He said the kits for the rapid antigen tests are being awaited and should be in Sri Lanka in about a week.

Another bone of contention among the public has been whether there is adequate RT-PCR testing and Dr. Herath says that on Thursday around 11,552 tests were carried out.

When asked whether there had been an RT-PCR machine breakdown, he said that arrangements are being made to repair the machine at the Mulleriyawa Hospital laboratory over the weekend.

With regard to the source of the latest clusters, he said that they are looking into it, but went onto explain that taking all measures, Sri Lanka was able to limit to a minimum, the virus leaking into society. These measures included limiting people coming into the country, putting them under quarantine, multiple RT-PCR testing and home quarantine.

“But there is always a small chance of a leak and that is not unexpected. It could be 1 in 100; 1 in 1,000; or 1 in 10,000. Even if it is 1 in 10,000, we have already brought almost 50,000 people from abroad, so there is a possibility that at least five people leaked into the community despite all these precautions,” he said.

Dr. Herath added: “This was expected because of the inherent nature of the barrier and protection methods. This is also why we have been urging people to practise preventive measures.”

Echoing similar views, Chief Epidemiologist Dr. Sudath Samaraweera said the source of the Minuwangoda cluster has not been found yet.

“We are still investigating the source,” he said, when asked by the Sunday Times about reports doing the rounds that it had begun with a flight crew of Ukrainian Airlines who had stayed at a hotel in Seeduwa.

Meanwhile, the Secretary of the Public Health Inspectors’ (PHIs’) Union, M. Balasooriya said that even though the Army Commander has stated something about a Ukrainian flight crew, the PHIs did not know about it.

“We were not involved in any investigation and this is why we are saying that there should be a deeper investigation,” he said.

With regard to the earlier quarantine process, Mr. Balasooriya said that people usually undergo the first 14 days of quarantining in designated centres or hotels under the supervision of the tri-forces, while the next 14-day home quarantine is under the PHIs in the respective areas where these people come back to.

He conceded that there have been co-ordination issues, as it was the returnees from abroad themselves who would inform the PHIs of their home quarantine. So there could be instances when these returnees do not tell the PHIs that they should be in home quarantine.

Usually the procedure is for the Epidemiology Unit to inform the regional health office, which in turn would pass on the information to the relevant PHI, he added. Regarding the change in the quarantining strategy, Mr. Balasooriya said that people were cooperating and were comfortable in their own homes.

Dr. Eranga Narangoda

All about COVID-19 and how it is handledSome invaluable insights are given to Sunday Times readers by Consultant Physician Dr. Eranga Narangoda who was at the forefront in the treatment of COVID-19 patients in Sri Lanka, at the National Institute of Infectious Diseases (NIID), from the start of the outbreak. Since August, he is attached to the Homagama Hospital.

Pointing out that those who get infected with COVID-19 can be grouped into three, Dr. Narangoda says that they are those with ‘mild’ disease; ‘severe’ disease; or are ‘critically’ ill.

Thereafter, he explains the symptoms and period of infection (when a person has the live virus in his/her body) of each group:

Mild disease – the main symptoms include fever, dry cough and sore throat. Even though in other countries patients also have shortness of breath, this symptom is not seen commonly among Sri Lankan patients.

Those with mild disease would be infective (others can catch COVID-19 from them) 2 days before the onset of symptoms and normally 7 to 10 days after developing symptoms.

After 10 days, the patient is not infective and may be discharged without an RT-PCR test, thus reducing the burden on the laboratories doing these tests.

In mild cases, the treatment is the management of symptoms: if there is cough, cough suppressants are given and for fever, antipyretics.

·      Severe disease – the two main symptoms are a higher respiratory rate and lower saturation of oxygen in the blood.

The respiration rate is the number of breaths a person takes per minute. The normal respiratory rate for an adult when resting is 12 to 20 breaths per minute. A respiratory rate under 12 or over 25 breaths per minute while resting is considered abnormal.

