Detection of SARS-CoV-2 using qRT-PCR in saliva obtained from asymptomatic or mild COVID-19 patients, comparative analysis with matched nasopharyngeal samples

Objectives The accurate detection of severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) is essential for the diagnosis of coronavirus disease 2019 (COVID-19). We compared the quantitative RT-PCR results between nasopharyngeal swabs and saliva specimens. Methods A COVID-19 outbreak occurred on a cruise ship at Nagasaki port, Japan. We obtained 123 nasopharyngeal swabs and saliva each from asymptomatic or mild patients in the late phase of infection. Results The intervals from the diagnosis to the sampling were 25.5 days for nasopharyngeal swabs and 28.9 days for saliva. The positive rate was 19.5% (24/123) for nasopharyngeal swabs and 38.2% (47/123) for saliva (P = 0.48). The quantified viral copies (mean ± SEM copies/5 μl) were 9.3±2.6 in nasopharyngeal swabs and 920±850 in saliva (P = 0.0006). Conclusions The advantages of saliva specimens include positive rate improvement and accurate viral load detection. Saliva may be used as a reliable sample for SARS-CoV-2 detection.

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Viral Load, Detection Rate and Sensitivity of Nasopharyngeal and Oropharyngeal Swab Sampling for Diagnosis of COVID-19

Ulum Islamiyyah ◽

10.33102/uij.vol33no3.319 ◽

2021 ◽

pp. 35-50

Author(s):

Eyzawiah Hassan ◽

Nuralia Akma Mohamad Mustafa ◽

Nor Azirah Salahuddin ◽

Siti Asmat Md Arepen

Keyword(s):

Viral Load ◽

Nasopharyngeal Swab ◽

Screening Methods ◽

Rt Pcr ◽

Pcr Assay ◽

Health Crisis ◽

Load Detection ◽

Negative Results ◽

Positive Rate ◽

Oropharyngeal Swab

The rapid spread of the COVID-19 pandemic has led to a major public health crisis. Accurate screening methods for COVID-19 infection is essential and crucial for case detection, isolation, prevention and control of the current pandemic. At present, nasopharyngeal and oropharyngeal swabs are typically used as the method of choice for the diagnosis of SARS-CoV-2 infection. We carried out a review on the accuracy of the two different sampling sites, the nasopharyngeal and oropharyngeal swab sampling, focusing on the viral load, detection of positive cases and sensitivity in real-time polymerase chain reaction (RT-PCR) assay in diagnosing COVID-19. A total of 25 articles related to the topic were selected out of 5221 articles searched online using Scopus, PubMed and Medline, Embase, Web of Science, and Google scholar with the keywords COVID-19, SARS-CoV-2, nasopharyngeal swab, oropharyngeal swab, nasal swab and throat swab. All full text original articles were obtained and reviewed. Nasopharyngeal swab had significantly higher SARS-CoV-2 load than oropharyngeal swab (mean Ct value ranging from 24.3-37.8, higher detection of positive rate (highest rate 62.5%) and sensitivity (highest sensitivity 98.3%, P<0.05) in RT-PCR assay compared to oropharyngeal swab. Based on the scientific literature review, both nasopharyngeal and oropharyngeal swabs were reported to have 30% probability of yielding false negative results; thus clinically suspicious patients with negative results should be viewed with concern. In conclusion, although several methods of COVID-19 screening and type of specimen are available, nasopharyngeal swab is the best option for large scale screening as it yields significantly higher viral load, higher detection of positive rate among cases and higher sensitivity in RT-PCR assay compared to oropharyngeal swab in detecting SARS-CoV-2.

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Evaluation of the performance of the COVID-19 rapid antigen tests in a tertiary level hospital in Bangladesh.

10.21203/rs.3.rs-1056525/v1 ◽

2021 ◽

Author(s):

Mohammad Jahidur Rahman Khan ◽

Md. Shahadat Hossain ◽

Samshad Jahan Shumu ◽

Md. Selim Reza ◽

Farzana Mim ◽

...

