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

Published

3 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

A ‘barbaric’ 24 hours in the ‘horrendous’ Russia-Ukraine war leaves Donald Trump’s peace plan in tatters

Published

2 hours ago

April 24, 2025

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A 'barbaric' 24 hours in the 'horrendous' Russia-Ukraine war leaves Donald Trump's peace plan in tatters

Events in Ukraine over the last 24 hours have been utterly barbaric. Bad even by the standards of this horrendous war.

Multiple Iranian drones and North Korean missiles laden with explosives brought carnage to swathes of the country, killing yet more civilians.

This was Russia’s answer to President Donald Trump’s peace plan and ultimatum. Normally, strangely reluctant to criticise Russia, even Trump was moved to implore Vladimir Putin to “STOP”.

Ukraine latest – Trump unhappy with Putin

But in truth, throughout Trump’s Ukraine peace process – if it can be called that – most of America’s pressure has been on Ukraine.

The peace plan that has emerged from direct US talks, which were mainly with Russia, is one-sided, and to Ukraine and its European partners, it is a surrender plan which is impossible for Ukraine to accept.

Even Russia’s supporter in this war, China, has problems with it, in particular with America’s proposal that Russia is rewarded for its invasion with sovereignty of Crimea.

Far from heading towards a peace deal, we are now, it seems, careering towards a crunch point that could see America give up on Ukraine completely, possibly blaming Kyiv for failure and renewing relations with Moscow.

Might will be proven right, and Vladimir Putin will be emboldened to do it all over again in a few years, possibly against other countries too. That is the fear in chancelleries across Europe.

There are two key questions now.

Does Trump mean he will walk away from trying to broker peace or supporting Ukraine entirely?

And if he does, can Ukraine carry on without US help?

European nations have said they will carry on supporting Ukraine. They see its survival and victory as essential for their own security.

They already give Ukraine €40bn in financial and military help. Ukraine would need another €20bn or so to fill the US gap – not that tall an order.

And they are beefing up their defence industries to do more to give Ukraine what it needs to fight Russia.

Ukraine’s defence increasingly depends on a homegrown drone industry, which doesn’t rely on American backing.

But Ukraine does need US intelligence, aerial defence support and satellite coverage provided by Starlink.

Were they to lose all that, they could be in trouble.

What exactly Trump does if and, as seems increasingly likely, when his deal fails, he is not making clear.

But what seems certain is America is caring less and less for Ukraine’s plight under this president.

That poses some urgent and pressing questions for Europe.

Its leaders have always said they will support Ukraine “whatever it takes, as long as it takes”.

Do they have the political will and unity to do that, even without America by their side?

World

Pakistan halts trade and India revokes visas as retaliatory measures ramp up after Kashmir killings

Published

12 hours ago

April 24, 2025

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Pakistan halts trade and India revokes visas as retaliatory measures ramp up after Kashmir killings

Pakistan has halted trade and India has revoked visas as tit-for-tat retaliatory actions ramp up between the two powers after an attack in Kashmir that killed 26 people.

The victims were mostly Indian tourists who had been visiting Pahalgam, a popular tourist destination in the Indian-held part of the territory, which both nuclear-armed nations claim as their own.

In response to the attack, India closed a border crossing, suspended a water-sharing treaty and downgraded diplomatic ties with Pakistan – which it blames for the assault.

The Indian government did not publicly produce any evidence connecting the attack to its neighbour, but said it had “cross-border” links to Pakistan.

Pakistan has denied the accusations and a previously unknown militant group calling itself Kashmir Resistance has claimed responsibility.

On Thursday, India’s foreign ministry said all visas issued to Pakistani nationals would be revoked, effective from Sunday.

It also advised Indian citizens not to travel to Pakistan and announced other measures including cutting the number of diplomatic staff and closing the only functional land border crossing between the nations.

In return, Pakistan said it was closing its airspace to all Indian-owned and operated airlines and suspending all trade with India – including to and from any third country.

Similarly, it also announced the cancellation of all visas under the SAARC Visa Exemption Scheme – which allows some people to have a “Special Travel” document exempting them from visas.

‘Act of war’

The moves are just the latest escalation of tensions between the two, as Pakistan warned that any suspension of water supplies by India would be viewed as an “act of war”.

Both Pakistan and India saw protesters turn out on the streets, calling on their respective governments to go further.

Pakistan’s Prime Minister Shehbaz Sharif chaired a meeting of the National Security Committee to respond to India’s measures.

He warned that any attempt to disrupt the Indus Waters Treaty would be met with “full force” from Pakistan.

The landmark treaty has so far survived two wars between the countries, in 1965 and 1971, as well as a major border skirmish in 1999.

It allows for a water-sharing system that is a lifeline for both countries – in particular for Pakistan’s agriculture.

‘Ends of the Earth’

It comes after Indian Prime Minister Narendra Modi promised to pursue those responsible for the attack “to the ends of the Earth”.

Speaking on Thursday at a public meeting in the eastern state of Bihar, he said: “I say to the whole world, India will identify, track, and punish every terrorist and their backers.

