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

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.

scholarly journals Triplex Real Time RT-PCR for N1, N2 and RP probes from CDC EUA SARS-CoV-2 diagnosis kit

2020 ◽  
Author(s):  
Byron Freire-Paspuel ◽  
Patricio Vega-Mariño ◽  
Alberto Velez ◽  
Marilyn Cruz ◽  
Miguel Angel Garcia-Bereguiain
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Real Time ◽  
Reverse Transcription ◽  
Clinical Performance ◽  
Rt Pcr ◽  
Reverse Transcription Pcr ◽  
Speed Up

AbstractCDC protocol for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include 3 targets for detection (N1, N2 and RP) labelled with FAM so 3 PCR reactions are required per sample. We developed a triplex, real-time reverse transcription PCR for SARS-CoV-2 that maintained clinical performance compared with CDC singleplex assay. This protocol could speed up detection and save reagents during current SARS-CoV-2 testing supplies shortage.

Identification of SARS-CoV-2 RNA in the conjunctival swab of an Italian pediatric patient affected with COVID-19: A case report

2020 ◽  
pp. 112067212097782
Author(s):  
Luciano Quaranta ◽  
Francesca Rovida ◽  
Ivano Riva ◽  
Carlo Bruttini ◽  
Ilaria Brambilla ◽  
...  
Keyword(s):  
Case Report ◽  
Severe Acute Respiratory Syndrome ◽  
Pediatric Patient ◽  
Ocular Involvement ◽  
Case Description ◽  
Rt Pcr ◽  
Reverse Transcription Pcr ◽  
Ocular Symptoms ◽  
Pediatric Clinic ◽  
Conjunctival Swab

Introduction: To report a case of identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA in ocular specimen in a pediatric patient affected with Coronavirus disease 2019 (COVID-19) with no signs of ocular involvement. Case description: A 11-year old male patient with confirmed COVID-19 infection was hospitalized at the Pediatric Clinic Clinic of the IRCCS Foundation and Hospital San Matteo, Pavia, Italy. Three days after hospital admission, because of the patient complaining very mild ocular symptoms, an ophthalmological evaluation was performed. No signs related to conjunctivitis or keratitis were found but a conjunctival swab was collected as well, based on patient’s medical history. The specific SARS-CoV-2 reverse transcription PCR (RT-PCR) was performed, unearthing the presence of viral RNA from the swab. On day 25 from hospitalization, the conjunctival swab was repeated, giving negative result. Conclusions: This is the first report of the identification of SARS-CoV-2 RNA in ocular specimen in a pediatric patient without signs of ocular involvement. However, despite the transmission through tears is theoretically possible, it is still unclear whether this could be considered as an important route for the spread of SARS-CoV-2.

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

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.

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

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252964
Author(s):  
Kenji Ota ◽  
Katsunori Yanagihara ◽  
Daisuke Sasaki ◽  
Norihito Kaku ◽  
Naoki Uno ◽  
...  
Keyword(s):  
Viral Load ◽  
Comparative Analysis ◽  
Severe Acute Respiratory Syndrome ◽  
Late Phase ◽  
Cruise Ship ◽  
Rt Pcr ◽  
Load Detection ◽  
Qrt Pcr ◽  
Positive Rate ◽  
Rate Improvement

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.

scholarly journals Rapid Diagnosis of Ebola Hemorrhagic Fever by Reverse Transcription-PCR in an Outbreak Setting and Assessment of Patient Viral Load as a Predictor of Outcome

2004 ◽  
Vol 78 (8) ◽  
pp. 4330-4341 ◽  
Author(s):  
Jonathan S. Towner ◽  
Pierre E. Rollin ◽  
Daniel G. Bausch ◽  
Anthony Sanchez ◽  
Sharon M. Crary ◽  
...  
Keyword(s):  
Viral Load ◽  
Reverse Transcription ◽  
Hemorrhagic Fever ◽  
Rt Pcr ◽  
Diagnostic Laboratory ◽  
Reverse Transcription Pcr ◽  
Ebola Hemorrhagic Fever ◽  
Antigen Capture ◽  
Gulu District ◽  
Multiple Samples

