RT-PCR Screening Tests for SARS-CoV-2 with Saliva Samples in Asymptomatic People: Strategy to Maintain Social and Economic Activities while Reducing the Risk of Spreading the Virus

The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to a succession of epidemic waves. It thus appears that monitoring the presence of SARS-CoV-2 in wastewater alone is insufficient, and it may be important in the future to also monitor the evolution of these variants. We used a real-time RT-PCR screening test for variants in the wastewater of our city to assess the effectiveness of direct SARS-CoV-2 sequencing from the same wastewater. We compared the genome sequencing results obtained over the large RS network and the smaller B7 network with the different distributions of the variants observed by RT-PCR screening. The prevalence of the “UK variant” in the RS and B7 networks was estimated to be 70% and 8% using RT-PCR screening compared to 95% and 64% using genome sequencing, respectively. The latter values were close to the epidemiology observed in patients of the corresponding area, which were 91% and 58%, respectively. Genome sequencing in sewage identified SARS-CoV-2 of lineage B.1.525 in B7 at 27% (37% in patients), whereas it was completely missed by RT-PCR. We thus determined that direct sequencing makes it possible to observe, in wastewater, a distribution of the variants comparable to that revealed by genomic monitoring in patients and that this method is more accurate than RT-PCR. It also shows that, rather than a single large sample, it would be preferable to analyse several targeted samples if we want to more appropriately assess the geographical distribution of the different variants. In conclusion, this work supports the wider surveillance of SARS-CoV-2 variants in wastewater by genome sequencing and targeting small areas on the condition of having a sequencing capacity and, when this is not the case, to developing more precise screening tests based on the multiplexed detection of the mutations of interest.

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Surveillance testing for SARS-COV-2 infection in an asymptomatic athlete population: a prospective cohort study with 123 362 tests and 23 463 paired RT-PCR/antigen samples

BMJ Open Sport & Exercise Medicine ◽

10.1136/bmjsem-2021-001137 ◽

2021 ◽

Vol 7 (2) ◽

pp. e001137

Author(s):

Kimberly Harmon ◽

Anabelle M de St Maurice ◽

Adam C Brady ◽

Sankar Swaminathan ◽

Doug F Aukerman ◽

...

Keyword(s):

Screening Programme ◽

Sports Participation ◽

High Specificity ◽

Turnaround Time ◽

Screening Tests ◽

Rt Pcr ◽

Pcr Screening ◽

Testing Approach ◽

Antigen Tests ◽

Antigen Testing

ObjectiveTo assess the diagnostic accuracy of antigen compared with reverse transcriptase (RT)-PCR testing in an asymptomatic athlete screening programme and to monitor infection in college athletes.MethodsQuidel Sofia-2 SARS-CoV-2 Antigen Tests were performed daily before sports participation for football, basketball, wrestling and water polo from 29 September 2020 to 28 February 2021. Paired RT-PCR and antigen tests were performed at least once a week. Positive antigen tests were confirmed with RT-PCR.Results81 175 antigen and 42 187 RT-PCR tests were performed, including 23 462 weekly paired antigen/RT-PCR screening tests in 1931 athletes. One hundred and seventy-two athletes had a positive screening RT-PCR (0.4%), of which 83 (48%) occurred on paired testing days. The sensitivity of antigen tests varied with the frequency of RT-PCR testing and prevalence of COVID-19. The sensitivity of antigen testing was 35.7% (95% CI: 17% to 60%) and specificity 99.8% (95% CI: 99.7% to 99.9%) with once-a-week RT-PCR testing after adjusting for school prevalence. Daily antigen testing was similar to RT-PCR testing two to three times a week in identifying infection. Antigen testing identified infection before the next scheduled PCR on 89 occasions and resulted in 234 days where potentially infectious athletes were isolated before they would have been isolated with RT-PCR testing alone. Two athletic-related outbreaks occurred; 86% of total infections were community acquired.ConclusionAntigen testing has high specificity with a short turnaround time but is not as sensitive as RT-PCR. Daily antigen testing or RT-PCR testing two to three times a week is similar. There are benefits and drawbacks to each testing approach.