Keyword(s):

Viral Load ◽

Real Time ◽

Sensitivity And Specificity ◽

Detection Rate ◽

High Sensitivity ◽

Rt Pcr ◽

College Hospital ◽

Medical College ◽

Qrt Pcr ◽

Antigen Tests

Abstract Background: While the COVID-19 pandemic is a worldwide crisis, tests with high sensitivity and specificity are essential for identifying and managing COVID-19 patients. Globally, several rapid antigen tests RATs for COVID-19 have been developed, but their clinical efficacy has not been well established. This study aimed to evaluate the performance of several rapid antigen tests (RATs) to diagnose SARS-CoV-2 infection.Methods: This prospective observational study was conducted at Shaheed Suhrawardy Medical College hospital from February 2021 to April 2021 in Dhaka, Bangladesh. This study included the patients admitted in this hospital at the COVID-19 isolation unit or referred from the triage facility of the outdoor department of this hospital suspected as COVID-19 case. Two nasopharyngeal samples were collected simultaneously. one sample was used on the spot for the RAT. The other was sent to the adjacent Shaheed Suhrawardy Medical College COVID-19 RT-PCR laboratory for real-time reverse transcription-polymerase chain reaction (qRT-PCR). The performance of the RAT was evaluated using the results of qRT-PCR as a reference.Results: A total of 223 patients were included in this study, and the real-time RT-PCR detected SARS-CoV-2 in 84 (37.7%) patients. Of these 84 patients, 9 (10.7%) were asymptomatic. The overall sensitivity and specificity of RATs were 78.6% and 99.3%, respectively. The sensitivity was 81.3% in symptomatic cases and 55.6% in asymptomatic cases. False-negatives were observed in 18 patients, 3 of whom were asymptomatic and had a low viral load (cycle threshold (Ct) > 30). The detection rate of RATs was 100% when the Ct value was up to 24. The detection rate was 42.3% when the Ct was >29. The detection rate of RATs was 92.3% when the onset of symptoms was within three days. The detection rate was 33.3% when the onset of symptoms was >7 days.Conclusions: RATs for COVID-19 used in this study delivered an acceptable performance in patients with high viral load and within the first week of the onset of symptoms. They can be used as a supplementary method to RT-PCR for the diagnosis of COVID-19 patients.

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AN EPIDEMIOLOGY-CLINICAL CORRELATION OF VIRAL LOAD AS MEASURED BY CYCLE THRESHOLD VALUE BY RT-PCR IN COVID-1

10.36106/4843504 ◽

2021 ◽

pp. 1-2

Author(s):

Atrikumar P. Patel ◽

Palak Shah ◽

Pavan Acharya ◽

Monila N. Patel

Keyword(s):

Polymerase Chain Reaction ◽

Viral Load ◽

Severe Acute Respiratory Syndrome ◽

Threshold Value ◽

Clinical Correlation ◽

Rt Pcr ◽

Chain Reaction ◽

Oropharyngeal Swab ◽

Polymerase Chain ◽

Novel Coronavirus

The 2019 novel coronavirus [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] was rst documented in December 2019 in Wuhan, China, and spread across the globe resulting in [1]. signicant global morbidity and mortality Diagnosis of COVID-19 is mainly done by nasopharyngeal and oropharyngeal swab RT-PCR (Reverse transcriptase - polymerase chain reaction). Real time RT-PCR is of great interest today for detection of SARS- CoV-2 due to its benets as a specic assay.

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High SARS-CoV-2 Viral Load in Urine Sediment Correlates with Acute Kidney Injury and Poor COVID-19 Outcome

Journal of the American Society of Nephrology ◽

10.1681/asn.2021010059 ◽

2021 ◽

pp. ASN.2021010059

Author(s):

Paulo Caceres ◽

Gina Savickas ◽

Shannon Murray ◽

Kausik Umanath ◽

Junior Uduman ◽

...

Keyword(s):

