Variants

Beware a More Transmissible and Deadly Variant, Warns Bill Gates (Who Has a Book to Promote)

Microsoft billionaire Bill Gates has warned there is a “way above 5%” risk the world has not yet seen the worst of the Covid pandemic. MailOnline has more.

The tech mogul and philanthropist said he did not want to sound “doom and gloom” but warned there was a risk an “even more transmissive and even more fatal” variant could be generated.

He said the risk of that happening is “way above 5%” and would mean the world has yet to see the worst of the pandemic.

It is not the first time he has made such a prediction. In December 2021, he warned his millions of Twitter followers to brace themselves for the worst part of the pandemic having previously cautioned in 2015 that the world was not ready for the next pandemic.

Gates told the FT: “We’re still at risk of this pandemic generating a variant that would be even more transmissive and even more fatal.

“It’s not likely, I don’t want to be a voice of doom and gloom, but it’s way above a 5% risk that this pandemic, we haven’t even seen the worst of it.”

COVID-19 has killed an estimated 6.2 million people worldwide since March 2020, but case numbers and deaths have been dropping in recent weeks.

Gates’s warning comes after Dr Tedros Adhanom Ghebreyesus, director-general of the World Health Organisation (WHO), this week warned that people still needed to be weary of the virus, and that decreases in overall testing and Covid surveillance in many countries left the world at risk to a resurgence of the virus.

Gates – who releases his new book How to Prevent the Next Pandemic on Tuesday – advised governments across the world to invest in a team of epidemiologists and computer modellers to help identify global health threats in the future.

More epidemiologists and computer modellers?!? Based on their track record of the last two years. I don’t think so!

Worth reading in full.

Omicron BA.2 is Even Milder Than Omicron BA.1, UKHSA Data Show

The latest U.K. Health Security Agency (UKHSA) Technical Briefing on variants of concern reports that the Omicron BA.2 variant, which is now dominant in the U.K. and in many countries around the world, is even milder than the original Omicron BA.1 variant, which was responsible for the very low death toll this winter.

The report states:

Analyses of sequenced cases up to March 8th 2022 have been undertaken to compare the risk of hospitalisation, as defined by admission as an inpatient, or presentation to emergency care that resulted in admission, transfer or death, following BA.2 compared to BA.1. This analysis adjusted for age, reinfection status, sex, ethnicity, local area deprivation and vaccination status. It also controlled for the effect of geography and specimen date. The risk of hospitalisation does not appear to be higher following a BA.2 infection than following a BA.1 infection (hazard ratio 0.94 95% CI: 0.88-1.00).

The hazard ratio of 0.94 means BA.2 comes with 6% lower risk of hospitalisation compared to BA.1. The 95% confidence interval (CI) of 0.88-1.00 means the researchers are 95% sure the variant is not a higher risk than BA.1, and it may be up to 12% lower. These figures are adjusted for confounders such as age and vaccination status, and also geography for some reason. Admittedly, it’s not a big drop, but it’s in the right direction, and it means up to 12% fewer people may be hospitalised in the current surge, which is a good thing.

Ex-WHO Scientist Claims Omicron BA.2 Variant is as Infectious as Measles – But What Do the Data Show?

A former World Health Organisation (WHO) official has claimed that the BA.2 subvariant of Omicron has a basic reproduction number (R0) of around 12 (each infected person passes it on to 12 others), making it as infectious as measles, the most contagious disease known, and nearly six times as infectious than the original Wuhan strain (with an R0 of 2.5). Here’s the report in MailOnline.

Professor Adrian Esterman, a leading epidemiologist in Australia, said BA.2 is 40% more transmissible than the original variant.

He claimed it would have a basic reproduction number (R0) of around 12, meaning if left to spread unchecked every infected person would pass it to a dozen others.

It would make the sub-strain five times more infectious than the original Wuhan virus and one of the most contagious diseases known to science.   

The claim would explain why the mutant virus was able to outstrip its parent strain in the U.K. in about a month and undermine China’s Zero Covid policy, which has until now managed to suppress every version of the virus.

Explaining his methodology, Professor Esterman said: “The basic reproduction number (R0) for BA.1 is about 8.2, making R0 for BA.2 about 12. This makes it pretty close to measles, the most contagious disease we know about.”