In the case of severe disease, the patient’s respiratory rate is over 30 breaths per minute and the patient becomes breathless. There are lung signs which are indicated by chest X-ray changes.

Meanwhile, the oxygen saturation level is how much oxygen there is in a person’s haemoglobin in red blood cells. The normal oxygen saturation level should be around 95–100.

Those with severe disease will be infective 2 days before the onset of symptoms and 18 to 20 days after developing symptoms.

The main treatment for those with severe disease is the provision of oxygen in the ICU and intravenous antibiotics. According to recent studies, there is also a place for dexamethasone in their treatment.

Critically ill – this is when the patient is in the ICU with organ failure, with vital organs being affected. These patients are on the ventilator.

Dr. Narangoda stresses that in addition to the three main symptoms of fever, dry cough and sore throat, which are also the symptoms of most common respiratory viral infections, there are two “more specific” symptoms linked to COVID-19.

They are:

• Altered taste
• Altered smell

“These two symptoms we don’t see in other respiratory diseases,” he says.

Pointing out that some of these symptoms persist for a few months after the patient has recovered, this Physician explains that these post-COVID issues include fatigue, breathlessness on exerting themselves, loss of appetite and changes in taste and smell.

“These may last several weeks after recovery, but don’t worry,” says Dr. Narangoda, adding that there is no need to test those people suffering from post-COVID syndrome. They are not infective as they do not have the live virus in their bodies.

Immunity from coronavirus

Once a person gets COVID-19, like most other respiratory diseases, the person is immune for about three months, explains Dr. Narangoda, reiterating that once that person’s antibody levels decrease, he/she can catch COVID-19 again. Therefore, the idea of ‘herd immunity’ does not really work. Even if a vaccine is produced after proper testing for safety and efficacy, people would have to keep taking boosters to ensure immunity.

This is why Dr. Narangoda urges everyone to take the simple precautions of thorough hand-hygiene, wearing face-masks and keeping a metre distance. Another very important point is not to touch the face, not just the nose and mouth but also the eyes, as the virus can enter the body this way as well.

Dr. Fernando believes that Sri Lanka may have had low-grade community transmission nearly all the time, but relaxing the social distancing measure over the months made it grow gradually. Thereafter, followed ‘super-spreading’ events, not confirmed as yet, such as the Minuwangoda and Peliyagoda clusters.

Here is Dr. Fernando’s analysis up to October 25:

October 15 – Fifty-year-old Patient A (who had got admitted to an outstation hospital’s medical ward on October 12) is transferred to the ICU around 3.30 p.m. Dr. X who attended on her from then on is not in Personal Protective Equipment (PPE) but wears two surgical masks.

Patient B who had got admitted to the medical ward of the same hospital on October 14 is transferred to the ICU on October 15 at 1.30 p.m. and Patient C from the oral and maxillofacial (OMF) surgical ward is brought to the ICU at 2.30 p.m. the same day. Patient A occupies the middle bed and Patients B & C those on either side.

Patient D is admitted to the same ICU at 5.30 p.m. after being brought to the OPD/PCU at 4.30 p.m. the same day with severe difficulty in breathing. His X-ray suggests pneumonia and he is kept in the ICU’s isolation cubicle and attended by Dr. X and other staff wearing PPE. He has to be intubated at 8.30 p.m. and is given CPR (cardiopulmonary resuscitation) by Dr. X and a nurse for 30 minutes before his death is confirmed at 10.30 p.m. Before that, at 9 p.m., a sample for RT-PCR testing is taken from him too.

When the sample is taken from Patient D, there have been no suspicion of Patients A, B & C being exposed to COVID-19. However, Patients A and B as well as D were known diabetics with very poor control. Patient A’s leg had been amputated. Patients A & B also had other co-morbidities. They had been transferred to the ICU from the same medical ward with a diagnosis of worsening “heart failure”.

