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Lessels says KZN sequencing team was in a Catch-22 situation

Dr Richard Lessels, of the now-globally famous KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), whose genome sequencing team alerted the world to the now-rampant COVID-19 Omicron variant, has confessed that he suffered “sleepless nights” when South Africans were banned from overseas travel virtually overnight, writes Chris Bateman.

Lessels says his researchers found themselves in a classic Catch-22 situation: if they'd withheld their preliminary findings on the highly infectious new variant any longer, they risked being accused of being grossly irresponsible and contributing to public harm.

He was asked about the controversy by Dr Noluthando Nematswerani, head of Discovery Health’s Clinical Policy Unit, after delivering a webinar update on KRISP’s Omicron research, on 7 December.

Nemetswerani asked him, with a wry grin, “Should you have gone out and told the world about Omicron?”

Taking a breath, Lessels answered, “There was a lot of criticism that we jumped the gun and scared people about the variant that led to the travel ban. The reality is that we feel…we have sleepless nights in terms of whether we did the wrong thing and that the travel bans are our responsibility. The reality is that the infection was already out. Sequencing in Botswana had already been shared openly on the global platform where all genomic sequences are shared – and it was noticed in the United Kingdom. It was tweeted in the UK and a journalist picked it up and posted the story on the Daily Mail online website, the most widely read online news website in the world. So, even if we’d held back from announcing it, it wouldn’t have made any difference. It would have become very clear, very quickly that something was happening in South Africa. We would have been accused of the opposite, of being clearly shown to be holding back information of global significance.

"As a group of scientists on the genetic sequencing network we’ve been clear from the start that we’ll be open and transparent. We’re part of a global response. Thankfully our politicians have taken the very sane approach that we’re part of a global pandemic response and that we share information on that basis. This time we saw a lot of outcry about the travel bans and other restrictions and the lack of support coming to Africa to deal with this ongoing challenge. Of course, we question ourselves as a group, but we maintain we did the right thing, not just for SA, but for the global response.”

Lessels fascinated his audience when asked how the Omicron mutation came about. He said there were a few hypotheses, but he "veered towards" one which suggests that it mutated from a chronic infection in one individual

“There are precedents in the world where somebody has a compromised immune system and can’t clear the virus. They then develop a more chronic infection over several months with an immune response evolution,” he explained. More work was needed to understand this, prevent it and deal with chronic infections so that the risk of this happening again could be reduced, he said.

He added that with normal circulation of the virus and transmission in the world, and in spite of inadequate surveillance or genomic sequencing, “there has to be a very big blind spot over a long period of time for us to completely miss the intermediate forms of this variant”.

Another theory was that the virus would have spread within an animal host where it evolved to get “better at transmitting in the animal species” before being “pulled back,” into the human population. He emphasised that there was no definitive evidence to support either hypothesis,

Fastest-ever spread

The Omicron variant spread outwards from Gauteng to all provinces within three weeks, the fastest transmission since COVID-19 was originally detected among a group of KwaZulu-Natal travellers returning from Italy on 1 March 2020. Initial laboratory studies indicate that Omicron might be shorter-lived than previous variants, but according to Dr Allison Glass, lead clinical virologist at Lancet laboratory’s molecular biology unit, it’s too early to draw any conclusions.

Glass says that uniquely, Omicron has the ability to re-infect people who caught COVID-19 in previous waves, or those already vaccinated, creating mild breakthrough infections. While hospital admissions have risen dramatically (admittedly from a low base at the beginning of November), there have been very few severely sick people, or deaths.

Staff in high care units and ICUs, overwhelmed during previous waves with doctors having to make morally impossible life and death choices between COVID-19 and non-COVID-19 patients, are cautiously holding their collective breath that this tendency will persist. However, they warn that even mild breakthrough or first-time infections have the potential to aggravate pre-existing conditions, adding to the routinely high critical care load over the festive season.

Describing some of the unique properties of Omicron, Lessels said: “It’s not just the just the number of mutations, but where they fall and what we understand. What also comes out clearly is that it’s very different from everything else we’ve seen. Though some mutations were familiar, we’ve never seen this combination of mutations. As we get more data and do more sequencing, we can then plug that in to build the family tree of viruses.”

He warned the anti-vaccination lobby against using the non-lethal characteristics of Omicron to dissuade people from getting vaccinated.

“A lot of the spread happens around the time of symptom development, not when people are in ICU or hospital. Our understanding about this virus and its evolution is still developing. We cannot let what we know so far feed into disinformation and misinformation, with people saying there’s nothing to worry about. There’s no evolutionary pressure on this virus to become less virulent. What we need is real world data on how the vaccine effectiveness is holding up against severe disease, hospitalisation and death. Over the next few weeks, the data will improve. Through the rest of December and into January we’ll gradually build up a picture of what we’re dealing with, not just in SA, but worldwide.”


See more from MedicalBrief archives:


Omicron: Some simple steps to deal with the new variant


State of play with Omicron – The discovery, the spread, the politics, and the science


UK quarantine: Out-of-pocket travellers to SA take government to court




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