The R0 number is the average number of people each BA.2 patient would infect, if there was no immunity in a population or behavioural changes. 

But most scientists say there is no reason to be concerned over the variant because it is just as mild as the original Omicron.

The BA.2 subvariant is now behind almost every case in England, or 83% of infections last week, according to official estimates.

It became dominant three weeks beforehand, accounting for 52% of all infections in the week to February 20th. 

The Office for National Statistics (ONS) estimates cases have been rising since mid-February, with one in 25 people in England estimated to have been infected last week.

Hospitalisations are also creeping up, but the majority appear to be incidental – when someone tests positive after admission for another illness. 

What Really Happened at the Start of the COVID-19 Pandemic?

At this two-year point in the pandemic, I’ve been revisiting what happened at the start to get a clearer idea of how things unfolded and whether what happened then can tell us anything useful about the virus. Here’s what we know.

In the last week of December 2019, a doctor in Wuhan noticed unusual pneumonia in six patients who all tested positive for a new coronavirus. We can surmise that to have hospitalised six unconnected people (not all linked to the Huanan market), the new virus must have been circulating in Wuhan for some weeks. Internal reporting of this cluster led to the first public message of a suspected pneumonia outbreak, with precautions advised, from the Wuhan Municipal Health Commission on December 31st. At this point there were just 27 identified cases in hospital, seven of them serious – which wouldn’t seem out of the ordinary for winter.

Despite this inauspicious start, Hubei province went on (according to official data) to have a deadly outbreak, though one that was notably slower burning and milder than later Covid outbreaks elsewhere. It totalled around 4,500 deaths out of a population of 57 million people, making it around a tenth as deadly as the first wave in the U.K., and peaked at 143 reported daily deaths on February 19th (suggesting the infection peak was late January). This doesn’t seem a particularly high death toll for a winter respiratory virus.

Notably, this initial deadly outbreak was very localised. Hubei was locked down on January 23rd, but prior to that the virus circulated freely for weeks, while millions of people left the province ahead of the lockdown. Despite this, no other province in China suffered a deadly outbreak (see below). While we might be inclined to question China’s official data, it fits with what happened in neighbouring countries – no other country in the region suffered a deadly outbreak of the new virus. South Korea’s outbreak peaked at six reported daily deaths on March 30th, Japan’s (which was the worst in the region) at 24 on May 1st.

Imperial Finally Acknowledges Pre-Existing Immunity to COVID-19. What Took It So Long?

T-cells from common cold coronaviruses can provide protection against COVID-19, an Imperial College London study has found. Reuters reports on the findings, which were published in Nature.

The study, which began in September 2020, looked at levels of cross-reactive T-cells generated by previous common colds in 52 household contacts of positive COVID-19 cases shortly after exposure, to see if they went on to develop infection.

It found that the 26 who did not develop infection had significantly higher levels of those T-cells than people who did get infected. Imperial did not say how long protection from the T-cells would last.

“We found that high levels of pre-existing T cells, created by the body when infected with other human coronaviruses like the common cold, can protect against COVID-19 infection,” study author Dr Rhia Kundu said.

The researchers suggest vaccines based on imitating the internal virus proteins that T-cells target may be more resilient to mutations and new variants as those proteins, unlike the spike protein targeted by the current vaccines, “mutate much less”.

Cross-immunity to SARS-CoV-2 from other coronaviruses has been proposed since early on in the pandemic as an important element in reaching herd immunity and endemicity (for example, it was mentioned in this Scientist article from March 2020), and became a particular focus of interest in the autumn of 2020 as evidence of it accumulated (see here, here and here). It’s good to have further confirmation of this from Imperial (and also recently from UCL), but it has to be said it’s pretty late to the party, and it’s not clear why a study which began in September 2020 during a public health emergency has taken 16 months to report, particularly when vaccines were brought to market in 10 months. The emphasis of the researchers is on the potential usefulness of the findings for developing new and more resilient vaccines, which contains a tacit admission that the existing vaccines are failing, but also leaves one wondering whether the research has only been published now that it is useful for making new pharmaceutical products. It might be added that the studies on the efficacy of generic off-label medicines against Covid are taking an awfully long time to report.