October 16th night – Patient A is diagnosed with COVID-19 and transferred to the IDH. She dies 6 days later on the 22nd.

October 24 – Patient B, around the same age as Patient A, from the same outstation hospital dies of COVID-19.

Dr. X who spent the longest time, over 20 hours in the ICU with Patient A, was awaiting the first RT-PCR test even on October 25. Eleven days had passed by.

Some doctors who had got exposed to Patient A before and after Dr. X for much shorter durations (even for 5 minutes) had got their RT-PCRs while being quarantined in the same hotel.

Some background into the scene at the ICU

Dr. X spent significant time very close to Patient A, examining her, listening to her heart and lungs, taking blood-gases and also catheterizing her. Dr. X was in the ICU except for about three hours of intermittent sleep. She was wearing a KN95 mask and a surgical gown over her dress from 4 to 8 p.m. and changed it to PPE at 8 p.m. to intubate and resuscitate Patient D. Thereafter, she changed into a surgical gown again after the death of Patient D.

Since Dr. X had to remove the KN95 mask, she could not get another KN95 as each doctor is given just one mask, with a request that it be re-used. Instead Dr. X used two surgical masks, one over the other.

Around 1 a.m. on October 16, Dr. X’s friend, another doctor, calls to give an important message. The person who usually brings dinner to the doctors’ quarters had said that the bride-groom at a wedding she attended in early October had become COVID-19 positive. This was while someone had told her that another person who attended the same wedding was in the hospital, with some breathing difficulty.

Dr. X then verifies that Patient A is the person who had been at the wedding and thinks that Patient A would need an RT-PCR in the morning. Patient A has said that she and the bride-groom, a relative, were not close to each other at the wedding on October 2, but it was the bride-groom who carried her in his arms to the van when she was leaving for the hospital on October 12.

So the deduction here is that the high-risk exposure occurred then from the bride-groom and Patient A became positive on October 16, through a very short incubation period.

To the time of Patient A’s transfer to the IDH, she was relatively stable (blood pressure & pulse remained stable and blood gases were normal) and she was on face-mask oxygen, which she moved frequently, without a significant drop in oxygen saturation. She also talked. She needed nebulization in-between.

Simultaneously, through contact tracing, the hospital too probably received the information on the 16th morning about Patient A’s exposure to the bride-groom at the October 2 wedding (later it was revealed that it was the home-coming). By that time there is a plan to send Patient A to another hospital on the 16th morning for a CT pulmonary angiography, but it is cancelled, an RT-PCR taken at around 9 a.m. and sent to the Ragama Hospital laboratory, which promises results the same night.

Patient C is then transferred quickly back to the OMF ward to avoid possible further exposure to Patient A.

But Patient B has to be kept there as he needs ICU treatment. On October 21, he is transferred to the COVID-19 isolation ward as he shows some improvement and the ICU needs disinfection. When his condition becomes worse again on October 23 night, he is re-admitted to the ICU and dies on the morning of October 24.

Patient B has undergone 3 RT-PCR tests on October 16, 18 and 23 during his hospital stay. The first two had been negative, while the third was positive, suggesting that he may have contracted COVID-19 from Patient A, while being in the bed next to her in the ICU.

On October 16, after the test sample is taken from Patient A, all ICU staff (including Dr. X) are told to stay in hospital without going home until the RT-PCR results come. It is around 9 p.m. when Patient A is found to be positive and Dr. X continues her ICU shift, but now wearing the PPE, to prevent another doctor getting exposed to Patient A.

From the time of Patient A’s admission to the ICU, it is Nurse M, wearing a KN95 mask and surgical gown over her uniform, who looks after her, not only providing nursing care but also psychological support. But after the test results come, Nurse N wearing PPE, is allocated Patient A and she accompanies her to the IDH at 2 a.m. on October 17.

We do not know what the Ct value of Patient A’s test was. If it was low, her infectiousness would have been high and thus with a high viral load, the incubation period in those she would have infected would be short.