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Microarray and RT-PCR screening for white spot syndrome virus immediate-early genes in cycloheximide-treated shrimp

Virology ◽

10.1016/j.virol.2005.01.047 ◽

2005 ◽

Vol 334 (2) ◽

pp. 327-341 ◽

Cited By ~ 101

Author(s):

Wang-Jing Liu ◽

Yun-Shiang Chang ◽

Chung-Hsiung Wang ◽

Guang-Hsiung Kou ◽

Chu-Fang Lo

Keyword(s):

White Spot Syndrome Virus ◽

Immediate Early Genes ◽

Immediate Early ◽

White Spot ◽

Rt Pcr ◽

Pcr Screening ◽

Early Genes ◽

White Spot Syndrome

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Cytochrome P450 Isoform Expression in Human Vascular Endothelial Cells

Hypertension ◽

10.1161/hyp.36.suppl_1.698-a ◽

2000 ◽

Vol 36 (suppl_1) ◽

pp. 698-698

Author(s):

Eduardo Barbosa-Sicard ◽

Eva Kaergel ◽

Dominik N Muller ◽

Horst Honeck ◽

Friedrich C Luft ◽

...

Keyword(s):

Endothelial Cells ◽

Arachidonic Acid ◽

Cytochrome P450 ◽

Vascular Endothelial Cells ◽

Arachidonic Acid Metabolism ◽

Vascular Endothelial ◽

Rt Pcr ◽

Pcr Screening ◽

Mediators Of Inflammation ◽

Derivatives Of

P29 Epoxy derivatives of arachidonic acid may act as important autocrine and paracrine mediators of endothelial function including regulation of vascular tone and control of inflammation. To identify potential candidates for catalyzing the synthesis of these and further arachidonic acid metabolites, we studied human vascular endothelial cells for the expression of individual cytochrome P450 isoforms belonging to the CYP families 1, 2, 3 and 4. An RT-PCR screening performed with subfamily- and isoform-specific primer pairs revealed mRNAs for the P450 forms 1A1, 1B1, 2C8, 2E1, 2J2, 3A7, 4A11 and 4F2. The identity of the RT-PCR products was confirmed by DNA sequencing. In addition, P450 1A2 mRNA was detected after induction with β-naphthoflavone which also enhanced the expresion of P450s 1A1 and 1B1. P450s 2B6 and 3A4 were not detectable. Similar P450 isoform patterns were obtained analyzing primary human endothelial cells originating from aorta, coronary arteries, dermal microvessels and umbilical veins, as well as an immortalized human endothelial cell line (HMEC-1). Further studies with HMEC-1 cells showed the expression of all human members of the P450 2C subfamily (2C8, 2C9, 2C18 and 2C19). We next used gaschromatography-mass spectrometry to identify the regioisomeric epoxeicosatrienoic acids produced by HMEC-1 cells. Among the P450 forms detected by the RT-PCR screening, P450 2C8 and 2J2 are the leading candidates for producing vasoactive epoxyeicosatrienoic acids. Using recombinant human P450 1A1, we then found that this P450 form catalyzes the formation of various regioisomeric hydroxy derivatives of arachidonic acid. We conclude that P450 1A1 known primarily for its role in polycyclic aromatic hydrocarbon metabolism, may interfere with endothelial arachidonic acid metabolism, particularly after its induction by drugs and xenobiotics. Furthermore, P450s 4A11 and 4F2 probably contribute to the degradation of lipid mediators of inflammation.

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Rapid Point-Of-Care Serology and Clinical History Assessment Increase Protection Provided by RT-PCR Screening: A Pilot Study Involving Three Nursing Homes in Brescia, a Hotspot of Lombardy

Frontiers in Public Health ◽

10.3389/fpubh.2021.649524 ◽

2021 ◽

Vol 9 ◽

Author(s):

Antonella Savio ◽

Stefano Calza ◽

Gianbattista Guerrini ◽

Valentina Romano ◽

Eleonora Marchina

Keyword(s):

