Detecting SARS-CoV-2 by Realtime RT-PCR in clinical samples collected in the North of Vietnam

2021 ◽  
Vol 30 (9) ◽  
pp. 11-17
Author(s):  
Hoang Vu Mai Phuong ◽  
Ung Thi Hong Trang ◽  
Nguyen Vu Son ◽  
Le Thi Thanh ◽  
Nguyen Le Khanh Hang ◽  
...  
Keyword(s):  
Viral Load ◽  
Average Rate ◽  
Clinical Samples ◽  
Viet Nam ◽  
Rt Pcr ◽  
Ct Value ◽  
The North ◽  
Viral Load Data ◽  
The Mean ◽  
High Level

From January to August 2020, Northern Viet Nam faced a COVID-19 outbreak, up to September 2020, there were 1122 confrmed cases of SARS-CoV-2, of which 465 cases were imported from Europe, America and Asia, 657 cases were identifed domestically. A total of 30,686 samples were collected during the SARS-CoV-2 outbreak in Northern Viet Nam and examined by Real-time RT-PCR using primers and probe from Charite - Berlin protocol. This study showed the initial results of SARS-CoV-2 detection and RNA quantitative in positive samples. The positive rate was 0.8%, ranging from 0.4 to 3.5% according to collection sites. Out of 251 positive samples, the mean Ct value was 28 (IQR: 22.3-32; range 14 - 38). The positive samples had a Ct value below 30 was 68.5%, there was no signifcant difference between the Ct value of the group ≤ 30 and > 30. The mean of the RNA copies/µl was 8.4.107, (IQR: 2.29.106 - 1.83.109 RNA copies/µl, range: 1.95.103 – 4.95.1011). In the group of imported COVID-19 cases, the rate of virus at low level was 29%, an average was 56% and at high level was 15%. In the community groups, the viral load data showed that the average rate at low, intermediate and high level were 20%, 63% and 17% respectively. The proportion of high-level viral load may raise an alert to start the quarantine process to reduce the transmission of SARS-CoV-2

scholarly journals Lower nasopharyngeal viral load during the latest phase of COVID-19 pandemic in a Northern Italy University Hospital

2020 ◽  
Vol 58 (9) ◽  
pp. 1573-1577 ◽  
Author(s):  
Nicola Clementi ◽  
Roberto Ferrarese ◽  
Marco Tonelli ◽  
Virginia Amato ◽  
Sara Racca ◽  
...  
Keyword(s):  
Viral Load ◽  
Pilot Study ◽  
Pcr Amplification ◽  
Clinical Severity ◽  
University Hospital ◽  
Rt Pcr ◽  
Viral Loads ◽  
Viral Load Data ◽  
The Mean ◽  
Polymerase Chain

AbstractObjectivesA milder clinical course of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been anecdotally reported over the latest phase of COVID-19 pandemic in Italy. Several factors may contribute to this observation, including the effect of lockdown, social distancing, lower humidity, lower air pollution, and potential changes in the intrinsic pathogenicity of the virus. In this regard, the clinical severity of COVID-19 could be attenuated by mutations in SARS-CoV-2 genome that decrease its virulence, as well as by lower virus inocula.MethodsIn this pilot study, we compared the reverse transcription polymerase chain reaction (RT-PCR) amplification profile of 100 nasopharyngeal swabs consecutively collected in April, during the peak of SARS-CoV-2 epidemic, to that of 100 swabs collected using the same procedure in May.ResultsThe mean Ct value of positive samples collected in May was significantly higher than that of samples collected in the previous period (ORF 1a/b gene: 31.85 ± 0.32 vs. 28.37 ± 0.5, p<0.001; E gene: 33.76 ± 0.38 vs. 29.79 ± 0.63, p<0.001), suggesting a lower viral load at the time of sampling. No significant differences were observed between male and females in the two periods, whilst higher viral loads were found in (i) patients over 60-years old, and (ii) patients that experienced severe COVID-19 during the early stages of the pandemic.ConclusionsThis pilot study prompts further investigation on the correlation between SARS-CoV-2 load and different clinical manifestation of COVID-19 during different phases of the pandemic. Laboratories should consider reporting quantitative viral load data in the molecular diagnosis of SARS-CoV-2 infection.

scholarly journals Viral Dynamics and Real-Time RT-PCR Ct Values Correlation with Disease Severity in COVID-19

