PCR testing to identify COVID-19 cases: What is Egypt’s policy?
Aside from the official protocol, the availability of PCR testing appears to vary across government sectors and within the medical community itself.
Illustration by Soheir Sharara

For almost a month in her daily updates on the number of new COVID-19 cases in Egypt, Health Minister Hala Zayed linked all newly-announced cases either to people who had come into contact with previously confirmed cases, or to people returning from abroad. That phrasing was featured in each of the ministry’s daily press statements from March 6 through April 7.

During the initial period of the outbreak of the coronavirus pandemic in Egypt, the Health Ministry was using similar metrics to decide who would receive a coronavirus test, known as a polymerase chain reaction (PCR) test: either people returning from abroad, or people who were in contact with a previously confirmed case who were also exhibiting symptoms of COVID-19.

Zayed emphasized the state’s policy towards limited testing on March 27, saying “It’s wrong to test the entire population.”

But since April 8, when Zayed stopped identifying the source of new infections, the ministry reduced the requirements for a free PCR test to anyone exhibiting severe symptoms of COVID-19, especially pneumonia, regardless of whether they were in contact with a previously confirmed case or not.

Mada Masr spoke with doctors and nurses to understand the Health Ministry’s policies towards PCR testing and how it has played out on the ground, with medical workers on the front lines of the pandemic taking exceptional measures — sometimes circumventing protocol — in order to secure and conduct PCR tests.

An evolving protocol

Ahmed Abdallah, a doctor at the Damietta Chest Hospital, says that after the number of confirmed cases in Egypt passed 1,000, the Health Ministry sent all hospitals a new protocol for running PCR tests. According to this new protocol, doctors needed to verify a combination of symptoms in suspected COVID-19 cases before authorizing a PCR test.

Patients first undergo a physical examination and have x-rays and lab work done. Doctors fill out a form authorizing a PCR test for patients with a high fever and a severe cough, and those whose x-rays show that they are suffering from pneumonia. Patients who complain of difficulty breathing or aches in the throat and chest but have inconclusive lab results are asked to return after two or three days for another examination, Abdallah says.

Before the total number of confirmed cases in Egypt passed 1,000, hospitals were using a points system to determine whether further lab tests were warranted, which could include a PCR test, according to Amir al-Bastaweesy, the head of cardio-thoracic surgery at Port Said’s Health Care Authority.

Doctors scored patients on a scale of one to 10 to determine the probability of infection. For example, if a patient had been in an area with confirmed COVID-19 cases — such as an office, a factory, street or neighborhood — they would receive one point, Bastaweesy explains. If the patient complains of a high fever, cough, difficulty breathing, fatigue or exhaustion, they are assigned one point for each symptom. Points are also added for elderly patients and anyone who suffers from a chronic illness. If the tallied score is eight out of 10 or higher, doctors transfer the patient to the nearest fever or chest hospital to do lab work to verify their symptoms and assess whether a PCR test is warranted, Bastaweesy says.

The point system has since been abandoned. Now, all patients arriving at hospitals complaining of symptoms consistent with the coronavirus automatically receive a blood test and a chest x-ray, Bastaweesy says. If the patient is diagnosed with pneumonia, doctors admit them to the hospital and take two swabs from the nose and throat for analysis using PCR technology.

If the test comes back positive, the patient is transferred to a quarantine hospital. If it comes back negative, the patient stays at the hospital for another three days to run the PCR test again. 

A negative PCR result does not necessarily mean the patient has not contracted COVID-19. They may have indeed contracted it, but the virus may not have replicated enough to show up in swabs collected to test for the virus from the mouth, throat, trachea, or elsewhere.

Bastaweesy says that PCR tests often result in “false negatives” — when the test comes out negative for patients infected with COVID-19. Therefore, according to Bastaweesy, hospitals in Egypt determine whether a patient has contracted COVID-19 by mostly relying on chest x-rays and blood tests rather than a PCR test.

