scholarly journals Viral Culture in Hospitalized Congregate Care Patients With Prolonged SARS-CoV-2 Viral RNA Detection

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. 734-735
Author(s):  
Thilaka Arunachalam ◽  
Amit Singh ◽  
Kathleen Stellrecht ◽  
Sarah Elmendorf ◽  
Tarani K Barman ◽  
...  

Abstract Prolonged detection of SARS-CoV-2 viral RNA has been observed in hospitalized congregate care patients following resolution of clinical symptoms. It is unknown whether patients with persistent PCR positivity pose a risk for COVID-19 transmission. The purpose of this study was to examine the results of serial PCR testing, viral load, and viral culture in patients awaiting discharge prior to a negative PCR test. We sampled 14 patients who were admitted from skilled nursing and/or rehabilitation facilities to a large academic medical center, had clinical signs and symptoms of COVID-19, and had multiple PCR-positive tests separated by at least 14 days. PCR-positive nasopharyngeal swabs were obtained from each patient for viral load quantification and viral culture. The mean age of patients was 72.5 years (55 – 92), with a mean peak SOFA score of 5.6 (1 – 11). Patients were hospitalized for a mean of 37.0 days (25 – 60). RNA was detected by PCR for a mean of 32.9 days (19 – 47). Mean viral load for the first PCR-positive nasopharyngeal swab collected at our hospital was 5.81 genomic copies/mL (2.12 – 9.72). Viral load decreased significantly with days from clinical symptom onset (R = -0.69, 95% CI, -0.80 – -0.55). Four out of 28 samples grew active virus via culture, with no active virus isolates after 2 days of symptom onset. Our viral culture data suggests that persistent PCR positivity may not correlate with infectivity, which has important implications for COVID-19 infection control precautions among older congregate care patients.

2021 ◽  
Author(s):  
Toshihito Nomura ◽  
Hiroki Kitagawa ◽  
Keitaro Omori ◽  
Norifumi Shigemoto ◽  
Masaki Kakimoto ◽  
...  

Abstract Approximately 5% of patients with coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 develop severe COVID-19. Severe COVID-19 requires respiratory management with mechanical ventilation and an extended period of treatment. Prolonged infectious virus shedding is a concern in severe COVID-19 cases, but few reports have examined the duration of infectious virus shedding. Therefore, we investigated the duration of infectious virus shedding in patients transferred to Hiroshima University Hospital with severe COVID-19 requiring mechanical ventilation. Nasopharyngeal swab specimens were collected and analyzed using both viral culture and reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) tests between December 2020 and February 2021. Of the 23 patients tested, the proportions of those with positive test results at first specimen collection on RT-qPCR and viral culture tests were 95·7% and 30·4%, respectively. All six patients with positive viral culture test results who were followed-up tested negative 24 days after symptom onset but remained positive on RT-qPCR. The longest negative conversion time was observed in a dialysis patient on immunosuppressive drugs. This study indicated that patients with severe COVID-19 remain culture positive for ≥ 10 days after symptom onset. Additionally, immunosuppressed patients with severe COVID-19 could consider isolation for ≥ 20 days.


2015 ◽  
Vol 36 (3) ◽  
pp. 241-248 ◽  
Author(s):  
Shital C. Shah ◽  
Dino P. Rumoro ◽  
Marilyn M. Hallock ◽  
Gordon M. Trenholme ◽  
Gillian S. Gibbs ◽  
...  

OBJECTIVETo identify clinical signs and symptoms (ie, “terms”) that accurately predict laboratory-confirmed influenza cases and thereafter generate and evaluate various influenza-like illness (ILI) case definitions for detecting influenza. A secondary objective explored whether surveillance of data beyond the chief complaint improves the accuracy of predicting influenza.DESIGNRetrospective, cross-sectional study.SETTINGLarge urban academic medical center hospital.PARTICIPANTSA total of 1,581 emergency department (ED) patients who received a nasopharyngeal swab followed by rRT-PCR testing between August 30, 2009, and January 2, 2010, and between November 28, 2010, and March 26, 2011.METHODSAn electronic surveillance system (GUARDIAN) scanned the entire electronic medical record (EMR) and identified cases containing 29 clinical terms relevant to influenza. Analyses were conducted using logistic regressions, diagnostic odds ratio (DOR), sensitivity, and specificity.RESULTSThe best predictive model for identifying influenza for all ages consisted of cough (DOR=5.87), fever (DOR=4.49), rhinorrhea (DOR=1.98), and myalgias (DOR=1.44). The 3 best case definitions that included combinations of some or all of these 4 symptoms had comparable performance (ie, sensitivity=89%–92% and specificity=38%–44%). For children <5 years of age, the addition of rhinorrhea to the fever and cough case definition achieved a better balance between sensitivity (85%) and specificity (47%). For the fever and cough ILI case definition, using the entire EMR, GUARDIAN identified 37.1% more influenza cases than it did using only the chief complaint data.CONCLUSIONSA simplified case definition of fever and cough may be suitable for implementation for all ages, while inclusion of rhinorrhea may further improve influenza detection for the 0–4-year-old age group. Finally, ILI surveillance based on the entire EMR is recommended.Infect Control Hosp Epidemiol 2015;00(0): 1–8