Diagnostics ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1091
Author(s):  
Ali A. Rabaan ◽  
Raghavendra Tirupathi ◽  
Anupam A Sule ◽  
Jehad Aldali ◽  
Abbas Al Mutair ◽  
...  
Keyword(s):  
Viral Load ◽  
Real Time ◽  
Disease Severity ◽  
False Negative ◽  
Influential Factors ◽  
Confirmatory Test ◽  
Acid Extraction ◽  
Rt Pcr ◽  
Viral Kinetics ◽  
Ct Value

Real-time RT-PCR is considered the gold standard confirmatory test for coronavirus disease 2019 (COVID-19). However, many scientists disagree, and it is essential to understand that several factors and variables can cause a false-negative test. In this context, cycle threshold (Ct) values are being utilized to diagnose or predict SARS-CoV-2 infection. This practice has a significant clinical utility as Ct values can be correlated with the viral load. In addition, Ct values have a strong correlation with multiple haematological and biochemical markers. However, it is essential to consider that Ct values might be affected by pre-analytic, analytic, and post-analytical variables such as collection technique, specimen type, sampling time, viral kinetics, transport and storage conditions, nucleic acid extraction, viral RNA load, primer designing, real-time PCR efficiency, and Ct value determination method. Therefore, understanding the interpretation of Ct values and other influential factors could play a crucial role in interpreting viral load and disease severity. In several clinical studies consisting of small or large sample sizes, several discrepancies exist regarding a significant positive correlation between the Ct value and disease severity in COVID-19. In this context, a revised review of the literature has been conducted to fill the knowledge gaps regarding the correlations between Ct values and severity/fatality rates of patients with COVID-19. Various databases such as PubMed, Science Direct, Medline, Scopus, and Google Scholar were searched up to April 2021 by using keywords including “RT-PCR or viral load”, “SARS-CoV-2 and RT-PCR”, “Ct value and viral load”, “Ct value or COVID-19”. Research articles were extracted and selected independently by the authors and included in the present review based on their relevance to the study. The current narrative review explores the correlation of Ct values with mortality, disease progression, severity, and infectivity. We also discuss the factors that can affect these values, such as collection technique, type of swab, sampling method, etc.

Paleomagnetic and geobarometric study of the mid-Cretaceous Whitehorse Pluton, Yukon Territory

1997 ◽  
Vol 34 (10) ◽  
pp. 1379-1391 ◽  
Author(s):  
M. J. Harris ◽  
D. T. A. Symons ◽  
W. H. Blackburn ◽  
C. J. R. Hart
Keyword(s):  
United States ◽  
British Columbia ◽  
Crystallization Temperature ◽  
Remanent Magnetization ◽  
Average Rate ◽  
Yukon Territory ◽  
Canadian Cordillera ◽  
The North ◽  
North American Craton ◽  
High Level

This is the first of several Lithoprobe paleomagnetic studies underway to examine geotectonic motions in the northern Canadian Cordillera. Except for one controversial study, estimates for terranes underlying the Intermontane Belt in the Yukon have been extrapolated from studies in Alaska, southern British Columbia, and the northwestern United States. The Whitehorse Pluton is a large unmetamorphosed and undeformed tonalitic body of mid-Cretaceous age (~112 Ma) that was intruded into sedimentary units of the Whitehorse Trough in the Stikinia terrane. Geothermobarometric estimates for eight sites around the pluton indicate that postmagnetization tilting has been negligible since cooling through the hornblende-crystallization temperature and that the pluton is a high-level intrusion. Paleomagnetic measurements for 22 of 24 sites in the pluton yield a well-defined characteristic remanent magnetization (ChRM) direction that is steeply down and northwards. The ChRM direction gives a paleopole of 285.5°E, 81.7°N (dp = 53°, dm = 5.7°). When compared with the 112 Ma reference pole for the North American craton, this paleopole suggests that the northern Stikinia terrane has been translated northwards by 11.0 ± 4.8° (1220 ± 530 km) and rotated clockwise by 59 ± 17°. Except for an estimate from the ~70 Ma Carmacks Group volcanics, this translation and rotation estimate agrees well with previous estimates for units in the central and southern Intermontane Belt. They suggest that the terranes of the Intermontane Belt have behaved as a fairly coherent unit since the Early Cretaceous, moving northward at a minimum average rate of 2.3 ± 0.4 cm/a between ~140 and ~45 Ma.

