“RAT Negative, PCR Positive” : Two Interpretations

“Antigen Negative, PCR positive.”

What does it mean ?

interpretations at the end

Our knowledge till date:

Corona viruses are the simplest and most ancient living things (?) on this earth. They just have a single strand of RNA inside their outer shell. This single RNA strand codes for all the living thing about it: the process of infecting humans and killing them.

This single strand is surrounded by a coat which consists of few proteins. That is all, Period.

Proteins are also called antigens as they can initiate an immune reaction in a host.

A SARS virus has got no heart, no brain or kidney not even a sperm or ovum to carry on its progeny. Unlike any other living thing, it does not eat, sleep, urinate or pass stool. But it multiplies. For this, it has to infect a living thing. In case of SARS, this living thing is a human lung cell. It is equipped with a spike protein that fits into the ACE pore on our lung cells. Once inside, it uses another of its personal protein- a Polymerase (a stitcher) to stitch new genomes inside our body. It also needs one more protein, a Protease ( a scissor) that trims the loose ends of this stitched fabric to unpack brand new daughter viruses. 

Thus each SARS virus has a Spike: a sort of a smart-key, to enter inside human cell and two enzymes to churn out thousands of daughter cells. That’s the thing that matter for us. Period.

We use

the Spike protein to manufacture Vaccines that will block its entry.

And two drugs, Molnupiravir ( blocks Polymerase) and  Paxlovid ( Protease blocker) to prevent its multiplication inside our body.

Testing-

Now, consider this carefully.

We have developed two types of tests to detect this virus inside our body. Each test targets different elements of the virus.

1. Rapid Antigen test (RAT): 

It detects the protein on the surface of the virus. If it is positive, you are bound to harbour the virus. because once the virus is dead, our system will break down all its protein. But the concentration of the protein must be sufficient enough to raise an alarm. Thus this test will miss smaller viral load. A condition called false negaitive. But when positive, it indicates infectiousness.

2. RTPCR Test- 

In this test, we try to detect the RNA at the core of the virus. RNAs are chemically Nucleic acids. The  nasal sample is churned in a liquid to extract all Nucleic acid present in it. A sophisticated machine, Thermal Cycler, amplifies the Nucleic Acid content and stains them.

This is a multiplier test. That means the machine amplifies the Nucleic acid content with each cycle, till it can read them. So it can detect very minute amount of nucleic acid in our sample. CT value is the number of cycles the material has to be amplified to detect the Nucleic Acid. Hence, higher the CT value, lower is the quantity,

There is one more caveat. When positive, it certifies that Nucleic Acid akin to SARS COV2 is detected in the sample. The test does not differentiate between live or dead or any old fragmented virus.

3. Life cycle of Omicron: 

The Virus has changed. Omicron behaves differently than its fore fathers, the wild wuhan and Delta strains.

Here is the new time table.

D-0:

Let us call the day the Omicron enters our body as D-0.

Now, the incubation period has been reduced to 3 days.

D-3:

I shall get fever, sore throat, dry cough and body pain or I may remain asymptomatic.

D-7:

The disease is over. I will no more be infective.

Infected versus Infectious:

Infected means I harbour a live virus inside me. But infectious means I have sufficient quantity of the virus in a strategic position ( in my nose or upper part of airway), so that it can dislodge during a bout of cough or vigorous breath and enter your nose.

Omicron like the earlier variants of the virus are infectious 2 days before the onset of symptoms to 3-5 days after this. That counts to 7 days.

The virus enters us through our nose and mouth not by blood or urine or skun.

In the above cases, the interpretations of 

“RAT -ve, PCR +ve” depends on the day the test is conducted.

If detected on:

D3 –

The viral load may not have been built up in me. RAT can be negave. But a PCR test will pick up the virus. This is called RAT false negative , even though I have got the infection.

If detected on

D10-

My RAT will be Negative but PCR will be Positive. PCR will remain positive till all the minute trace of NA are cleared from my nose. This can take 10-12 weeks.

PCR Positive is not significant after 10th day of infection.

Infected and infectiousness are two different things.

PCR test may pick up the rare case of Covid-19 that is missed by the Rapid test, RAT will pick up all the infectious persons.

Therefore while USA has ended isolation 5 days after you test positive, GOI, MOHFW has terminated Isolation after the 7th day.

Rationality:

If my pharmacist is positive today, there is 70% chances that it will be Omicron. He will remain asymptomatic, if he has no co-morbid conditions.

There will be very few harm, if on the 8th day, my oharmacist uses a N95 mask and dispense medicine rather than staying at home. Otherwise, the way Health Care Workers ( HCW) are getting infected, the routine business in health care is going to stop.