How the spread of Omicron went from patient zero to all around the globe

Published

4 years ago

November 29, 2021

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The speed with which new variants of the COVID-19 virus spread around the world can leave government’s scrambling to catch up. What is sometimes more remarkable is the speed with which those new variants are detected.

It has taken barely two weeks from the initial testing of ‘patient zero’, before potentially the entire globe is readying itself to examine COVID test samples to see if they contain the Omicron variant.

Patient zero, called n=1 or the index case by the scientific community, arrived at Hong Kong International Airport on 11 November, having flown in from South Africa via Doha in Qatar, on flight QR818.

He had been in South Africa for almost three weeks, and had tested negative the day before he began his trip there.

On his return to the territory on the Qatar Airways flight, the 36-year-old was in seat 31A, and was showing no symptoms when he checked into the Regal Airport Hotel in Chek Lap Kok, to begin his mandatory quarantine. He also tested negative on his return.

Hong Kong has some of the most stringent regulations on arrival in the world.

Anyone coming from a “high-risk” country can only board flights for the territory if they are fully-vaccinated Hong Kong residents and even then they have to undergo compulsory isolation for 21 days in a designated quarantine hotel when they arrive.

While in quarantine, they must undergo six COVID tests and then they must monitor themselves for the following seven days, after which they are tested again 26 days after the day of their arrival.

The man in question had fulfilled all the requirements, having received the Pfizer vaccine on 13 May and 4 June, and outwardly there were no signs his case was anything unusual.

But two days into his quarantine, he was tested again, on 13 November, and after showing a high viral load was sent to hospital the next day.

Meanwhile, another passenger that had arrived in Hong Kong the day before the man who later became patient zero, was staying in a room opposite him on the fifth floor of the same quarantine hotel.

He tested negative twice before, on 18 November, a result showed he too had a high viral load and he was also rushed to hospital.

Like all arrivals who test positive after coming to Hong Kong, they were give case numbers – 12388 and 12404.

Early conclusions from Hong Kong’s health authorities were that case 12404 might have been infected with the variant as air flowed into the corridor when case 12388 opened his hotel room door as he was not wearing a surgical mask.

While the test results from the Hong Kong travellers were being analysed, other researchers in South Africa and Botswana were also looking into a newly emerging variant.

Just three days after the Hong Kong traveller went to his quarantine hotel, a number of people were being routinely tested in the South African province of Gauteng.

At around the same time, South Africa, and particularly Gauteng, began to see a sudden uptick in cases.

South African scientists began to come to the conclusion they were seeing something new after detecting a group of related SARS-CoV-2 viruses that were turning up in large numbers, compared to other variants.

Out of the specimens collected between 14 and 23 November, more than 70% were of the same type.

They raised the alarm on 22 November.

The next day the new variant was picked up by GISAID, the open-access database of flu viruses and coronavirus variants that has been critical to spreading news around the world about emerging forms of COVID-19.

On 24 November, it was given a new name under the criteria given to emerging COVID variants – B.1.1.529.

On the same day, the new variant was reported to the World Health Organisation, which convened its technical advisory group – similar to WHO’s equivalent to SAGE – to assess what should be done.

The UK, responding to the rapidly evolving situation, designated the virus type a variant under investigation, VUI-21NOV-01, on 25 November.

As it did so, cases in South Africa were shooting up.

Professor Sharon Peacock of COG-UK Genomics UK Consortium, which oversees sequencing in the UK, said on Friday: “The number of recorded COVID-19 infections on 16 November 2021 was 273 cases. By 25 November this had risen to more than 1,200 cases.

“More than 80% of these were from Gauteng province. Cases in Gauteng province initially appeared to be clustered, but over time there has been more widespread dispersal of infections across the province.

“An analysis of the R value (a measure of growth rate) is 1.47 for South Africa as a whole, but initial estimates for Gauteng province are 1.93. Based on this measurement, it indicates that growth rate of cases is considerably higher in Gauteng province than the rest of the country.

“Around 100 B.1.1.529 genomes have now been identified in South Africa, mostly from Gauteng province. But this region is also where the sequencing has been targeted, and the question is whether the variant is present over a wider geographic area.”

In total, according to the European Centre for Disease Control, South African investigators examined 77 samples in Gauteng taken between 12 and 20 November looking for a specific mutation that suggested Omicron was present, and found it in all cases.

The results, say the ECDC, suggest that Omicron is already dominant in Gauteng and is present in significant proportions in most parts of South Africa.

The question is, what does this mean for the rest of the world?

It is clear that Omicron has been in the UK for several days.

