Immunity diagram
Credit: EUROIMMUN, a PerkinElmer company

Nonspecific, innate immune response is the first line of defense against invading pathogens. Cells of the innate immune system such as macrophages, natural killer cells, and dendritic cells prevent the spread of foreign pathogens throughout the body.

An innate immune response also triggers specific adaptive immune responses. These include cells that engulf the pathogen, inform other immune cells about the invading pathogen, and produce an inflammatory response to marshal the forces of the adaptive immune system.

In severe cases of infection, inflammatory responses can grow into an inflammatory cytokine storm that injures tissues causing widespread damage that manifests as severe fevers, inflammation, fatigue, nausea, and can even result in death. TNF-α, IL-1β, IL-6, and IL-8 are considered the main components of a cytokine-storm.1

Measuring pro-inflammatory cytokines (e.g., IL-6) in blood in both adults and pediatric patients has several potential applications in the management of COVID-19 such as risk evaluation, monitoring progression of disease, assessment of prognosis, selection of treatment, and monitoring response to therapy.2

Adaptive immune response occurs following exposure to a foreign antigen either from a pathogen or a vaccination. There are two broad classes of such responses—antibody (humoral) and cell-mediated immune responses, mediated by B and T lymphocytes, respectively.

Antibodies can bind specifically to antigens from the foreign substance to block their attachment to host cells and mark it for destruction by the immune system. Measurement of such antibodies by immunoassays can help in understanding the role of B-cell mediated humoral immunity against the infection.

In the second class of adaptive immune response (cell-mediated immune response), activated T cells help clear the infection either by directly killing the virus-infected host cell or by producing signaling molecules such as interferon-gamma that can hinder viral replication and enable macrophages to destroy the pathogen.

In COVID-19, approximately 13% of symptomatic patients and 40% of asymptomatic patients become negative for antibodies against SARS-CoV-2 within eight weeks. Additionally, approximately 20% of patients have recovered from COVID-19 infection without detectable antibody titer.3

In such cases, it is possible that the body’s cellular immunity response plays a role in fighting the infection. Robust cellular immune response against SARS-CoV-2 was present up to six months following asymptomatic and mild-to-moderate infection in adults.4 Vaccination against SARS-CoV-2 also induces a strong T-cell response that persists for at least six months.5 Therefore, for novel infections such as COVID-19, it is crucial to measure the entire spectrum of immune response, including innate and adaptive immune responses.

Infectious disease diagnostics cover a spectrum—there are tests to tell you whether you carry the pathogen, and there are tests to tell you whether your immune defenses can mount an adequate cellular or humoral response against the pathogen.

Then, there are tests that tell you whether a person carrying a pathogen can transmit the disease or not. To address whether a person is contagious, we need to understand if we are detecting the live virus or just the viral genomic traces from virus particles that have already been destroyed by the host’s immune system.

RT-PCR tests facilitate detection of the viral genetic material in patient samples. However, such molecular tests are sensitive and if a patient is positive, especially low-positive, these tests do not tell us if we are detecting live virus that can be transmitted to other people or if we are just detecting viral RNA traces.6

Cycle threshold (Ct) is a numerical value generated during a RT-PCR test that gives the number of reaction cycles needed for a sample to amplify and cross a cut-off to be considered positive for the presence of the target. For instance, if the Ct value for an RT-PCR is 38 cycles, a sample with a Ct value below the cutoff, would be considered to contain the target.

Recent data suggests that a higher Ct value for SARS-CoV-2 RT-PCR tests is associated with viral RNA traces that are no longer contagious.7 However, more evidence is needed to prove this theory.

Moreover, not all molecular tests detect the same target in the pathogen genome, and they may require different numbers of RT-PCR cycles before the target is detected. Therefore, it is difficult to set up a global cut-off value for live versus non-live virus based on the Ct values of RT-PCR tests.

The traditional method to determine if the virus is still infectious is to take a sample from the patient and culture it with cells. If the cells are infected, then the virus is infectious, and the patient is contagious. If the cells are not infected, it means that the person is not contagious. However, as viral culture is very time consuming and requires high biosafety levels and laboratory standards, these cannot be designed for routine diagnostic testing.

It has also been debated whether viral antigen tests can detect infectious virus where a high antigen concentration indicates a high virus concentration which could be associated with the live virus.8 However, such claims need further experimental validation.

Currently, high quality RT-PCR assays are still the best option to detect pathogens and conclude on the potential of a patient to transfer a pathogen to somebody else. We do not have a sensitive and specific molecular or antigen test that correlates to the presence of live virus detected by traditional viral culture assays.



  1. Liu Y, Qi G, Bellanti JA, Moser R, Ryffel B, Zheng SG. 2020. Regulatory T cells: A potential weapon to combat COVID-19? MedComm (Beijing). 10.1002/mco1002.1012.
  2. Liu BM, Martins TB, Peterson LK, Hill HR. 2021. Clinical significance of measuring serum cytokine levels as inflammatory biomarkers in adult and pediatric COVID-19 cases: A review. Cytokine. 142:155478-155478.
  3. Long Q-X, Tang X-J, Shi Q-L, et al. 2020. Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections. Nature Medicine. 26(8):1200-1204.
  4. Zuo J, Dowell AC, Pearce H, et al. 2021. Robust SARS-CoV-2-specific T cell immunity is maintained at 6 months following primary infection. Nature Immunology. 
  5. Guerrera G, Picozza M, D’Orso S, et al. 2021. BNT162b2 vaccination induces durable SARS-CoV-2 specific T cells with a stem cell memory phenotype. Sci Immunol.
  6. Joynt GM, Wu WK. 2020. Understanding COVID-19: what does viral RNA load really mean? Lancet Infect Dis. 20(6):635-636.
  7. Jefferson T, Spencer EA, Brassey J, Heneghan C. 2020. Viral cultures for COVID-19 infectious potential assessment – a systematic review. Clin Infect Dis.
  8. Pekosz A, Cooper CK, Parvu V, et al. 2020. Antigen-based testing but not real-time PCR correlates with SARS-CoV-2 virus culture. medRxiv. 2020:2020.2010.2002.20205708.


Iswariya Venkataraman, PhD, is associate director, scientific affairs, at EUROIMMUN, a PerkinElmer company.

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