Nursing Homes ◽

Close Contact ◽

Fisher Exact Test ◽

Rt Pcr ◽

Positive Serology ◽

Serological Screening ◽

Pcr Screening ◽

Exact Test ◽

Viral Spread

Background: COVID-19 outbursts have been registered worldwide within care homes with asymptomatic transmission combined with shortage/inaccuracy of diagnostic tests undermining the efforts at containment of the disease. Nursing facilities in Lombardy (Italy) were left with no, or limited, access to testing for 8 weeks after the outbreak of COVID-19.Methods: This study includes 246 residents and 286 workers of three different nursing homes in Brescia-Lombardy. Clinical questionnaires and rapid serology tests were devised to integrate the data of the first available RT-PCR screening. Follow-up serology after 60-days was performed on 67 of 86 workers with positive serology or clinically suspicious.Findings: Thirty-seven residents and 18 workers had previous positive RT-PCR. Thorough screening disclosed two additional RT-PCR-positive workers. Serology screening revealed antibodies in 59 residents and 48 workers, including 32/37 residents and all workers previously positive at RT-PCR. Follow up serology disclosed antibodies in two additional workers with recent symptoms at the time of screening. The professionals in close contact with residents had more infections (47/226–20.79% vs. 1/60–1.66%; p = 0.00013 Fisher exact-test). A suspicious clinical score was present in 44/64 residents and in 41/50 workers who tested positive with either method with totally asymptomatic disease more frequent among residents 28.1 vs. 10.0% (p = 0.019 Fisher exact-test).Interpretation: Based on the available RT-PCR ± results at the time of symptoms/contacts, our integrated clinical and serological screening demonstrated sensitivity 89% and specificity 87%. This multimodal assessment proved extremely useful in understanding the viral spread in nursing homes, in defining its stage and in implementing protective measures. Rapid serology tests demonstrated efficient and particularly suited for older people less able to move/cooperate.

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A rapid RT-PCR screening assay incorporating multiplexed validated control genes for CBF rearrangements at diagnosis in AML

Pathology ◽

10.1080/0031302042000224593 ◽

2004 ◽

Vol 36 (4) ◽

pp. 335-342

Author(s):

Russell J. Saal ◽

Paula V. Marlton ◽

Georgina Timson ◽

Devinder S. Gill ◽

Marcus Waugh ◽

...

Keyword(s):

Rt Pcr ◽

Screening Assay ◽

Pcr Screening

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Impact of the COVID-19 epidemic at a high-volume facility in gynecological oncology in Tokyo, Japan: a single-center experience

Journal of Ovarian Research ◽

10.1186/s13048-020-00711-x ◽

2020 ◽

Vol 13 (1) ◽

Cited By ~ 1

Author(s):

Yuya Nogami ◽

Yusuke Kobayashi ◽

Kosuke Tsuji ◽

Megumi Yokota ◽

Hiroshi Nishio ◽

...

Keyword(s):

Infectious Disease ◽

Ovarian Cancer ◽

Clinical Decision Making ◽

High Volume ◽

Treatment Delay ◽

Emerging Infectious Disease ◽

Ovarian Tumors ◽

Screening Tests ◽

Rt Pcr ◽

First Case

Abstract Background The number of cases of novel coronavirus disease 2019 (COVID-19) in Japan have risen since the first case was reported on January 24, 2020, and 6225 infections have been reported as of June 30, 2020. On April 8, 2020, our hospital began screening patients via pre-admission reverse transcriptase-polymerase chain reaction (RT-PCR) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and chest computed tomography (CT). Although no patients exhibited apparent pneumonia, treatment delay or changes in treatment plans were required for a few patients based on the results of screening tests. During an emerging infectious disease pandemic, the likelihood of being infected, as well as the disease itself, affects clinical decision making in several ways. We summarized and presented our experience. Case presentation After the introduction of pre-admission screening, RT-PCR and CT were performed in 200 and 76 patients, respectively, as of June 30, 2020. The treatment of five patients, including two patients with cervical cancer, two patients with ovarian tumors, and one patient with ovarian cancer, was affected by the results. Two asymptomatic RT-PCR-positive patients did not develop COVID-19, but their treatment was delayed until the confirmation of negative results. The other three patients were RT-PCR-negative, but abnormal CT findings suggested the possibility of COVID-19, which delayed treatment. The patients receiving first-line preoperative chemotherapy for ovarian cancer had clinically evident exacerbations because of the treatment delay. Conclusion During the epidemic phase of an emerging infectious disease, we found that COVID-19 has several other effects besides its incidence. The postponing treatment was the most common, therefore, treatment of ovarian tumors and ovarian cancer was considered to be the most likely to be affected among gynecological diseases. Protocols that allow for easy over-diagnosis can be disadvantageous, mainly because of treatment delays, and therefore, the protocols must be developed in light of the local infection situation.

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An Evidence-Based Approach to Plum Pox Virus Detection by DASI-ELISA and RT-PCR in Dormant Period

Virology Research and Treatment ◽

10.4137/vrt.s495 ◽

2008 ◽

Vol 1 ◽

pp. VRT.S495 ◽

Cited By ~ 1

Author(s):

Antonio Olmos ◽

Edson Bertolini ◽

Nieves Capote ◽

Mariano Cambra

Keyword(s):

