scholarly journals Viral cultures for COVID-19 infectious potential assessment – a systematic review

2020 ◽  
Author(s):  
T Jefferson ◽  
E A Spencer ◽  
J Brassey ◽  
C Heneghan
Keyword(s):  
Rt Pcr ◽  
Live Virus ◽  
Cycle Threshold ◽  
Viral Loads ◽  
Additional Information ◽  
Viral Culture ◽  
Unit Increase ◽  
Specimen Test ◽  
Virus Culture ◽  
Infectious Potential

Abstract Objective to review the evidence from studies relating SARS-CoV-2 culture with the results of reverse transcriptase polymerase chain reaction (RT-PCR) and other variables which may influence the interpretation of the test, such as time from symptom onset Methods We searched LitCovid, medRxiv, Google Scholar and the WHO Covid-19 database for Covid-19 to 10 September 2020. We included studies attempting to culture or observe SARS-CoV-2 in specimens with RT-PCR positivity. Studies were dual extracted and the data summarised narratively by specimen type. Where necessary we contacted corresponding authors of included papers for additional information. We assessed quality using a modified QUADAS 2 risk of bias tool. Results We included 29 studies reporting attempts at culturing, or observing tissue infection by, SARS-CoV-2 in sputum, nasopharyngeal or oropharyngeal, urine, stool, blood and environmental specimens. The quality of the studies was moderate with lack of standardised reporting. The data suggest a relationship between the time from onset of symptom to the timing of the specimen test, cycle threshold (Ct) and symptom severity. Twelve studies reported that Ct values were significantly lower and log copies higher in specimens producing live virus culture. Two studies reported the odds of live virus culture reduced by approximately 33% for every one unit increase in Ct. Six of eight studies reported detectable RNA for longer than 14 days but infectious potential declined after day 8 even among cases with ongoing high viral loads. Four studies reported viral culture from stool specimens. Conclusion Complete live viruses are necessary for transmission, not the fragments identified by PCR. Prospective routine testing of reference and culture specimens and their relationship to symptoms, signs and patient co-factors should be used to define the reliability of PCR for assessing infectious potential. Those with high cycle threshold are unlikely to have infectious potential.

scholarly journals Viral cultures for COVID-19 infectivity assessment. Systematic review

2020 ◽  
Author(s):  
Tom Jefferson ◽  
Elizabeth Spencer ◽  
Jon Brassey ◽  
Carl Heneghan
Keyword(s):  
Strong Relationship ◽  
Threshold Level ◽  
Rt Pcr ◽  
Live Virus ◽  
Cycle Threshold ◽  
Viral Loads ◽  
Additional Information ◽  
Viral Culture ◽  
Unit Increase ◽  
Virus Culture

Objective To review the evidence from studies comparing SARS-CoV-2 culture, with the results of reverse transcriptase polymerase chain reaction (RT-PCR). Methods We searched LitCovid, medRxiv, Google Scholar and the WHO Covid-19 database for Covid-19 using the terms viral culture or viral replication and associated synonyms up to 10 September 2020. We carried out citation matching and included studies reporting attempts to culture or observe SARS-CoV-2 matching with cutoffs for RT-PCR positivity. One reviewer extracted data for each study and a second reviewer checked end edited the extraction and summarised the narratively by sample: fecal, respiratory, environment, blood or mixed. Where necessary we wrote to corresponding authors of the included or background papers for additional information. We assessed quality using a modified QUADAS 2 risk of bias tool. This is the fourth version of this review that was first published on the 4th of August and updated on the 21t of August, on the 3rd and 10th of September. Results We included 29 studies reporting culturing or observing tissue invasion by SARS-CoV in sputum, naso or oropharyngeal, urine, stool, blood and environmental samples from patients diagnosed with Covid-19. The data are suggestive of a relation between the time from collection of a specimen to test, cycle threshold and symptom severity. The quality of the studies was moderate with lack of standardised reporting. Twelve studies reported that Ct values were significantly lower and log copies higher in samples producing live virus culture. Five studies reported no growth in samples based on a Ct cut-off value. These values ranged from CT > 24 for no growth to Ct > 34 or more. Two studies report a strong relationship between Ct value and ability to recover infectious virus and that the odds of live virus culture reduced by 33% for every one unit increase in Ct. A cut-off RT-PCR Ct > 30 was associated with non-infectious samples. One study that analysed the NSP, N and E gene fragments of the PCR result reported different cut-off thresholds depending on the gene fragment analysed. The duration of RNA shedding detected by PCR was far longer compared to detection of live culture. Six out of eight studies reported RNA shedding for longer than 14 days. Yet, infectivity declines after day 8 even among cases with ongoing high viral loads. A very small proportion of people re-testing positive after hospital discharge or with high Ct are likely to be infectious. Conclusion Prospective routine testing of reference and culture specimens are necessary for each country involved in the pandemic to establish the usefulness and reliability of PCR for Covid-19 and its relation to patient factors. Infectivity is related to the date of onset of symptoms and cycle threshold level. A binary Yes / No approach to the interpretation RT-PCR unvalidated against viral culture will result in false positives with possible segregation of large numbers of people who are no longer infectious and hence not a threat to public health.