After one of the first cases in England was revealed to have been identified in Brentwood, Essex County Council said staff, customers and delivery workers who visited a branch of KFC on Brentwood High Street on Friday 19 November, between 1pm and 5pm, should take a PCR test immediately – suggesting a person with the variant was in the restaurant at the time.

Likewise, they asked anyone in the congregation of the town’s Trinity Church on Sunday 21 November to do the same.

Essex’s director of public health Dr Mike Gogarty told the BBC’s World At One programme that the person in question was tested on 20 November and has contracted the variant from someone who had been in contact with someone who had been to South Africa – in a clear case of community transmission.

He said: “We are talking probably about two weeks from now since that person returned from Africa.”

Both the UK cases identified on Saturday, which also included one in Nottingham, were linked to travel in South Africa. A third case in the London borough of Westminster, who had previously been in southern Africa, has since left the country.

But while South Africa, like the UK, has an effective system to sequence COVID test samples, many other countries in Africa do not.

Omicron has been detected early in Botswana, but there are concerns it may be widespread in several other nations in southern Africa.

Some 98 samples were sequenced in Botswana to allow the identification of six cases of Omicron by Friday, reported the ECDC, but in the same period countries like Kenya sequenced just five cases, with no Omicron cases.

Israel, one of the world’s most vaccinated countries, said on Friday it had also detected the country’s first case of Omicron in a traveller who had returned from Malawi. Two other suspected cases were also placed in isolation.

On that day, as the world became aware of the extent of the spread, markets reacted with oil prices plunging and airlines shares suffering major losses.

A case was also confirmed in Belgium and on Saturday suspected cases were reported in Germany, Italy and the Czech Republic.

Denmark and Australia announced two cases and the Netherlands identified 13 Omicron cases in dozens of COVID-positive travellers from South Africa on Sunday.

On Monday, further cases were announced in Portugal, where 13 players and staff members of Lisbon soccer team Belenenses were found to be positive for the variant even though only one player had been recently to South Africa.

Countries across the planet have reacted by closing their borders or reintroducing severe travel restrictions.

While scientists have raised the alarm, and have said they expected it to spread, many say there is no more cause for concern in terms of the impact on people, than there might have been if the Delta variant stays dominant.

Reacting to the news cases had been discovered in Scotland, Professor Rowland Kao, the Sir Timothy O’Shea Professor of Veterinary Epidemiology and Data Science at the University of Edinburgh, said: “It is now clear that the Omicron variant has been spreading around the world for some days, if not weeks prior to the alarms being raised, and this is only to be expected for a virus which transmits as easily as SARS-CoV-2, and with international travel now substantial (even though not quite at the level pre-pandemic).

“Evidence of community spread in two locations in Scotland (ie cases with no obvious risks other than community spread) and no obvious source yet, are strong indicators that we shall see more cases in Scotland arise over the next few days and weeks.

“As always, anything individuals can do to mitigate spread (physical distancing, taking lateral flow tests when appropriate and being aware of COVID symptoms and testing) will be beneficial.

“However it is important to remember that the omicron variant may not pose an increased health risk – it may in fact cause milder infections. However we shall only know for sure in the next few weeks.”

World

Israeli soldier describes arbitrary killing of civilians in Gaza

Published

17 hours ago

July 7, 2025

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Israeli soldier describes arbitrary killing of civilians in Gaza

An Israeli reservist who served three tours of duty in Gaza has told Sky News in a rare on-camera interview that his unit was often ordered to shoot anyone entering areas soldiers defined as no-go zones, regardless of whether they posed a threat, a practice he says left civilians dead where they fell.

“We have a territory that we are in, and the commands are: everyone that comes inside needs to die,” he said. “If they’re inside, they’re dangerous you need to kill them. No matter who it is,” he said.

Speaking anonymously, the soldier said troops killed civilians arbitrarily. He described the rules of engagement as unclear, with orders to open fire shifting constantly depending on the commander.

The soldier is a reservist in the Israel Defence Force’s 252nd Division. He was posted twice to the Netzarim corridor; a narrow strip of land cut through central Gaza early in the war, running from the sea to the Israeli border. It was designed to split the territory and allow Israeli forces to have greater control from inside the Strip.

He said that when his unit was stationed on the edge of a civilian area, soldiers slept in a house belonging to displaced Palestinians and marked an invisible boundary around it that defined a no-go zone for Gazans.

“In one of the houses that we had been in, we had the big territory. This was the closest to the citizens’ neighbourhood, with people inside. And there’s an imaginary line that they tell us all the Gazan people know it, and that they know they are not allowed to pass it,” he said. “But how can they know?”

People who crossed into this area were most often shot, he said.

