SARS-CoV-2: PCR, Viral Load and CTs

There is no doubt that PCR (Polymerase Chain Reaction) is the star test of this pandemic, being widely used worldwide for the identification of SARS-CoV-2.

In Life Length we have multiple posts in which we explain how PCR works, but, in summary, this technique mainly isolates and amplifies the viral RNA, in such a way that several amplification cycles are carried out to produce a detectable amount of genetic material. .

The minimum amplification cycles to detect RNA are called CT (Cycle Thresholds).

In our reports, you will find 3 different values of CT because our PCR detects and amplifies 3 different regions of the coronavirus genome – ORF 1ab, N Protein and S Protein – unlike other laboratories that detect only 2 regions.

You will also find in our reports a section that indicates the viral load that results from calculating the weighted average of the CTs of each gene.

In this way, the greater the number of cycles necessary to detect a gene, the less amount of this gene is in the initial sample. Therefore, it can be said that the CT value provides an inverse measure as follows:

Values between 0 and 25: High viral load
Values between 25 and 32: Average viral load
Values greater than 32: Low viral load

Therefore, as we indicated in our results reports, lower CT numbers indicate a higher viral load, which means a more severe case; greater contagion capacity and, in general, longer time to recover and obtain a non-contagious (negative) result.

Why do we indicate virality and CT in our reports? What has led us to provide this level of detail that other laboratories do not provide?

As experts on the subject such as Dr. Julio García, spokesman for the Spanish Society of Infectious Diseases Microbiology (Seimc) have already communicated in the media: “A higher viral load leads to greater infectivity: there is more of the virus and it is more likely that those viruses reach a susceptible host. ”

Logically, a greater capacity for infection leads to a greater number of potential infections, especially if prevention measures are not followed properly.

Knowing our own infection capacity can be essential to prevent new infections around us.

In addition, the 3 different CT values can be useful in identifying the strains or, better said, variants that are appearing in recent months.

In Spain so far 2 variants of COVID-19 have been detected; the British and the South African variant. Although the N Protein and ORF1ab regions remain intact, both variants present mutations in the S Protein gene region, making it undetectable. This leads to positive samples in SARS-CoV-2 without the S Protein gene – which is not amplified in any cycle – CTs of this region with very high or indeterminate values are given. That is, if a high viral load is observed in N Protein and ORF1ab, but low or undeterminated in S Protein, it is most likely a sample from a patient infected with the South African or British variants.

For more information on the new variants, you can consult our previous blog on this topic.

Although there is currently an open debate within the scientific community about the usefulness of the CT value (since it is an imperfect measure), what is clear is that having a higher viral load is associated with being more infectious and that the value of CT is the only tool that PCR gives us to determine this viral load.