Author(s):  
Jianping Huang ◽  
Tingting Mao ◽  
Shufei Li ◽  
Lianpeng Wu ◽  
Xueqin Xu ◽  
...  

ABSTRACTOBJECTIVETo investigate the dynamics of viral RNA, IgM, and IgG and their relationships in patients with SARS-CoV-2 pneumonia over an 8-week period.DESIGNRetrospective, observational case series.SETTINGWenzhou Sixth People’s HospitalPARTICIPANTSThirty-three patients with laboratory confirmed SARS-CoV-2 pneumonia admitted to hospital. Data were collected from January 27 to April 10, 2020.MAIN OUTCOME MEASURESThroat swabs, sputum, stool, and blood samples were collected, and viral load was measured by reverse transcription PCR (RT-PCR). Specific IgM and IgG against spike protein (S), spike protein receptor binding domain (RBD), and nucleocapsid (N) were analyzed.RESULTSAt the early stages of symptom onset, SARS-CoV-2 viral load is higher in throat swabs and sputum, but lower in stool. The median (IQR) time of undetectable viral RNA in throat swab, sputum, and stool was 18.5 (13.25-22) days, 22 (18.5-27.5) days, and 17 (11.5-32) days, respectively. In sputum, 17 patients (51.5%) had undetectable viral RNA within 22 days (short persistence), and 16 (48.5%) had persistent viral RNA more than 22 days (long persistence). Three patients (9.1%) had a detectable relapse of viral RNA in sputum within two weeks of their discharge from the hospital. One patient had persistent viral RNA for 59 days or longer. The median (IQR) seroconversion time of anti-S IgM, anti-RBD IgM, and anti-N IgM was 10.5 (7.75-15.5) days, 14 (9-24) days, and 10 (7-14) days, respectively. The median (IQR) seroconversion time of anti-S IgG, anti-RBD IgG, and anti-N IgG was 10 (7.25-16.5) days, 13 (9-17) days, and 10 (7-14) days, respectively. By week 8 after symptom onset, IgM were negative in many of the previously positive patients, and IgG levels remained less than 50% of the peak levels in more than 20% of the patients. In about 40% of the patients, anti-RBD IgG levels were 4-times higher in convalescence than in acute phase. SARS-CoV-2 RNA coexisted with antibodies for more than 50 days. Anti-RBD IgM and IgG levels, including anti-RBD IgM levels at presentation and peak time, were significantly higher in viral RNA short persistence patients than in long persistence patients.CONCLUSIONThis study adds important new information about the features of viral load and antibody dynamics of SARS-CoV-2. It is clear from these results that the viral RNA persists in sputum and stool specimens for a relatively long time in many patients. Anti-RBD may also serve as a potential protective antibody against SARS-CoV-2 infection, as viral persistence appears to be related to anti-RBD levels. Earlier treatment intervention also appears to be a factor in viral persistence.WHAT IS ALREADY KNOWN ON THIS TOPICThere are several reports about the serum antibodies against SARS-CoV-2. However, most of them evaluate diagnostic accuracy. Only two articles report dynamics of SARS-CoV-2 viral RNA and antibodies with serial samples, but the observation periods are within 30 days. None of the studies investigate the profiles of SARS-CoV-2 viral load and antibodies in a long period. Three reports investigate profiles in respiratory samples, but there are no reports on the dynamics of the viral load in stool samples.WHAT THIS STUDY ADDSIn both sputum and stool, SARS-CoV-2 RNA persists for a long time. The anti-RBD antibodies may involve in the clearance of SARS-CoV-2 infection. After eight weeks from symptom onset, IgM were negative in many of the previously positive patients, and IgG levels remained less than 50% of the peak levels in more than 20% of the patients. In about 40% of the patients, anti-RBD IgG levels increased 4-time higher in convalescence than in acute phase. Long persistence of SARS-CoV-2 viral RNA in sputum and stool presents challenges for management of the infection. The IgM/IgG comb test is better than single IgM test as a supplement diagnostic tool. Anti-RBD may be a protective antibody, and is valuable for development of vaccines.


