The fast-spreading B.1.1.7 variant of COVID-19 was not present in the community in Sri Lanka until April 08, Prof Neelika Malavige of the University of Sri Jayawardenapura said.
Speaking to EconomyNext in a phone interview this morning, Malavige denied claims that authorities had known for at least two months that the strain was in the community.
Malavige, Professor in Microbiology at the Department of Immunology and Molecular Medicine, Faculty of Medicine, University of Sri Jayewardenepura, said that though her team found one or two cases of B.1.1.7 in the community towards end-January/early February this year, subsequent testing of primary, secondary and even tertiary contacts of those cases had not resulted in a single positive identification of the highly transmissible variant.
“We did not see any sign of B.1.1.7 in our PCRs until April 08,” she said.
However, in a previous correspondence on February 13, the professor said three people in the community had tested positive for the UK strain towards end-January.
“[The strain] possibly leaked into the community due to some failure in the quarantine process,” Malavige said in that interview, adding that leaks were natural and to be expected even in the toughest quarantine regimes in the world.
She said at the time that three Sri Lankans from the community had tested positive for B.1.1.7. “Since we identified the variant in the community very early, we might be able to contain it,” she said.
A statement from the Sri Jayawardenapura University (SJU) released on February 12 also said: “While most of the [92 samples that were genome sequenced] belonged to the previously circulating B.1.411 lineage (Sri Lankan lineage), a few viruses belonging to the B.1.1.7 (UK lineage) was detected from Colombo, Avissawella, Biyagama and Vavinya and from a few individuals in the quarantine centres.” (Emphasis ours)
Acknowledging the wording in the statement and that there was no subsequent clarification or announcement from either the SJU or the Ministry of Health of this apparent re-evaluation, Malavige said today that the SJU had later concluded that only one of the positive B.1.1.7 cases was from the community and not three as previously thought.
All other positive cases, she said, were from quarantine centres.
“As soon as that information was out, the one or two positive cases were contact-traced and everyone was quarantined for 14 days. After that, no other samples tested positive for B.1.1.7,” said Malavige.
“Thousands of samples from all over the country were sent to us for screening, but until April 08, we just didn’t detect it again in the community,” she added.
The professor said that the SJU lab routinely receives samples from quarantine centres and offices of the Regional Directors of Health Services (RDHS). The RDHS offices, which used to only send samples from the community, now send samples from the quarantine centres too.
“So you can see how we can sometimes get the location wrong,” she said.
Earlier this year, two people had tested positive for B.1.1.7, one from Vavuniya and the other from a construction site in Colombo. The Vavuniya case, Malavige said today, was definitely from a quarantine centre.
The construction worker’s movements were then retraced using GPS locations on his phone but none of his contacts tested positive for B.1.1.7.
“We screened thousands of samples and didn’t find the British variant again. It was not a case of finding it in the community and then proceeding to ignore it,” she said.
Meanwhile the COVID-19 caseload in Sri Lanka was on the decline. What used to be a positivity rate of around 30% in December last year had declined to 10 to 15 percent by January in Colombo, said Malavige, after which it gradually fell. By March, the SJU lab was seeing “very few positives” – 3 or 4 out of 600.
If the UK strain was indeed not in the community in February or March, how then did it suddenly spread among thousands of people in April alone? Was it a quarantine leak some months prior? Did it arrive through a tourist, or perhaps a visiting cricketer? Authorities have yet to answer this question.
One of the more surprising decisions of late by the health ministry, as has been highlighted by lab technologist Ravi Kumudesh and others, is Sri Lanka’s sudden and inexplicable drop in PCR tests. The number of daily tests dropped significantly, and the only explanation offered by the health ministry’s epidemiology unit was that, because cases were on the decline, the corresponding drop in close contacts meant there weren’t many people left to test.
Malavige agrees that testing went down.
“I don’t know why. I do know what the epid unit said. In April when we got random samples from the Colombo Municipal Council (CMC) area which we covered, on some days we didn’t get any positives,” she said.
The professor maintains that, apart from the two cases detected in end-January/early February, genome sequencing of samples collected from the community until March 31 only showed B.1.411, the Sri Lankan strain of SARS-CoV-2, the virus that causes COVID-19.
“After that, we didn’t see anything unusual,” she said.
That is, until the Avurudu holidays.
Following an outbreak in the first week of April, the SJU lab sequenced samples that showed what is known as an S drop – the absence or malfunction of the virus’s S gene in the test due to a specific mutation in the gene.
The TaqPath COVID-19 diagnostic test kit, which according to Malavige is widely used in Sri Lanka, results in an S drop when a sample with this specific mutation is tested, potentially signalling – though not confirming – the presence of B.1.1.7.
“This is a characteristic of the UK variant,” she said.
B.1.1.7, she said, is one of three variants of concern, as declared by the World Health Organisation (WHO); the other two being the South African and Brazil strains. A variant of concern is more transmissible, or is associated with more disease severity, or evades immunity (meaning it can infect people who have already had COVID-19 or have received a vaccine).
The UK strain is known for its high transmissibility. Whether it causes more disease severity is less certain. But given the increased transmissibility and the ceiling on the number of intensive care units (ICU) in the system, said Malavige, the mortality rate invariably increases – potentially up to 55 percent according to one paper published in Nature.