“It was like pretty much everyone that comes into the territory, and it might be like a teenager riding his bicycle,” he said.

The soldier described a prevailing belief among troops that all Gazans were terrorists, even when they were clearly unarmed civilians. This perception, he said, was not challenged and was often endorsed by commanders.

“They don’t really talk to you about civilians that may come to your place. Like I was in the Netzarim road, and they say if someone comes here, it means that he knows he shouldn’t be there, and if he still comes, it means he’s a terrorist,” he said.

“This is what they tell you. But I don’t really think it’s true. It’s just poor people, civilians that don’t really have too many choices.”

He said the rules of engagement shifted constantly, leaving civilians at the mercy of commanders’ discretion.

“They might be shot, they might be captured,” he said. “It really depends on the day, the mood of the commander.”

He recalled an occasion of a man crossing the boundary and being shot. When another man came later to the body, he too was shot.

Later the soldiers decided to capture people who approached the body. Hours after that, the order changed again, shoot everyone on sight who crosses the “imaginary line”.

At another time, his unit was positioned near the Shujaiya area of Gaza City. He described Palestinians scavenging scrap metal and solar panels from a building inside the so-called no-go zone.

“For sure, no terrorists there,” he said. “Every commander can choose for himself what he does. So it’s kind of like the Wild West. So, some commanders can really decide to do war crimes and bad things and don’t face the consequences of that.”

The soldier said many of his comrades believed there were no innocents in Gaza, citing the Hamas-led 7 October attack that killed around 1,200 people and saw 250 taken hostage. Dozens of hostages have since been freed or rescued by Israeli forces, while about 50 remain in captivity, including roughly 30 Israel believes are dead.

He recalled soldiers openly discussing the killings.

“They’d say: ‘Yeah, but these people didn’t do anything to prevent October 7, and they probably had fun when this was happening to us. So they deserve to die’.”

He added: “People don’t feel mercy for them.”

“I think a lot of them really felt like they were doing something good,” he said. “I think the core of it, that in their mind, these people aren’t innocent.”

In Israel, it is rare for soldiers to publicly criticise the IDF, which is seen as a unifying institution and a rite of passage for Jewish Israelis. Military service shapes identity and social standing, and those who speak out risk being ostracised.

The soldier said he did not want to be identified because he feared being branded a traitor or shunned by his community.

Still, he felt compelled to speak out.

“I kind of feel like I took part in something bad, and I need to counter it with something good that I do, by speaking out, because I am very troubled about what I took and still am taking part of, as a soldier and citizen in this country,” he said

“I think the war is… a very bad thing that is happening to us, and to the Palestinians, and I think it needs to be over,” he said.

He added: “I think in Israeli community, it’s very hard to criticise itself and its army. A lot of people don’t understand what they are agreeing to. They think the war needs to happen, and we need to bring the hostages back, but they don’t understand the consequences.

“I think a lot of people, if they knew exactly what’s happening, it wouldn’t go down very well for them, and they wouldn’t agree with it. I hope that by speaking of it, it can change how things are being done.”

We put the allegations of arbitrary killings in the Netzarim corridor to the Israeli military.

In a statement, the IDF said it “operates in strict accordance with its rules of engagement and international law, taking feasible precautions to mitigate civilian harm”.

“The IDF operates against military targets and objectives, and does not target civilians or civilian objects,” the statement continued.

The Israeli military added that “reports and complaints regarding the violation of international law by the IDF are transferred to the relevant authorities responsible for examining exceptional incidents that occurred during the war”.

On the specific allegations raised by the soldier interviewed, the IDF said it could not address them directly because “the necessary details were not provided to address the case mentioned in the query. Should additional information be received, it will be thoroughly examined.”

The statement also mentioned the steps the military says it takes to minimise civilian casualties, including issuing evacuation warnings and advising people to temporarily leave areas of intense fighting.

“The areas designated for evacuation in the Gaza Strip are updated as needed. The IDF continuously informs the civilian population of any changes,” it said.

World

Australian mother guilty of murdering three people with poisonous mushrooms

Published

19 hours ago

July 7, 2025

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Australian mother guilty of murdering three people with poisonous mushrooms

An Australian mother has been found guilty of murdering her estranged husband’s parents and an aunt by serving them a beef wellington laced with poisonous mushrooms.

Erin Patterson, 50, invited her former parents-in-law, Don and Gail Patterson, both 70, and Gail Patterson’s sister, Heather Wilkinson, 66, to the fatal lunch on 29 July 2023.

The mother-of-two, from the state of Victoria in southern Australia, has also been convicted of the attempted murder of Mrs Wilkinson’s husband Reverend Ian Wilkinson.