Maha Gaafar, a professor of clinical pathology and medical analysis at Cairo University’s Faculty of Medicine, says that PCR tests can be misleading and that studies conducted on the coronavirus during the past month show that x-rays and lab tests can also be effective in confirming a COVID-19 diagnosis, especially through complete blood count (CBC) analysis. 

Research has shown that CBC results showing a white blood cell count lower than 4,000 may indicate a COVID-19 infection (white blood cell counts in adults normally range between 4,000 and 11,000). Other indicators can be found in x-rays and chest scans, where positive cases exhibit clots that take a certain shape that doctors can easily identify, she explains.

Those with mild symptoms can only undergo a PCR test if they have been in contact with a confirmed COVID-19 case, as per the Health Ministry protocol. So, if there is no prior contact with a confirmed case, symptoms must be severe to warrant a test. 

The World Health Organization (WHO) said on March 28 that Egypt has the capability to conduct up to 200,000 PCR tests. As of April 23, the Health Ministry had conducted over 90,000 PCR tests, according to the ministry spokesperson. In addition, 200,000 rapid diagnostic tests had also been conducted. 

According to Bastaweesy, the ministry has significantly widened the number of PCR tests being conducted. At the beginning of the outbreak, PCR testing was limited to fever and chest hospitals. Now, he says, the ministry is supplying PCR testing kits to smaller health units.

Abdallah says no country in the world can test its entire population. The correct approach in dealing with an infectious disease, he says, is to ration testing. If the state decides to take swabs from 100,000 citizens and they all come back negative, many could nevertheless contract the virus afterward.

Who is able to get a PCR test?

Aside from the official protocol, the availability of PCR testing appears to vary across government sectors and within the medical community itself.

Prisons are a case in point. On April 16, the Interior Ministry announced in a video posted on its official Facebook page that it had taken precautionary measures and conducted a full medical review of detainees to ensure that there were no COVID-19 cases inside Egypt’s prisons. The video featured footage of several detainees having swabs taken for PCR tests, including the prominent journalist Khaled Dawoud, who has been held in remand detention since September, and activist Ahmed Douma, who is serving a 15-year sentence.

The Interior Ministry did not indicate how many detainees have been tested. In addition, prison visitations have been suspended since March 10, which means families have not been able to check on their imprisoned relatives for the past seven weeks as the virus continues to spread in Egypt.

Meanwhile, a judicial source told Al-Watan newspaper on April 12 that, consistent with the Health Ministry’s plan for early detection and “community protection,” medical examinations were conducted on all deputy ministers and lawyers working at the Justice Ministry. The following day, the ministry issued a press release saying that all tests came back negative.

The Justice Ministry statement did not clarify why the tests were conducted — whether some of its staff were exhibiting symptoms or had come into contact with a confirmed case, or whether the tests were linked to a wider state plan for early detection within certain government bodies.

While the Health Ministry’s new protocol has widened the scope of tests being conducted, not everyone suspected of having contracted the coronavirus is provided an equal opportunity to get a PCR test.

Sorayah al-Sheikh, a member of parliament representing Shubra al-Kheima, recalls witnessing 46 members of one family contracting the virus in the neighborhood of Bahteem, including two who died as a result. According to Sheikh, the story began on March 27, when a 55-year-old poulter went to the Nile Hospital for Health Insurance in Shubra al-Kheima complaining of high fever and bone pain. Doctors diagnosed him as having a regular cold, prescribed painkillers, and asked him to return two days later for re-examination. Four days later, his symptoms worsened. After his fourth visit to the hospital, doctors admitted him and took swabs for a PCR test, which came back positive.

The Health Ministry’s preventive medicine department then took swabs from people he had been in contact with and found that 45 members of his family had contracted the virus, including his 73-year-old mother who died on April 6 before reaching a quarantine hospital. The next day, the poulter died. None of his family members were able to attend the funeral because they had all been transferred to quarantine hospitals.