Whether any increased severity is due to this logistical equation or whether it actually causes severity on its own remains a question, but Malavige is inclined to believe the latter.
The samples sequenced in early April showed the S drop which, Malavige said, showed that something was not right, though it could not be confirmed at the time that B.1.1.7 was indeed the culprit.
Some 800 samples subsequently collected from all primary and secondary contacts all tested negative, after which the SJU team took a break for the Avurudu holidays.
“SJU is not bound to do PCRs. We do it voluntarily as a duty and have been since February 2020. Every person working in our lab is doing 100% voluntary work. No one in our lab had taken a break, so we took one for Avurudu,” she said.
Work resumed on April 19, but during the break, patients from a bank head office in Colombo had been rushed to hospital. After Samples were collected and, on April 19, promptly sequenced. Sixteen out of 17 showed the S drop.
“And then we saw stars,” said Malavige.
The S drop was observed in samples from Kurunegala too. On April 23, Malavige and her team, flanked by officials, went before the media and announced the detection of a new, much more transmissible strain of the novel coronavirus, pending confirmation.
“The authorities were very concerned,” she said.
Then came the long weekend, and pictures that went viral on social media revealed reckless travels and unmasked gatherings that likely took the newer, deadlier – and as Malavige calls it, nastier – strain everywhere.
Should the government have declared a lockdown? Or at least imposed movement restrictions? Authorities have been repeatedly criticised for shifting the blame to the public and for placing the burden of containing the spread on an exhausted populace.
“Whether restrictions should’ve been imposed when the strain was detected, I do not know. What happened during Avurudu was alarming and shocking. But I’m not going to blame the public. The people were kept inside a cage for a long time. It’s human nature to want to be free.
“Whether that cage should’ve been kept closed for a longer period, that is the question. If the UK strain hadn’t come to Sri Lanka, yes, we would’ve seen a spike in cases after Avurudu regardless, but it wouldn’t have been like the situation we’re seeing now,” said Malavige.
While there is no disputing that the public has a part to play, the authorities’ more questionable decisions have been met with bitter criticism from medical experts, union representatives and others. Scepticism has also been expressed about the sincerity of the SJU team, with some alleging certain biases on their part – an allegation that Malavige flatly denies.
“I have no political affiliation at all. Neither does Dr Chandima Jeewandara,” she said. Dr Jeewandara is Director, Allergy Immunology and Cell Biology Unit of the University of Sri Jayawardenepura.
“I think the government has made enough and more mistakes. We can talk about who did what wrong after we have doused the fire, but right now let’s douse the fire,” said Malavige.
However, the professor does contend that the authorities are doing everything they can to take charge of the situation.
“I believe they do understand the gravity of the situation. I believe they’re trying their best to do what they can because the priority now is to reduce cases and manage the severe cases,” she said.
With the politics out of the way, Malavige spoke of the dangers of the new strain.
As deadly as it is, so far even the UK strain has resulted in a majority of asymptomatic cases in Sri Lanka. But that’s not the reassurance it sounds like.
“Let’s put it this way. Let’s say with the Sri Lankan variant, 0.1% needed ICU care. If it becomes 1% now or even 0.5%, that will really tip the balance. If people who get severe disease increase from 1 percent to 5 percent, that too will tip the balance. These are not actual figures based on real data, but you get the idea,” she said. (This data, incidentally, is not yet available).
B.1.1.7 has been responsible for a sudden increase in ICU admissions, particularly of younger patients with severe symptoms including breathing difficulties. Prof Malavige said the proportion of those who develop pneumonia and therefore need oxygen and high dependency care/ICU care are on the rise.
The data on this too, is unavailable, and ‘young’ remains undefined, and Malavige calls for getting out hospital statistics to better understand the situation.
“How prepared are we to increase the facilities to rapidly accommodate these patients who develop severe disease? Right now the important thing is to prevent casualties. If we have increasing case loads, we can’t keep expanding facilities because there’s a ceiling,” she said.
“We have to reduce cases. How do we do that and at the same time maximise facilities? These are the burning questions we must address,” she added.
The priority now, the professor said, is to strategise.
“We’re now in a crisis,” she said, adding that it’s critical that people limit non-essential movement.
“I don’t go out unless I absolutely have to because I know the danger. If there is a fire somewhere, nobody has to tell me not to go in there. If you see fire, you move, you don’t jump in.”
But what of the thousands for whom staying put is a luxury? What of essential workers, daily wage earners and others to whom a lockdown of any kind spells doom?
“It would be less dangerous for those thousands who have to be out if everyone else stayed at home. For essential workers and daily wage earners to be out and about, those who can afford to stay home, must stay home,” the professor said.
Asked if Sri Lanka is in danger of becoming another India in terms of an unmitigated public health crisis, Malavige said: “That’s a difficult question. We should not let the Indian variant come here. We’ve got enough problems in our hands. We don’t need double trouble.”
She is, however, cautiously optimistic that the situation will be brought under control – if Sri Lanka acts now.
“We’ll be able to contain it, but not tomorrow. We’re still in the exponentially rising stage. Normally anything rises, then plateaus and then falls,” she said.
“I hope this plateaus soon,” she added.