ABSTRACT The largest outbreak on record of Ebola hemorrhagic fever (EHF) occurred in Uganda from August 2000 to January 2001. The outbreak was centered in the Gulu district of northern Uganda, with secondary transmission to other districts. After the initial diagnosis of Sudan ebolavirus by the National Institute for Virology in Johannesburg, South Africa, a temporary diagnostic laboratory was established within the Gulu district at St. Mary's Lacor Hospital. The laboratory used antigen capture and reverse transcription-PCR (RT-PCR) to diagnose Sudan ebolavirus infection in suspect patients. The RT-PCR and antigen-capture diagnostic assays proved very effective for detecting ebolavirus in patient serum, plasma, and whole blood. In samples collected very early in the course of infection, the RT-PCR assay could detect ebolavirus 24 to 48 h prior to detection by antigen capture. More than 1,000 blood samples were collected, with multiple samples obtained from many patients throughout the course of infection. Real-time quantitative RT-PCR was used to determine the viral load in multiple samples from patients with fatal and nonfatal cases, and these data were correlated with the disease outcome. RNA copy levels in patients who died averaged 2 log10 higher than those in patients who survived. Using clinical material from multiple EHF patients, we sequenced the variable region of the glycoprotein. This Sudan ebolavirus strain was not derived from either the earlier Boniface (1976) or Maleo (1979) strain, but it shares a common ancestor with both. Furthermore, both sequence and epidemiologic data are consistent with the outbreak having originated from a single introduction into the human population.

A mechanistic model of developing immunity to Teladorsagia circumcincta infection in lambs

Parasitology ◽  
2010 ◽  
Vol 138 (3) ◽  
pp. 322-332 ◽  
Author(s):  
D. R. SINGLETON ◽  
M. J. STEAR ◽  
L. MATTHEWS
Keyword(s):  
Immune Response ◽  
Mechanistic Model ◽  
Meta Analysis ◽  
Large Data ◽  
Acquired Immunity ◽  
Domestic Sheep ◽  
Data Set ◽  
Immune Priming ◽  
Helminth Infections ◽  
Faecal Egg Counts

SUMMARYAcquired immunity influences the severity of parasitic disease, but modelling the effects of acquired immunity in helminth infections has proved challenging. This may be due to a lack of suitable immunological data, or to the perceived complexity of modelling the immune response. We have developed a model of T. circumcincta infection in domestic sheep that incorporates the effects of acquired immunity on parasite establishment and fecundity. A large data set from commercially managed populations of Scottish Blackface sheep was used, which included relationships between IgA activity and worm length, and between worm length and fecundity. Use was also made of a recently published meta-analysis of parasite establishment rates. This realistic but simple model of nematode infection emulates observed patterns of faecal egg counts. The end-of-season faecal egg counts are remarkably robust to perturbations in the majority of the parameters, possibly because of priming of the immune system early in the season, reducing parasite establishment and growth and, therefore, faecal egg counts. Lowering the amount of early infection leads to higher end-of-season egg counts. The periparturient rise in egg counts in ewes appears to have an important role in supplying infection for the priming of the immune response. This feedback in the immune priming suggests that nematode infections may be difficult to eliminate.

scholarly journals Detection of SARS Coronavirus in Patients with Severe Acute Respiratory Syndrome by Conventional and Real-Time Quantitative Reverse Transcription-PCR Assays

2004 ◽  
Vol 50 (1) ◽  
pp. 67-72 ◽  
Author(s):  
Leo L M Poon ◽  
Kwok Hung Chan ◽  
On Kei Wong ◽  
Timothy K W Cheung ◽  
Iris Ng ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Real Time ◽  
N Gene ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Reverse Transcription Pcr ◽  
Copy Numbers ◽  
Stool Samples ◽  
Pcr Assays