Meanwhile, medical workers who are on the front lines of the pandemic and are highly susceptible to infection find themselves having to use personal and professional ties in order to get tested. Hoda Yehia, a nurse at the New Qasr al-Aini Hospital, managed to undergo three PCR tests in under a week. She was favored due to her strong relationships with medical colleagues and to the interference of the head of the Nurses Syndicate on her behalf.

Yehia, who is now in quarantine at the Imbaba Fever Hospital, tells Mada Masr that she began to feel body aches and fatigue on Friday, April 10. The following day, she developed a fever of 38 degrees Celsius. At the time, she was working a 24-hour shift at the thoracic care department. Yehia informed a colleague who, after examining her, told her she was suffering from a throat infection and recommended a chest x-ray if the symptoms continued until Sunday.

“My fever rose to 39 degrees on Sunday, so I went to the hospital and had regular x-rays taken. It showed pneumonia,” Yehia says. A doctor told her to head to a fever hospital immediately to undergo a PCR test but she responded that she was too fatigued and could not make it. The doctor negotiated with the hospital administration on her behalf, and throat and nasal swabs were taken at New Qasr al-Aini’s emergency room. 

Yehia returned home and isolated herself from her husband and children. The following day, her colleagues called and told her that the PCR test results came back negative. But her symptoms continued to worsen. On Tuesday, she had difficulty breathing, so doctors told her to come to the hospital for a CT scan. The scan showed that she was suffering from pneumonia and that there were clots in her lungs, pointing to a coronavirus infection.

“They told me, ‘the scan indicates it’s coronavirus, but the PCR test says it’s not, so we can’t send you to a quarantine hospital. Isolate yourself at home. I returned home on Tuesday. The next day, they told me to come for another swab, which they took, and I went back home again,” Yehia says. On Wednesday afternoon, she was experiencing breathing difficulty. After speaking to her colleagues, an ambulance was sent to her home to take her to the Imbaba Fever Hospital, but she refused: “I told them that I don’t need an ambulance. I was afraid of people kicking us out of the apartment if they find out I contracted coronavirus. I bore the load and took a cab to the fever hospital.”

“Everyone interfered on my behalf. The head of thoracic care at the [New Qasr al-Aini Hospital] and the head of the Nurses Syndicate called the director of the Imbaba Fever Hospital. They even cleared a special room in isolation care at the Imbaba Fever Hospital for me,” Yehia says. 

“When I reached the fever hospital, they told me that the second swab they took at [New Qasr al-Aini Hospital] also came back negative. They took two other swabs from the nose and throat. While we waited for the results, they thankfully gave me medication provided to patients in quarantine hospitals and medication to dissolve the clots,” she says.

Exceptions for medical staff tasked with detecting and treating COVID-19 cases extend to private hospitals. A nurse working at a private hospital in Maadi, who asked to remain anonymous, tells Mada Masr that swabs are regularly taken to conduct PCR testing for the hospital’s medical staff. She says the private hospital cut a deal with officials at the Abbasseya Fever Hospital to analyze swabs from its medical staff as well as patients suspected of being infected with the coronavirus. If the results come back positive, the fever hospital informs the Health Ministry directly. 

As the number of cases in Egypt began to increase, the same private hospital was able to obtain several PCR testing kits to conduct tests in its own lab. This is in contravention to warnings by the health minister against any private hospital violating ministry policy by running its own PCR tests.

The nurse says the private hospital took swabs from her for PCR testing in March and April, which stands in contrast to her experience at the government-run New Qasr al-Aini Hospital, where she also works. Despite an increasing number of doctors and nurses contracting the coronavirus at New Qasr al-Aini Hospital — including a nursing supervisor — the hospital’s management refused to take any swabs from the nurse or over 100 of her colleagues as they did not exhibit any symptoms of the coronavirus.

The WHO has repeatedly called on Egypt to increase testing across the country and not to limit tests to patients whose symptoms have already progressed. John Jabbour, the WHO’s representative in Egypt said that conducting testing in a methodological and scientific manner will help in detecting new cases and verifying official data about the size of the outbreak.

“I wish everyone would get swabbed, I think that’s the solution,” says Abdallah.


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