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Cycle Threshold (Ct) value of RT-PCR can tell us if a SARS-CoV-2 infected person can spread disease

By Rajeev Chitguppi, Dental Tribune South Asia
August 24, 2020

Currently, all SARS-CoV-2 detection measures make use of RT-PCR test, and its results are generally reported as either positive or negative, which tells us if a person is infected. However, to contain the pandemic, what we need to know is whether that person is infectious or in other words, 'can he spread the disease?' It's important to know that the RT-PCR test does provide an additional measure of the viral load in the sample. This reading is called the cycle threshold (Ct) value. Evidence suggests that reporting this Ct value (calculated viral load) can assist in a better interpretation of the condition, and also in taking clinical decisions.

Our main objective is to prevent the spread of COVID-19 pandemic, for which we must identify and isolate infectious people. Hence, it is critical that those with a high viral load are isolated and not allowed to transmit the virus to others.

Quantitative vs Qualitative data

Currently, all detection measures viz. diagnosis, screening, and surveillance depend on a reverse transcriptase–quantitative polymerase chain reaction (RT-qPCR) test, and we report its results as either positive or negative.

However, it's essential to know that the RT-PCR test does provide a measure of the viral load in the sample, and the reading is called the cycle threshold (Ct) value. Evidence suggests that reporting this Ct value (calculated viral load) can assist in the better interpretation of the condition and support the clinical decisions.

Measuring infectivity by viral culture

RT-PCR testing can tell us whether there is a detectable virus present in an individual. Still, it does not accurately tell us whether that individual is infectious or is capable of spreading the disease. Infectivity in cell culture is the standard for determining whether a patient is contagious.

In the absence of viral culture data, one can use viral load or cycle threshold (Ct) values derived from RT-PCR as a proxy for the likelihood of transmission. The Ct is the number of replication cycles required for a signal of RT-PCR product to cross a determined threshold.

Early studies on symptoms and viral shedding

Early studies showed the highest viral load in throat swabs at the time of symptom onset and inferred that infectiousness peaked on or before symptom onset.

Another early study showed pharyngeal virus shedding to be very high during the first week of symptoms, with a peak happening on day 4.

Correlation between symptoms and Ct values: (JAMA Internal Medicine, 6 Aug 2020)

In this cohort study, both asymptomatic and symptomatic SARS-CoV-2 patients showed similar Ct values. Viral molecular shedding was prolonged. Since asymptomatic/ presymptomatic transmission of SARS-CoV-2 infection may be a critical factor in community spread, population-based surveillance and isolation of asymptomatic patients may be required.

Infectivity: Ct values & viral culture

In a German study (click here to read) the researchers could readily isolate the virus during the first week of symptoms from a significant fraction of samples. Still, no isolates were obtained from samples taken after day eight despite ongoing high viral loads. The study recommended an early discharge with ensuing home isolation for patients who are beyond day 10 of symptoms with less than 100,000 viral RNA copies per ml of sputum. Both criteria predict that there is a little residual risk of infectivity, based on cell culture.

In a French study published in April 2020, the researchers at the Méditerranée Infection University Hospital Institute in Marseille, France collected 183 samples from 155 patients. Out of the 183 samples obtained, 174 were nasopharyngeal swabs, and 9 were sputum samples. They assessed the patient samples for SARS-CoV-2 RNA positivity using real-time RT-PCR targeting the E gene. All 183 samples were inoculated in cell cultures. The objective was to correlate viral load to cultivable viruses.

Among the 183 samples inoculated in the studied period, 129 led to virus isolation. Of these, 124 samples had detectable cytopathic effect between 24 and 96 h. Blind subcultures allowed obtaining five additional isolates only.

The study found a significant relationship between Ct value and culture positivity rate.

  1. Samples with Ct values of 13–17 all led to a positive culture.
  2. Culture positivity rate then decreased progressively according to Ct values to reach 12% at 33 Ct.
  3. No culture was obtained from samples with Ct > 34.
  4. The five additional isolates obtained after blind subcultures had Ct between 27 and 34 (low viable virus load).

Thus the study found a strong correlation between Ct value and sample infectivity in a cell culture model. The authors could deduce that with this system, patients with Ct values equal or above 34 do not excrete infectious viral particles.

A study done in Manitoba (May 2020) evaluated the relationship between cycle threshold (Ct) values (wrt E gene SARS-CoV-2 RT-PCR  from respiratory samples), symptom onset to test (STT) and infectivity in cell culture. They took SARS-CoV-2 RT-PCR confirmed positive samples and determined their ability to infect Vero cell lines. The study observed no growth in samples with a Ct > 24 or STT > 8 days. The authors concluded that the infectivity of patients with Ct >24 and the duration of symptoms >8 days might be low.

For every 1 unit increase in Ct, the odds ratio for infectivity decreased by 32%. The high specificity of Ct and STT suggests that Ct values greater than 24, along with the duration of symptoms lasting longer than eight days may be used in combination to determine the period of infectivity in patients. 

Contrary evidence

One study, published in the NEJM in May 2020, coming from a skilled nursing facility in Kings County, Washington, found viral growth in a patient sample with a cycle threshold (Ct) value of 34, as well as viral growth in asymptomatic and presymptomatic individuals. However, a systematic review from Stanford University analysing this study said that the findings from an elder care facility might not reflect the general population. Reasons are two-fold.

  1. It is difficult to recognise early signs and symptoms of respiratory viral infections in the elderly
    populations due to impaired immune responses associated with ageing and the high prevalence of pre-existing and underlying conditions, such as chronic cough and cognitive impairments.
  2. Elderly and infirm patients have blunted physiological responses that may allow them to remain asymptomatic during infection.

Latest systematic review (21 Aug 2020)

The latest systematic review on this topic MedRxiv, 21 Aug 2020 included 17 studies that suggested a correlation between the time from collection of a specimen to test, cycle threshold (as a proxy for viral load) and symptom severity. The quality of the studies was moderate with lack of standardised reporting and lack of testing of PCR against viral culture or infectivity in animals limiting our current ability to quantify the relationship between the variables and ultimately the usefulness of PCR use for assessing infectiousness of patients. However, the authors mention that the infectivity appeared to decline after about a week of viral shedding around the cycle threshold value of 24. 

10 Comments

  • Chirag V Sheth says:

    Clinical reference for this study

  • Meenu ji says:

    If ct value is explained visually, it will be more clearer

  • ashok thathoo says:

    very informative

  • Bhavesh parmar says:

    My real time PCR report is
    N gene(CT) 29
    Orf Gene (CT) 28
    S gene (CT) 28
    So what is my CT value ?

  • Rajesh naik says:

    If CT value is 24.20 is high or low risk

  • Nilesh attal says:

    If ct value is 27 and 28 is it high or low infection for person above 50 years

  • Vikas says:

    My ct value is 16 whdit is myvstsus

  • Sunny says:

    Sir
    If n gene 12.85
    S gene 12.08
    Then what is Ct value

  • Subhash kakkar says:

    Iwas suffering from respiratory problem since 30th August and got my corona test on 3rd September positive with ctv23 and got admitted in hospital for 15 days during which I was put on oxygen for12 days. After spending 15 days in hospital I am under home quarantine till today for a weak, now I cNnot stand and walk even. For how many days more I would have to remain in isolation from my family. Can still I spread the virus among my family and friends. For how many days it will take me able to see my family or visitors and physiotherapist to provide
    me massage or physiotherapy to me

  • Sarvesh says:

    N gene – 23
    Orflab -21
    S gene – 22

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