Testing Strategies For The Delta Variant: A Hospital Guide

how are hospitals testing for delta variant

The Delta variant of COVID-19 has been associated with increased transmissibility and illness of greater severity. Hospitals have been keen to understand the prevalence of the Delta variant among their patients. For instance, UF Health Jacksonville doctors are using genome sequencing to test COVID samples and determine the percentage of their patients infected with the Delta variant. Nucleic acid amplification tests (NAATs), including PCR tests, are considered the gold standard for COVID-19 tests and can effectively detect the Delta variant. Antigen tests, including self-tests or at-home tests, are rapid but generally less likely to detect the virus than NAATs. Vaccination has proven to be effective in reducing the risk of infection, severe illness, and death from the Delta variant, and treatments such as antiviral medications and monoclonal antibodies have been shown to be effective for those infected.

Characteristics Values
Testing Method Nucleic acid amplification tests (NAATs), including PCR tests, are the "gold standard" for COVID-19 tests. Antigen tests are also used, which are rapid tests with results available in 15-30 minutes.
Sample Collection Specimens are collected from the nose or mouth and transported to a laboratory for testing.
Testing Frequency Hospitals may not test every sample due to cost and time constraints.
Testing Purpose To determine the prevalence of the Delta variant among COVID-19 patients and plan accordingly.
Treatment For severe COVID-19, the standard treatment includes remdesivir, corticosteroids, and prophylactic heparin. Molnupiravir and Nirmatrelvir are two additional antivirals in the approval process. Vaccination remains the best protection against the Delta variant.

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Genetic sequencing to identify the Delta variant

Genetic sequencing is a method used to identify the Delta variant of the SARS-CoV-2 virus. It involves decoding the genes of the virus to understand its spread, evolution, and specific mutations. This process is different from the clinical tests used to diagnose patients with COVID-19, as it focuses on identifying and tracking specific variants.

Genomic sequencing is employed by researchers to identify and track specific variants of SARS-CoV-2, including the highly contagious Delta variant. This technique is not the same as the viral tests used to detect current infections. Viral tests include Nucleic Acid Amplification Tests (NAATs) and antigen tests, which detect the presence of the virus but do not distinguish between different variants.

To identify the Delta variant specifically, scientists compare the mutations in the viral genomes of samples collected from the community to the original Wuhan strain. Groupings of specific mutations are used to define viral variants or lineages. For the Delta variant, the presence of the L452R mutation is often indicative, with a high percentage of samples exhibiting this mutation being proven to be the Delta variant upon sequencing.

At UF Health Jacksonville, doctors and scientists utilized genetic sequencing to determine the prevalence of the Delta variant among their COVID-19 patients. They employed a machine that analyzed the genetic sequencing of the current strain and compared it to the samples they were testing. This allowed them to identify that 9 out of 10 patients at their facility had the Delta variant.

Genetic sequencing plays a crucial role in understanding the spread and evolution of the SARS-CoV-2 virus, particularly in tracking specific variants like the highly contagious Delta variant. By employing this technique, researchers can gain valuable insights into the mutations of the virus and make informed decisions to mitigate its impact.

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Nucleic acid amplification tests (NAATs)

NAATs can be performed in laboratory facilities by trained personnel or in point-of-care (POC) settings. Some NAATs can even be self-administered at home or in other non-healthcare locations. The type of specimen collected for a NAAT test can vary, including specimens from the upper or lower respiratory tract, urine, swab, or saliva. Saliva is an acceptable specimen type for SARS-CoV-2 testing, and some NAATs have been authorized for use with saliva specimens.

NAATs use a variety of methods to amplify nucleic acids and detect the virus, including Reverse Transcription Polymerase Chain Reaction (RT-PCR), Polymerase Chain Reaction (PCR), Rolling Circle Amplification (RCA), Loop-Mediated Isothermal Amplification (LAMP), Recombinase Polymerase Amplification (RPA), and CRISPR-related amplification. These tests usually involve some form of nucleic acid hybridization, where the sample is probed with an artificially produced complementary strand of DNA or RNA that is labeled for easy detection.

NAATs have several advantages, including high sensitivity and specificity. They can be used to detect a variety of infections, including COVID-19, cancers, and bacterial and viral infections. NAATs have also revolutionized bio-detection by providing greater possibilities in novel diagnoses, achieving high efficiency, specificity, and cost-effectiveness. However, NAATs also have limitations, such as lengthy run times, large reaction volumes, and complex protocols.

