Archive for July, 2022

Where are we in the pandemic?

The bottom line here is that anyone making the statement ‘coming out of the Covid environment’ has not kept up with the data, which demonstrate the following:

1. Transmission is ~ 98% via airborne aerosols, known since March 2020 and firmly established by initial rules on masking and regions where this is maintained.

2. The pandemic is unabated. Cases remain high, with several waves a year. This to the extent that hospital beds fill up every wave, world-wide health care workers are burning out due to overwork and waiting lists are getting so long that the best option is becoming the avoidance of ill health.

3. Deaths are lower due to vaccines, but SARS-CoV-2 is an adept immune escapologist

4. Long Covid is a growing socio-economic problem, a consequence is the loss of members of an organisation’s workforce.

5. Viral persistence is measurable 15 months after recovery, and among the targets is bone marrow and the immune system.

6. There is no cure and no efficacious treatment, and this is true  for acute infection (when you have overt symptoms for ~ 10 days), viral persistence (months/years, see below) and LongCovid (see below). This is in contrast to HIV.

The consequences of the above are that organisations need to:

A. Explicitly state that masks are expected to preserve the health of yourself and of your co-workers and provide masks to the workforce.

B. Explicitly provide details on ventilation of rooms occupied by the workforce and/or install HEPA filters in all such rooms.

C. Expect those with even partial symptoms have a clear LFTs before returning to work.

D. Provide updates on the status of current variants, how much we don’t know and the extent to which Public Health surveillance is reliable.

Anything else is a gross dereliction of duty on the part of an organisation’s management.

Below I take each of the above statements and provide the evidence, including links. If any reader from my workplace, the University of Liverpool can come up with an argument based on evidence why we should not take all possible measures against transmission, then I will accept that the University does not need to take such measures. Until then, not doing so remains a gross dereliction of duty.


Transmission is ~98% by airborne aerosols. Aerosols DO NOT drop to the ground, they remain airborne, and the only protection is to reduce their concentration. This is achieved by two complementary routes:

Masks to reduce the amount of aerosols put into the air by an infected person;

Ventilation and filtration to ensure rapid dilution.

Some resources and comments on these

A nice article in PNAS on how secondary physical measures work, which should be on the desk of every organisations’ Health and Safety Office.

A very simple message from JAMA in an article on this subject

“Because no single approach is 100% effective in preventing COVID-19, prevention measures work best when layered, including vaccination and nonpharmacologic interventions that reduce inhalation of infectious particles.”

The same article makes further excellent points. One on the long-term implications for building design

“Reducing contaminants in shared air by improving air handling systems in buildings is an attractive, broadly effective structural measure that does not require repeated individual actions.”

There is a nice Sci-Comm piece here.

The evidence on the efficacy of the different layers of is that you are safer in a small room with an unvaccinated person, both wearing a FFP2/N95 masks, than in the same room, both vaccinated but  without masks.

We should of course as far as possible have all measures in place.

Pandemic is unabated

Data acquisition is being dismantled, so it is essential to employ critical faculties. The testing programme is no longer functional, since you cannot report the results of tests purchased privately. Moreover, the excellent ONS survey will soon be limited, so we will have even less information on the number infected later in the year, and the only proxy will then be NHS data on admissions and bed occupancy.

For the record the ONS survey data are here and for the week ending 29 June 2022 for England the estimated number of people testing positive for COVID-19 was 2,154,000 (95% credible interval: 2,062,600 to 2,247,100), equating to 3.95% of the population, or around 1 in 25 people.

There are very useful analyses of these data, which I recommend, e.g., @TravellingTabby on Twitter who maintains an excellent data web page from the ONS data

The idea that the virus is attenuating is WRONG. As usually small numbers, large effect sizes, when we go to a good sized study (130 k patients) there is no evidence that Omicron is milder

Deaths are lower

The estimate from WHO is that vaccines have avoided 20 M deaths. However, excess deaths over historical average still substantial. The problem is that the efficacy of the vaccines is good, but not nearly good enough. This is compounded by giving the virus a free reign so that natural selection can operate at extremely high throughput. The result is a virus that was already good at immune escape is now a master. Some data in the links below.