Acute Kidney Injury ◽

Viral Load ◽

Severe Acute Respiratory Syndrome ◽

Medical Care ◽

Kidney Injury ◽

Viral Infectivity ◽

Viral Detection ◽

Urine Sediment ◽

Viral Receptor ◽

Qrt Pcr

BackgroundAcute kidney injury (AKI) is a complication of coronavirus disease 2019 (COVID-19) that is associated with high mortality. Despite documented kidney tropism of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there are no consistent reports of viral detection in urine or correlation with AKI or COVID-19 severity. Here we hypothesize that quantification of SARS-CoV-2 viral load in urine sediment from COVID-19 patients correlates with occurrence of AKI and mortality. MethodsSARS-CoV-2 viral load in urine sediments (U-viral load) was quantified by qRT-PCR in 52 patients with PCR-confirmed COVID-19 diagnosis, hospitalized between March 15th and June 8th, 2020. Immunolabeling of SARS-CoV-2 proteins Spike and Nucleocapsid was performed in two COVID-19 kidney biopsies and urine sediments. Viral infectivity assays were performed from 32 urine sediments. ResultsTwenty COVID-19 patients (39%) had detectable SARS-CoV-2 U-viral load, of which 17 (85%) developed AKI with an average U-viral load 4-times higher than non-AKI COVID-19 patients. U-viral load was highest (7.7-fold) within two weeks after AKI diagnosis. A higher U-viral load correlated with mortality but not with albuminuria or AKI stage. SARS-CoV-2 proteins partially colocalized with the viral receptor ACE2 in kidney biopsies in tubules and parietal cells, and in urine sediment cells. Infective SARS-CoV-2 was not detected in urine sediments. ConclusionOur results further support SARS-CoV-2 kidney tropism. A higher SARS-CoV-2 viral load in urine sediments from COVID-19 patients correlated with increased incidence of AKI and mortality. Urinary viral detection could inform medical care of COVID-19 patients with kidney injury to improve prognosis.

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Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020

Eurosurveillance ◽

10.2807/1560-7917.es.2020.25.32.2001483 ◽

2020 ◽

Vol 25 (32) ◽

Cited By ~ 43

Author(s):

Anika Singanayagam ◽

Monika Patel ◽

Andre Charlett ◽

Jamie Lopez Bernal ◽

Vanessa Saliba ◽

...

Keyword(s):

Viral Load ◽

Severe Acute Respiratory Syndrome ◽

Respiratory Tract ◽

Symptom Onset ◽

Infectious Virus ◽

Upper Respiratory Tract ◽

Threshold Values ◽

Rt Pcr ◽

Cycle Threshold ◽

Upper Respiratory

Severe acute respiratory syndrome coronavirus 2 viral load in the upper respiratory tract peaks around symptom onset and infectious virus persists for 10 days in mild-to-moderate coronavirus disease (n = 324 samples analysed). RT-PCR cycle threshold (Ct) values correlate strongly with cultivable virus. Probability of culturing virus declines to 8% in samples with Ct > 35 and to 6% 10 days after onset; it is similar in asymptomatic and symptomatic persons. Asymptomatic persons represent a source of transmissible virus.

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Is a stable positive rate of <0.1% an indication of a fresh outbreak of SARS-CoV-2 infection?

International Journal of Infection Control ◽

10.3396/ijic.v17.20927 ◽

2021 ◽

Author(s):

Alberto Boretti

Keyword(s):

Polymerase Chain Reaction ◽

Viral Load ◽

New Zealand ◽

Vulnerable Populations ◽

Healthy Population ◽

Rt Pcr ◽

Chain Reaction ◽

Positive Rate ◽

Polymerase Chain ◽

The Government

This letter gives a short analysis of the rate of positive SARS-CoV-2 tests in New Zealand and the restrictions that were implemented in response to these rates changing. Concerned about the growth of the number of positive cases of SARS-CoV-2 infection, the New Zealand government introduced stricter lockdown measures on August 16, 2020, and on August 18, 2020, it postponed elections planned for September. Growth in the number of positive cases was an artifact of the number of tests growing at a higher rate than the number of positive cases. The positive rate on August 16 was 0.05% (13 positive cases from 26,014 tests). On August 2, the positive rate was higher at 0.18% (three positive cases from 1,692 tests), despite the government considering that the virus was eradicated at this time. A better approach to this pandemic would be the development of policies based on the positive rate, not solely on positive case numbers, and to include viral load using reverse transcription polymerase chain reaction (RT-PCR) tests with an appropriate cycle threshold to properly identify infectious cases. It is also advised to protect vulnerable populations and avoid unnecessary limitations to the healthy population. The SARS-CoV-2 pandemic will last longer than several months, and the sooner life gets back to nearly normal, the better.

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Dynamics of SARS-CoV-2 Variants of Concern in Brazil, Early 2021

Frontiers in Public Health ◽

10.3389/fpubh.2021.784300 ◽

2021 ◽

Vol 9 ◽

Author(s):

José Eduardo Levi ◽

Cristina Mendes Oliveira ◽

Bianca Della Croce ◽

Paulo Telles ◽

Annelise Correa Wengerkievicz Lopes ◽

...