Abstract Background: A novel coronavirus (CoV) was recently identified as the agent for severe acute respiratory syndrome (SARS). We compared the abilities of conventional and real-time reverse transcription-PCR (RT-PCR) assays to detect SARS CoV in clinical specimens. Methods: RNA samples isolated from nasopharyngeal aspirate (NPA; n = 170) and stool (n = 44) were reverse-transcribed and tested by our in-house conventional RT-PCR assay. We selected 98 NPA and 37 stool samples collected at different times after the onset of disease and tested them in a real-time quantitative RT-PCR specific for the open reading frame (ORF) 1b region of SARS CoV. Detection rates for the conventional and real-time quantitative RT-PCR assays were compared. To investigate the nature of viral RNA molecules in these clinical samples, we determined copy numbers of ORF 1b and nucleocapsid (N) gene sequences of SARS CoV. Results: The quantitative real-time RT-PCR assay was more sensitive than the conventional RT-PCR assay for detecting SARS CoV in samples collected early in the course of the disease. Real-time assays targeted at the ORF 1b region and the N gene revealed that copy numbers of ORF 1b and N gene sequences in clinical samples were similar. Conclusions: NPA and stool samples can be used for early diagnosis of SARS. The real-time quantitative RT-PCR assay for SARS CoV is potentially useful for early detection of SARS CoV. Our results suggest that genomic RNA is the predominant viral RNA species in clinical samples.

scholarly journals Evaluation of Antibody Response in Symptomatic and Asymptomatic COVID-19 Patients and Diagnostic Assessment of New IgM/IgG ELISA Kits

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 161
Author(s):  
Hadeel T. Al-Jighefee ◽  
Hadi M. Yassine ◽  
Maryam A. Al-Nesf ◽  
Ali A. Hssain ◽  
Sara Taleb ◽  
...  
Keyword(s):  
Immune Response ◽  
Severe Acute Respiratory Syndrome ◽  
Antibody Response ◽  
Diagnostic Assessment ◽  
Enzyme Linked Immunosorbent Assay ◽  
Rt Pcr ◽  
Serum Samples ◽  
Time Intervals ◽  
Low Sensitivity ◽  
Pcr Test

This study aims to study the immune response and evaluate the performances of four new IgM and five IgG enzyme-linked immunosorbent assay (ELISA) kits for detecting anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies against different antigens in symptomatic and asymptomatic coronavirus disease 2019 (COVID-19) patients. A total of 291 samples collected from symptomatic and asymptomatic RT–PCR-confirmed patients were used to evaluate the ELISA kits’ performance (EDI, AnshLabs, DiaPro, NovaLisa, and Lionex). The sensitivity was measured at three different time-intervals post symptoms onset or positive SARS-CoV-2 RT–PCR test (≤14, 14–30, >30 days). The specificity was investigated using 119 pre-pandemic serum samples. The sensitivity of all IgM kits gradually decreased with time, ranging from 48.7% (EDI)–66.4% (Lionex) at ≤14 days, 29.1% (NovaLisa)–61.8% (Lionex) at 14–30 days, and 6.0% (AnshLabs)–47.9% (Lionex) at >30 days. The sensitivity of IgG kits increased with time, peaking in the latest interval (>30 days) at 96.6% (Lionex). Specificity of IgM ranged from 88.2% (Lionex)–99.2% (EDI), while IgG ranged from 75.6% (DiaPro)–98.3% (Lionex). Among all RT–PCR-positive patients, 23 samples (7.9%) were seronegative by all IgG kits, of which only seven samples (30.4%) had detectable IgM antibodies. IgM assays have variable and low sensitivity, thus considered a poor marker for COVID-19 diagnosis. IgG assays can miss at least 8% of RT–PCR-positive cases.

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

2020 ◽  
Vol 25 (32) ◽  
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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