PCR viral presence (nasal / throat mucous swab) tests, when positive, indicate that the viral RNA, but not necessarily viable/infectious virus, is present in the mucous swab. When symptoms and a positive test are found, it likely means the person is infected. It is also possible they are fortunate enough to just have a random virus in their mucous but not actually in their body (not likely, but may occur). Sometimes people who have recovered will have mucous remnants that contain viruses which may be the cause of some “had COVID, recovered, tested negative, then later retested positive again” cases. False positives can also be caused by non-viable viruses that cannot infect but do contain RNA. Positive/negative results, the Ct count, and patient physiology should interpreted by a professional.
The PCR viral/antigen presence test uses an “amplification” technique that enables the most sensitive equipment to detect fewer than 50 viruses in a sample. “During the exponential amplification phase, the quantity of the target DNA template (amplicon) doubles every cycle… However, the efficiency of amplification is often variable among primers and templates.”. The viral sample is placed in a reagent chemical that, when temperature cycled, results in a new copy for (nearly) every RNA/DNA copy in the sample, thus doubling the population with each cycle. The reagent also adds markers to the copies such that, at some point, the markers fluoresce with a light intensity bright enough to be detected by the equipment. The cycle where this occurs is known as the Ct. There is also a closely related measurement known as Cq. Lower values mean more RNA was present because it took fewer cycles of doubling to reach the point where fluorescence was detected.
The resources below provide a more complete and accurate understanding.
Real-time polymerase chain reaction – Wikipedia
Reverse transcription polymerase chain reaction – Wikipedia
“RT-PCR” redirects here. For real-time polymerase chain reaction, also called quantitative real time polymerase chain reaction (qPCR) or kinetic polymerase chain reaction, see Real-time polymerase chain reaction.
"new CDC guidance … says PCR tests should be set at 28 CT or lower."
"The state lab at the Kansas Department of Health initially used a 42 CT on its most commonly performed test; on January 7, they reduced it to 35."https://t.co/laJf2flQLw
— ReallyCorrect.com (@ReallycorrectC) May 25, 2021
You’re Infected With the Coronavirus. But How Infected?
Knowing the amount of virus carried in the body could help doctors predict the course of a patient’s illness.
“Viral culture was positive only in samples with a cycle-threshold value of 28.4 or less. The incidence of culture positivity decreased with an increasing time from symptom onset and with an increasing cycle-threshold value (Table S3).”
Duration of Culturable SARS-CoV-2 in Hospitalized Patients with Covid-19 | NEJM
Correspondence from The New England Journal of Medicine — Duration of Culturable SARS-CoV-2 in Hospitalized Patients with Covid-19
SARS-CoV-2 Cycle Threshold: A Metric That Matters (or Not) | AACC.org
The cycle threshold (Ct) in reverse transcription polymerase chain reaction (RT-PCR) SARS-CoV-2 tests is gaining currency as a potential marker for severe disease in patients with COVID-19 illness. Amid mounting evidence in the clinical literature, however, some in the laboratory community are urgin…
To Interpret the SARS-CoV-2 Test, Consider the Cycle Threshold Value
(See the Brief report by Tang Xiao et al on pages 2249–51.)
FAQs on Testing for SARS-CoV-2
Answers to FAQs relating to the development and performance of tests for SARS-CoV-2.
Analytical Validation of a COVID-19 qRT-PCR Detection Assay Using a 384-well Format and Three Extraction Methods
The COVID-19 global pandemic is an unprecedented health emergency. Insufficient access to testing has hampered effective public health interventions and patient care management in a number of countries. Furthermore, the availability of regulatory-cleared reagents has challenged widespread implementa…
Epidemiological Correlates of Polymerase Chain Reaction Cycle Threshold Values in the Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
Cycle threshold values were lower among coronavirus disease 2019 patients under 18 years of age and those reporting upper respiratory symptoms at sample collect
Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets
This is a comparative analysis of the performance of the primer–probe sets from four open-source molecular diagnostic assays for SARS-CoV-2 recommended by the World Health Organization.
