No SARS-CoV-2 detection in the German CAPNETZ cohort of community acquired pneumonia before COVID-19 peak in March 2020

Abstract Purpose The first SARS-CoV-2 cases in Europe were reported in January 2020. Recently, concern arose on unrecognized infections before this date. For a better understanding of the pandemic, we retrospectively analyzed patient samples for SARS-CoV-2 from the prospective CAPNETZ study cohort. Methods We used nasopharyngeal swab samples from a cohort of well characterized patients with community acquired pneumonia of the CAPNETZ study group, recruited from different geographic regions across Germany, Austria, the Netherlands, and Switzerland between 02nd December 2019 and 28th April 2020. Multiplex real-time RT-PCR for a broad range of respiratory pathogens and SARS-CoV-2 real-time RT-PCR were performed on all samples. Results In our cohort, respiratory pathogens other than SARS-CoV-2 were detected in 21.5% (42/195) of patients with rhinovirus as the most frequently detected pathogen. The detection rate increased to 29.7% (58/195) when SARS-CoV-2 was included. No SARS-CoV-2 positive sample was detected before end of March 2020. Conclusions Respiratory viral pathogens accounted for a considerable number of positive results but no SARS-CoV-2 case was identified before the end of March 2020.

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First Report of Hepatitis E Virus in Shellfish in Southeast Italy

Applied Sciences ◽

10.3390/app11010043 ◽

2020 ◽

Vol 11 (1) ◽

pp. 43

Author(s):

Gianfranco La Bella ◽

Maria Grazia Basanisi ◽

Gaia Nobili ◽

Valentina Terio ◽

Elisabetta Suffredini ◽

...

Keyword(s):

Real Time ◽

Hepatitis E Virus ◽

Potential Role ◽

Hepatitis E ◽

Developed Countries ◽

Rt Pcr ◽

Viral Pathogens ◽

Apulia Region ◽

Causative Agents

Hepatitis E virus (HEV) represents one of the principal causative agents of hepatitis globally. Among the five HEV genotypes affecting humans, genotypes 3 and 4 are zoonotic and are the main source of hepatitis E in developed countries. HEV has been detected in several foods. The present work investigated the presence of this virus in shellfish sold at retail in the Apulia region of Italy. The presence of HEV RNA was assessed by real-time RT-PCR in 225 shellfish samples collected during 2018. Overall, two (0.89%) of these samples tested positive for HEV RNA. To our knowledge, this is the first notification of the detection of HEV in mussels sold at retail in the Apulia region. These data highlight the potential role of shellfish as a vehicle for the transmission of viral pathogens.

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PO 8565 PREVALENCE AND CLINICAL SIGNIFICANCE OF RESPIRATORY VIRUSES AND BACTERIA DETECTED IN TUBERCULOSIS PATIENTS COMPARED TO HOUSEHOLD CONTACT CONTROLS IN TANZANIA

BMJ Global Health ◽

10.1136/bmjgh-2019-edc.142 ◽

2019 ◽

Vol 4 (Suppl 3) ◽

pp. A54.2-A54

Author(s):

Francis Mhimbira ◽

Jerry Hella ◽

Hellen Hiza ◽

Emmanuel Mbuba ◽

Magreth Chiryamkubi ◽

...

Keyword(s):