scholarly journals Evaluation of Sample Pooling for Screening of SARS CoV-2

2020 ◽  
Author(s):  
Andargachew Mulu ◽  
Dawit Hailu Alemayehu ◽  
Fekadu Alemu ◽  
Dessalegn Abeje Tefera ◽  
Sinknesh Wolde ◽  
...  
Keyword(s):  
Ad Hoc ◽  
Clinical Sample ◽  
Diagnostic Testing ◽  
Positive Sample ◽  
Clinical Samples ◽  
Global Public Health ◽  
Rt Pcr ◽  
Resource Saving ◽  
Public Health Importance ◽  
Ct Value

AbstractBackgroundThe coronavirus disease (COVID-19) pandemic has revealed the global public health importance of robust diagnostic testing. To overcome the challenge of nucleic acid (NA) extraction and testing kit availability efficient method is urgently needed.ObjectivesTo establish an efficient, time and resource-saving and cost-effective methods, and to propose an ad hoc pooling approach for mass screening of SARS-CoV-2MethodsDirect clinical sample and NA pooling approach was used for the standard reverse transcriptase polymerase chain reaction (RT-PCR) test of the SARS CoV-2 targeting the envelop (E) and open reading frame (ORF1ab) genomic region of the virus. In this approach, experimental pools were created using SARS CoV-2 positive clinical samples spiked with up to 9 negative samples prior to NA extraction step to have a final extraction volume of 200 μL (maximum dilution factor of 10). Viral NA was also subsequently extracted from each pool and tested using the SARS CoV-2 RT-PCR assay.ResultsWe found that a single positive sample can be amplified and detected in pools of up to 7 samples depending on the ct value of the original sample, corresponding to high, medium, and low SARS CoV-2 viral copies/reaction. However, to minimize false negativity of the assay with pooling strategies and with unknown false negativity rate of the assay under validation, we recommend poling of 4 in 1 using the standard protocols of the assay, reagents and equipment. The predictive algorithm indicated a pooling ratio of 4 in 1 was expected to retain accuracy of the test irrespective of the ct value (relative RNA copy number) of the sample spiked and result in a 237% increase in testing efficiency.ConclusionsThe approaches showed its concept in easily customized and resource-saving manner and would allow expanding of current screening capacities and enable the expansion of detection in the community.

scholarly journals #27: Comparison of RT-PCR Cycle Threshold Values from Respiratory Specimens in Symptomatic and Asymptomatic Children with SARS CoV-2 Infection

2021 ◽  
Vol 10 (Supplement_2) ◽  
pp. S10-S11
Author(s):  
John Strutner ◽  
Nanda Ramchandar ◽  
Shruti Dubey ◽  
Mary Gamboa ◽  
Michelle K Vanderpool ◽  
...  
Keyword(s):  
Medical Record ◽  
Electronic Medical Record ◽  
Tertiary Care ◽  
Severe Illness ◽  
Rt Pcr ◽  
Respiratory Specimen ◽  
Cycle Threshold ◽  
Ct Value ◽  
Asymptomatic Children ◽  
The Mean

Abstract Background Understanding viral kinetics of SARS-CoV-2 is important to assess risk of transmission, manage treatment, and determine the need for isolation and protective equipment. Children have been noted to have less severe illness than adults and may have less transmission potential. We sought to determine whether children deemed to be asymptomatic had a difference in the PCR cycle threshold (Ct) value of respiratory samples from symptomatic children with SARS CoV-2 infection. Methods This was a retrospective cross-sectional study to compare PCR Ct values of 728 children who tested positive for SARS-CoV-2 by respiratory samples collected over a 4-month period. The study was a single center review of patients who tested positive for SARS-CoV-2 by RT-PCR from a respiratory specimen at a large tertiary care children’s hospital. Inclusion criteria included children 0–18 years of age who tested positive for SARS-CoV-2 by RT-PCR from a respiratory specimen for whom clinical information was available in the electronic medical record. Results We analyzed 728 children who tested positive for SARS-CoV-2 by RT-PCR from a respiratory sample over a 4-month period and for whom data was available in the electronic medical record. Overall, 71.2% of infected children were symptomatic. The mean Ct value for symptomatic patients (Ct mean 19.9, SD 6.3) was significantly lower than asymptomatic patients (Ct mean 23.5, SD 6.5) (P value &lt; 0.001, CI95th 2.6 - 4.6). The mean PCR Ct value was lowest in children less than 5 years of age. Conclusions and Relevance In this retrospective review of children who tested positive by RT-PCR for SARS CoV-2, the mean Ct was significantly lower in symptomatic children and was lowest in children under 5 years of age.

