As China buckles under a surge in Covid-19 cases, sparking fears of a new coronavirus mutant being unleashed on the world, South Africa has identified its first case of the so-called kraken sub-variant, described by the World Health Organisation (WHO) as the most highly-tranmissible so far.
Local health authorities were quick to dismiss fears about XBB.1.5, now the dominant strain in the US and detectable in at least 28 other countries, but MedicalBrief notes the development is a fresh reminder that the pandemic is far from over, as leading scientists have cautioned.
The National Coronavirus Command Council met this week to assess the potential dangers of the XBB.1.5 sub-variant and determined that there was no cause for alarm yet. News24 reports that the Ministerial Advisory Committee on Covid-19 is expected to meet in the next few days to finalise the details around the provision of additional Covid-19 booster jabs to eligible adults, Health Minister Joe Phaahla said on Tuesday.
He said this would see adults aged 50 and older eligible for five vaccine doses and those between 18 and 49 eligible for four.
The additional doses are expected to be available later this month, and the public will be able to mix and match between the two vaccines available in South Africa.
TimesLIVE, however, reports that although there have been no major differences in severity identified between cases caused by XBB.1.5 and those from other variants, the WHO is planning an updated assessment on the variant’s risks as it causes a huge surge of infections on the east coast of America, among other countries.
In South Africa, the first recorded case was discovered in gene sequencing carried out by researchers at Stellenbosch University from a 27 December sample, according to Professor Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation, who added that no effect on cases, hospitalisations or deaths have been seen elsewhere in the country so far, and currently, there was no need to panic.
The report on the detection of the XBB.1.5 variant case had been submitted to the Department of Health, reports The Mercury.
“We discovered that it is still the Omicron variant in circulation, but a sublineage, identified as XBB.1.5.” He said they had detected only one genome of the XBB.1.5 variant from 100 samples, “meaning it is at a very low prevalence”.
Covid-19 vaccines currently in circulation would still be effective against the new variant.
“We had our last wave in May 2022 but thanks to population immunity, meaning immunity through previous infection and vaccination, it was not deadly and we didn’t see a big increase in hospital admissions.
“We are not expecting another wave of infections or the need for any restrictions but people who are concerned should get a booster vaccine to ensure that if they are infected, they don’t get severe disease.”
News24 reports that the country has been advised to ramp up its Covid-19 testing, however.
The WHO's Maria Van Kerkhove said XBB.1.5 spreads rapidly because of the mutations it contains, allowing it to adhere to cells and replicate easily.
While the WHO did not have any data on severity yet, or a clinical picture of its impact, it saw no indication that its severity had changed.
“We are concerned about its growth advantage, in particular in some countries in Europe and in the US… specifically the northeast part of the United States, where XBB.1.5 has rapidly replaced other circulating variants,” she said.
“Our worry is how transmissible it is… and the more this virus circulates, the more opportunities it has to change.”
Statistics from the US Centres for Disease Control and Prevention (CDC) showed the strain is behind 41% of cases in America, reports the Daily Mail.
In the UK, meanwhile, data from GISAID and CoVariants.org suggests that XBB.1.5 was responsible for just under 8% of cases in the two weeks to 2 January.
But the latest figures from the Sanger Institute, one of the UK’s largest Covid surveillance centres, suggests XBB.1.5 is behind up to half of all Covid cases in the worst-hit regions.
Latest NHS figures show there are 9 459 hospital patients with Covid and 4 128 with flu. The total of 13 587 is 13% of all available ward beds, or one in every eight.
Both figures are expected to rise in the coming days and hospitals are already 94% full.
XBB.1.5 has gained 14 new mutations to the virus’ spike proteins compared with its ancestor strains, which appear to have given it enhanced antibody-resistance.
This means people who are vaccinated or have had a previous infection are more susceptible to an infection – though not necessarily severe illness.
But what worries the WHO is the prospect of XBB.1.5 being the gateway to a scarier variant. The more infections that occur, the more opportunities the virus has to mutate and evolve.
The F486P vaccines could make it more resistant to antibodies brought on by the Covid vaccine.
Some lab tests have indicated it can better evade jab-induced immunity, although the jury is still out in the real world.
Meanwhile, the WHO has accused China of under-representing its number of Covid hospitalisations and deaths as fears increase about the rapid spread of the virus in that country.
News24 reports that Chinese state media played down the severity of a surge of Covid-19 infections before a briefing by its scientists to the WHO, which was hoping for a “detailed discussion” on the evolution of the virus.
China’s sudden turnaround on Covid controls on 7 December, as well as the accuracy of its case and mortality data, have come under increasing scrutiny at home and abroad.
The Los Angeles Times reports that “the coronavirus has indeed taken advantage of its opportunity to spread through a population of 1.4 bn people that is under-vaccinated and has little to no prior exposure to the virus”.
