County of Los Angeles (hereafter, LA County) sustained a large outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To learn about the transmission history, we carried out surveillance viral genome sequencing to determine 142 viral genomes from unique patients seeking care at the University of California, Los Angeles (UCLA) Health System. 86 of these genomes were from samples collected before April 19, 2020. RESULTS: We found that the early outbreak in LA County, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe. We identified a USA-specific strain, B.1.43, which was found predominantly in California and Washington State. While samples from LA County carried the ancestral B.1.43 genome, viral genomes from neighboring counties in California and from counties in Washington State carried additional mutations, suggesting a potential origin of B.1.43 in Southern California. We quantified the transmission rate of SARS-CoV-2 over time, and found evidence that the public health measures put in place in LA County to control the virus were effective at preventing transmission, but might have been undermined by the many introductions of SARS-CoV-2 into the region. CONCLUSION: Our work demonstrates that genome sequencing can be a powerful tool for investigating outbreaks and informing the public health response. Our results reinforce the critical need for the USA to have coordinated inter-state responses to the pandemic.

Retrospective Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Symptomatic Patients Prior to Widespread Diagnostic Testing in Southern California.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused one of the worst pandemics in recent history. Few reports have revealed that SARS-CoV-2 was spreading in the United States as early as the end of January. In this study, we aimed to determine if SARS-CoV-2 had been circulating in the Los Angeles (LA) area at a time when access to diagnostic testing for coronavirus disease 2019 (COVID-19) was severely limited. METHODS: We used a pooling strategy to look for SARS-CoV-2 in remnant respiratory samples submitted for regular respiratory pathogen testing from symptomatic patients from November 2019 to early March 2020. We then performed sequencing on the positive samples. RESULTS: We detected SARS-CoV-2 in 7 specimens from 6 patients, dating back to mid-January. The earliest positive patient, with a sample collected on January 13, 2020 had no relevant travel history but did have a sibling with similar symptoms. Sequencing of these SARS-CoV-2 genomes revealed that the virus was introduced into the LA area from both domestic and international sources as early as January. CONCLUSIONS: We present strong evidence of community spread of SARS-CoV-2 in the LA area well before widespread diagnostic testing was being performed in early 2020. These genomic data demonstrate that SARS-CoV-2 was being introduced into Los Angeles County from both international and domestic sources in January 2020.

Lower Severe Acute Respiratory Syndrome Coronavirus 2 Viral Shedding Following Coronavirus Disease 2019 Vaccination Among Healthcare Workers in Los Angeles, California.

Among 880 healthcare workers with a positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) test, 264 (30.0%) infections were identified following receipt of at least 1 vaccine dose. Median SARS-CoV-2 cycle threshold values were highest among individuals receiving 2 vaccine doses, corresponding to lower viral shedding. Vaccination might lead to lower transmissibility of SARS-CoV-2.

Investigation of SARS-CoV-2 Epsilon Variant and Hospitalization Status by Genomic Surveillance in a Single Large Health System During the 2020-2021 Winter Surge in Southern California.

OBJECTIVES: This study aimed to assess whether the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Epsilon variant (B.1.429/427) is more virulent, leading to more hospitalization and more severe disease requiring intensive care unit (ICU) admission. METHODS: SARS-CoV-2 genomic surveillance was performed on respiratory samples from 231 unique patients, collected at a single large health system in Southern California between November 2020 and March 2021 during the winter surge. RESULTS: The frequencies of the Epsilon variant among outpatients, hospitalized patients, and ICU patients were indifferent. CONCLUSIONS: Our study suggests that the Epsilon variant is not associated with increased hospitalization and ICU admission.

Predictors of SARS-CoV-2 Infection in Youth at a Large, Urban Healthcare Center in California, March-September 2020.

Objective: To understand which social, epidemiologic, and clinical risk factors are associated with SARS-CoV-2 infection in youth accessing care in a large, urban academic institution. Methods: We conducted a prospective cohort study with case-control analyses in youth who received testing for SARS-CoV-2 at our academic institution in Los Angeles during the first wave of the COVID-19 pandemic (March-September 2020). Results: A total of 27,976 SARS-CoV-2 assays among 11,922 youth aged 0-24 years were performed, including 475 youth with positive SARS-CoV-2 results. Positivity rate was higher among older, African American, and Hispanic/Latinx youth. Cases were more likely to be from non-English-speaking households and have safety-net insurance. Zip codes with higher proportion of Hispanic/Latinx and residents living under the poverty line were associated with increased SARS-CoV-2 cases. Youth were more likely to have positive results if tested for exposure (OR 21.5, 95% CI 14.6-32.1) or recent travel (OR 1.5, 95% CI 1.0-2.3). Students were less likely to have positive results than essential worker youth (OR 0.5, 95% CI 0.3-0.8). Patterns of symptom presentation varied significantly by age group; number of symptoms correlated significantly with age in SARS-CoV-2 cases (r = 0.030, p < 0.001). SARS-CoV-2 viral load did not vary by symptom severity, but asymptomatic youth had lower median viral load than those with symptoms (21.5 vs. 26.7, p = 0.009). Conclusions: Socioeconomic factors are important drivers of SARS-CoV-2 infection in youth. Presence of symptoms, exposure, and travel can be used to drive testing in older youth. Policies for school reopening and infection prevention should be tailored differently for elementary schools and universities.

Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples.