scholarly journals Effect of Lopinavir/Ritonavir Treatment On COVID-2019 Transmissibility: A Possible Option To Reduce Isolation Time

2021 ◽  
Author(s):  
Dong-Min Kim ◽  
Jae Keun Chung ◽  
Choon-Mee Kim ◽  
Mi-Seon Bang ◽  
Misbah Tariq ◽  
...  
Keyword(s):  
Viral Load ◽  
Lower Respiratory Tract ◽  
Antiviral Agent ◽  
Healthcare Systems ◽  
Rt Pcr ◽  
Load Duration ◽  
Viral Shedding ◽  
Number Of Patients ◽  
The Mean ◽  
Hospital Wards

Abstract Owing to the coronavirus disease 2019 (COVID-19) pandemic, there is a shortage of hospital wards to accommodate the increasing number of patients, especially in intensive care units. Healthcare systems are collapsing in many countries. Therefore, it is necessary to reduce isolation time. We examined the effect of lopinavir/ritonavir administration in patients with SARS-CoV-2. To assess the viral load, duration and clearance of viable virus; cell culture and RT-PCR were performed in parallel. No viable SARS-CoV-2 could be detected after administration of lopinavir/ritonavir with median time of viable viral clearance being one day after administration. The mean viral load in both upper and lower respiratory tract samples of lopinavir/ritonavir administered group was significantly lower than the group who were not treated with any antiviral agent. The duration of viable viral shedding was shorter in patients with lopinavir/ritonavir treatment compared with those without treatment. This study suggests that lopinavir/ritonavir treatment offers a possible method to reduce isolation time of patients infected with the SARS-CoV-2.

Detection of blaVIM and blaIMP Carbapenemase-Producing Pseudomonas aeruginosa from Clinical Samples in Iran

2021 ◽  
Author(s):  
Mohammad Reza Zolfaghari
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Cross Sectional Study ◽  
Clinical Samples ◽  
Sectional Study ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Cross Sectional ◽  
High Prevalence ◽  
Polymerase Chain ◽  
High Level

Background and Aims: The prevalence of carbapenemase-producing Pseudomonas aeruginosa (P. aeruginosa) strains has been recently reported worldwide. Therefore, accurate and rapid detection of carbapenemase-producing isolates is essential. So, this study aimed to detect blaVIM and blaIMP carbapenemase-producing strains using the modified Hodge test (MHT) and reverse transcription-polymerase chain reaction (RT-PCR). Materials and Methods: In this cross-sectional study, P. aeruginosa  strains were collected from clinical samples (blood, urine, wound, and other liquids body) in Firoozgar and Shahid Motahari Hospitals in Tehran and Velayat Hospital in Rasht Province, from May to December 2018. After identifying the isolates using the standard microbial tests, carbapenemase-producing strains were isolated by the modified hodge test. After that, the detection of blaVIM and blaIMP genes was performed by RT-PCR technique. Results: One hundred P. aeruginosa were isolated from different clinical samples. Among these, 74 (74%) isolates were considered as carbapenemase positive using MHT. The frequencies of blaVIM and blaIMP genes were obtained as 83% and 11%, respectively. Conclusions: The results of this study indicate a high level of resistance to most of the antibiotics tested and a high prevalence of blaVIM gene in P. aeruginosa strains.

scholarly journals Is Viral Load a Prognostic Indicator for Outcome of Covid-19 Patients? A Prospective Cohort Study in Iran

2021 ◽  
Author(s):  
Mohammad Hosein Taziki Balajelini ◽  
Abdolhalim Rajabi ◽  
Masoud Mohammadi ◽  
Alijan Tabarraei ◽  
Seyed Mohammad Hadi Razavi Nikoo ◽  
...  
Keyword(s):  
Cohort Study ◽  
Viral Load ◽  
Clinical Symptoms ◽  
Study Groups ◽  
Prognostic Indicator ◽  
Nasopharyngeal Swab ◽  
Ct Value ◽  
The Mean ◽  
Severity Of The Disease ◽  
Time Of Admission

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.

scholarly journals Virus Load and Incidence Olfactory, Gustatory, Respiratory, Gastrointestinal Disorders in COVID-19 Patients: A Retrospective Cohort Study

