Detection of SARs CoV-2 during initial phase of pandemic from population of banas kantha district of Gujarat-India with special emphasis on pooled samples

Corona virus (SARs CoV-2) has caused immense effect on morbidity and mortality of the population globally. We undertook this study as we are a part of one of the network laboratories of ICMR to test the patient’s sample by RT PCR for the ORF 1 ab gene of corona virus. : For a period of one and half months (14 April to 31 May 2020) we tested the nasopharynx and oro-pharynx swab samples sent to us in VTM from the assigned districts of Gujarat. All the samples were subjected to RT PCR method by following standard methods. Total of 9.04%(256/2833) population was positive and 4.73%(139/2833) belonged to age groups 21-40 and 2.33% (66/2833) to 41-60yrs. Above the age of 60yrs there were only 0.95% (22/2833) cases which were positive. It was advantageous to pool the samples. Out of the number of pools prepared, we reported around 80% negative and rest were positive in pools. The study also included association of viral load and infectivity. We found that 12% of the asymptomatic people and 5.1% of symptomatic individuals had high viral load. : It is seen that the incidence of Novel corona virus -19 detection by RT PCR is a reliable method and the establishment of the Ct value and infectivity of the patient to the health care workers and relatives needs to be taken care of. Also, the study presents asymptomatic patients having high viral loads being highly infective.

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Insufficient Sensitivity of RNA Dependent RNA Polymerase Gene of SARS-CoV-2 Viral Genome as Confirmatory Test using Korean COVID-19 Cases

10.20944/preprints202002.0424.v1 ◽

2020 ◽

Cited By ~ 10

Author(s):

Soyoun Kim ◽

Dong-Min Kim ◽

Baeckseung Lee

Keyword(s):

Diagnostic Methods ◽

Confirmatory Test ◽

Test Results ◽

Rt Pcr ◽

Viral Loads ◽

Asymptomatic Patients ◽

Pcr Method ◽

Who Guideline ◽

Rna Polymerase Gene ◽

Insufficient Sensitivity

Since mid-December of 2019, coronavirus disease 2019 (COVID-19) has been spreading from Wuhan, China. As of February 21, total 75,773 confirmed cases worldwide have spread to more than two dozen countries. Transmission of COVID-19 can occur early in the course of infection since SARS-CoV-2 viral loads in asymptomatic patients are similar to that in the symptomatic patients. Therefore, more sensitive diagnostic methods are needed to detect early phase of the infection to prevent secondary or tertiary spreads. Here, we compare the RT-PCR confirmatory test results using two different SARS-CoV-2 viral RNAs from two Korean COVID-19 confirmed cases.RT-PCR method targeting the RdRP gene, which was recommended by WHO guideline, was less sensitive than targeting N genes (as per CDC guideline). Because many countries follow the WHO guideline, our findings may contribute to the early diagnosis of COVID-19.

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Viral load and antibody levels in patients with COVID-19

GSC Advanced Research and Reviews ◽

10.30574/gscarr.2021.8.3.0180 ◽

2021 ◽

Vol 8 (3) ◽

pp. 010-018

Author(s):

Iva Christova ◽

Iva Trifonova ◽

Teodora Gladnishka ◽

Elena Dragusheva ◽

Georgi Popov ◽

...

Keyword(s):

Viral Load ◽

High Viral Load ◽

Igg Antibodies ◽

Rt Pcr ◽

Serum Samples ◽

Weekly Basis ◽

Specific Antibody Response ◽

Viral Loads ◽

Antibody Levels ◽

Kinetics Of

Relations between viral load, antibody levels and COVID-19 severity are not well studied and results from such investigations are controversial. In this study, we investigated kinetics of viral load and antibody responses to SARS-CoV-2 in 20 patients with COVID-19 and analysed the association with disease severity. The patients were followed on weekly basis within the first month after the onset and then once per month for the next 4 months. Serum samples were tested for IgA, IgM, and IgG antibodies against SARS-CoV-2 using ELISA tests. SARS-CoV-2 viral load in nasopharyngeal swabs was measured by quantitative Realtime RT-PCR. For vast majority of the patients, the viral loads were at their highest levels at presentation and then declined gradually. Despite development of specific antibody response 7-11 days after the onset of COVID-19, SARS-CoV-2 RNA was still detected in nasopharyngeal swabs of most of the patients. There was no direct link between viral load and severity of COVID-19: some of mild and some of severe cases started with a high viral load. There was a relationship between the time from the onset of the disease and the viral load: the highest viral load was in the first days. In more severe cases, there was a tendency for slower reduction in viral load and longer detection of SARS-CoV-2 virus. Levels of the specific antibodies increased earlier and to higher levels and were present for longer time in patients with more severe manifestations of COVID-19 than in those with milder disease.