Need to identify the gaps

While appreciating the tireless work done by the Medical Officers of Health (MOHs), health administrators and teams working in the field of COVID-19, it is important to identify the gaps and rectify them as Sri Lanka is now experiencing as many as 500 new cases a day.

Following Patient A’s diagnosis, 55 health staff including 14 doctors are sent for quarantine in different places, mostly hotels.

Meanwhile, the reason for the decision (written instructions from the Health Ministry) that Dr. X should wait 11 days until October 26 to do the first RT-PCR is questionable. It is noteworthy that Patient B who had more or less similar exposure as Dr. X in the ICU could get 3 RT-PCRs by October 23.

When we use this knowledge on the local situation, Nurse M’s RT-PCR test came positive on October 25 and she was transferred to the IDH, while Dr. X was still awaiting her first PCR, despite similar, close and prolonged exposure in an enclosed environment. The doctor’s test was finally performed on October 26 and was negative. The PPE possibly helped Nurse N to be PCR negative.

The possibilities for Dr. X’s negative result:

The surgical mask (or wearing 2 surgical masks) was highly effective, while Dr. X practised social distancing properly in the ICU even though PPE was not worn for over 12 hours of her stay there.

Dr. X developed asymptomatic disease after a short incubation of only 2 to 3 days due to the exposure to a high viral load from Patient A. By Day 11, she was able to run through the illness and recover, resulting in the RT-PCR becoming negative, though she had got the disease. (The Ct value correlates with the viral load and infectiousness, but not so much with the symptomatic or asymptomatic nature of the illness).

Even if Dr. X was truly positive and continued to shed the virus, depending on the time of the onset of illness, the RT-PCR may give a false negative (30% chances). We will know for sure if an antibody (sp IgG) test is done on Dr. X at 3 weeks, with nearly 99% sensitivity.

There seems to be confusion as to when RT-PCR tests should be performed.

We need to divide the people who need this testing into two groups:

Positive cases – For those who are already confirmed as positive, it is not essential to do a test after Day 10 (as instructed by the Health Ministry) and a follow-up test between Days 11 to 14. This is because the shedding of the replicable virus is extremely rare (almost not reported in healthcare workers).

Suspected exposure or contacts – In those where we are looking for evidence of infection, doing a test after 10 days of heavy or high-risk exposure is inadequate. An argument that may be put forward is that as they are in quarantine from Day 1 (maybe it’s not essential to do so on Day 1 as the shortest incubation is 2 days and they will not transmit it to others during this period).

However, there are many possibilities if we apply this rule to the community, when considering what happened at Kuliyapitiya.

There was a wedding at a Katunayake church on September 29. The building was well-ventilated and about 40-50 attended the wedding.

The homecoming was at a hotel in Udubaddawa close to Kuliyapitiya on October 2 with about 350 in attendance.

There was also a prayer session for about 73 people in a smaller congested and enclosed space in Kuliyapitiya on October 4, visited by the newly-married couple to give refreshments.

Some people attended all three functions, while others attended one or two.

The index case (first) in this cluster is thought to be the bride-groom but whether he contracted it from someone else at either functions is not clear from the information available.

This came to light when the person who sought treatment at the fever corner of the Kuliyapitiya Hospital became positive following a routine sample taken on October 12. When her contacts were traced it was found that she had attended all 3 functions (on the 29th, 2nd and 4th) and that led to tracing all who attended these functions.

The newly-wed couple had their PCRs done on the 14th and the groom was positive but the bride negative. A few members of the groom’s family when tested on the 16th became positive. They kept on tracing more from the 3 functions and the most number was from those who attended the prayer meeting. However, the two priests who attended it tested negative.

Many of the PCRs from the contacts were done around October 20, while the others may still be undergoing testing.