All four fell ill after eating a meal of beef wellington, mashed potatoes and green beans at Patterson’s home in the town of Leongatha, the court was told.

Prosecutors said Patterson knowingly laced the beef pastry dish with deadly death cap mushrooms, also known as Amanita phalloides, at her home.

The guests ate their meals off four large grey dinner plates, while Patterson ate from a smaller, tan-coloured plate, the court heard.

Mrs Wilkinson and Mrs Patterson died on Friday 4 August 2023, while Mr Patterson died a day later.

Reverend Wilkinson spent seven weeks in hospital but survived.

Her estranged husband Simon Patterson, with whom she has two children, was also invited to the lunch and initially accepted but later declined, the trial heard.

The jury was told that prosecutors had dropped three charges that Patterson had attempted to murder her husband, who she has been separated from since 2015.

Reverend Wilkinson said that immediately after the meal, Patterson fabricated a cancer diagnosis, suggesting the lunch was put together so that she could ask them the best way to tell her children about the illness.

The prosecution said she did this to justify the children’s absence.

The defence did not dispute that Patterson lied about having cancer.

The trial attracted intense interest in Australia – with podcasters, journalists and documentary-makers descending on the town of Morwell, around two hours east of Melbourne, where the court hearings took place.

A sentencing date is yet to be scheduled.

What makes death cap mushrooms so lethal?

The death cap is one of the most toxic mushrooms on the planet and is involved in the majority of fatal mushroom poisonings worldwide.

The species contains three main groups of toxins: amatoxins, phallotoxins, and virotoxins.

From these, amatoxins are primarily responsible for the toxic effects in humans.

The alpha-amanitin amatoxin has been found to cause protein deficit and ultimately cell death, although other mechanisms are thought to be involved.

The liver is the main organ that fails due to the poison, but other organs are also affected, most notably the kidneys.

The effects usually begin after a short latent period and can include gastrointestinal disorders followed by jaundice, seizures, coma, and eventually, death.

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World

Israel attacks Houthi targets at three ports and power plant in Yemen

Published

23 hours ago

July 7, 2025

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Israel attacks Houthi targets at three ports and power plant in Yemen

Israel says its military has attacked Houthi targets at three ports and a power plant in Yemen.

Defence minister Israel Katz confirmed the strikes, saying they were carried out due to repeated attacks by the Iranian-backed rebel group on Israel.

Mr Katz said the Israeli military attacked the Galaxy Leader ship which he claimed was hijacked by the Houthis and was being used for “terrorist activities in the Red Sea”.

It came after the Israel Defense Forces (IDF) issued an evacuation warning for people at Hodeidah, Ras Issa, and Salif ports – as well as the Ras al Khatib power station, which it said is controlled by Houthi rebels.

The IDF said it would carry out airstrikes on those areas due to “military activities being carried out there”.

Afterwards, Mr Katz confirmed the strikes at the ports and power plant.

Earlier in the day, a ship was reportedly set on fire after being attacked in the Red Sea.

A private security company said the assault, off the southwest coast of Yemen, resembled that of the Houthi militant group.

It was the first such incident reported in the vital shipping corridor since mid-April.

The vessel, identified as the Liberian-flagged, Greek-owned bulk carrier Magic Seas, had taken on water after being hit by sea drones, maritime security sources said. The crew later abandoned the ship.

The Houthi rebels have been launching missile and drone attacks against commercial and military ships in the region in what the group’s leadership called an effort to end Israel’s offensive against Hamas in Gaza.

Between November 2023 and January 2025, the Houthis targeted more than 100 merchant vessels with missiles and drones, sinking two of them and killing four sailors.

The Houthis paused attacks in a self-imposed ceasefire until the US launched an assault against the rebels in mid-March.

That ended weeks later and the Houthis have not attacked a vessel, though they have continued occasional missile attacks targeting Israel.

A renewed Houthi campaign against shipping could again draw in US and Western forces to the area.

The ship attack comes at a sensitive moment in the Middle East.

A possible ceasefire in the Israel-Hamas war hangs in the balance and Iran is weighing up whether to restart negotiations over its nuclear programme.

It follows American airstrikes last month, which targeted its most-sensitive atomic sites amid an Israeli war against the Islamic Republic that ended after 12 days.

How did the Houthis come to control much of Yemen?

A civil war erupted in Yemen in late 2014 when the Houthis seized Sanaa.

Worried by the growing influence of Shia Iran along its border, Saudi Arabia led a Western-backed coalition in March 2015, which intervened in support of the Saudi-backed government.

The Houthis established control over much of the north and other large population centres, while the internationally recognised government based itself in the port city of Aden.