Clinical Significance ◽

Bacterial Pathogens ◽

Severe Disease ◽

Respiratory Viruses ◽

Household Contact ◽

Nasopharyngeal Swab ◽

Respiratory Pathogens ◽

Viral Pathogens ◽

Tuberculosis Patients ◽

Study Participants

BackgroundThe study aim is to describe the prevalence of respiratory pathogens in tuberculosis (TB) patients and in their household contact controls, and to determine the clinical significance of respiratory pathogens in TB patients.MethodsWe studied 489 smear-positive adult TB patients and 305 household contact controls without TB with nasopharyngeal swab samples within an ongoing prospective cohort study in Dar es Salaam, Tanzania, between 2013 and 2015. We used multiplex real-time PCR to detect 16 respiratory viruses and seven bacterial pathogens from nasopharyngeal swabs.ResultsThe median age of the study participants was 33 years; 61% (484/794) were men, and 21% (168/794) were HIV-positive. TB patients had a higher prevalence of HIV (28.6%; 140/489) than controls (9.2%; 28/305). Overall prevalence of respiratory viral pathogens was 20.4% (160/794; 95% CI 17.7%–23.3%) and of bacterial pathogens 38.2% (303/794; 95% CI 34.9%–41.6%). TB patients and controls did not differ in the prevalence of respiratory viruses (Odds Ratio [OR] 1.00, 95% CI 0.71–1.44), but respiratory bacteria were less frequently detected in TB patients (OR 0.70, 95% CI 0.53–0.94). TB patients with both respiratory viruses and respiratory bacteria were likely to have more severe disease (adjusted OR [aOR] 1.6, 95% CI 1.1–2.4; p 0.011). TB patients with respiratory viruses tended to have more frequent lung cavitations (aOR 1.6, 95% CI 0.93–2.7; p 0.089).ConclusionRespiratory viruses are common for both TB patients and household controls. TB patients may present with more severe TB disease, particularly when they are co-infected with both bacteria and viruses.

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Comparison of Six RNA Extraction Methods for the Detection of Classical Swine Fever Virus by Real-Time and Conventional Reverse Transcription–PCR

Journal of Veterinary Diagnostic Investigation ◽

10.1177/104063870501700609 ◽

2005 ◽

Vol 17 (6) ◽

pp. 574-578 ◽

Cited By ~ 41

Author(s):

Ming Y. Deng ◽

He Wang ◽

Gordon B. Ward ◽

Tammy R. Beckham ◽

Thomas S. McKenna

Keyword(s):

Real Time ◽

Classical Swine Fever Virus ◽

Rna Extraction ◽

Classical Swine Fever ◽

Extraction Methods ◽

Rt Pcr ◽

Total Rna ◽

Reverse Transcription Pcr ◽

Rna Extraction Methods ◽

Positive Results

Six RNA extraction methods, i.e., RNAqueous kit, Micro-to-midi total RNA purification system, NucleoSpin RNA II, GenElute mammalian total RNA kit, RNeasy mini kit, and TRIzol LS reagent, were evaluated on blood and 7 tissues from pig infected with classical swine fever virus (CSFV). Each of the 6 extraction methods yielded sufficient RNA for positive results in a real-time reverse transcription–PCR (RT-PCR) for CSFV, and all RNA, except the one extracted from blood by TRIzol LS reagent, yielded positive results in both a conventional RT-PCR for CSFV and a conventional RT-PCR for an endogenous gene encoding β-actin. The RNA extracted from blood by TRIzol LS reagent became positive in both conventional RT-PCR assays when it was diluted to 1:2, 1:4, or up to 1:64 in nuclease-free water. It is concluded that all 6 methods are more or less useful for the detection of CSFV by real-time and conventional RT-PCR in swine blood and tissues. However, some of the 6 reagents offer certain advantages not common to all 6 extraction procedures. For example, RNA extracted by the TRIzol LS reagent constantly had the highest yield; that by the RNAqueous kit had the highest A260/A280 ratio for almost all samples; and that by the NucleoSpin RNA II and the GenElute mammalian total RNA kit was most likely to be free of contaminations with genomic DNA.

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Comparison of Luminex xTAG® RVP fast assay and real time RT-PCR for the detection of respiratory viruses in adults with community-acquired pneumonia

Journal of Medical Virology ◽

10.1002/jmv.24463 ◽

2016 ◽

Vol 88 (7) ◽

pp. 1173-1179 ◽

Cited By ~ 4

Author(s):

Vivian Luchsinger ◽

Yara Prades ◽

Mauricio Ruiz ◽

Rolando Pizarro ◽

Patricio Rossi ◽

...