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PCR tests

Nucleic acid amplification tests (NAATs), including PCR tests, are considered the "gold standard" for COVID-19 tests. They are more likely to detect the virus than antigen tests. PCR tests identify genetic material, be it partial, alive, or dead. They are not designed to identify an active infectious disease, determine an acute infection, ongoing infectiousness, or actual disease.

Doctors at UF Health Jacksonville used genetic sequencing to determine the prevalence of the Delta variant in their hospital. They were motivated by the lack of testing by the state health department, which only tests a random sample of COVID-19 tests and not those coming into hospitals.

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Antigen tests

The AffiDX SARS-CoV-2 antigen lateral-flow test has been evaluated with patient samples confirmed to be Delta variant positive, and for a Ct<29, the test correctly identified all positive cases. Other commercially available lateral-flow tests have also been evaluated, with varying results. The Sure Status COVID-19 Antigen Card Test (Premier Medical Corporation) showed higher sensitivity for the alpha, beta, and gamma variants compared to the delta variant. Conversely, the Flowflex SARS-CoV-2 Antigen Rapid Test (ACON Laboratories) showed higher sensitivity for the delta variant compared to other Ag-RDT kits.

A study by UMass Chan Medical School and associated researchers supported by the NIH Rapid Acceleration of Diagnostics (RADx) initiative found that at-home antigen tests performed similarly in detecting the Omicron and Delta variants compared to polymerase chain reaction (PCR) tests. The study analyzed data from 5,726 participants in a prospective cohort study and found that 82% of delta-infected individuals tested positive using at-home antigen tests within 48 hours of their first positive PCR test.

Another study assessed the performance of at-home antigen tests in detecting the Delta and Omicron variants by measuring the likelihood of a positive result compared to a PCR test and the likelihood of a positive result based on the number of days since the first positive PCR test. The study found that overall, 82% of delta-infected individuals tested positive using at-home antigen tests within 48 hours of their first positive PCR test.

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Preventing the spread of COVID-19

The Delta variant of SARS-CoV-2 is associated with increased transmissibility and more severe illness. As hospitals continue to manage outbreaks, it is important to understand how to prevent the spread of COVID-19.

Firstly, testing is a crucial tool in preventing the spread of COVID-19. If you have symptoms or have been exposed to someone with suspected or confirmed COVID-19, it is important to get tested, regardless of your vaccination status. Testing options include viral tests, which look for a current infection, and antibody tests, which indicate previous infection. Nucleic acid amplification tests (NAATs), including PCR tests, are highly effective in detecting the virus and are considered the "gold standard". Antigen tests, on the other hand, provide rapid results in 15-30 minutes but are less sensitive than NAATs. Self-tests or at-home tests are also available as antigen tests. It is important to follow the testing instructions carefully and repeat testing if necessary, especially with negative antigen test results.

In addition to testing, vaccination is a powerful tool in preventing the spread of COVID-19, including the Delta variant. Vaccinated individuals are protected from developing severe cases of COVID-19 and are less likely to be hospitalized or die from the disease. The vaccines significantly reduce the risk of infection and are especially effective in preventing severe illness and death. For individuals over 60 or with certain medical conditions, booster shots are important to maintain protection against COVID-19.

Other practices to prevent the spread of COVID-19 include good hand hygiene, wearing masks, and social distancing, especially in indoor settings. These measures, combined with testing and vaccination, can help reduce the transmission of COVID-19 and protect against the Delta variant.

By following these measures and staying vigilant, we can all play a part in preventing the spread of COVID-19 and keeping ourselves and our communities safe.

Frequently asked questions

Hospitals are testing for the Delta variant through genetic sequencing. This involves taking specimens from a patient's nose or mouth and using a machine to compare the genetic sequencing of the current strain with the sample being tested.

Nucleic acid amplification tests (NAATs), including PCR tests, are used to detect the Delta variant. Antigen tests are also used, but they are less likely to detect the virus.

Hospitals can determine if a patient has the Delta variant by performing an epidemiological investigation, which includes epidemiologic analysis, detailed case reviews, serial SARS-CoV-2 reverse transcriptase–polymerase chain reaction (RT–PCR) testing, viral culture, environmental swabbing, and whole-genome sequencing (WGS).

If a patient tests positive for the Delta variant, they are usually hospitalized and treated with antiviral medication such as remdesivir, corticosteroids, and prophylactic heparin. In addition, vaccinated patients who test positive for the Delta variant are at a lower risk of developing severe illness or dying from the virus.

Hospitals may not be able to test all patients for the Delta variant due to cost and time constraints. However, by conducting their own testing, hospitals can better plan and allocate resources.

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