Virus Detection ◽

Screening Tests ◽

Plum Pox Virus ◽

Evidence Based ◽

Rt Pcr ◽

Likelihood Ratios ◽

Dormant Period ◽

Plant Materials ◽

Calculation Of Parameters ◽

Post Test

An evidence-based approach, such as those developed in clinical and veterinary medicine, was applied to the detection of Plum pox virus (PPV) during the dormant period. A standardized methodology was used for the calculation of parameters of the operational capacity of DASI-ELISA and RT-PCR in wintertime. These methods are routinely handled to test the sanitary status of plants in national or international trading and in those cases concerning export-import of plant materials. Diagnosis often has to be performed during the dormant period, when plant material is commercialized. Some guidelines to interpret diagnostic results of wintertime are provided in an attempt to minimize risks associated with the methods and over-reliance on the binary outcome of a single assay. In order to evaluate if a complementary test increased the confidence of PPV diagnosis when discordant results between DASI-ELISA and RT-PCR are obtained, NASBA-FH also was included. Likelihood ratios of each method were estimated based on the sensitivity and specificity obtained in wintertime. Subsequently, a Bayesian approach was performed to calculate post-test probability of PPV infection in spring. Results of evidence-based approach show that different PPV prevalences require different screening tests. Thus, at very low PPV prevalence levels DASI-ELISA should be used as the election method, whilst at the highest PPV prevalence levels RT-PCR should be performed. NASBA-FH could be used at medium prevalences to clarify discordances between DASI-ELISA and RT-PCR.

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Factors Affecting SARS-CoV-2 (COVID-19) Pandemic, including Zoonotic, Human Transmission and Chain of Infection. Reducing Public Health Risk by Serum Antibody Testing, Avoiding Screening in Unhygienic Places and False PCR Reporting. A Scientific Review

10.20944/preprints202006.0284.v1 ◽

2020 ◽

Author(s):

Kamran Mahmood Ahmed Aziz ◽

Abdullah Othman ◽

Waleed Alqahtani ◽

Sumaiya Azhar

Keyword(s):

High Risk ◽

Infection Control ◽

False Positive ◽

Serum Antibody ◽

Screening Tests ◽

Current Evidence ◽

Rt Pcr ◽

Antibody Testing ◽

Term Survival ◽

Live Virus

Since December 2019, a rapid increase in the number of SARS-CoV-2 (COVID-19) cases was reported worldwide, despite strict infection control and lock down measures. Current paper investigated the actual facts behind this rapid increase in the number of cases. Study of genomic sequence reveals that domestic and wild animals were likely ancestors and zoonotic source for SARS-CoVs, MERS-CoVs, and SARS-CoV-2. Strong evidence suggest that these viruses already existed and replicated in animals and humans during past several decades, exhibiting diverse mutations, evolutions and self-limiting diseases, except during outbreaks. Serious zoonotic reservoir investigations are required to investigate animal transmission of SARS-CoVs and SARS-CoV-2 to limit current pandemic. This might be the reason of increasing number of cases via animals. SARS-CoV-2 has been retrospectively isolated in different studies in August 2019, several months before Wuhan announced. Hence, there is a possibility that viruses existed, went undetected, infecting subclinically, in past several years, and SARS-CoV-2 antigens and neutralizing antibodies may have been present in humans since long time. This might be another reason of increasing number of cases by screening as mass screening and antigen or antibody testing was not carried out in the past years. Randomized controlled trials are required to investigate human to human transmission by touch, as the current evidence is limited with conflicting results. As all SARS-CoVs are basically respiratory viruses, droplet precautions and infection control measures are essential, especially for hospital staff. Increased number of SARS-CoV-2 asymptomatic, or subclinical cases are detected worldwide. This silent phase of transmission can be beneficial for humans. Lack of symptoms eventually lessen virus transmission and reduce the pathogen's long-term survival and provide humoral herd immunity up to several years. Hence, seropositivity with diverse antibodies develops against mutating SARS-CoVs which will confer strong immunity during epidemics. Strategies such as identification, contact tracing and quarantine are costly and practically difficult. Hence, asymptomatic persons can continue their work with droplet precautions and standard infection control procedures, while symptomatic or sick persons can isolate themselves in their homes without the need for strict quarantine until clinical recovery, with reduced hospital visits and minimizing chances of hospital acquired infections. RT-PCR has low sensitivity and specificity, carries a high risk of handling live virus antigens, and requires difficult protocols. As viral load also sharply declines after few days of onset of infection, this technique might overlook infection. Furthermore, SARS-CoV-2 infection may be present in blood when oropharyngeal swabs are negative by RT-PCR. Additionally, RT-PCR usually gives false negative and false positive results and must be interpreted cautiously. This might be again a reason of increasing number of cases by false positive RT-PCR reporting. Moreover, antibodies against SARS-CoVs develop robustly in serum even by reduced amount of antigens. In contrast to RT-PCR, ELISA for diagnosing antibodies against SARS-CoV-2 demonstrates 100% specificity and 100% sensitivity, even in clinically asymptomatic individuals. These antibodies can be used for serologic surveys, monitoring and screening. However, screening tests for SARS-COV-2 should be avoided in unhygienic public places by nasopharyngeal swabs, which carry a high risk of further transmission, co-infection or superinfection. Such highly infectious virus must be isolated and tested in highly sterilized laboratory. Further strict international laws and policies are required to stop the possible spread of experimental viruses, biological warfare and bioterrorism.