“Right now the pandemic situation in China is not transparent,” said Wang Pi-sheng, the head of Taiwan’s epidemic command centre “We have a limited grasp on its information, and it’s not very accurate.”
“Data remains essential for WHO to carry out regular, rapid and robust risk assessments of the global situation,” WHO director-general Tedros Adhanom Ghebreyesus said last week.
About two weeks after the easing of zero COVID rules, hospitals in Hebei province had run out of beds in their intensive care units. Patients were forced to lie on the floor and incoming ambulances were turned away.
A study by Hong Kong University said the death toll would be nearly 1m if the government can’t provide enough booster shots and antiviral treatments. Modellers at the Institute for Health Metrics and Evaluation at the University of Washington say China would hit the 1m mark if the virus is allowed to spread unchecked, but added that the government would probably reinstate some pandemic control measures to prevent that from happening.
Airfinity, a health analytics firm based in London, has a more pessimistic outlook: 1.7m deaths by 1 May. It estimates the current wave of infections will peak this week, with 3.7m new cases in one day, followed by a quicker, second wave that will peak on 3 March, with 4.2m new cases.
Yet despite these predictions, the country’s Foreign Ministry labelled travel entry curbs imposed by some countries as “simply unreasonable”, saying they “lacked scientific basis”.
President Cyril Ramaphosa and the National Coronavirus Command Council had signed off on a decision to refrain from implementing restrictions on travellers from affected countries, such as China and the US, and no restrictions would be placed on South Africans.
Last week, Italian authorities said almost half of the 212 passengers, who arrived at Milan Airport from China had tested positive for Covid-19.T
The LA Times reports that the Traveller Genomic Surveillance programme set up shop at Los Angeles International Airport last week specifically to monitor viral specimens from China.
“New variants can arise anywhere there’s uncontrolled infection, and Covid is spreading through China like wildfire,” said Harvard University infectious-disease specialist Dr Jonathan Li.
The WHO has urged Chinese health officials to regularly share specific and real-time information on the outbreak, and data on hospitalisations, deaths and vaccinations, after reports that 100 ambulances full of Covid cases arrive at hospitals every day, and doctors have said 70% of Shanghai “is infected with Covid”.
The Communist Party’s official newspaper cited Chinese experts as saying the illness caused by the virus was relatively mild for most people.
“Severe and critical illnesses account for 3% to 4% of infected patients currently admitted to designated hospitals in Beijing,” said Tong Zhaohui, vice president of the Beijing Chaoyang Hospital.
Kang Yan, head of West China Tianfu Hospital of Sichuan University, said that in the past three weeks 46 patients had been admitted to intensive care units, representing about 1% of symptomatic infections.
However, the emergencies area at the Zhongshan Hospital in Shanghai was packed with patients last week, a Reuters witness said.
Some were in beds in the corridor receiving IV treatment while dozens were queuing around them, waiting to see a doctor. It was unclear how many were there with Covid.
Around the cities of Baoding and Langfang outside Beijing, hospitals have run out of intensive care beds and staff as severe cases surge, reports AP.
Xu Wenbo of the Chinese Centre for Disease Control and Prevention said last week 50 of the 130 Omicron versions detected in China had resulted in outbreaks. The country is creating a national genetic database “to monitor in real time” how different strains were evolving and the potential implications for public health.
Soaring figures
China has so far insisted on using only Chinese-made vaccines, which are seen as less effective than Western ones based on mRNA technology, and the European Union has offered free Covid-19 vaccines to the country.
Beijing has not responded to the offer yet, an EU spokesperson said, but the move comes after Germany shipped 11 500 BioNTech Covid shots to China last month for use by German nationals there.
Health officials also insist that the variants spreading throughout the country are the same versions of Omicron that have already been identified elsewhere. Should a new version of the virus be found, the country would report it, said Zunyou.
But scientists worry that the Chinese surge could unleash a new coronavirus mutant on the world: it could be similar to Omicron variants circulating there now, it could be a combination of strains. Or something entirely different, they say.
“China has a population that is very large and there’s limited immunity. And that seems to be the setting in which we may see an explosion of a new variant,” Dr Stuart Campbell Ray, an infectious disease expert at Johns Hopkins University told AP.
Every new infection offers a chance for the coronavirus to mutate, and the virus is spreading rapidly in China. The country has largely abandoned its “zero COVID” policy, and although overall reported vaccination rates are high, booster levels are lower, especially among older people. Domestic vaccines have proven less effective against serious infection than Western-made messenger RNA versions. Many were given more than a year ago, meaning immunity has waned.
The result? Fertile ground for the virus to change.
“When we’ve seen big waves of infection, it’s often followed by new variants being generated,” Ray said.
Dr Shan-Lu Liu, who studies viruses at Ohio State University, said many existing Omicron variants have been detected in China, including BF.7, which is extremely adept at evading immunity and is possibly driving the current surge.
Experts said a partially immune population like China’s puts particular pressure on the virus to change.
