• August 4th, 2020

Covid-19 testing: From swab to result… a behind-the-scenes look at the steps involved



The Namibia Institute for Pathology (NIP) has ramped up testing for Covid-19 in recent weeks, despite a backlog of cases. This week, New Era had the opportunity of witnessing first-hand the testing process at the NIP Windhoek laboratory. 
Testing for Covid-19 is a process that is cumbersome, intense and sensitive, according to medical technologists employed at NIP when New Era joined the team for a typical day at the frontline. We arrived at the NIP laboratory at 08h00 on Monday morning and already found medical technologists preparing for the day ahead by changing into personal protective equipment (PPE). 

The day starts off with a morning meeting chaired by the chief technologist. At this meeting, the team discusses challenges experienced from the previous day before moving to their designated duty desks to kick-start the production process. 
The technologists responsible for receiving and sorting out samples operate from their desks, while the next step of handling is done from the biosafety cabinet. 

There are more than 10 technologists in the laboratory, excluding those that are helping out to reduce the backlog. We also observed that there is an excess workload on Mondays due to the weekend backlog. It is an all-hands-on-deck approach and one that requires a high level of concentration to avoid contaminating the test results. Not even cellphones are allowed inside the laboratory. 
The NIP uses a molecular assay to diagnose Covid-19. The polymerase chain reaction (PCR) techniques are used to make copies of a targeted piece of the virus’s ribonucleic acid (RNA).

Steps 

Receiving 
The first step of the process is receiving the sample in the laboratory. The medical technologists receive samples in sealed containers carried in yellow plastics accompanied by forms with the patients’ details. They then create a unique number that will be used to create a worksheet. The process of receiving takes between two and three hours. After creating a worksheet, a barcode is verified to ensure it matches with the submitted patient forms.

Sorting and matching
The next stage is sorting and matching. During this process, technologists sort samples and classify them according to their merits, because some are considered urgent, critical and others normal. The samples that are marked urgent and critical are given priority. During this step, the technologists also confirm whether the tubes are properly sealed and labelled with correct names and reference numbers. 

Verification
This process entails ensuring the accuracy of name, case number as well as the unique number assigned to every sample.  

Worksheet and labelling 
The next step is worksheet and labelling after verification of the sample. Lab officials create the worksheet by entering the unique and case numbers created. The worksheet also contains two controls (negative and positive) as well as a space for comment. The barcode stickers are then printed out and used to label the tubes carrying the specimen. The information is also scanned and entered on a system for capturing, making it easier to access and track. 

Manual extraction
The next step entails manual extraction for RNA. In this step, the RNA is separated from the sample that has been received. This process will then choose 94 samples for extraction because the instrument (Abbott molecular Covid-19 test) can only take up to 94 samples.

Incubation
The 94 extracted samples are then placed in the incubator for 10 minutes to kill the virus.

Automation extraction and expose procedure
After the incubation, an automation extraction and expose procedure is done using the testing instrument. Physicians are able to access critical information by early detection of pathogens and subtle changes in the patient’s genes. It does both extracting and exposes the sample for amplification. The controls are there to guide the process which takes three to four hours.

Amplification
During the amplification process, the reverse transcriptase is added to RNA (94) tubes to convert it to deoxyribonucleic acid (DNA). The DNA is then added to a primer. The primers act as the foundation for the targeted DNA to be copied. The genetic materials from the virus are then copied in a PCR machine that runs several cycles. If the person is infected with Covid-19, after a few cycles a single strand of DNA will be produced during this stage. The technologists explained that after each cycle, more copies of DNA are produced up until the cycles are completed or the primers have been used up in the reactions. This process can produce millions of copies of the DNA. 

Addition
In the addition process, fluorescent dye is added to the copies of the DNA to determine whether the outcome is positive or negative. This process takes 30 minutes. 

Resulting 
The last process is resulting. This is where the outcome is confirmed and approved by the head of department before  being signed off by the surveillance officials from the ministry of health. The information is then handed over to the minister for public announcement. New Era observed that the entire testing process could take up to eight to ten hours depending on the samples processed. By the time we left the laboratory, it was already 18:30 and no single result was produced as yet, as the process only finished at around 20h00. – ljason@nepc.com.na 
 


Loide Jason
2020-07-30 15:19:13 | 5 days ago

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