Keyword(s):

Real Time ◽

Respiratory Viruses ◽

Community Acquired Pneumonia ◽

Rt Pcr

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Prevalence of Bovine viral diarrhea virus in cattle herds from Basrah and Nassirya Provinces by direct and indirect Elisa and Real time qPCR

Al-Qadisiyah Journal of Veterinary Medicine Sciences ◽

10.29079/vol11iss2art184 ◽

2012 ◽

Vol 11 (2) ◽

pp. 1

Author(s):

B. A. Jarullah, J. Aed Gati, and A. Saleh

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Indirect Elisa ◽

Positive Sample ◽

Enzyme Linked Immunosorbent Assay ◽

Rt Pcr ◽

Diarrhea Virus ◽

Virus Rna ◽

Two Samples ◽

Cattle Herds

The current study was conducted to investigate the prevalence of BVD virus in Basrah and Nassirya city by using ELISA and RT-PCR. Two hundreds and eighty two samples of non vaccinated cattle sera samples collected from two regions of Iraq (188 samples from Nassirya city and 92 samples from Basrah city). Samples tested by Enzyme Linked Immunosorbent Assay (ELISA) antigen capture. Positive results were 20 samples ( 8 sample in Thi-Qar and 12 positive samples from Basrah). All samples submitted to indirect ELISA(IDEXX HerdCheck ELISA )for detect BVDV antibodies .Genotyping of all 20 positive samples to antigen detection were tested by Real time PCR, using Cador BVDV ½ kit, after extraction of virus RNA by QIAamp mini kit. The results revealed that there were 20 positive sample according to direct ELISA(Ag detection), while 66 sample were positive to indirect ELISA, as well as, the result of RT-PCR showed that there were two sample positive to BVDV type-1 (one sample form each city).Key words: BVDV, Genotype, ELISA, Iraq, Real time PCR.

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Development, Evaluation of the PNA RT-LAMP Assay for Rapid Molecular Detection of SARS-CoV-2

10.21203/rs.3.rs-558645/v1 ◽

2021 ◽

Author(s):

Chinbayar Bat-Ochir ◽

Yeon-Sook Kim ◽

Han Gyeul Kim ◽

See Sok Lee ◽

Han Woo Lee ◽

...

Keyword(s):

Real Time ◽

Lamp Assay ◽

Study Data ◽

Molecular Diagnostic ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Clinical Sensitivity ◽

Clinical Accuracy ◽

Absolute Detection Limit ◽

Development Evaluation

Abstract Dual-labeled PNA probe used RT-LAMP molecular rapid assay targeting SARS-CoV-2 ORF1ab and N genes was developed, and the analytical, clinical performances for detection of SARS-CoV-2 RNA extracted from clinical nasopharyngeal swab specimens were evaluated in this study. Data showed that this assay is highly specific for SARS-CoV-2, and the absolute detection limit is 1 genomic copy per microliter of viral RNA which can be considered to be comparable to gold-standard molecular diagnostic method real-time reverse transcriptase PCR. Both clinical sensitivity and specificity against a commercial real-time RT-PCR assay were determined as identical. In conclusion, the PNA RT-LAMP assay showed high analytical and clinical accuracy which are identical to real-time RT-PCR which has been routinely used for the detection of SARS-CoV-2.

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Pooling for SARS-CoV-2 Control in Care Institutions

10.21203/rs.3.rs-42489/v1 ◽

2020 ◽

Author(s):

Jorge J. Cabrera Alvargonzalez ◽

Sonia Rey Cao ◽

Sonia Pérez Castro ◽

Lucía Martínez Lamas ◽

Olaia Cores Calvo ◽

...