2021 ◽  
Author(s):  
Katie R. Mollan ◽  
Joseph J. Eron ◽  
Taylor J. Krajewski ◽  
Wendy Painter ◽  
Elizabeth R. Duke ◽  
...  

Background: SARS-CoV-2 infectious virus isolation in the upper airway of COVID-19 patients is associated with higher levels of viral RNA. However, comprehensive evaluation of the relationships between host and disease factors and infectious, replication competent virus is needed. Methods: Symptomatic COVID-19 outpatients were enrolled from the United States. Clinical symptoms were recorded via patient diary. Nasopharyngeal swabs were collected to quantitate SARS-CoV-2 RNA by reverse transcriptase polymerase chain reaction and for infectious virus isolation in Vero E6-cells. SARS-CoV-2 antibodies were measured in serum using a validated ELISA assay. Findings: Among 204 participants within one week of reported symptom onset (median=5, IQR 4-5 days), median age was 40 (min-max: 18-82 years), median nasopharyngeal viral RNA was 6.5 (IQR 4.7-7.6 log10 copies/mL), and 26% had detectable SARS-CoV-2 antibodies at baseline. Infectious virus was recovered in 7% of participants with antibodies compared to 58% of participants without antibodies (probability ratio (PR)=0.12, 95% CI: 0.04, 0.36; p=0.00016). Infectious virus isolation was also associated with higher levels of viral RNA (mean RNA difference +2.6 log10, 95% CI: 2.2, 3.0; p<0.0001) and fewer days since symptom onset (PR=0.79, 95% CI: 0.71, 0.88 per day; p<0.0001). Interpretation: The presence of SARS-CoV-2 antibodies is strongly associated with clearance of infectious virus isolation. Seropositivity and viral RNA are likely more reliable markers of infectious virus suppression than subjective measure of COVID-19 symptoms. Virus-targeted treatment and prevention strategies should be administered as early as possible and ideally before seroconversion. Funding: Ridgeback Biotherapeutics, LP and NIH ClinicalTrials.gov Identifier: NCT04405570


Author(s):  
Daniel Owusu ◽  
Mary A Pomeroy ◽  
Nathaniel M Lewis ◽  
Ashutosh Wadhwa ◽  
Anna R Yousaf ◽  
...  

Abstract Background To better understand severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding and infectivity, we estimated SARS-CoV-2 RNA shedding duration, described participant characteristics associated with the first negative rRT-PCR test (resolution), and determined if replication-competent viruses was recoverable ≥10 days after symptom onset. Methods We collected serial nasopharyngeal specimens from 109 individuals with rRT-PCR–confirmed COVID-19 in Utah and Wisconsin. We calculated viral RNA shedding resolution probability using the Kaplan-Meier estimator and evaluated characteristics associated with shedding resolution using Cox proportional hazards regression. We attempted viral culture for 35 rRT-PCR–positive nasopharyngeal specimens collected ≥10 days after symptom onset. Results The likelihood of viral RNA shedding resolution at 10 days after symptom onset was approximately 3%. Time to shedding resolution was shorter among participants aged &lt;18 years (adjusted hazards ratio [aHR], 3.01; 95% confidence interval [CI], 1.6–5.6) and longer among those aged ≥50 years (aHR, 0.50; 95% CI, .3–.9) compared to participants aged 18–49 years. No replication-competent viruses were recovered. Conclusions Although most patients were positive for SARS-CoV-2 for ≥10 days after symptom onset, our findings suggest that individuals with mild to moderate COVID-19 are unlikely to be infectious ≥10 days after symptom onset.


2021 ◽  
Author(s):  
Mohammad Hosein Taziki Balajelini ◽  
Abdolhalim Rajabi ◽  
Masoud Mohammadi ◽  
Alijan Tabarraei ◽  
Seyed Mohammad Hadi Razavi Nikoo ◽  
...  