An inactivated virus, incapable of causing infection and symptoms, can fool a PCR viral presence test into a false positive infection indication because the RNA still exists even though the virus is inactivated / non-viable.
“A positive PCR result does NOT prove active replication of a virus. It does NOT prove infectious virus is present.”
“PCR methods do have some serious limitations for environmental viral analysis, including small sample volumes, the presence of PCR-inhibitory substances, and an inability to differentiate between infective and noninfective viruses.”
“Enteric viruses that are important causes of human disease must often be detected by reverse transcription polymerase chain reaction (RT-PCR), a method that commonly yields positive results with samples that contain only inactivated virus.”
Coronavirus Disease 2019 (COVID-19)
CDC provides credible COVID-19 health information to the U.S.
What does a positive PCR result mean…or not mean?
The polymerase chain reaction (PCR) has remained a hugely important laboratory tool for decades. Subtle changes to the enzymes and drastic change to detection of a result have occurred in that span, but the tool
Are you infectious if you have a positive PCR test result for COVID-19? – CEBM
Tom Jefferson, Carl Heneghan, Elizabeth Spencer, Jon Brassey PCR detection of viruses is helpful so long as its accuracy can
Dynamic profile of RT-PCR findings from 301 COVID-19 patients in Wuhan, China: A descriptive study
With the spread of Coronavirus Disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection, its effect on…
Laboratory diagnosis of COVID-19
This was a non-systematic review of the literature on the laboratory diagnosis of COVID-19.Searches in PubMed and Google Scholar for articles made available in 2020, using the terms “diagnosis” OR “diagnostic” OR “diagnostic tests” OR “tests” …
Application of PCR-Based Methods To Assess the Infectivity of Enteric Viruses in Environmental Samples
The advent of the PCR has greatly enhanced our ability to detect human enteric viral pathogens in the environment, including water, municipal wastes, sewage, food, air, and fomites ([2][1], [3][2], [59][3], [69][4], [79][5]). This is especially true for those viruses which do not grow in cell
Pretreatment to Avoid Positive RT-PCR Results With Inactivated Viruses – PubMed
Enteric viruses that are important causes of human disease must often be detected by reverse transcription-polymerase chain reaction (RT-PCR), a method that commonly yields positive results with samples that contain only inactivated virus. This study was intended to develop a pretreatment for sample…
Methods to prevent PCR amplification of DNA from non-viable virus were not successful for infectious laryngotracheitis virus
Molecular-based testing of poultry dust has been used as a fast, sensitive and specific way to monitor viruses in chicken flocks but it provides no information on viral viability. Differentiation of viable and nonviable virus would expand the usefulness of PCR-based detection. This study tested thre…
Application of PCR-Based Methods To Assess the Infectivity of Enteric Viruses in Environmental Samples
This article has been cited by other articles in PMC.
Vaccines (immunizations): MedlinePlus Medical Encyclopedia
Vaccines are used to boost your immune system and prevent serious, life-threatening diseases.
Role of Cell Culture for Virus Detection in the Age of Technology
Viral disease diagnosis has traditionally relied on the isolation of viral pathogens in cell cultures. Although this approach is often slow and requires considerable technical expertise, it has been regarded for decades as the “gold standard” …
Nanopore sequencing the SARS-CoV-2 genome: introduction to protocol
During this online seminar, Phillip James, who is the Applications Manager for the UK at Oxford Nanopore Technologies, provides an in-depth introduction to sequencing the SARS-CoV-2 genome using the their protocol including advice for best performance.
Diagnostics for SARS-CoV-2 detection: A comprehensive review of the FDA-EUA COVID-19 testing landscape
The rapidly spreading outbreak of COVID-19 disease is caused by the SARS-CoV-2 virus, first reported in December 2019 in Wuhan, China. As of June 17, 2020, this virus has infected over 8.2 million people but ranges in symptom severity, making it difficult …
What is the Illumina method of DNA sequencing?
Illumina sequencing has been used to sequence many genomes and has enabled the comparison of DNA sequences to improve understanding of health and disease.
Biosafety level – Wikipedia
Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy
The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying…
Loading…
Reload document 
Open in new tab 