As Dr. Mike Yeadon explained in his October 2020 piece for the Daily Sceptic, “What SAGE Has Got Wrong“, the assumption of a lack of pre-existing immunity and hence universal susceptibility was one of the great errors made by Government advisers throughout the pandemic and which led to an over-reaction that continues to this day. Now that Imperial researchers have acknowledged the existence of prior immunity, will Neil Ferguson’s modelling team update its assumptions?

Here Comes the French Variant…

Scientists at the IHU Mediterranee Infection in Marseille, France, have announced the discovery of a new variant of SARS-CoV-2, which they say has more mutations than Omicron and may be more resistant to vaccines. Firstpost has the story.

Here’s what we know so far of this new COVID-19 variant:

• Researchers say that it contains 46 mutations – even more than Omicron – which makes it more resistant to vaccines and infectious.
• Some 12 cases have been spotted so far near Marseille, with the first linked to travel to the African country Cameroon.
• Tests show the strain carries the N501Y mutation – first seen on the Alpha variant – that experts believe can make it more transmissible
• According to the scientists, it also carries the E484K mutation, which could mean that the IHU variant will be more resistant to vaccines.
• It is yet to be spotted in other countries or labelled a variant under investigation by the World Health Organisation.

The variant was discovered on December 9th, so we might have expected it to have spread a bit further and faster by now if it is going to make a big impact – Omicron, by comparison, was already on its way to world domination by this point. So this may be just one of many non-event variants.

France is currently experiencing a strong winter surge dominated by the Omicron variant and the Government is responding by tightening the vaccine passport regime.

Vaccine Escape Mutations “Will Become a Major Mechanism of Transmission”, Say Researchers

When the vaccine rollout got underway, some scientists argued that mass vaccination would set up an evolutionary selection pressure in favour of vaccine-resistant strains, potentially prolonging the pandemic.

For example, Robert Malone and Peter Navarro wrote the following in the Washington Times:

The more people you vaccinate, the greater the number of vaccine-resistant mutations you are likely to get, the less durable the vaccines will become, ever more powerful vaccines will have to be developed, and individuals will be exposed to more and more risk … If the entire population has been trained via a universal vaccination strategy to have the same basic immune response, then once a viral escape mutant is selected, it will rapidly spread through the entire population

To avoid being locked into an arms race with the virus, they argued that only the most vulnerable should be vaccinated. They were calling, in other words, for focused protection.

However, many scientists were sceptical that this constituted a good enough reason to hold off on mass vaccination. After all, people were dying of Covid now, and the ‘arms race argument’ was in any case speculative.

It’s important to note: the premise of Malone and Navarro’s argument – that vaccination can drive viral evolution – is accepted by many of those who support the mass rollout of Covid vaccines. At a press conference in January, the UK’s Chief Scientific Adviser Sir Patrick Vallance said the following:

The more you vaccinate, the more you put evolutionary pressure on the virus. So it’s true that, as you get up to very high levels of vaccination, the virus is then struggling to find out what to do, and that eventually will become an issue.

The part of Malone and Navarro’s argument that is in dispute, it seems, is that the ensuing arms race will prove unmanageable. For example, Vallance followed his comments above by saying, “the virus probably will mutate at that point, and that means that different vaccines will be needed in due course.”

A Doctor Writes… What We Know About the Omicron Variant So Far

There follows a guest post from our in-house doctor, formerly a senior medic in the NHS, on what we know so far about the Omicron Covid variant. He’s also written about the scandal of the Downing Street parties – Secret Santa-Gate – asking: “If Covid really was such a mortal threat as the Government have led the public to believe, do readers really think that Downing Street apparatchiks would be flocking to packed parties in small rooms? I suspect not.

It’s now two weeks since the world first heard of the Omicron variant. Travel restrictions and mask mandates were immediately reimposed on the U.K. population and have since been tightened further. Reports in the press this morning are trailing the reimposition of more curbs on liberty in the U.K. over the next few weeks. In today’s update, I will examine what we have learnt about the new variant and to what extent it may affect the situation in the NHS. This update is a bit data-heavy, so apologies in advance for the graphic fest.