Frequent and widespread testing of members of the population who are asymptomatic for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the mitigation of the transmission of the virus. Despite the recent increases in testing capacity, tests based on quantitative polymerase chain reaction (qPCR) assays cannot be easily deployed at the scale required for population-wide screening. Here, we show that next-generation sequencing of pooled samples tagged with sample-specific molecular barcodes enables the testing of thousands of nasal or saliva samples for SARS-CoV-2 RNA in a single run without the need for RNA extraction. The assay, which we named SwabSeq, incorporates a synthetic RNA standard that facilitates end-point quantification and the calling of true negatives, and that reduces the requirements for automation, purification and sample-to-sample normalization. We used SwabSeq to perform 80,000 tests, with an analytical sensitivity and specificity comparable to or better than traditional qPCR tests, in less than two months with turnaround times of less than 24 h. SwabSeq could be rapidly adapted for the detection of other pathogens.

SARS-CoV-2 Infection Detection by PCR and Serologic Testing in Clinical Practice.

Patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be diagnosed by PCR during acute infection or later in their clinical course by detection of virus-specific antibodies. While in theory complementary, both PCR and serologic tests have practical shortcomings. A retrospective study was performed in order to further define these limitations in a clinical context and to determine how to best utilize these tests in a coherent fashion. A total of 3,075 patients underwent both PCR and serology tests at University of California, Los Angeles (UCLA), in the study period. Among these, 2,731 (89%) had no positive tests at all, 73 (2%) had a positive PCR test and only negative serology tests, 144 (5%) had a positive serology test and only negative PCR tests, and 127 (4%) had positive PCR and serology tests. Approximately half of the patients with discordant results (i.e., PCR positive and serology negative or vice versa) had mistimed tests in reference to the course of their disease. PCR-positive patients who were asymptomatic or pregnant were less likely to generate a detectable humoral immune response to SARS-CoV-2. On a quantitative level, the log number of days between symptom onset and PCR test was positively correlated with cycle threshold (CT) values. However, there was no apparent relationship between PCR CT and serologic (arbitrary units per milliliter) results.

Performance Characteristics of Severe Acute Respiratory Syndrome Coronavirus 2 RT-PCR Tests in a Single Health System: Analysis of >10,000 Results from Three Different Assays.

The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the approval of numerous molecular diagnostic assays with various performance and technical capacities. There are limited data comparing performance among assays. We conducted a retrospective analysis of >10,000 test results among three widely used RT-PCR assays for coronavirus disease 2019 (CDC, Simplexa Direct, and TaqPath) to assess performance characteristics. We also retested remnant weakly positive specimens to assess analytical sensitivity. All assays had strong linear correlation and little bias among CT values for PCR targets. In patients with first-test negative results (n = 811), most (795, 98.0%) remained negative for all subsequent testing. Retesting of weakly positive specimens (CT > 30) showed sensitivities as follows: TaqPath (97.8%), CDC (91%), Simplexa (75.3%). Our analysis showed no performance difference among PCR targets within the same assay, suggesting a single target is sufficient for SARS-CoV-2 detection. Lower respiratory tract specimens had a higher negative predictive value (100%) than upper respiratory tract specimens (98%), highlighting the utility of testing lower respiratory tract specimens when clinically indicated. Negative predictive value did not increase on further repeated testing, providing strong evidence for discouraging unnecessary repeated testing for SARS-CoV-2.

Diagnostic yield of repeat testing for SARS-CoV-2: Experience from a large health system in Los Angeles.

OBJECTIVE: To determine the diagnostic yield of repeat testing for SARS-CoV-2. METHODS: A retrospective analysis was performed of all SARS-CoV-2 test results within the UCLA Health System between March 9th and April 29th, 2020. All patients with repeat test results were identified and those with discordant results were reviewed. RESULTS: Between March 9th and April 29th there were 10,165 SARS-CoV-2 test results, of which 630 (6.2%) were positive. Among the 904 patients with repeat test results, 808 (89.4%) were initially negative and 96 (10.6%) were initially positive. Among the 808 patients with an initial negative test, 15 (1.9%) subsequently tested positive. Eleven cases with an initial negative SARS-CoV-2 test and without a known prior positive SARS-CoV-2 test were reviewed; 6 were employed as healthcare workers and 10 were positive on the second test. CONCLUSIONS: We found a low diagnostic yield of repeat testing for SARS-CoV-2 in our health system. Repeat testing might prove useful in certain clinical scenarios, such as in healthcare workers, when symptoms develop after a negative test, and in hospitalized patients with a high clinical suspicion for COVID-19.

Clinical and Epidemiologic Evaluation of Inconclusive COVID-19 PCR Results Using a Quantitative Algorithm.

OBJECTIVES: The inconclusive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase chain reaction (PCR) result causes confusion and delay for infection prevention precautions and patient management. We aimed to develop a quantitative algorithm to assess and interpret these inconclusive results. METHODS: We created a score-based algorithm by combining laboratory, clinical, and epidemiologic data to evaluate 69 cases with inconclusive coronavirus disease 2019 (COVID-19) PCR results from the Centers for Disease Control and Prevention (CDC) assay (18 cases) and the TaqPath assay (51 cases). RESULTS: We determined 5 (28%) of 18 (CDC assay) and 20 (39%) of 51 (TaqPath assay) cases to be false positive. Lowering the cycle threshold cutoff from 40 to 37 in the TaqPath assay resulted in a dramatic reduction of the false-positive rate to 14%. We also showed testing of asymptomatic individuals is associated with a significantly higher probability of having a false-positive result. CONCLUSIONS: A substantial percentage of inconclusive SARS-CoV-2 PCR results can be false positive, especially among asymptomatic patients. The quantitative algorithm we created was shown to be effective and could provide a useful tool for clinicians and hospital epidemiologists to interpret inconclusive COVID-19 PCR results and provide clinical guidance when additional PCR or antibody test results are available.