2021 ◽  
Author(s):  
Mohammad Hosein Taziki Balajelini ◽  
Abdolhalim Rajabi ◽  
Masoud Mohammadi ◽  
Hadi Razavi Nikoo ◽  
Alijan Tabarraei ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Cohort Study ◽  
Viral Load ◽  
Retrospective Cohort Study ◽  
Retrospective Cohort ◽  
Gastrointestinal Symptoms ◽  
Chain Reaction ◽  
Ct Value ◽  
The Mean ◽  
Polymerase Chain

Objectives: This study investigated the relationship between viral load and the incidence and recovery of olfactory and gustatory dysfunction (OD and GD), incidence of respiratory and gastrointestinal symptoms in COVID-19 patients. Design: A Retrospective Cohort Study. Setting and Participants: In total 599 outpatients’ cases polymerase chain reaction (PCR)–confirmed COVID-19-positive patients in Golestan province were included in the study. Main Outcome Measures: The incidence of OD, GD, their severity and the time of recovery was determined. The association of these variables with cycle threshold (CT) values of SARS-CoV-2 polymerase chain reaction was assessed. Results: The mean age of patients was 38.27 ± 13.62 years. The incidence of general symptoms included myalgia 70.1%, headache 51.8%, fever 47.7%, and dyspnea 21.4%. 41.9% of patients had gastrointestinal symptoms, including abdominal pain 26.5%, diarrhea 25.2%, nausea 20.5%, and vomiting 12.9%. 12.2% of patients had comorbidity. The trimester recovery rates of OD and GD were 93.94% and 94.74%, respectively. The mean recovery time of OD and GD was 14.56±13.37 and 13.8±3.77 days, respectively. The mean CT value in all patients was 27.45±4.55. There were significant associations between CT value with headache (P=0.04), GD (P=0.002) and OD (P=0.001). Conclusions: The intensity and the recovery of OD and GD in Covid-19 patients may be affected by initial viral load. Unlike to respiratory and gastrointestinal symptoms, the OD and GD were associated with lower viral load. Therefore, it may be recommended to use these clinical symptoms as an indicator in the initial screening of patients during pandemics.

scholarly journals Multicenter comparison of the Cobas 6800 system with the RealStar RT-PCR kit for the detection of SARS-CoV-2

2020 ◽  
Author(s):  
Marc Wirden ◽  
Linda Feghoul ◽  
Mélanie Bertine ◽  
Marie-Laure Nere ◽  
Quentin Le Hingrat ◽  
...  
Keyword(s):  
Regression Analysis ◽  
Linear Regression Analysis ◽  
Regression Line ◽  
Clinical Samples ◽  
Altman Analysis ◽  
Rt Pcr ◽  
Bland Altman Analysis ◽  
Deming Regression ◽  
The Mean ◽  
Pcr Assays

ABSTRACTBackgroundRT-PCR testing is crucial in the diagnostic of SARS-CoV-2 infection. The use of reliable and comparable PCR assays is a cornerstone to allow use of different PCR assays depending on the local equipment. In this work, we provide a comparison of the Cobas® (Roche) and the RealStar® assay (Altona).MethodsAssessment of the two assays was performed prospectively in three reference Parisians hospitals, using 170 clinical samples. They were tested with the Cobas® assay, selected to obtain a distribution of cycle threshold (Ct) as large as possible, and tested with the RealStar assay with three largely available extraction platforms: QIAsymphony (Qiagen), MagNAPure (Roche) and NucliSENS-easyMag (BioMérieux).ResultsOverall, the agreement (positive for at least one gene) was 76%. This rate differed considerably depending on the Cobas Ct values for gene E: below 35 (n = 91), the concordance was 99%. Regarding the positive Ct values, linear regression analysis showed a determination correlation (R2) of 0.88 and the Deming regression line revealed a strong correlation with a slope of 1.023 and an intercept of -3.9. Bland-Altman analysis showed that the mean difference (Cobas® minus RealStar®) was + 3.3 Ct, with a SD of + 2.3 Ct.ConclusionsIn this comparison, both RealStar® and Cobas® assays provided comparable qualitative results and a high correlation when both tests were positive. Discrepancies exist after 35 Ct and varied depending on the extraction system used for the RealStar® assay, probably due to a low viral load close to the detection limit of both assays.

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