scholarly journals Pre-test symptom duration and cycle threshold values for SARS-CoV-2 reverse transcription-PCR (RT-PCR) predict COVID-19 mortality

Author(s):  
Emily Happy Miller ◽  
Jason Zucker ◽  
Delivette Castor ◽  
Medini K Annavajhala ◽  
Jorge L Sepulveda ◽  
...  

Abstract Background The relationship between SARS-CoV-2 viral load and patient symptom duration in both in- and outpatients, and the impact of these factors on patient outcomes, are currently unknown. Understanding these associations is important to clinicians caring for patients with COVID-19. Methods We conducted an observational study between March 10–May 30, 2020 at a large quaternary academic medical center in New York City. Patient characteristics, laboratory values, and clinical outcomes were abstracted from the electronic medical records. Of all patients tested for SARS-CoV-2 during this time (N=16,384), there were 5,467 patients with positive tests, of which 4,254 had available Ct values and were included in further analysis. Univariable and multivariable logistic regression models were used to test associations between Ct values, duration of symptoms prior to testing, patient characteristics and mortality. The primary outcome is defined as death or discharge to hospice. Results Lower Ct values at diagnosis (i.e. higher viral load) were associated with significantly higher mortality among both in- and out-patients. Interestingly, patients with a shorter time since the onset of symptoms to testing had a worse prognosis, with those presenting less than three days from symptom onset having 2-fold increased odds of death. After adjusting for time since symptom onset and other clinical covariates, Ct values remained a strong predictor of mortality. Conclusions SARS-CoV-2 RT-PCR Ct value and duration of symptoms are strongly associated with mortality. These two factors add useful information for clinicians to risk stratify patients presenting with COVID-19.

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S314-S314
Author(s):  
Lillian B Brown ◽  
Lisa Gail Winston ◽  
Barbara Haller ◽  
Phong Pham ◽  
Beatrice Marcelo ◽  
...  

Abstract Background Most diagnostic tests for SARS-CoV-2, the causative agent of COVID-19, are RT-PCR based. This method is sensitive but cannot distinguish replicating from non-replicating virus. RT-PCR cycle threshold (Ct) values are inversely correlated with viral load, and higher Ct values have been correlated with lower in vitro viral infectivity. However, relatively few data exist on the association between Ct values and patients’ duration of symptoms remains unclear. We thus evaluated Ct values and symptom duration in a cohort of patients hospitalized with COVID-19. Methods We assessed all patients admitted to San Francisco General Hospital between April 1 and May 18, 2020 with confirmed COVID-19 infection based on RT-PCR testing (Abbott m2000 platform). We included patients having diagnostic testing for suspected COVID-19 and patients having asymptomatic testing per hospital policy. For symptomatic patients, date of symptom onset was abstracted from hospital records, and time from symptom onset to test date was calculated. RT-PCR Ct values were manually extracted. Median Ct and IQR were calculated for patients with < 10 days of symptoms, ≥10 days of symptoms, and asymptomatic disease. Between-group comparisons were performed using the Kruskal-Wallis test. Results Among 61 patients with positive RT-PCR tests, 40 patients reported < 10 days of symptoms at the time of testing, 15 reported ≥10 days of symptoms, and 6 were asymptomatic. The median Ct value was 14.2 cycles (IQR, 10.2, 18.3) among patients reporting < 10 days of symptoms, 19.7 cycles (IQR, 15.3, 23.9) among patients reporting ≥10 days of symptoms, and 26.3 (IQR, 25.0, 29.1) among asymptomatic patients. Ct values were significantly lower among patients with < 10 days of symptoms compared to patients with >=10 days of symptoms (p=0.01) and when compared to asymptomatic patients (p=0.0002) [Figure]. Cycle threshold (Ct) by days of symptoms at time of testing Conclusion SARS-CoV-2 RT-PCR cycle threshold values were higher (indicating lower viral load) in patients with longer symptom duration and were highest in asymptomatic patients. These results add to emerging data suggesting that strategies for optimal isolation of patients in both community and hospital settings could be informed by a combination of symptom duration and RT-PCR Ct values. Disclosures All Authors: No reported disclosures


Vaccines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 659
Author(s):  
Luca Coppeta ◽  
Ottavia Balbi ◽  
Zaira Grattagliano ◽  
Grazia Genga Mina ◽  
Antonio Pietroiusti ◽  
...  