South Africa is widely regarded as the epicentre of Omicron. Having spent considerable time working in that wonderful country, I can attest to the expertise of my South African medical colleagues, particularly in the field of infectious diseases. So, when Dr. Fareed Abdullah writes from the Steve Biko Hospital in Pretoria that the data so far on the Omicron variant suggests it is very much milder than the Delta variant, I’m inclined to take him seriously.

I encourage readers to examine this document themselves – this extract is worth quoting in full:

In summary, the first impression on examination of the 166 patients admitted since the Omicron variant made an appearance, together with the snapshot of the clinical profile of 42 patients currently in the Covid wards at the SBAH/TDH complex, is that the majority of hospital admissions are for diagnoses unrelated to Covid. The SARS-CoV-2 positivity is an incidental finding in these patients and is largely driven by hospital policy requiring testing of all patients requiring admission to the hospital.

Using the proportion of patients on room air as a marker for incidental Covid admission as opposed to severe Covid (pneumonia), 66% of patients at the SBAH/TDH complex are incidental Covid admissions. This very unusual picture is also occurring at other hospitals in Gauteng. On December 3rd, Helen Joseph Hospital had 37 patients in the Covid wards of whom 31 were on room air (83%); and the Dr. George Mukhari Academic Hospital had 80 patients of which 14 were on supplemental oxygen and one on a ventilator (81% on room air).

Chris Whitty Worried That the Public Won’t Accept New Covid Restrictions

Chris Whitty has said that his “greatest worry at the moment” is whether, should new restrictions be implemented to fight Covid variants, the Government can “still take people with us” and ensure public compliance with tightening Covid laws. The Chief Medical Officer further stated that it will now be harder to gain public acceptance for more restrictions given that the “people put up with two years of their lives being interfered with”. BBC News has the story.

England’s Chief Medical Officer Chris Whitty has said his “greatest worry” is whether people will accept fresh curbs on activities to tackle Covid variants.

His comments came after the Government announced quarantines on travellers from some African countries following the emergence of a new strain.

Whitty said he questioned whether “we could take people with us” if restrictions had to be imposed.

But he added that “my overall view is, I think we will”.

England has been through three national lockdowns since Covid first struck. There have also been many local restrictions imposed at various points during the past 20 months.

Whitty told a panel discussion hosted by the Local Government Association: “My greatest worry at the moment is that people… if we need to do something more muscular at some point, whether it’s for the current new variant or at some later stage, can we still take people with us?”

He admitted that some of the changes the public has had to make have been “very destructive” to society and the economy. However, despite his worries, Whitty struck a positive note, saying he believed the Government will be able to maintain public support for Covid measures.

“I think the extraordinary thing has been the ability of the U.K. population, with very, very small exceptions, to just accept that there are things we collectively have to do to protect one another and do collectively, including things that have been very destructive to social and economic situations for individuals and families,” he said.

“Obviously, we want to avoid having to do those at all if we can, and to do the minimum ones necessary, but will we be able to maintain public support?

I think my overall view is, I think we will.”

There have been a further 50,091 Covid cases in the U.K. and another 160 deaths within 28 days of a positive test, the latest Government figures show.

Both deaths and the number of people admitted to hospital continue to trend lower despite the rise in cases. It is likely we’re seeing the impact of the booster campaign protecting the most vulnerable people and keeping them out of hospital.

Worth reading in full.

No Evidence New Delta Sub-Variant AY.4.2 is Anything to Worry About

There’s a new variant in town. Or rather, a sub-variant – AY.4.2, an offshoot of the Delta variant, said by some scientists to be up to 10-15% more transmissible. As of the end of September it made up around 6% of new cases and is on an upward trajectory.

Variants detected in England (Wellcome Sanger Institute)

However, there’s no reason to panic – and, for a change, that’s the message coming from the top. The Prime Minister’s official spokesman said: “There’s no evidence to suggest that this variant… the AY.4.2 one… is more easily spread. There’s no evidence for that…”

Francois Balloux, Director of the University College London Genetics Institute, said while the variant is “likely to be up to 10% more transmissible”, it is not comparable to Delta when it arrived in the U.K, which was at least 50% more infectious than Alpha.

Professor Balloux played down the likely impact of the increased transmissibility on infections, adding: