Dental Tribune India

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. 

89 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

  • Staro says:

    keep in mind that Ct value is a direct function of the concentration – once you add 100 ng of RNA isolate to the RT reaction – you may get Ct 30; if you start a reaction with 1 microgram – Ct will be shifted to 25, etc. You use commercial positive and negative control samples for gating.

  • Dhruba Raj Mishra says:

    my PCR test conducted on 29th is as under:
    N-gen Ct-value =16.8
    E-gen CT-value =15.6
    ORF 1ab CT Value = 16.2
    What is the range to be negative and positive , i am 64 years old, yr answer is expected

  • Pratap says:

    my PCR test conducted on 01th is as under:
    N-gen Ct-value =16
    E-gen CT-value =16
    ORF 1ab CT Value = 16
    I am 32 years old, yr answer is expected to how will be my report in negative after how many days. I lost my Smell and taste feeling. Pl Doctor or any suggest me for best results.

  • Yogesh Shrestha says:

    MY grand daughter is 6 Year old
    Her PCR Test conducted on 4th October 2020
    ORF1ab gene=29.71
    N gene = 30.64
    E gene = 27.81
    How we can safely accompany her

  • sanjay says:

    If the E-Gene ct value is 31 and orf 1ab-Gene ct value is also 31. What its mean. will this person can spread infection to other family members.

  • prakash dhavale says:

    test detected positive
    My CT value is 13, what is means
    it is high or low
    Please answer

  • Nayankumar Modi says:

    My CT value 31.83 pl advise

  • KP Chhusyaki says:

    How can I determine my Ct value from this Real Time RT-PCR positive as N gene-24, ORF-20 and S gene-20?

  • FuriousFuk says:

    I wish they just put the freaking Ct Values in a table with corresponding implications! Dafuq i just read!? i need a Semester of Bio-English terms to understand what they imply…

  • Kabiraj says:

    Hi, My name is Kabiraj and I am 62 years male. My PCR test result shows:
    SARS-COV-2 (ORF1ab gene) : Detected ( CT Value: 15.18)
    SARS-COV-2 (N gene) : Detected ( CT Value: 15.61)
    SARS-COV-2 (E gene) : Detected ( CT Value: 15.83)
    What it suggests?

  • Akhil Reddy says:

    China considers CT value of 40 and above as non-infectious. India considers CT value of 35 as non-infectious

  • Ajay Sinha says:

    My Ct value is 37+
    what does it mean when my anti body test is 5,97?

  • Sunil kumar jena says:

    Ct value <35…it will be risk ??
    Target gene=33
    E-gene=32

  • Sunil kumar jena says:

    Ct value <35…it will be risk or not ?
    Target gene=33
    E-gene=32

  • GR Choudhary says:

    My ct value is e 19 and n 19.62

  • Anil Jain says:

    यदि E- Gene CT -18 hai aur ORF 1ab bhi 18 hai to kya ye उच्च जोखिम है या निम्न जोखिम है, कृपया बताएं

  • Amit Parulkar says:

    My rt pcr test on 15th showed detected (22)
    What kind of risk do I have, I do not have any symptoms

  • Reena Kanuga says:

    My CT value is 15 pls reply

  • Om Shrestha says:

    N gene ct value is 28
    Orf ct value is 29
    For 3 yrs child what does its meaning
    N how can we improve the value at home isolation

  • John Tallinn says:

    I do not believe the FDA allows labs to report quantitative data under EUA.

  • Past 22 days I tested my covid and it was coming out positive and my ct value is 22 . Then after again 17 days I have tested my covid and found positive .Does I am infectious now?? And what gonna be my ct value no

  • Ravi says:

    I have tested for Covid and CT value is observed as >30. What it indicates and how many days it will take to recover.

  • Somnath Biswas says:

    Ct.value is 31 ,no symptoms ,already 7 days have passed is the patient can spread covid now

  • Somali Mohanty says:

    I was detected as positive with CT value 32.58 and I do not have any symptoms. What risk do I have currently and in future?

  • Sachin says:

    my Brother wife was detected as positive with CT value E-Gene- 31.12 And RdRP/N 31.12 and do not have any symptoms. What risk do I have currently and in future?

    And My Brother Son corona positive , do not have any symptoms. What risk do I have currently and in future?

  • Vishal kumar says:

    I m 38 years old boy, corona’s symptom (fever & cough) was appeared on 27/09/2020 whereas i was got tested rt PCR on 04/10/2020 and the result was Confirmatory Gene Ct Value :-25. Accordingly, Medicines were prescribed by the Doctor to me on 05/10/2020. I faced Fever continuously till 11/10/2020 and cough till 16/10/2020. Further, i was got tested rt PCR on 21/10/2020 and result is Negative. Sir, my questions are as under:
    1) what does its value mean “Confirmatory Gene Ct Value :-25”
    2) can i break my isolation period.

  • Bijay says:

    My PCR test conducted shows ct value of 18 to. All the three parameters. What does it mean for me a 62 year diabetes

  • Trina banerjee says:

    My father’s e gene ct value was 32.2
    And orfla gene ct value is 32
    What does that mean, please do answer

  • Biman Kumar Kundu says:

    My son age 32,was having cold and slight sore throat on 23rdOct.On 24th Oct visited Doctor for medical care.Doctor gave medicines and adviced for Covid 19 test. Result came+be with Ct vaue 26.Pl advice

  • MUKESH PANDYA says:

    my wife 61yrs old, RT PCR value 32. 10th day after detection she has been asked to discharge. what are the possibilities of spreading virus. does she require home quarantine and how many days. what are the chances of repulsion. what is the best practice to stay healthy

  • Rakesh says:

    E GENE 31; ORF Lab 33; N GENE 33.
    Please tell me my ct value and my risk.

  • Ram Krishna Shrestha says:

    My N-Gene is 33
    E-Gene is 32
    And ORF 1ab is 32
    What about may covid risk is covid infection transfer to Other people or not

  • Tarun Mankad says:

    My son’s e gene, n gene and ORF 1ab all are 24 what is intentisity ? Pl send response immediately.

  • Somnath Dey says:

    My RT PCR report is showing
    CT value (RDRP / N gene): 32.54
    CT value (E gene):30.83
    I don’t have any symptoms.
    What is my risk and transferring to others also.

  • RAHUL SAJAN AHIRE says:

    My father CT values are n 20 orf1ab 21& s21. His age is 66.admitted to hospital. Please suggest his infectivity and further care to be taken care.
    Please guide

  • Manoj kumar says:

    My RT PCR report is showing
    CT value (RDRP / N gene): 33
    CT value (E gene):3
    I don’t have any symptoms.
    What is my risk if I have already completed 14 days isolation.

    Please suggest me whether I can come from isolation.

    Answer from Dr Rajeev Chitguppi

    If you never developed/ do not have any symptoms, you can discontinue your isolation and other precautions after the 10th day of testing PCR positive. You have already completed 14 days.

  • Sudha says:

    My husband ORF gene 18.33
    N gene 19.51
    S gene 17.48 is this dangerous r not

  • Priti says:

    My husband’s report is positive with N gen ct-16.17 & RDRP
    Ct-17.12
    IS IT Serious or normal or he can spread that virus

  • Neha Gangwal says:

    RdRp gene 26.95
    E gene 25.94

  • PARVEEN says:

    MY WIFE AGED 54 HAS BEEN DIAGNOSED COVID POSITIVE TODAY WITH CT VALUE
    E Gene 19.270 and
    N gene\RDRP 19.450
    PLEASE SUGGEST HOW TO DEAL WITH IT

  • Nitin sahni says:

    My covid report is negative but my mother and father infected their covid ct is 15.98 for mother her age is 57 and father 16.11 and he is 60 years old. Is this cureable????

  • Nirmesh Singh says:

    My test report has come today, I am positive & My CT value is 22, what does this mean.

  • Rachs says:

    My CT value is 30 can i mixed with my other family members.
    Is it safe?

  • sanjay kala says:

    my CT value is 15.33(SARS CoV-2 Ct Value 15.33), 1 can I spread the disease among family members and for how many days. what medication I should take…my throat is bad and I have fever about 102.6.

  • Jigar Shah says:

    On 10th Nov my rt PCR count is 27
    Is it high viral load or I have to be quarantine

    I am quarantine from last 15 days

  • Sheetal says:

    My mother is covid positive with CT 24.5 ..which stage of covid indicates this value

  • Anil Pandit says:

    My E GENE Ct VALUE is 24 and RdRp GENE Ct VALUE is 26. Would like to know about infection levels and what is the possibility of spreading this virus to my family. Don’t have any problem with me.

  • Anita says:

    My husband N- Gene ct value is 31:00 & CRF- 1ab ct value is 29:00 what is the meaning of this value

  • kapil khanal says:

    My ct values are as follows-
    N-Gene=34
    E-Gene=34
    ORF 1ab=33

    What do I do? I don’t have any other symptoms except partial smell loss.

  • Krishna Keshaw Verma says:

    My E gene 23
    ORF 1ab 25
    N gene 25

    What is my ct value

  • arun anand says:

    i was negative in rtpcr but still have irritation in throat and whhezing while breathing

  • Ajay Pal Sharma says:

    I was tested positive on 5th August & negative on 13th August discharge on 15th August now on 13th November I again tested positive with CT value of 26 with no symptom is I can spread the desees or not & what medication I take

  • Jhulen Shrestha says:

    ORF 1ab 33,
    N Gene 35,
    E Gene 34
    After 16 days I don’t have any symtoms. What is the meaning of this CT value?