scholarly journals Persistence of live virus in critically ill patients infected with SARS-COV-2: a prospective observational study

Critical Care ◽  
2022 ◽  
Vol 26 (1) ◽  
Author(s):  
Duane J. Funk ◽  
Jared Bullard ◽  
Sylvan Lother ◽  
Gloria Vazquez Grande ◽  
Lauren Garnett ◽  
...  
Keyword(s):  
Observational Study ◽  
Prospective Observational Study ◽  
Severity Of Illness ◽  
Vero Cells ◽  
Rt Pcr ◽  
Icu Patients ◽  
Live Virus ◽  
Cycle Threshold ◽  
Viral Culture ◽  
Culture Negative

Abstract Background Research on the duration of infectivity of ICU patients with COVID-19 has been sparse. Tests based on Reverse Transcriptase polymerase chain reaction (RT-PCR) detect both live virus and non-infectious viral RNA. We aimed to determine the duration of infectiousness based on viral culture of nasopharyngeal samples of patients with COVID-19. Methods Prospective observational study in adult intensive care units with a diagnosis of COVID-19 Pneumonia. Patients had repeated nasopharyngeal sampling performed after day 10 of ICU admission. Culture positive rate (based on viral culture on Vero cells in a level 4 lab) and Cycle threshold from RT-PCR were measured. Results Nine patients of the 108 samples (8.3%, 95% CI 3.9–15.2%) grew live virus at a median of 13 days (interquartile range 11–19) after their initial positive test. 74.1% of patients were RT-PCR positive but culture negative, and the remaining (17.6%) were RT-PCR and culture negative. Cycle threshold showed excellent ability to predict the presence of live virus, with a Ct < 25 with an AUC of 0.90 (95% CI 0.83–0.97, p < 0.001). The specificity of a Ct > 25 to predict negative viral culture was 100% (95% CI 70–100%). Conclusion 8.3% of our ICU patients with COVID-19 grew live virus at a median of 13 days post-initial positive RT-PCR test. Severity of illness, use of mechanical ventilation, and time between tests did not predict the presence of live virus. Cycle threshold of > 25 had the best ability to determine the lack of live virus in these patents.

scholarly journals Clinical utility of cycle threshold values in the context of COVID-19

2020 ◽  
Author(s):  
Sonia N. Rao ◽  
Davide Manissero ◽  
Victoria Steele ◽  
Josep Pareja
Keyword(s):  
Viral Load ◽  
Troponin I ◽  
Severe Disease ◽  
Clinical Information ◽  
High Sensitivity ◽  
Clinical Value ◽  
Cycle Threshold ◽  
Viral Loads ◽  
Ct Value ◽  
Viral Culture

Abstract BackgroundThe ability to predict likely prognosis and infectiousness for patients with COVID-19 would aid patient management decisions. Diagnosis is usually via real-time PCR and it is unclear whether the semi-quantitative capability of this method, determining viral load through cycle threshold (Ct) values, can be leveraged.ObjectivesWe aim to review available knowledge on correlations between SARS-COV-2 Ct values and patient- or healthcare-related outcomes to determine whether Ct values provide useful clinical information.SourcesA PubMed search was conducted on 1st June 2020 based on a search strategy of (Ct value OR viral load) AND SARS-CoV-2. Data was extracted from studies reporting on the presence or absence of an association between Ct values, or viral loads determined via Ct value, and clinical outcomes.ContentData from 18 studies were relevant for inclusion. One study reported on the correlation between Ct values and mortality and one study reported on the correlation between Ct values and progression to severe disease; both reported a significant association (p < 0.001 and p = 0.008, respectively). Fourteen studies reported on the correlation between Ct value or viral loads determined via Ct value and disease severity and an association was observed in 8 (57%) studies. Studies reporting on the correlation of viral load with biochemical and haematological markers showed an association with at least one marker, including increased lactate dehydrogenase (n = 4), decreased lymphocytes (n = 3) and increased high-sensitivity troponin I (n = 2). Two studies reporting on the correlation with infectivity showed that lower Ct values were associated with higher viral culture positivity.ImplicationsData suggest that lower Ct values may be associated with worse outcomes, and that Ct values may be useful in predicting the clinical course and prognosis of patients with COVID-19; however, further studies are warranted to confirm clinical value.