“We will pursue them to the ends of the Earth.”

Police in Indian Kashmir published notices on Thursday naming three suspected militants it claimed were “involved in” the attack.

Two of the three suspects were Pakistani nationals, according to the notice.

A contested Kashmir

India and Pakistan each administer a part of Kashmir, but both claim the territory in its entirety.

The region has a long, volatile and complex history.

Recent years has seen India claim that violence in the area has calmed – despite a bloody rebellion against New Delhi raging for decades.

India claims the militancy in Kashmir is Pakistan-backed terrorism.

Pakistan denies this. In a statement Thursday, the country said it supported the self-determination of the Kashmiri people.

Many Muslim Kashmiris, in a Muslim-majority territory, consider the militants part of a home-grown struggle for freedom.

Diplomatic relations between the two were already weak before the latest escalation as Pakistan had expelled India’s envoy after India revoked the semi-autonomous status of Kashmir in 2019.

This deepened tensions in the region but things have largely held stable after the two countries renewed a previous ceasefire agreement in 2021.

Tens of thousands of people have been killed in Kashmir since the uprising began in 1989, but violence has tapered off in recent years and tourism has surged in the scenic region.

Until the most recent episode, tourists have not been the targets of such attacks.

World

Trump accuses Zelenskyy of harming peace talks on Ukraine war and tells him to ‘get it done’

Published

23 hours ago

April 24, 2025

admin

Trump accuses Zelenskyy of harming peace talks on Ukraine war and tells him to 'get it done'

Donald Trump has claimed a deal to end Russia’s war on Ukraine is “very close” as he heaped pressure on Volodymyr Zelenskyy to “get it done”.

Hours after US secretary of state Marco Rubio withdrew from high-level talks in London on ending the conflict, the American president appeared to vent frustration about Mr Zelenskyy on his Truth Social platform.

“We are very close to a deal, but the man with ‘no cards to play’ should now, finally, GET IT DONE,” Mr Trump said.

“I look forward to being able to help Ukraine, and Russia, get out of this complete and total MESS, that would have never started if I were president!”

Ukraine war latest: ‘We are very close to deal’, Trump claims

Mr Trump also criticised Mr Zelenskyy for telling the Wall Street Journal that Ukraine would not accept giving up Crimea as part of a peace deal with Russia.

And he accused the Ukrainian president of harming peace negotiations with “inflammatory statements”.

Reports say that the US president’s seven-point peace plan to end the war includes a proposal that America would formally recognise Russian sovereignty over Crimea – which was annexed in 2014 and which Ukraine maintains is its territory.

“It’s inflammatory statements like Zelenskyy’s that makes it so difficult to settle this war,” Mr Trump added. “He has nothing to boast about!

“The situation for Ukraine is dire – He can have peace or, he can fight for another three years before losing the whole country.”

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Speaking later at the White House on Wednesday, Mr Trump said: “I think we have a deal with Russia. We have to get a deal with Zelenskyy.

“I thought Zelenskyy would be easier to deal with, but so far it’s harder. I think we have a deal with both.”

Asked if he was planning to meet Mr Putin soon in Saudi Arabia, he said “probably not, but I hope to meet with him soon thereafter”.

The peace plan, reported by US media over the weekend, would freeze the frontlines in Ukraine as part of the agreement.

London talks on ending war downgraded

It comes after Mr Rubio withdrew from a planned meeting in London on Wednesday, which the UK’s Foreign Secretary David Lammy and Defence Secretary John Healey did attend.

The downgraded talks were also attended by Keith Kellogg, the US envoy for Ukraine, along with other officials from France, Germany and Ukraine.

Mr Rubio said last week that the US may “walk away” from negotiations due to a lack of progress with Russia and Ukraine – a warning now repeated by vice president JD Vance.

The UK Foreign Office said in a statement that there had been significant progress at the talks on Wednesday, and added: “All parties reiterated their strong support for President Trump’s commitment to stopping the killing and achieving a just and lasting peace.”

‘Emotions have run high’ – Zelenskyy

On Wednesday evening, the Ukrainian president said “emotions have run high today” but stressed all sides “expressed their views and respectfully received each other’s positions” during the London talks.

Mr Zelenskyy said on social media: “The American side shared its vision. Ukraine and other Europeans presented their inputs.

“And we hope that it is exactly such joint work that will lead to lasting peace.”

He also said, however, that “Ukraine will always act in accordance with its constitution,”.

And he posted a screenshot of the Crimea Declaration – which says the US refuses to recognise Russia’s claim to Crimea – made by former US secretary of state Mike Pompeo in 2018, during Mr Trump’s first term as president.

It also comes after Ukrainian officials said nine people were killed and almost 50 injured in the city of Marhanets after a Russian drone hit a bus carrying workers on Wednesday morning.

Russia also launched “a massive” drone attack on the central Ukrainian region of Poltava, injuring at least six people, the emergency service said in a post on the Telegram messaging app.