None of the contacts traced from the wedding were positive and only two who attended the home-coming were positive. However, these two people had a family member in their household who attended the prayer meeting. So it is debatable where they contracted the virus from.

Of the 73 who were at the prayer meeting, about half did not go to the wedding or the home-coming.

So there could be many possibilities – a complete outsider could have brought the infection to the prayer meeting, infecting several others including the bride-groom.

As in the case of Dr. X, there is a theoretical possibility that depending on the length of exposure to the time the testing was done, some will become negative when there is enough time for them to get the disease with a short incubation and finish the viral shedding to give a negative result. The other question is how was the bride negative? A possibility is that she contracted the virus and completed the viral shedding.

Another possibility is that when RT-PCRs are done on a massive scale, the results get delayed for days and those awaiting the results, some who may be infected, can spread the virus.

All these scenarios show how complex it is to limit community spread with our contact-tracing and testing protocols. When in doubt, the best is to apply the ‘Precautionary Principle’ which is, when something is scientifically plausible but uncertain, action should be taken to avoid harm. If there is a doubt, the benefit of the doubt should be given to the public.

The use of rapid antigen testing as a field test to increase detection efficiency and prevent the spread. Unlike many months ago, now WHO-approved sensitive rapid antigen tests are available.

Perform follow-up antibody testing to determine the extent of spread. Though detectable antibodies may not last long, testing them at 3 weeks can solve the puzzle in many cases.

The analysis should be based on transmission dynamics, taking into account the ‘incubation period’ and the ‘period of infectivity’.

The incubation period is 2-14 days for 99% and over 14 days (14-27) for 1%. The median incubation is only about 5 days.

The true period of infectivity is very unlikely to be longer than 8 days or safely almost never 10 days from the onset of illness and there are no reports of household or healthcare workers contracting the disease after Day 6 from a confirmed case.

The RT-PCR test on a nasopharyngeal swab is only 70% sensitive and 1/3rd are false negatives.

Both symptomatic (with symptoms) and asymptomatic (without symptoms) patients can transmit the disease. In the ‘asymptomatic’ group there could be some pre-symptomatics who are a lot more infectious than the fully asymptomatics and the symptomatics in the late stages. When symptomatic they are mostly infectious in the first 3 to 4 days.

Though the RT-PCR tests can be positive for 2 to 4 weeks in some cases, the replicable virus that grows in cultures is not isolated after 8 days of infection, according to most studies. This tells us that up to even 1/3rd to 2/3rd of all PCR tests could still be “falsely” positive in patients who have got infected with the virus sometime earlier but not truly infective at the time of the test. This is due to the detection of parts of the dead virus.

However, the proportion of truly infective patients who are asymptomatic could also vary from 40-90% in different settings and populations. In communities or set-ups where people are wearing their masks all the time and practise social distancing rules stringently, there would be a large majority of cases under the ‘asymptomatic’ or ‘mildly symptomatic’ groups explained by the ‘inoculum theory’.

Therefore, the best bet is to design Sri Lanka’s strategy on the ‘inoculum theory’ to face the next waves of COVID-19. This would not see an implementation of lockdowns but living with the new normal. Under the inoculum theory, ‘exposure to a lower inoculum or dose of any virus can make subsequent illness far less likely to be severe’. If all people wear effective masks and stringently follow social distancing practices all the time over a long period, the asymptomatic and mildly symptomatic proportion of the infected cases would go up.

The curfews are designed with the hope that things will be back to normal soon. But we are now at a stage where such normalcy can be a couple of years away. We have to see how life can go on by transforming every member of the public to be disciplined and stringently practise social distancing every minute, so that we will do everything to avoid getting infected or infecting others. In the remote event of transmission, the dose of inoculum will be very minute and a large majority will be asymptomatic or mildly symptomatic and the death rates will be very small. However, protecting the elderly and the vulnerable will need special attention even with this strategy. Regional lockdowns than curfews may be needed only when rapidly expanding clusters emerge.