Keyword(s):

Scale Up ◽

Positive Sample ◽

Care Homes ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Average Delay ◽

Global Rate ◽

Local Experience ◽

Expected Performance ◽

Pooling Strategies

Abstract Background Workers and residents in Care Homes are considered at special risk for the acquisition of SARS-CoV-2 infection, due to the infectivity and high mortality rate in the case of residents, compared to other containment areas. The role of presymptomatic people in transmission has been shown to be important and the early detection these people is critical for the control of new outbreaks. Pooling strategies have proven to preserve SARS-CoV-2 testing resources.The aims of the present study, based in our local experience, were (a) to describe SARS-CoV-2 prevalence in institutionalized people in Galicia (Spain) during the Coronavirus pandemic and (b) to evaluate the expected performance of a pooling strategy using RT-PCR for the next rounds of screening of institutionalized people.Methods 25,386 Nasopharyngeal swab samples from the total of the residents and workers at Care Homes in Galicia (March to May 2020) were tested using RT-PCR. Prevalence and distribution of positive detection in Care Homes was calculated. Pools of 19 negative samples and one positive sample were tested using RT-PCR as well. Prevalence and distribution of positive detection in Care Homes was calculated. Results Distribution of SARS-CoV-2 infection at Care Houses was uneven. As the virus circulation global rate was low in our area, the number of people at risk of acquiring the infection continues to be very high. In this work, we have successfully demonstrated that pooling of different groups of samples at low prevalence clusters, can be done with a small average delay on quantification cycle (Cq) values. Conclusions A new surveillance system with guaranteed protection is required for small clusters, previously covered with individual testing. Our proposal for Care Houses, once prevalence zero is achieved, would include successive rounds of testing using a pooling solution for transmission control preserving testing resources. Scale-up of this method may be of utility to confront larger clusters to avoid the viral circulation and keeping them operative.

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Sensitivity of Nasopharyngeal Swabs and Saliva for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2

Clinical Infectious Diseases ◽

10.1093/cid/ciaa848 ◽

2020 ◽

Cited By ~ 26

Author(s):

Alainna J Jamal ◽

Mohammad Mozafarihashjin ◽

Eric Coomes ◽

Jeff Powis ◽

Angel X Li ◽

...

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Real Time ◽

Saliva Sample ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Sample Pair

Abstract We enrolled 91 consecutive inpatients with COVID-19 at 6 hospitals in Toronto, Canada, and tested 1 nasopharyngeal swab/saliva sample pair from each patient using real-time RT-PCR for severe acute respiratory syndrome coronavirus 2. Sensitivity was 89% for nasopharyngeal swabs and 72% for saliva (P = .02). Difference in sensitivity was greatest for sample pairs collected later in illness.

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Visual Detection of SARS-CoV-2 RNA by Conventional PCR-Induced Generation of DNAzyme Sensor

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2020.586254 ◽

2020 ◽

Vol 7 ◽

Author(s):

Anbalagan Anantharaj ◽

Soon Jyoti Das ◽

Patil Sharanabasava ◽

Rakesh Lodha ◽

Sushil K. Kabra ◽

...

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Visual Detection ◽

Fluorescence Probe ◽

Scale Validation ◽

Unmet Need ◽

Pilot Scale ◽

Molecular Diagnostic ◽

Nasopharyngeal Swab ◽

Rt Pcr

The gold standard for the diagnosis of SARS-CoV-2, the causative agent of COVID-19, is real-time polymerase chain reaction (PCR), which is labor-intensive, expensive, and not widely available in resource-poor settings. Therefore, it is imperative to develop novel, accurate, affordable, and easily accessible assays/sensors to diagnose and isolate COVID-19 cases. To address this unmet need, we utilized the catalytic potential of peroxidase-like DNAzyme and developed a simple visual detection assay for SARS-CoV-2 RNA using a conventional thermal cycler by the PCR-induced generation of DNAzyme sensor. The performance of RT-PCR DNAzyme-based sensor was comparable to that of real-time PCR. The pilot scale validation of RT-PCR DNAzyme-based sensor has shown ~100% sensitivity and specificity in clinical specimens (nasopharyngeal swab, n = 34), with a good correlation (Spearman r = 0.799) with the Ct-value of fluorescence probe-based real-time PCR. These findings clearly indicate the potential of this inexpensive, sensitive, and specific molecular diagnostic test to extend our testing capabilities for the detection of SARS-CoV-2 to curtail COVID-19 transmission.

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