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than one hundred million people since the beginning of the worldwide pandemic. In this study, data from a large hospital in central Italy was used to evaluate the impact of the first dose of the BNT162b2 mRNA vaccine on SARS-CoV-2 infections in terms of the prevalence of symptomatic cases, symptom duration, and viral clearance timing. All vaccinated Healthcare Workers (HCWs) with positive RT-PCR by nasopharyngeal (NP) swabs were divided into two cohorts (positive RT-PCR within day 12 and positive RT-PCR between day 13 and day 21 after first dose administration) and compared for the presence and duration of symptoms and the timing of viral clearance. The same variables were evaluated across HCWs with positive RT-PCR within 6 days after first dose administration and non-vaccinated HCWs with positive RT-PCR between 1 October 2020 and 28 February 2021. Eighteen HCWs tested positive on RT-PCR by NP swab from day 1 to day 12 after the 1st dose administration (incidence rate 6.2 × 10−4) and 5 HCWs from day 13 to day 21 (incidence rate 2.3 × 10−4). Symptom duration and viral clearance timing are significantly shorter in the cohort of HCWs with positive RT-PCR 12 days after the first dose of the BNT162b2 mRNA vaccine. The administration of the first dose proved effective in reducing presence, symptom duration, and viral clearance even in HCWs vaccinated for less than 6 days. These results could have implications on public health and post-exposure prophylaxis.


2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S264-S265
Author(s):  
Corey J Medler ◽  
Lejla Jakupovic ◽  
Allison J Weinmann ◽  
Rachel Kenney ◽  
Susan L Davis ◽  
...  

Abstract Background The COVID-19 pandemic has revealed new challenges for antimicrobial stewardship. Optimal medical treatment is not completely understood at this time. The epidemiology and outcomes of bacterial co-infections are not well-established; however, empiric antibiotic (abx) use is anecdotally common. The purpose of this study is to characterize empiric antimicrobial drug selection and timing in COVID-19 and evaluate the impact on patient outcomes. Methods Cross-sectional cohort study for COVID-19 positive inpatients from March 1, 2020 to June 1, 2020 at an academic medical center and 4 community hospitals. Inclusion: patients with a documented positive COVID-19 PCR nasopharyngeal swab. Exclusion: patients less than 18 years; deceased or transitioned to hospice within 24 hours of admission. Primary endpoint: empiric abx drug, initiation, duration and indication. Additional data collected: severity of illness, co-infection diagnosis, microbiology, and adverse drug effects (ADE). Clinical outcomes included time to recovery by COVID-19 ordinal outcome, clinical status at day 15, and readmission. Results 400 patients were included with 27% from the ICU. COVID symptom category included mild (23.8%), moderate (53%), severe (15%), and critical (8.3%). 322 (80.5%) received abx at any time during hospital stay, 301 (93.5%) started within 1 day of admission. Most common documented indication community-acquired pneumonia (69%). Identified 43 (10.8%) microbiologically confirmed co-infections, including 5 MRSA and 7 Pseudomonas. Median duration of initial abx 4 days. 54/322 (16.8%) had abx restarted after discontinuation. Median days to recovery without abx was 10 days (7 – 14) and 14 days (9 – 20) with abx. Patient characteristics and outcomes described in table 1. 74 abx related ADE were identified: gastrointestinal 37 and renal 22. Conclusion It’s difficult to distinguish bacterial and Covid-19 in coinfections in patients ill enough to be hospitalized. Longer courses of empiric abx therapy were prevalent as the severity of illness increased. However, the low frequency of microbiologically confirmed bacterial co-infections results in potentially unnecessary abx exposure. This exposure increases risk of abx ADE and may not improve clinical outcome. Disclosures All Authors: No reported disclosures


Author(s):  
M D Soffer ◽  
L L Shook ◽  
K James ◽  
M R Sawyer ◽  
A Ciaranello ◽  
...  

Abstract Background Reports of SARS-CoV2 infection have focused on pregnant women hospitalized due to moderate to severe COVID-19 disease or asymptomatic women diagnosed through universal screening at the time of obstetric admission. Many pregnant women who have symptomatic SARS-CoV2 infection may not meet criteria for hospitalization; however, whether and how these women can be managed safely in outpatient setting is not well described. Objective We sought to describe the time to symptom and viral clearance and to identify predictors of hospitalization in order to better understand the safety of monitoring pregnant patients with symptomatic COVID-19 in the outpatient setting. Study Design We performed a retrospective cohort study of pregnant patients with symptomatic, confirmed COVID-19 illness at a large academic medical center. Patients had systematic telehealth follow up by a clinician team to assess for symptoms, provide virtual prenatal care, and arrange in-person visits when appropriate in a dedicated outpatient center. Data was collected via chart abstraction. Results Of 180 pregnant patients presenting with symptoms and undergoing RT-PCR testing, 67 patients with confirmed COVID-19 infection were identified during the study period. Nineteen (28%) required acute care given worsening of COVID-19 symptoms, and 95% of these were directed to this acute care setting due to symptom severity telehealth evaluation. Nine women (13%) were admitted to the hospital given worsening symptoms, 3 required ICU care, 2 required ventilatory support, and 2 required delivery. Women with the presenting symptoms of fever, cough, shortness of breath, chest pain, or nausea and vomiting were more likely to require admission. The median duration from initial positive test to RT-PCR viral clearance was 26 days. Disease progression, time to viral clearance and duration of symptoms did not vary significantly by trimester of infection. Conclusions Management of the majority of pregnant women with symptomatic COVID-19 illness can be accomplished in the outpatient setting with intensive and protocol-driven monitoring for symptom progression.


PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258970
Author(s):  
Amanda Caplan ◽  
Kelly W. Bates ◽  
Carla Brioni ◽  
Aileen Santos ◽  
Linda M. Sabatini ◽  
...  

Background Studies of outpatients with mild or moderate COVID-19 are uncommon. We studied: 1) association of symptoms with reverse transcriptase polymerase chain reaction (RT-PCR) test results; and 2) association of initial RT-PCR cycle threshold (Ct) in relation to duration of RT-PCR positivity in outpatients with mild or moderate COVID-19. Methods This was a cohort study of outpatients with confirmed COVID-19 and at least one symptom. Participants had repeat nasopharyngeal swabs and symptom checklists every 3–5 days until two consecutive RT-PCR tests were negative. RT-PCR tests were used to assess viral load. Antibody tests for COVID-19 were performed at 2 weeks, 4 weeks, and 8 weeks after symptom onset. Results Twenty-five patients (nine females) were enrolled, ranging in age from 19–58 (median age 28 years). All patients reported at least one symptom, with a median of six symptoms per patient. Symptoms persisted for 6–67 days (median duration 18 days). In all 25 patients, blood samples collected a median of 13 days after symptom onset were positive for SARS-CoV-2 antibodies in 15 (60%). After a median of 28 days following symptom onset, 23/23 patients with available samples tested positive for antibodies. The longest duration of positive RT-PCR test was 49 days from first positive PCR test (Mean = 27.4, SD = 12.5, Median = 24). Initial Ct was significantly associated with longer duration (β = -1.3, SE = 0.3, p<0.01 per 1 cycle higher) of RT-PCR positivity. Conclusions In mildly or moderately ill COVID-19 outpatients, RT-PCT tests remained positive for as long as 49 days and test positivity and symptom duration correlated with initial viral load.


2021 ◽  
Author(s):  
Lael M. Yonker ◽  
Julie Boucau ◽  
James Regan ◽  
Manish Chandra Choudhary ◽  
Madeleine D. Burns ◽  
...  

Background: Data on viral factors causing pediatric disease and guidance for pediatric-specific considerations have lagged behind adults throughout the COVID-19 pandemic. As COVID-19 infections and deaths increase in the pediatric population, characterization of SARS-CoV-2 viral dynamics in children would enable data-driven public health guidance. Methods: Nasal swabs collected from children with COVID-19 were analyzed. Viral load was quantified by RT-PCR; viral culture was assessed by direct observation of cytopathic effects and semiquantitative viral titers. Correlations with age or symptom duration were analyzed. SARS-CoV-2 whole genome amplification was compared with contemporaneous Massachusetts sequences to assess for clustering patterns. Results: Ninety-seven children with COVID-19 (median age 10 years, range 2 weeks-22 years) were included in this study. Age did not impact SARS-CoV-2 viral load in nasal secretions: children of all ages were equally likely to carry live, replicating virus. Children within the first five days of illness had higher viral loads and rates of culture positivity, and viral load in hospitalized children (n=30) did not differ from hospitalized adults (n=21) with similar duration of symptoms. While pediatric SARS-CoV-2 sequences were representative of those in the community, novel variants were identified. Conclusions: Children can carry high quantities of live, replicating virus, creating a potential reservoir for transmission and evolution of genetic variants. As guidance around social distancing and masking evolves following vaccine uptake in older populations, a clear understanding of SARS-CoV-2 infection dynamics in children is critical for rational development of public health policies and vaccination strategies to mitigate the impact of COVID-19.  


2020 ◽  
Vol 41 (S1) ◽  
pp. s114-s115
Author(s):  
Alexandra Johnson ◽  
Bobby Warren ◽  
Deverick John Anderson ◽  
Melissa Johnson ◽  
Isabella Gamez ◽  
...  