  • Sini says:

    My ct values is 18 advice

  • Earven says:

    Need to know E gene and N gene meaning and calculation . What is CT value . Is this sum of E gen and N gene CT VALUE
    E Gene 12.450
    N Gene\RDRP 13.380

  • Pradeep says:

    If my COVID -19 RNA VIRUS PCR
    Screening (E gene) Ct Value Confirmatory (RdRp & N gene) Ct Value
    POSITIVE (LOW VIRAL LOAD)
    24.95 26.75
    Negative
    RT-PCR
    and my age is 56 what is it , I kno it’s a low virus detected and non communicable but what are the risk factors

  • Praveen Goyal says:

    My N gene CT Value is 19.82 and ORF1ab gene CT value is 17.21. my age is 35 i got positive report.
    pls advise

  • Sayantan Samanta says:

    Ct VALUES
    SARS-COV2 (COVID-19 Virus) QUALITATIVE, REAL TIME PCR POSITIVE E GENE :32.9
    RdRp + N GENE :33.6
    It is low or strong ??

  • Pankajkumar omprakash gujarati says:

    N gene(ct value)15
    ORF 1ab(ct value)15
    S gene(ct value). 16
    It is low or strong

  • Pankajkumar omprakash gujarati says:

    N gene(ct value)15
    ORF 1ab(ct value)15
    S gene(ct value). 16
    My report pls tell me law or high virus

  • Usha Bisht says:

    On 5th Nov,2020 tested with Covid Positive with ct 19 and now on 21st again tested with Covid Positive with ct 30. Now, when I have to test again for negative

  • Rinky says:

    my E gene is 24, orflab is 25, N gene is 26 what it mean

  • Gaurav Khanna says:

    Sir
    My age is 37 years

    My report Target Gene CT Value s 31.44%

    Covid19 is detected

    Same is done from Throcare

    Please confirm this is normal or Middle or High range

  • YSJAMWAL says:

    N gene(ct value) 22.83
    ORF 1ab(ct value) 21.72

    My report pls tell me low or high virus

  • Deepak Kumbhat says:

    N- Gene ct value is 18
    ORF1ab- Gene ct value is 18
    Age 46 male
    Please advice

  • Harishchander says:

    E gene Ct value 25.14
    RdRp gene Ct Value 26.96
    With result Positive
    Now i have no any type problem with my body.what I do for Negative report. Is it high or low risk. Please guide me

  • Harish chander says:

    E gene Ct value 25.14 and RdRp gene Ct value 26.96 with Positive result. I am 52years old male. I have no any type problem with my body. Now I what to do for Negative. Is it high or low risk. Please guide me. Thanks.

  • Rashmin Vaja says:

    My wife sangeeta is admitted in bkc covid centre at phase 2 , CKD.
    JUST NOW I got her rt CPR report is positive.
    ORF 1ad gen is 23.4

    N gene is 25.62
    I am very frightened. Please explain me what is condition of patient. Is she out of danger.

  • Ritu Patel says:

    My name is Ritu Patel
    Postive on 20th nov 2020 ct value (32)and after 14 days reports are this
    ORF 1ab Gene : * TARGET DETECTED
    N gene : * TARGET DETECTED
    Conclusion : * COVID-19 POSITIVE (CT VALUE: 28-29 )
    How many days to recover for nagative?

  • HIMANSHU KUMAR says:

    MY CT VALUE IS 36 AFTER 18 DAYS OF FIRST TEST WHEN MY CT VALUE IS 19.
    PLEASE SUGGEST SEVERITY OF DISEASE.

  • MM sector 9 says:

    My N-Gene ct value is 33 and ORF1 ab-gene ct value is 31
    test 13.12.20.i am 68 years old. No symptom other than cough which is chronic.
    How to interpret it.

  • dipesh parekh says:

    If CT value is 27.71 is high or low risk

  • Vinod Kumar says:

    if CT is 17.49 is it low or high risk

  • NISHITH V SHAH says:

    My Rt pcr done on 25 dec. Result on 26dec. Ct value 20. It is low risk or high risk. N gane and S gane they write “Detected ” . Pl give me reply. Thanks

  • RAJENDRA Wadi says:

    My ct value is 23 what it means.

  • SOHANLAL says:

    pl.how to take care of patient.
    what is real treatment.

  • Nadim Daher says:

    My ct value is 23 what it means and what is the estimated time to quorantine isolate at home my age is 81 years very mild symptoms

  • Nadim Daher says:

    What it means ct 23 and how many moredays of home isolatio and when I do new pcr test my age 80 years

Leave a Reply

Your email address will not be published. Required fields are marked *

© 2021 - All rights reserved - Dental Tribune International