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Evaluation of the SARS-CoV-2 positivity ratio and upper respiratory tract viral load among asymptomatic individuals screened before hospitalization or surgery in Flanders, Belgium

PLoS ONE ◽

10.1371/journal.pone.0259908 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0259908

Author(s):

Laura Heireman ◽

Steven Abrams ◽

Peggy Bruynseels ◽

Reinoud Cartuyvels ◽

Lize Cuypers ◽

...

Keyword(s):

Viral Load ◽

Respiratory Tract ◽

Age Group ◽

Test Results ◽

Rt Pcr ◽

Median Viral Load ◽

Viral Loads ◽

Asymptomatic Patients ◽

Positivity Ratio ◽

Second Wave

Introduction The incidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections in the Belgian community is mainly estimated based on test results of patients with coronavirus disease (COVID-19)-like symptoms. The aim of this study was to investigate the evolution of the SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) positivity ratio and distribution of viral loads within a cohort of asymptomatic patients screened prior hospitalization or surgery, stratified by age category. Materials/Methods We retrospectively studied data on SARS-CoV-2 real-time RT-PCR detection in respiratory tract samples of asymptomatic patients screened pre-hospitalization or pre-surgery in nine Belgian hospitals located in Flanders over a 12-month period (1 April 2020–31 March 2021). Results In total, 255925 SARS-CoV-2 RT-PCR test results and 2421 positive results for which a viral load was reported, were included in this study. An unweighted overall SARS-CoV-2 real-time RT-PCR positivity ratio of 1.27% was observed with strong spatiotemporal differences. SARS-CoV-2 circulated predominantly in 80+ year old individuals across all time periods except between the first and second COVID-19 wave and in 20–30 year old individuals before the second COVID-19 wave. In contrast to the first wave, a significantly higher positivity ratio was observed for the 20–40 age group in addition to the 80+ age group compared to the other age groups during the second wave. The median viral load follows a similar temporal evolution as the positivity rate with an increase ahead of the second wave and highest viral loads observed for 80+ year old individuals. Conclusion There was a high SARS-CoV-2 circulation among asymptomatic patients with a predominance and highest viral loads observed in the elderly. Moreover, ahead of the second COVID-19 wave an increase in median viral load was noted with the highest overall positivity ratio observed in 20–30 year old individuals, indicating they could have been the hidden drivers of this wave.

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Relationships between Viral Load and the Clinical Course of COVID-19

Viruses ◽

10.3390/v13020304 ◽

2021 ◽

Vol 13 (2) ◽

pp. 304

Author(s):

Hiroyuki Tsukagoshi ◽

Daisuke Shinoda ◽

Mariko Saito ◽

Kaori Okayama ◽

Mitsuru Sada ◽

...

Keyword(s):

Viral Load ◽

Early Stage ◽

Fatal Case ◽

Epidemiological Data ◽

High Viral Load ◽

Viral Loads ◽

Severe Stage ◽

Asymptomatic Patients ◽

Positive Rate

To predict the clinical outcome of coronavirus disease-2019 (COVID-19), we examined relationships among epidemiological data, viral load, and disease severity. We examined viral loads of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) in fatal (15 cases), symptomatic/survived (133 cases), and asymptomatic cases (138 cases) using reverse transcription quantitative real-time PCR (RT-qPCR). We examined 5768 nasopharyngeal swabs (NPS) and attempted to detect the SARS-CoV-2 genome using RT-qPCR. Among them, the viral genome was detected using the method for the 370 NPS samples with a positive rate of 6.4%. A comparison of each age showed that the fatal case was higher than the survived case and asymptomatic patients. Survived cases were older than asymptomatic patients. Notably, the viral load in the fatal cases was significantly higher than in symptomatic or asymptomatic cases (p < 0.05). These results suggested that a high viral load of the SARS-CoV-2 in elderly patients at an early stage of the disease results in a poor outcome. We should, therefore, intervene early to prevent a severe stage of the disease in such cases.

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Pooled Saliva Specimens for SARS-CoV-2 Testing

Journal of Clinical Microbiology ◽

10.1128/jcm.02486-20 ◽

2020 ◽

Author(s):

Bidisha Barat ◽

Sanchita Das ◽

Valeria De Giorgi ◽

David K. Henderson ◽

Stacy Kopka ◽

...