scholarly journals Detection by PCR of Enteroviruses in Cerebrospinal Fluid during a Summer Outbreak of Aseptic Meningitis in Switzerland

1998 ◽  
Vol 36 (9) ◽  
pp. 2408-2412 ◽  
Author(s):  
Meri Gorgievski-Hrisoho ◽  
Jean-Daniel Schumacher ◽  
Nevenka Vilimonovic ◽  
Daniel Germann ◽  
Lukas Matter
Keyword(s):  
Cell Culture ◽  
Cerebrospinal Fluid ◽  
Aseptic Meningitis ◽  
Diagnostic Techniques ◽  
Rt Pcr ◽  
Echovirus 30 ◽  
Reverse Transcription Pcr ◽  
Viral Culture ◽  
Test Kit ◽  
Virus Culture

Enteroviruses (EV) are among the most common causes of aseptic meningitis. Standard diagnostic techniques are often too slow and lack sensitivity to be of clinical relevance. EV RNA can be detected within 5 h by a commercially available reverse transcription-PCR (RT-PCR) test kit. Cerebrospinal fluid (CSF) samples from 68 patients presenting with aseptic meningitis during a summer outbreak in Switzerland were examined in parallel with cell culture and commercial RT-PCR. RT-PCR was positive in all 16 CSF specimens positive by cell culture (100%). In addition, 42 of 52 (80%) CSF samples negative by cell culture were PCR positive. In 26 of these 42 (62%) patients, viral culture from other sites (throat swab or stool) was also positive. The CSF virus culture took 3 to 7 days to become positive. Echovirus 30 was the type most often isolated in this outbreak. The sensitivity of CSF RT-PCR based on clinical diagnosis during this aseptic meningitis outbreak in patients with negative bacterial culture results was 85%, i.e., considerably higher than the sensitivity of CSF virus culture (24%). We conclude that this commercial RT-PCR assay allows a positive diagnosis with minimal delay and may thus influence clinical decisions.

scholarly journals Clinical evaluation of the SD Biosensor saliva antigen rapid test with symptomatic and asymptomatic, non-hospitalized patients

2021 ◽  
Author(s):  
Zsofia Igloi ◽  
Jans Velzing ◽  
Robin Huisman ◽  
Corine Geurtsvankessel ◽  
Anoushka Comvalius ◽  
...  
Keyword(s):  
Clinical Evaluation ◽  
Rapid Test ◽  
Hospitalized Patients ◽  
Rt Pcr ◽  
Cycle Threshold ◽  
Virus Culture

AbstractPerformance of saliva antigen rapid test was evaluated in non-hospitalized patients, with or without symptoms. Overall sensitivity was 66.1% compared to RT-PCR in saliva. Using cycle threshold <30 cutoff or virus culture as reference, sensitivity increased to 88.6% or 96.7% respectively. Specificity was 99.6%.

scholarly journals Just 2% of SARS-CoV-2-positive individuals carry 90% of the virus circulating in communities

2021 ◽  
Author(s):  
Qing Yang ◽  
Tassa K Saldi ◽  
Erika Lasda ◽  
Carolyn J Decker ◽  
Camille L Paige ◽  
...  
Keyword(s):  
Rt Pcr ◽  
Live Virus ◽  
Viral Loads ◽  
University Of Colorado ◽  
Pandemic Response ◽  
Asymptomatic Individuals ◽  
The University ◽  
Analyze Data

We analyze data from the Fall 2020 pandemic response efforts at the University of Colorado Boulder (USA), where more than 72,500 saliva samples were tested for SARS-CoV-2 using quantitative RT-PCR. All samples were collected from individuals who reported no symptoms associated with COVID-19 on the day of collection. From these, 1,405 positive cases were identified. The distribution of viral loads within these asymptomatic individuals was indistinguishable from what has been previously reported in symptomatic individuals. Regardless of symptomatic status, approximately 50% of individuals who test positive for SARS-CoV-2 seem to be in non-infectious phases of the disease, based on having low viral loads in a range from which live virus has rarely been isolated. We find that, at any given time, just 2% of individuals carry 90% of the virions circulating within communities, serving as viral super-carriers and possibly also super-spreaders.