Abstract Background: Covid-19 has different clinical symptoms and severity. Predicting its progress and results is clinically important. Hence, in this study, we investigated the relationship between virus load and the outcomes in Golestan Province. Methodology: We conducted a retrospective cohort study of COVID-19 diagnosed with RT-PCR testing from May 2020 to December 2020. According to the severity of the disease, the study groups were divided into three groups: outpatient, inpatient, and inpatient with death. SARS-CoV-2 viral load was assessed using cycle threshold (Ct) values from a reverse transcription-polymerase chain reaction assay applied to nasopharyngeal swab samples. Demographic properties, Clinical characteristics, and CT values of the studied patients were compared. Data were analyzed using STATA Version 16.0 software.Results: Of 1318 included subjects, 599 were outpatient, and 719 were hospitalized. Of the hospitalized patients, 487 were recovered and 232 died. The mean age (year) of patients was 48.81±18.40 and 51.9% were female. There were significant differences between the age and the severity of the disease, the mean age of patients who died was higher than other patients (p<0.001). The mean CT value of all patients was 26.80±4.43, which was higher in outpatients than inpatients' cases (p <0.001). We did not find any significant differences for the Ct values between recovered and dead cases (p=0.66). CT value levels were not significantly different between age and sex groups. Conclusions: According to the results of the study, CT value can be used only as a factor to determine the severity of the disease at the time of admission, but the load of the virus is not a factor to predict the outcome.


2021 ◽  
Vol 26 (41) ◽  
Author(s):  
Guillaume André Durand ◽  
Franck de Laval ◽  
Albane de Bonet d’Oléon ◽  
François Xavier Le Flem ◽  
Yann Morin ◽  
...  

We investigated a COVID-19 outbreak at a fire station in Marseille, France. Confirmed cases were defined as individuals with positive SARS-CoV-2 reverse transcription (RT)-PCR and/or neutralising antibodies. All 85 firefighters at work during the outbreak period were included after questioning and sampled for RT-PCR and viral neutralisation assay. Twenty-three firefighters were confirmed positive, 19 of them were symptomatic, and four asymptomatic cases were confirmed by virus neutralisation. A total of 22 firefighters had specific neutralising antibodies against SARS-CoV-2. Neutralising antibodies were found in four asymptomatic and 18 symptomatic cases. Eleven symptomatic cases had high titres (≥ 1:80). The earliest detection of neutralising antibodies was 7 days after symptom onset, and 80% had neutralising antibodies 15 days after onset. One viral culture was positive 13 days after onset. The attack rate was 27%. We identified two introductions of the virus in this outbreak, through a presymptomatic and a paucisymptomatic case. Asymptomatic cases were not the source of a third generation of cases, although they worked without wearing a mask, indicating that asymptomatic cases did not play a significant role in this outbreak. Management and strategy based on early research of clinical signs associated with self-quarantine was effective.


2021 ◽  
Author(s):  
Asaf Biber ◽  
Michal Mandelboim ◽  
Geva Harmelin ◽  
Dana Lev ◽  
Li Ram ◽  
...  

Background: Ivermectin, an antiparasitic agent, also has antiviral properties. Our aim was to assess whether ivermectin can shorten the viral shedding in patients at an early stage of COVID19 infection. Methods: The double blinded trial compared patients receiving ivermectin 0.2 mg/kg for 3 days vs. placebo in non-hospitalized COVID19 patients. RT-PCR from a nasopharyngeal swab was obtained at recruitment and then every two days. Primary endpoint was reduction of viral-load on the 6th day (third day after termination of treatment) as reflected by Ct level>30 (non-infectious level). The primary outcome was supported by determination of viral culture viability. Results: Eighty nine patients were eligible (47 in ivermectin and 42 in placebo arm). Their median age was 35 years. Females accounted for 21.6%, and 16.8% were asymptomatic at recruitment. Median time from symptom onset was 4 days. There were no statistical differences in these parameters between the two groups. On day 6, 34 out of 47 (72%) patients in the ivermectin arm reached the endpoint, compared to 21/ 42 (50%) in the placebo arm (OR 2.62; 95% CI: 1.09 to 6.31). In a multivariable logistic regression model, the odds of a negative test at day 6 was 2.62 time higher in the ivermectin group (95% CI: 1.06 to 6.45). Cultures at days 2 to 6 were positive in 3/23 (13.0%) of ivermectin samples vs. 14/29 (48.2%) in the placebo group (p=0.008). Conclusions: There were significantly lower viral loads and viable cultures in the ivermectin group, which could lead to shortening isolation time in these patients.