The Tweetorial from Deepti Gurdasani covers a recent Science paper that demonstrates immune escape and that T-cell immunity to Omicron is poor at best

The paper is here.

Long Covid

This occurs in a significant number of people after they recover from acute infection. The risk only reduced a little by vaccination according to this large study of 33 k people infected after vaccination with over 13 M controls!

A key take home message from this paper is:

Altogether, the findings suggest that vaccination before infection confers only partial protection in the post-acute phase of the disease; hence, reliance on it as a sole mitigation strategy may not optimally reduce long-term health consequences of SARS-CoV-2 infection. The findings emphasize the need for continued optimization of strategies for primary prevention of BTI and will guide development of post-acute care pathways for people with BTI. 

Importantly, the risk of LongCovid increases with each infection.

The ONS (UK) data form early April 2022 indicate 1.7 million people with LongCovid in the UK (2.7% of the population), and it also affects the young…:

“40,000 aged 2-11 (confidence intervals 32K-48K) 59,000 aged 12-16 (confidence intervals 52K-66K) That’s a total of 99,000 children “

For those aged 17-24, that’s 89,000 (CI 77K-102K)

For those with an illness duration of at least A YEAR: 14,000 aged 2-11 (confidence intervals 9K-19K) 17,000 aged 12-16 (confidence intervals 13K-20K) That’s a total of 31,000 children. For those aged 17-24, that’s 45,000 (CI 36K-54K).

Unfortunately, those affected cannot pursue their usual lives and work, studies, hobbies, etc., are largely or completely suspended.

There is good evidence that micro clots are part of the problem and it seems likely that viral persistence in our organs may also contribute.

Viral persistence

Data from autopsies demonstrate viral persistence in organs in even moderate cases (so no hospitalisation) up to 15 months post infection. These data are likely to get worse, rather than better as we progress into the pandemic and we acquire more time-dependent data.

There is no cure and vaccines are an aid, but not a solution

The drugs we have are merely re-purposing existing ones, and their efficacy is modest, at best. It will be some time, 5 to 10 years  perhaps, before we have drugs that specifically target SARS-CoV-2 functions such as its polyprotein protease. There is good evidence for microclots playing a role in LongCovid, but we haven’t yet got a clinical trial running with preregistered outcomes etc. – so far we have case reports only.

Current vaccines are losing efficacy against variants more adept at immune escape, an entirely predictable outcome given near zero measures to reduce transmission, so the virus has had an evolutionary field day exploring host-pathogen interactions, to our detriment of course.

The future without measures beyond vaccination

Attrition of the workforce, most pronounced in those exposed to large numbers of humans in small spaces, such as healthcare and education.

Attrition of the student population able to undertake studies.

The outcome is that society is not sustainable, in the same way that Medieval societies were not sustainable in the face of population loss due to the Plague. One only has to consider the complex chain of skills that underpin basic everyday aspects of life:

The mobile phone, needs cutting edge sills in materials, chips, telecommunications networks, GPS satellites, electricity production, and of course software in all elements of the chain. 

Take out 10% of the workforce and we struggle. Currently over 2.7 % of the population are affected, ~0.9 % to the extent they cannot work, and this after just 2.5 years of the pandemic. What can we withstand? 5%, 10 %? I don’t know, but I cannot see a valid argument for testing the hypothesis that society can withstand X% of LongCovid. If you have one, let me know.

The Future 

Future A We continue to ignore the evidence, and see whether our society can withstand the impact of a large % of its population with LongCovid requiring care and being unable to work. This is a course of action taken by an ideologue, and is not possible for a scientist to act in this way, since in science we critically evaluate evidence.

Future B We apply mitigation measures so as to reduce the frequency of transmission, reduce infections and so the number with LongCovid, until such time as the pandemic is over and/or we have drugs that really work. This is the course of action of any organisation that has the well being of its staff (and students) as a core value, it is evidence- and knowledge-driven, and aims to be sustainable, that is to exist in a recognisable form in 10-50 years time.

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