scholarly journals Rapid diagnosis of SARS-CoV-2 pneumonia on lower respiratory tract specimens

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Vanessa De Pace ◽  
Patrizia Caligiuri ◽  
Valentina Ricucci ◽  
Nicola Nigro ◽  
Barbara Galano ◽  
...  
Keyword(s):  
Intensive Care ◽  
Viral Load ◽  
Lower Respiratory Tract ◽  
Diagnostic Performance ◽  
High Viral Load ◽  
Load Cycle ◽  
Rt Pcr ◽  
Cycle Threshold ◽  
Viral Loads ◽  
Rapid Pcr

Abstract Background The ongoing SARS-CoV-2 pandemic requires the availability of accurate and rapid diagnostic tests, especially in such clinical settings as emergency and intensive care units. The objective of this study was to evaluate the diagnostic performance of the Vivalytic SARS-CoV-2 rapid PCR kit in lower respiratory tract (LRT) specimens. Methods Consecutive LRT specimens (bronchoalveolar lavage and bronchoaspirates) were collected from Intensive Care Units of San Martino Hospital (Genoa, Italy) between November 2020 and January 2021. All samples underwent RT-PCR testing by means of the Allplex™ SARS-CoV-2 assay (Seegene Inc., South Korea). On the basis of RT-PCR results, specimens were categorized as negative, positive with high viral load [cycle threshold (Ct) ≤ 30] and positive with low viral load (Ct of 31–35). A 1:1:1 ratio was used to achieve a sample size of 75. All specimens were subsequently tested by means of the Vivalytic SARS-CoV-2 rapid PCR assay (Bosch Healthcare Solutions GmbH, Germany). The diagnostic performance of this assay was assessed against RT-PCR through the calculation of accuracy, Cohen’s κ, sensitivity, specificity and expected positive (PPV) and negative (NPV) predictive values. Results The overall diagnostic accuracy of the Vivalytic SARS-CoV-2 was 97.3% (95% CI: 90.9–99.3%), with an excellent Cohen’s κ of 0.94 (95% CI: 0.72–1). Sensitivity and specificity were 96% (95% CI: 86.5–98.9%) and 100% (95% CI: 86.7–100%), respectively. In samples with high viral loads, sensitivity was 100% (Table 1). The distributions of E gene Ct values were similar (Wilcoxon’s test: p = 0.070), with medians of 35 (IQR: 25–36) and 35 (IQR: 25–35) on Vivalytic and RT-PCR, respectively (Fig. 1). NPV and PPV was 92.6% and 100%, respectively.Table 1 Demographic characteristics and data sample type of the study cases (N = 75) Male, N (%) 56 (74.6%) Age (yr), Median (IQR) 65 (31–81) BAS, N (%) 43 (57.3%)  Negative 30.2%  Positive—High viral load [Ct ≤ 30] 27.9%  Positive—Low viral load [Ct 31–35] 41.9% BAL, N (%) 32 (42.7%)  Negative 37.5%  Positive—High viral load [Ct ≤ 30] 40.6%  Positive—Low viral load [Ct 31–35] 21.9% Data were expressed as proportions for categorical variables. Specimens were categorized into negative, positive with high viral load [cycle threshold (Ct) ≤ 30] and positive with low viral load (Ct of 31–35). BAS bronchoaspirates, BAL bronchoalveolar lavage, Ct cycle threshold Conclusions Vivalytic SARS-CoV-2 can be used effectively on LRT specimens following sample liquefaction. It is a feasible and highly accurate molecular procedure, especially in samples with high viral loads. This assay yields results in about 40 min, and may therefore accelerate clinical decision-making in urgent/emergency situations.

scholarly journals Clinical effect and antiviral mechanism of T-705 in treating severe fever with thrombocytopenia syndrome

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Hao Li ◽  
Xia-Ming Jiang ◽  
Ning Cui ◽  
Chun Yuan ◽  
Shao-Fei Zhang ◽  
...  
Keyword(s):  
Viral Load ◽  
Supportive Care ◽  
Fatal Outcome ◽  
Animal Experiments ◽  
Case Fatality ◽  
Rt Pcr ◽  
Cycle Threshold ◽  
Viral Loads ◽  
Severe Fever