Keyword(s):

Viral Load ◽

Screening Program ◽

High Viral Load ◽

Load Cycle ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Viral Loads ◽

Viral Transport ◽

Average Loss ◽

Positive Agreement

We evaluated saliva (SAL) specimens for SARS-CoV-2 RT-PCR testing by comparison of 459 prospectively paired nasopharyngeal (NP) or mid-turbinate (MT) swabs from 449 individuals with the aim of using saliva for asymptomatic screening. Samples were collected in a drive-through car line for symptomatic individuals (N=380) and in the emergency department (ED) (N=69). The percent positive and negative agreement of saliva compared to nasopharyngeal swab were 81.1% (95% CI: 65.8% – 90.5%) and 99.8% (95% CI: 98.7% – 100%), respectively. The percent positive agreement increased to 90.0% (95% CI: 74.4% – 96.5%) when considering only samples with moderate to high viral load (Cycle threshold (Ct) for the NP <=34). Pools of five saliva specimens were also evaluated on three platforms: bioMérieux NucliSENS easyMAG with ABI 7500Fast (CDC assay), Hologic Panther Fusion®, and Roche COBAS® 6800. The average loss of signal upon pooling was 2-3 Ct values across the platforms. The sensitivity of detecting a positive specimen in a pool compared with testing individually was 94%, 90%, and 94% for CDC 2019-nCoV Real-Time RT-PCR, Panther Fusion® SARS-CoV-2 assay, and cobas® SARS-CoV-2 test respectively, with decreased sample detection trending with lower viral load. We conclude that although pooled saliva testing, as collected in this study, is not quite as sensitive as NP/MT testing, saliva testing is adequate to detect individuals with higher viral loads in an asymptomatic screening program, does not require swabs or viral transport media for collection, and may help to improve voluntary screening compliance for those individuals averse to various forms of nasal collections.

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Pooled Saliva Specimens for SARS-CoV-2 Testing

10.1101/2020.10.02.20204859 ◽

2020 ◽

Author(s):

Bidisha Barat ◽

Sanchita Das ◽

Valeria De Giorgi ◽

David K. Henderson ◽

Stacy Kopka ◽

...

Keyword(s):

Viral Load ◽

Screening Program ◽

High Viral Load ◽

Load Cycle ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Lower Viral Load ◽

Viral Loads ◽

Viral Transport ◽

Positive Specimen

AbstractWe evaluated saliva (SAL) specimens for SARS-CoV-2 RT-PCR testing by comparison of 459 prospectively paired nasopharyngeal (NP) or mid-turbinate (MT) swabs from 449 individuals with the aim of using saliva for asymptomatic screening. Samples were collected in a drive-through car line for symptomatic individuals (N=380) and in the emergency department (ED) (N=69). The percent positive and negative agreement of saliva compared to nasopharyngeal swab were 81.1% (95% CI: 65.8% – 90.5%) and 99.8% (95% CI: 98.7% – 100%), respectively. The sensitivity increased to 90.0% (95% CI: 74.4% – 96.5%) when considering only samples with moderate to high viral load (Cycle threshold (Ct) for the NP <=34). Pools of five saliva specimens were also evaluated on three platforms: bioMérieux NucliSENS easyMAG with ABI 7500Fast (CDC assay), Hologic Panther Fusion, and Roche COBAS 6800. The median loss of signal upon pooling was 2-4 Ct values across the platforms. The sensitivity of detecting a positive specimen in a pool compared with testing individually was 100%, 93%, and 95% for CDC 2019-nCoV Real-Time RT-PCR, Panther Fusion® SARS-CoV-2 assay, and cobas® SARS-CoV-2 test respectively, with decreased sample detection trending with lower viral load. We conclude that although pooled saliva testing, as collected in this study, is not quite as sensitive as NP/MT testing, saliva testing is adequate to detect individuals with higher viral loads in an asymptomatic screening program, does not require swabs or viral transport media for collection, and may help to improve voluntary screening compliance for those individuals averse to various forms of nasal collections.

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An analysis of SARS-CoV-2 viral load by patient age

10.1101/2020.06.08.20125484 ◽

2020 ◽

Cited By ~ 66

Author(s):

Terry C. Jones ◽

Barbara Mühlemann ◽

Talitha Veith ◽

Guido Biele ◽

Marta Zuchowski ◽

...