Background: Stethoscopes are a known vector for microbial transmission; however, common strategies used to clean stethoscopes pose certain barriers that prevent routine cleaning after every use. We aimed to determine whether using readily available alcohol-based hand rub (ABHR) would effectively reduce bacterial bioburden on stethoscopes in a real-world setting. Methods: We performed a randomized study on inpatient wards of an academic medical center to assess the impact of using ABHR (AlcareExtra; ethyl alcohol, 80%) on the bacterial bioburden of stethoscopes. Stethoscopes were obtained from healthcare providers after routine use during an inpatient examination and were randomized to control (no intervention) or ABHR disinfection (2 pumps applied to tubing and bell or diaphragm by study personnel, then allowed to dry). Cultures of the tubing and bell or diaphragm were obtained with premoistened cellulose sponges. Sponges were combined with 1% Tween20-PBS and mixed in the Seward Stomacher. The homogenate was centrifuged and all but ~5 mL of the supernatant was discarded. Samples were plated on sheep’s blood agar and selective media for clinically important pathogens (CIPs) including S. aureus, Enterococcus spp, and gram-negative bacteria (GNB). CFU count was determined by counting the number of colonies on each plate and using dilution calculations to calculate the CFU of the original ~5 mL homogenate. Results: In total, 80 stethoscopes (40 disinfection, 40 control) were sampled from 46 physicians (MDs) and MD students (57.5%), 13 advanced practice providers (16.3%), and 21 nurses (RNs) and RN students (26.3%). The median CFU count was ~30-fold lower in the disinfection arm compared to control (106 [IQR, 50–381] vs 3,320 [986–4,834]; P < .0001). The effect was consistent across provider type, frequency of recent usual stethoscope cleaning, age, and status of pet ownership (Fig. 1). Overall, 26 of 80 (33%) of stethoscopes harbored CIP. The presence of CIP was lower but not significantly different for stethoscopes that underwent disinfection versus controls: S. aureus (25% vs 32.5%), Enterococcus (2.5% vs 10%), and GNB (2.5% vs 5%). Conclusions: Stethoscopes may serve as vectors for clean hands to become recontaminated immediately prior to performing patient care activities. Using ABHR to clean stethoscopes after every use is a practical and effective strategy to reduce overall bacterial contamination that can be easily incorporated into clinical workflow. Larger studies are needed to determine the efficacy of ABHR at removing CIP from stethoscopes as stethoscopes in both arms were frequently contaminated with CIP. Prior cleaning of stethoscopes on the study day did not seem to impact contamination rates, suggesting the impact of alcohol foam disinfection is short-lived and may need to be repeated frequently (ie, after each use).Funding: NoneDisclosures: NoneDisclosures: NoneFunding: None


2021 ◽  
pp. 000348942110212
Author(s):  
Nathan Kemper ◽  
Scott B. Shapiro ◽  
Allie Mains ◽  
Noga Lipschitz ◽  
Joseph Breen ◽  
...  

Objective: Examine the effects of a multi-disciplinary skull base conference (MDSBC) on the management of patients seen for skull base pathology in a neurotology clinic. Methods: Retrospective case review of patients who were seen in a neurotology clinic at a tertiary academic medical center for pathology of the lateral skull base and were discussed at an MDSBC between July 2019 and February 2020. Patient characteristics, nature of the skull base pathology, and pre- and post-MDSBC plan of care was categorized. Results: A total of 82 patients with pathology of the lateral skull base were discussed at a MDSBC during an 8-month study period. About 54 (65.9%) had a mass in the internal auditory canal and/or cerebellopontine angle while 28 (34.1%) had other pathology of the lateral skull base. Forty-nine (59.8%) were new patients and 33 (40.2%) were established. The management plan changed in 11 (13.4%, 7.4-22.6 95% CI) patients as a result of the skull base conference discussion. The planned management changed from some form of treatment to observation in 4 patients, and changed from observation to some form of treatment in 4 patients. For 3 patients who underwent surgery, the planned approach was altered. Conclusions: For a significant proportion of patients with pathology of the lateral skull base, the management plan changed as a result of discussion at an MDSBC. Although participants of a MDSBC would agree of its importance, it is unclear how an MDSBC affects patient outcomes.


2020 ◽  
Vol 41 (S1) ◽  
pp. s84-s84
Author(s):  
Lorinda Sheeler ◽  
Mary Kukla ◽  
Oluchi Abosi ◽  
Holly Meacham ◽  
Stephanie Holley ◽  
...  

Background: In December of 2019, the World Health Organization reported a novel coronavirus (severe acute respiratory coronavirus virus 2 [SARS-CoV-2)]) causing severe respiratory illness originating in Wuhan, China. Since then, an increasing number of cases and the confirmation of human-to-human transmission has led to the need to develop a communication campaign at our institution. We describe the impact of the communication campaign on the number of calls received and describe patterns of calls during the early stages of our response to this emerging infection. Methods: The University of Iowa Hospitals & Clinics is an 811-bed academic medical center with >200 outpatient clinics. In response to the coronavirus disease 2019 (COVID-19) outbreak, we launched a communications campaign on January 17, 2020. Initial communications included email updates to staff and a dedicated COVID-19 webpage with up-to-date information. Subsequently, we developed an electronic screening tool to guide a risk assessment during patient check in. The screening tool identifies travel to China in the past 14 days and the presence of symptoms defined as fever >37.7°C plus cough or difficulty breathing. The screening tool was activated on January 24, 2020. In addition, university staff contacted each student whose primary residence record included Hubei Province, China. Students were provided with medical contact information, signs and symptoms to monitor for, and a thermometer. Results: During the first 5 days of the campaign, 3 calls were related to COVID-19. The number of calls increased to 18 in the 5 days following the implementation of the electronic screening tool. Of the 21 calls received to date, 8 calls (38%) were generated due to the electronic travel screen, 4 calls (19%) were due to a positive coronavirus result in a multiplex respiratory panel, 4 calls (19%) were related to provider assessment only (without an electronic screening trigger), and 2 calls (10%) sought additional information following the viewing of the web-based communication campaign. Moreover, 3 calls (14%) were for people without travel history but with respiratory symptoms and contact with a person with recent travel to China. Among those reporting symptoms after travel to China, mean time since arrival to the United States was 2.7 days (range, 0–11 days). Conclusion: The COVID-19 outbreak is evolving, and providing up to date information is challenging. Implementing an electronic screening tool helped providers assess patients and direct questions to infection prevention professionals. Analyzing the types of calls received helped tailor messaging to frontline staff.Funding: NoneDisclosures: None


2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S188-S189
Author(s):  
Deepika Sivakumar ◽  
Shelbye R Herbin ◽  
Raymond Yost ◽  
Marco R Scipione

Abstract Background Inpatient antibiotic use early on in the COVID-19 pandemic may have increased due to the inability to distinguish between bacterial and COVID-19 pneumonia. The purpose of this study was to determine the impact of COVID-19 on antimicrobial usage during three separate waves of the COVID-19 pandemic. Methods We conducted a retrospective review of patients admitted to Detroit Medical Center between 3/10/19 to 4/24/21. Median days of therapy per 1000 adjusted patient days (DOT/1000 pt days) was evaluated for all administered antibiotics included in our pneumonia guidelines during 4 separate time periods: pre-COVID (3/3/19-4/27/19); 1st wave (3/8/20-5/2/20); 2nd wave (12/6/21-1/30/21); and 3rd wave (3/7/21-4/24/21). Antibiotics included in our pneumonia guidelines include: amoxicillin, azithromycin, aztreonam, ceftriaxone, cefepime, ciprofloxacin, doxycycline, linezolid, meropenem, moxifloxacin, piperacillin-tazobactam, tobramycin, and vancomycin. The percent change in antibiotic use between the separate time periods was also evaluated. Results An increase in antibiotics was seen during the 1st wave compared to the pre-COVID period (2639 [IQR 2339-3439] DOT/1000 pt days vs. 2432 [IQR 2291-2499] DOT/1000 pt days, p=0.08). This corresponded to an increase of 8.5% during the 1st wave. This increase did not persist during the 2nd and 3rd waves of the pandemic, and the use decreased by 8% and 16%, respectively, compared to the pre-COVID period. There was an increased use of ceftriaxone (+6.5%, p=0.23), doxycycline (+46%, p=0.13), linezolid (+61%, p=0.014), cefepime (+50%, p=0.001), and meropenem (+29%, p=0.25) during the 1st wave compared to the pre-COVID period. Linezolid (+39%, p=0.013), cefepime (+47%, p=0.08) and tobramycin (+47%, p=0.05) use remained high during the 3rd wave compared to the pre-COVID period, but the use was lower when compared to the 1st and 2nd waves. Figure 1. Antibiotic Use 01/2019 to 04/2019 Conclusion Antibiotics used to treat bacterial pneumonia during the 1st wave of the pandemic increased and there was a shift to broader spectrum agents during that period. The increased use was not sustained during the 2nd and 3rd waves of the pandemic, possibly due to the increased awareness of the differences between patients who present with COVID-19 pneumonia and bacterial pneumonia. Disclosures All Authors: No reported disclosures


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