Keyword(s):

Immune Response ◽

Viral Load ◽

Severe Acute Respiratory Syndrome ◽

Vaccine Coverage ◽

Large Data ◽

Rt Pcr ◽

Data Set ◽

Local Factors ◽

Reverse Transcription Pcr ◽

Mean Cycle

Brazil is the country with the second-largest number of deaths due to the coronavirus disease-2019 (COVID-19). Two variants of concern (VOCs), Alpha (B.1.1.7) and Gamma (P.1), were first detected in December 2020. While Alpha expanded within an expected rate in January and February 2021, its prevalence among new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases started to decrease in March, which coincided with the explosion of Gamma variant incidence all over the country, being responsible for more than 95% of the new cases over the following months. A significantly higher viral load [i.e., mean cycle threshold (Ct) values] for Gamma in comparison to non-VOC samples was verified by the analysis of a large data set of routine reverse transcription–PCR (RT–PCR) exams. Moreover, the rate of reinfections greatly increased from March 2021 onward, reinforcing the enhanced ability of Gamma to escape the immune response. It is difficult to predict the outcomes of competition between variants since local factors like frequency of introduction and vaccine coverage play a key role. Genomic surveillance is of uttermost importance for the mitigation of the pandemic.

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Comparing The Viral Load of Severe Acute Respiratory Syndrome Coronavirus 2 in Different Human Specimens

Kurdistan Journal of Applied Research ◽

10.24017/covid.15 ◽

2020 ◽

pp. 131-145

Author(s):

Ali Hattem Hussain

Keyword(s):

Viral Load ◽

Rectal Swab ◽

Throat Swab ◽

Meta Analysis ◽

Threshold Value ◽

Load Cycle ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Load Detection ◽

Respiratory Specimens

This meta-analysis study analyzed the data of 47 recent studies with data related SARS-COV-2 viral load detection in different human specimens. 1099 patients were tested for SARS-COV-2 viral load using up to 19 different respiratory and non-respiratory specimens using RT-PCR by targeting different types of viral genes of which ORF1ab is the most commonly used target gene. 9909 specimens were taken from the patients. The mean of viral load cycle threshold value is 17.8 (±11.7), with a median of 15.95 with minimum value of 0.2 and a maximum value of 36.5. Nasopharyngeal swab has the highest positivity rate (90.5%) for viral load detection followed by Bronchoalveolar lavage, nasal swab, nasopharyngeal aspirate, throat swab and sputum. For the non-respiratory specimen, stool and rectal swab are most appropriate specimens followed by blood. The urine is not appropriate specimen for viral load detection due to very low sensitivity. The sputum was positive up to 23 days in a daily manner since start of symptoms except for the days 19, 21, and 23 that were negative for the virus. Three specimens, the nasopharyngeal swab, throat swab, and rectal swab, showed positive RT-PCR results before the appearance of COVID-19 clinical features. Possible positive results can be present up to 43 days in throat swab, stool, and rectal swab. After negative conversion of respiratory specimens, the viral shedding can continue more than one month from stool and rectal swab. The 3rd day since onset of symptoms is the most day of testing (223/2935). The highest positivity of SARS-COV-2 viral load was recorded in day 16 since the onset of symptoms.

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Severe acute respiratory syndrome coronavirus 2 viral load in respiratory and feces specimens of children with coronavirus disease 2019

Future Virology ◽

10.2217/fvl-2020-0180 ◽

2021 ◽

Author(s):

Xiang Ma ◽

Liang Su ◽

Lu Cheng ◽

Zhaohua Zhang ◽

Jing Sun ◽

...

Keyword(s):

Viral Load ◽

Severe Acute Respiratory Syndrome ◽

Respiratory Specimen ◽

Virus Load ◽

The Third ◽

Positive Rate ◽

Kinetics Of ◽

Positive Results ◽

Respiratory Specimens

Background: The viral load kinetics of children with coronavirus disease 2019 is not clear. Materials & methods: The viral load of throat, nasal and feces specimens of 10 children with coronavirus disease 2019 were detected and analyzed. Results: The virus load of nasal and throat specimen decreased extremely and all respiratory specimens tested negative on the third week after they were admitted. All children showed positive PCR results in their feces. A total of 70% children showed positive results at the fourth week and 40% children showed positive results in their feces at the fifth week. All children tested negative on the sixth week. Conclusion: The positive rate of stool in children was higher than that in adults and the shedding time of stool was longer than that of respiratory specimen.

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