Keyword(s):

Viral Load ◽

Old Age ◽

Small Difference ◽

Age Groups ◽

Rt Pcr ◽

Aged Patients ◽

Patient Age ◽

Infected People ◽

Viral Loads ◽

Patient Âgé

AbstractAs children are under-represented in current studies aiming to analyse transmission of SARS-coronavirus 2 (SARS-CoV-2), their contribution to transmission is unclear. Viral load, as measured by RT-PCR, can inform considerations regarding transmission, especially if existing knowledge of viral load in other respiratory diseases is taken into account. RT-PCR threshold cycle data from 3303 patients who tested positive for SARS-CoV-2 (out of 77,996 persons tested in total, drawn from across Germany) were analysed to examine the relationship between patient age and estimated viral load. Two PCR systems were used. In data from the PCR system predominantly used for community and cluster screening during the early phase of the epidemic (Roche LightCycler 480 II), when such screening was frequent practice, viral loads do not differ significantly in three comparisons between young and old age groups (differences in log10 viral loads between young and old estimated from raw viral load data and a Bayesian mixture model of gamma distributions collectively range between −0.11 and −0.43). Data from a second type of PCR system (Roche cobas 6800/8800), introduced into diagnostic testing on March 16, 2020 and used during the time when household and other contact testing was reduced, show a credible but small difference in the three comparisons between young and old age groups (differences, measured as above, collectively range between −0.43 and −0.83). This small difference may be due to differential patterns of PCR instrument utilization rather than to an actual difference in viral load. Considering household transmission data on influenza, which has a similar viral load kinetic to SARS-CoV-2, the viral load differences between age groups observed in this study are likely to be of limited relevance. Combined data from both PCR instruments show that viral loads of at least 250,000 copies, a threshold we previously established for the isolation of infectious virus in cell culture at more than 5% probability, were present across the study period in 29.0% of kindergarten-aged patients 0-6 years old (n=38), 37.3% of those aged 0-19 (n=150), and in 51.4% of those aged 20 and above (n=3153). The differences in these fractions may also be due to differences in test utilization. We conclude that a considerable percentage of infected people in all age groups, including those who are pre- or mild-symptomatic, carry viral loads likely to represent infectivity. Based on these results and uncertainty about the remaining incidence, we recommend caution and careful monitoring during gradual lifting of non-pharmaceutical interventions. In particular, there is little evidence from the present study to support suggestions that children may not be as infectious as adults.

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Clinical importance of reporting SARS-CoV-2 viral loads across the different stages of the COVID-19 pandemic

10.1101/2020.07.10.20149773 ◽

2020 ◽

Author(s):

Milo Moraz ◽

Damien Jacot ◽

Matthaios Papadimitriou-Olivgeris ◽

Laurence Senn ◽

Gilbert Greub ◽

...

Keyword(s):

Viral Load ◽

Universal Screening ◽

Clinical Importance ◽

Screening Strategy ◽

Rt Pcr ◽

Chain Reaction ◽

Viral Loads ◽

Asymptomatic Patients ◽

Admission Screening ◽

Polymerase Chain

On April 25th, corresponding to the first deconfinement phase after the end of the lockdown in Switzerland, a universal admission screening strategy for COVID-19 was introduced in our hospital. All patients, including asymptomatic patients were tested for SARS-CoV-2 by quantitative reverse transcription polymerase chain reaction (RT-PCR). In addition to a qualitative answer, providing viral load values to the RT-PCR results not only helped the clinician to evaluate the stage of the infection but addressed patient contagiousness and guided infection control decisions. Here, we discuss the importance of reporting viral load values when a shift from a symptomatic to a universal screening strategy was performed.

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

BMC Infectious Diseases ◽

10.1186/s12879-021-06591-w ◽

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.

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Corona Virus (COVID-19) Awareness Assessment - A Survey Study Amongst the Indian Population

Journal of Clinical and Medical Research ◽

10.37191/mapsci-2582-4333-2(3)-041 ◽

2020 ◽

Author(s):

Gabriela Fernandes

Keyword(s):

Health Care ◽

Social Media ◽

Health Care Workers ◽

Indian Population ◽

Age Groups ◽

Survey Study ◽

Social Distancing ◽

Corona Virus ◽

Care Workers ◽

Amount Of Knowledge

Aim: The aim of this survey study was to assess the level of awareness amongst Indian population regarding the COVID-19. Method: A survey was conducted amongst 745 individuals to assess their level of awareness regarding COVID-19 and steps to be taken for its prevention. Result: The results revealed that a considerable percentage of individuals learned about the pandemic through social media and news and were aware of the mode of spread of the virus and also steps to be taken to prevent it from spreading. But considerable percentage of people was also not fully aware regarding the age groups this virus will be affecting. Conclusion: Upon understanding the percentage of people not aware about the age groups this virus will be affecting, keeping in mind good amount of knowledge amongst individuals about maintaining hygiene and social distancing, this survey would help the health care workers to create awareness regarding the effect of this virus on different age groups to help prevent carelessness amongst youth in following the regime.

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