AbstractSevere fever with thrombocytopenia syndrome (SFTS) virus (SFTSV) is an emerging tick-borne virus with high fatality and an expanding endemic. Currently, effective anti-SFTSV intervention remains unavailable. Favipiravir (T-705) was recently reported to show in vitro and in animal model antiviral efficacy against SFTSV. Here, we conducted a single-blind, randomized controlled trial to assess the efficacy and safety of T-705 in treating SFTS (Chinese Clinical Trial Registry website, number ChiCTR1900023350). From May to August 2018, laboratory-confirmed SFTS patients were recruited from a designated hospital and randomly assigned to receive oral T-705 in combination with supportive care or supportive care only. Fatal outcome occurred in 9.5% (7/74) of T-705 treated patients and 18.3% (13/71) of controls (odds ratio, 0.466, 95% CI, 0.174–1.247). Cox regression showed a significant reduction in case fatality rate (CFR) with an adjusted hazard ratio of 0.366 (95% CI, 0.142–0.944). Among the low-viral load subgroup (RT-PCR cycle threshold ≥26), T-705 treatment significantly reduced CFR from 11.5 to 1.6% (P = 0.029), while no between-arm difference was observed in the high-viral load subgroup (RT-PCR cycle threshold <26). The T-705-treated group showed shorter viral clearance, lower incidence of hemorrhagic signs, and faster recovery of laboratory abnormities compared with the controls. The in vitro and animal experiments demonstrated that the antiviral efficacies of T-705 were proportionally induced by SFTSV mutation rates, particularly from two transition mutation types. The mutation analyses on T-705-treated serum samples disclosed a partially consistent mutagenesis pattern as those of the in vitro or animal experiments in reducing the SFTSV viral loads, further supporting the anti-SFTSV effect of T-705, especially for the low-viral loads.

scholarly journals Preanalytical Issues and Cycle Threshold Values in SARS-CoV-2 Real-Time RT-PCR Testing: Should Test Results Include These?

ACS Omega ◽  
2021 ◽  
Author(s):  
Ilka Engelmann ◽  
Enagnon Kazali Alidjinou ◽  
Judith Ogiez ◽  
Quentin Pagneux ◽  
Sana Miloudi ◽  
...  
Keyword(s):  
Real Time ◽  
Test Results ◽  
Threshold Values ◽  
Rt Pcr ◽  
Cycle Threshold

scholarly journals Prolonged SARS-CoV-2-RNA Detection from Nasopharyngeal Swabs in an Oncologic Patient: What Impact on Cancer Treatment?

2021 ◽  
Vol 28 (1) ◽  
pp. 847-852
Author(s):  
Anna Ferrari ◽  
Marco Trevenzoli ◽  
Lolita Sasset ◽  
Elisabetta Di Liso ◽  
Toni Tavian ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Cancer Treatment ◽  
Cancer Patients ◽  
Clinical Symptoms ◽  
Palliative Radiotherapy ◽  
Rt Pcr ◽  
Cancer Treatments ◽  
Global Challenge ◽  
Viral Culture ◽  
Pcr Assays

The pandemic of SARS-CoV-2 is a serious global challenge affecting millions of people worldwide. Cancer patients are at risk for infection exposure and serious complications. A prompt diagnosis of SARS-CoV-2 infection is crucial for the timely adoption of isolation measures and the appropriate management of cancer treatments. In lung cancer patients the symptoms of infection 19 may resemble those exhibited by the underlying oncologic condition, possibly leading to diagnostic overlap and delays. Moreover, cancer patients might display a prolonged positivity of nasopharyngeal RT-PCR assays for SARS-CoV-2, causing long interruptions or delay of cancer treatments. However, the association between the positivity of RT-PCR assays and the patient’s infectivity remains uncertain. We describe the case of a patient with non-small cell lung cancer, and a severe ab extrinseco compression of the trachea, whose palliative radiotherapy was delayed because of the prolonged positivity of nasopharyngeal swabs for SARS-CoV-2. The patient did not show clinical symptoms suggestive of active infection, but the persistent positivity of RT-PCR assays imposed the continuation of isolation measures and the delay of radiotherapy for over two months. Finally, the negative result of SARS-CoV-2 viral culture allowed us to verify the absence of viral activity and to rule out the infectivity of the patient, who could finally continue her cancer treatment.

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