Author(s):  
Muge Cevik ◽  
Matthew Tate ◽  
Oliver Lloyd ◽  
Alberto Enrico Maraolo ◽  
Jenna Schafers ◽  
...  

Background Viral load kinetics and the duration of viral shedding are important determinants for disease transmission. We aim i) to characterise viral load dynamics, duration of viral RNA, and viable virus shedding of SARS-CoV-2 in various body fluids and ii) to compare SARS-CoV-2 viral dynamics with SARS-CoV-1 and MERS-CoV. Methods: Medline, EMBASE, Europe PMC, preprint servers and grey literature were searched to retrieve all articles reporting viral dynamics and duration of SARS-CoV-2, SARS-CoV-1 and MERS-CoV shedding. We excluded case reports and case series with < 5 patients, or studies that did not report shedding duration from symptom onset. PROSPERO registration: CRD42020181914. Findings: Seventy-nine studies on SARS-CoV-2, 8 on SARS-CoV-1, and 11 on MERS-CoV were included. Mean SARS-CoV-2 RNA shedding duration in upper respiratory tract, lower respiratory tract, stool and serum were 17.0, 14.6, 17.2 and 16.6 days, respectively. Maximum duration of SARS-CoV-2 RNA shedding reported in URT, LRT, stool and serum was 83, 59, 35 and 60 days, respectively. Pooled mean duration of SARS-CoV-2 RNA shedding was positively associated with age (p=0.002), but not gender (p = 0.277). No study to date has detected live virus beyond day nine of illness despite persistently high viral loads. SARS-CoV-2 viral load in the upper respiratory tract appears to peak in the first week of illness, while SARS-CoV-1 and MERS-CoV peak later. Conclusion: Although SARS-CoV-2 RNA shedding in respiratory and stool can be prolonged, duration of viable virus is relatively short-lived. Thus, detection of viral RNA cannot be used to infer infectiousness. High SARS-CoV-2 titres are detectable in the first week of illness with an early peak observed at symptom onset to day 5 of illness. This review underscores the importance of early case finding and isolation, as well as public education on the spectrum of illness. However, given potential delays in the isolation of patients, effective containment of SARS-CoV-2 may be challenging even with an early detection and isolation strategy. Funding: No funding was received.


2020 ◽  
Author(s):  
Paloma Merino-Amador ◽  
Jesús Guinea ◽  
Irene Muñoz-Gallego ◽  
Patricia González-Donapetry ◽  
Juan-Carlos Galán ◽  
...  

AbstractThe standard RT-PCR assay for COVID-19 is laborious and time-consuming, limiting the availability of testing. Rapid antigen-detection tests are faster and less expensive; however, the reliability of these tests must be validated before they can be used widely. The objective of this study was to determine the reliability of the PanbioTM COVID-19 Ag Rapid Test Device (PanbioRT) (Abbott) for SARS-CoV-2 in nasopharyngeal swab specimens. This was a prospective multicenter study in ten Spanish university hospitals of patients from hospital units with clinical symptoms or epidemiological criteria for COVID-19. Patients whose onset of symptoms or exposure was more than 7 days earlier were excluded. Two nasopharyngeal exudate samples were taken to perform the PanbioRT and a diagnostic RT-PCR test. Among the 958 patients studied, 359 (37.5%) were positive by RT-PCR and 325 (33.9%) were also positive by the PanbioRT. Agreement was 95.7% (kappa score: 0.90). All 34 false-negative PanbioRT results were in symptomatic patients, with 23.5% of them at 6–7 days since the onset of symptoms and 58.8% presenting CT >30 values for RT-PCR, indicating a low viral load. Overall sensitivity and specificity for the PanbioRT were 90.5% and 98.8%, respectively. The PanbioRT provides good clinical performance as a point-of-care test, with even more reliable results for patients with a shorter clinical course of the disease or a higher viral load. While this study has had a direct impact on the national diagnostic strategy for COVID-19 in Spain, the results must be interpreted based on the local epidemiological context.


Sign in / Sign up

Export Citation Format

Share Document