In China, most people have never been exposed to the coronavirus. China’s vaccines rely on an older technology producing fewer antibodies than messenger RNA vaccines.
Given those realities, Dr Gagandeep Kang, who studies viruses at the Christian Medical College in Vellore, India, said it remains to be seen if the virus will follow the same pattern of evolution in China as it has in the rest of the world after vaccines came out. “Or,” she asked, “will the pattern of evolution be completely different?”
South African virologist and epidemiologist Professor Salim Abdool Karim says that while the emergence of Pathogen X, the potential driver of a new global pandemic, is uppermost in public health experts’ minds, new data from Discovery Health Medical Scheme members show that the long-term consequences of Covid-19 infections will have a massive impact on health systems in years to come.
Included in this threat are the new variant of the SARS-CoV-2 virus, a potentially severe flu virus, and other viruses that jump from animals to humans (zoonotic diseases), like Ebola.
Karim told Daily Maverick there are three scenarios for the next three to five years.
“The first is that we need to acknowledge and appreciate that we are still living in a pandemic. It hasn’t left us.
“In South Africa, the emergency of Covid-19 is receding, and people are not dying in the same way as in 2020. But this doesn’t apply to the whole world,” he said.
“Many countries are still dealing with waves of infections, like China, and also the US, which has 400 deaths daily from Covid. In South Africa, we are still in double digits. Some days we record a low three to four deaths and other days 20 to 30 deaths. People are still dying, but not to the extent that we were concerned about in 2020.”
Karim says two descendants of the Omicron subvariant BA.5 are the latest mutations of the virus.
“They can escape almost every antibody that is available. That means none of the monoclonal antibodies works against them,” he said.
“The other problem is they will escape vaccine-induced immunity,” Karim added. “That is our ongoing concern – that we may get to a new variant that has a high level of escape and that this will spread.”
One fear about the unknown is whether the virus will mutate to the extent that it can escape a sizeable amount of the body’s T-cell response.
He says the second problem South Africa faces is a pandemic of long Covid-19 for the next three to five years, and health problems caused by infections currently occurring as well as those from the past.
“Statistics released by Discovery show that heart disease has doubled. That is how serious it is,” said Karim.
“The third problem is whether we could have a new pandemic even though the Covid-19 pandemic is not finished yet. The answer to that is that it is an ever-present threat and it will come from three groups of viruses.
“Influenza will always remain a threat. We are due at some point soon for a flu pandemic. These come in cycles every decade or so, but we haven’t had one for a while,” he said.
“We don’t know what is coming next. It poses a problem. It hasn’t been a problem because of masking and social distancing. We had no flu in South Africa in 2020 and 2021, then the flu came back this year. We could be seeing a significant flu outbreak in the next winter.”
Karim says there is also the potential for a new coronavirus.
“There are thousands of these, so we live with this threat. We had three in the past 20 years: SARS and then MERS and then came SARS-CoV-2. We are likely to see another coronavirus in the next decade.”
The third of the viral threats are viruses in the same class as Ebola, which causes haemorrhagic fever.
Meanwhile, on the subject of zoonoses, scientists at Washington State University recently discovered a virus in a Russian bat that would could infect humans and is related to SARS-CoV-2.
A team led by researchers at the university’s Paul G Allen School for Global Health said the virus is known as Khosta-2.
They identified spike proteins from the bat virus that can infect human cells and are resistant to both monoclonal antibodies and serum from SARS-CoV-2 vaccine recipients.
“Our research further demonstrates that (these types of viruses) circulating in wildlife outside Asia – even in places like western Russia where the Khosta-2 virus was found – also pose a threat to global health and ongoing vaccine campaigns against SARS-CoV-2,” said Michael Letko, Washington State University virologist.
He said the discovery underscores the importance of finding a universal vaccine for this class of viruses.
AP article – China’s COVID-19 surge raises odds of new coronavirus mutant (Open access)
LA Times article – Coronavirus Today: What’s going on in China? (Open access)
News24 article – China media plays down Covid severity as WHO seeks detail on variants (Open access)
TimesLIVE article – South Africa has first case of most transmissible Covid-19 variant (Open access)
The Mercury PressReader article – No need to panic over Kraken strain (Open access)
News24 – SA will not impose restrictions on travellers from China – health dept (Open access)
Daily Maverick article – The real spectre of Pathogen X and another global pandemic (Open access)
See more from MedicalBrief archives:
COVID cases soar in China, ‘impossible’ to track
COVID restrictions loosen after countrywide protests in China
South Africans still dying but COVID vaccine drive slows to a trickle
‘Acceptable loss’ debate as COVID-19 becomes plague of the elderly
Scepticism from EU experts over abolition of all COVID curbs in England
Zoonotic diseases: Sindbis, Langya and monkeypox outbreaks keep scientists on alert
WHO records 1m COVID deaths in 2022