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Natural History of Post-Allogeneic HSCT EBV-Reactivation: A Single Center Retrospective Survey.

Blood ◽

10.1182/blood.v106.11.3232.3232 ◽

2005 ◽

Vol 106 (11) ◽

pp. 3232-3232

Author(s):

Helene M. Schoemans ◽

Koen Theunissen ◽

Marc Boogaerts ◽

Johan Maertens

Keyword(s):

Opportunistic Infections ◽

Screening Tests ◽

Rt Pcr ◽

Post Transplantation ◽

Hematopoietic Stem ◽

Allogeneic Hsct ◽

Ebv Reactivation ◽

Number Of Patients ◽

Significant Difference

Abstract Epstein Barr Virus (EBV) reactivation occurs in about 50% of the allogeneic hematopoietic stem cell transplantation (HSCT) population in the first year post-transplantation. About 1-7% of these patients run the risk of developing a post-transplant lymphoproliferative disorder (PTLD). Several authors have thus advocated systematic screening by EBV real time PCR (RT-PCR) to initiate pre-emptive treatment of reactivations using Rituximab (van Esser 2002). However, the positive predictive value of EBV RT-PCR is only of 40% (van Esser 2001), implying that this algorithm overtreats a number of patients. Methods: We have retrospectively analyzed 60 consecutive allogeneic HSCT patients transplanted in our center between 1/1/2004 and 31/3/2005. Four patients were excluded because of absence of EBV follow-up (n=2) or autologous reconstitution (n=2). EBV reactivation (EBV (+)) was defined by at least two consecutive episodes of EBV RT-PCR above 1000 copies/ml of whole blood. Any other result was considered as negative (EBV (−)). Results: 1175 EBV RT-PCR samples were collected over a median follow up of 215 days (range: 21–511). The population observed was essentially adults (median age 42 years, range: 1–65) with leukemia (29 leukemia, 11 lymphomas, 16 other diseases), mixed graft types (26 matched sibling donors, 26 matched unrelated donors, 4 haploidentical donors; 77% peripheral blood stem cells; 20% CD34+ selection) and mixed conditioning (52% non-myeloablative conditioning containing ATG, and 48% full conditioning). The EBV(+) and EBV(−) cohorts were similar for all characteristics analyzed. We observed a median of 18 EBV RT-PCR per patient (range: 4–105), with a median interval between two tests of 7 days (range: 3–45). There were 30 true reactivations, 2 intermittent reactivations (non consecutive EBV titer rises above threshold), 8 isolated reactivations and 16 patients with no reactivation episode. EBV RT-PCR was first performed at a median of 6 days post HSCT (range: 0–245), and reactivation was noted at a median of 44 days post HSCT (range: 6–375). There were no significant difference in PCR follow up (first day of screening, median test interval and length of biological follow up) except for the total number of screening tests per patient, which was higher in the EBV(+) group (p= 0.01). There was only one case of biopsy-proven PTLD in the EBV(+) cohort. No patient was administered Rituximab post- HSCT. Survival curves of the two cohorts were similar regardless of EBV reactivation (log-rank, p= 0.201). Discussion: The incidence of EBV reactivation (n= 30; 54%) and of PTLD (n=1;1.7%) were standard compared to previous studies, resulting in a standard specificity of 47% for EBV screening. However, within our limited group of patients, we could not show any significant differences in mortality between the EBV(+) and EBV (−) cohorts. Therefore, absence of preventive treatment for EBV reactivation did not result in an increase in mortality in our EBV reactivating cohort. This suggests that systematic prophylactic use of Rituximab may not affect overall mortality, whilst potentially increasing the risk of other opportunistic infections. Conclusion: Further prospective studies are needed to better define the patients at risk for developing EBV-related PTLD, within the EBV reactivating allogeneic transplant patients group, before prophylactic treatment of reactivation becomes a routine procedure.

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