Monday 27 April 2020

Epidemiology is Hard

Here we go again!

-No, there is no evidence of 30 strains, or 8 strains or even 2 strains of SARS-CoV2. There is currently 1 strain and the genome of the virus seems pretty stable. If you heard information about MANY strains it is either bulls*** or somebody is talking about phylogenetic ‘strains’ (in fact they shouldn’t really use term strain in my opinion, but many people does which makes it a bit more confusing for non-scientists) so changes in the viral genome which can help us track spread around the world and create something like viral ‘family tree’. All of those changes are very small and does not change function of any of the viral proteins.
- When I say ‘no evidence’ means there is no evidence YET, but that can change when we will get new data or information. Or might not change at all. When WHO says there is ‘no evidence’ that COVID infection gives you immunity for recurring infections it means that we don’t have that data yet, so we cannot say if this immunity exists or not. It is very early and that is a new pathogen. We cannot tell if the immunity exists and how long it lasts cause not enough time has passed for us to perform tests and get this data. But the data and research so far looks promising, it seems that most of the people develop some level of immunity. How long it lasts? It is hard to say, but hopefully, at least several months as with SARS-1. I know that many of you read scary stories from Asian countries that people are getting re-infected after being discharged from the hospitals but:

*it is only very small number of all the people who got discharged from the hospital

*there is a chance that some of those second positives are false positives. There is no test, which would be 100% false proof, and there are human errors as well.

*there is a big chance that test picks up fragments of ‘dead’ virions, which just did not get cleared out by immune cells yet. Many of those tests were followed by tries to culture those virions in laboratory, and they could not get ‘live’ viruses from it so it seems that what was there was already dead.

*it might have been just first infection which just did not get fully cleared out and reappeared after some time, BUT most (if not all) of those cases has either no symptoms or very mild symptoms after second positive test. Most of the studies say that people with second positive test probably are unable to infect others.

Also having antibodies doesn’t mean you are not immune. I know. Confusing, but immunology is a b****. I’m saying that as person who tortured herself by doing entire course in immunology during my MSc degree, and now is writing DPhil partially in immunology. Don’t do that to yourself. I think immunology is one of the most confusing biological fields out there. Seriously, having antibodies, not having antibodies, having one type of antibodies but no other types of antibodies does not tell us if we have immunity to the pathogen or not 

. There are also B cells, T cells, CD4/CD8, TLRs, and million of other super weird things which makes me cry at night.

- There were some reports about COVID-19 causing blood clots in healthy young adults in US. I just wanted to say that morbidly obese is not healthy. I would also argue that obese is not healthy and yes, being obese makes you more prone to develop severe symptoms of COVID. That’s also because of immunological stuff - inflammation and fat tissue are quite related. Strokes and obesity are also related.

-And just one more thing, comparing countries and measures they used to battle pandemics really does not make sense especially when bringing extreme examples. Like for example - Hong Kong. No, they did not ‘won’ with COVID because they all use masks. They are very small country, which makes it easier to control. They have previous experiences in fighting similar epidemics (SARS-1). And last but not least, people in Hong Kong know how to use masks. And yes, you are more prone to get infections if you are using masks wrong. They are not silver bullet. There is no silver bullet.

- If you feel ill, got cough, fever etc. It is still very possible you have seasonal flu or flu-like illness. It doesn’t mean it is COVID. It does mean though you should stay at home.

 Speaking as a Rocket Scientist... medicine is hard. General Practice requires a degree of intuition and observation that would make Sherlock Holmes proud. Immunology,  the study of immune systems - extremely complex systems - where our tools for investigating them are so crude  - is like trying to analyse a large scale integrated circuit using a jewellers loupe and flint axe.

Sunday 26 April 2020


Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases, Welch et al, Scientific Reports volume 8, Article number: 2752 (2018).


Airborne-mediated microbial diseases such as influenza and tuberculosis represent major public health challenges. A direct approach to prevent airborne transmission is inactivation of airborne pathogens, and the airborne antimicrobial potential of UVC ultraviolet light has long been established; however, its widespread use in public settings is limited because conventional UVC light sources are both carcinogenic and cataractogenic. By contrast, we have previously shown that far-UVC light (207–222 nm) efficiently inactivates bacteria without harm to exposed mammalian skin. This is because, due to its strong absorbance in biological materials, far-UVC light cannot penetrate even the outer (non living) layers of human skin or eye; however, because bacteria and viruses are of micrometer or smaller dimensions, far-UVC can penetrate and inactivate them. We show for the first time that far-UVC efficiently inactivates airborne aerosolized viruses, with a very low dose of 2 mJ/cm2 of 222-nm light inactivating >95% of aerosolized H1N1 influenza virus. Continuous very low dose-rate far-UVC light in indoor public locations is a promising, safe and inexpensive tool to reduce the spread of airborne-mediated microbial diseases.

Monochromatic 222 nm UV light: Development of a safe, cost-effective technology for the efficient reduction of bacterial and viral infection and transmission , Park et al, NIH Grant Project 1R41AI125006-01

...research from Columbia University Medical Center demonstrated that single- wavelength far-UVC photons can kill bacteria and viruses while it cannot penetrate either the human stratum corneum (the outer dead-cell skin layer), nor the ocular cornea, nor the corneal tear-film layer, nor even the cytoplasm of individual human cells. In particular, the results teste both in vitro and in vivo have shown that several far-UVC wavelengths (such as 207 and 222 nm) are as efficient as conventional mercury containing germicidal UV lamp in inactivating both drug-resistant bacteria (e.g. MRSA) and viruses (e.g. H1N1), but these two far UVC wavelengths induce no damage to skin or to eyes, for a wide range of clinical endpoints, in contrast to a conventional broad-spectrum germicidal lamp.

Laser Focus World - 207nm and 222nm

Scientists have known for decades that broad-spectrum UVC light, which has a wavelength of between 200 to 400 nm), is highly effective at killing bacteria and viruses by destroying the molecular bonds that hold their DNA together. This conventional UV light is routinely used to decontaminate surgical equipment.

"Unfortunately, conventional germicidal UV light is also a human health hazard and can lead to skin cancer and cataracts, which prevents its use in public spaces," says study leader David J. Brenner.

Several years ago, Brenner and his colleagues hypothesized that far-UVC could kill microbes without damaging healthy tissue. "Far-UVC light has a very limited range and cannot penetrate through the outer dead-cell layer of human skin or the tear layer in the eye, so it’s not a human health hazard. But because viruses and bacteria are much smaller than human cells, far-UVC light can reach their DNA and kill them," said Brenner.

Excimer lamp sources
Brenner and his group use filtered excimer lamps emitting in the 207 to 222 nm wavelength range. For example, 207 nm light is emitted by a krypton-bromine (Kr-Br) excimer lamp, while 222 nm is emitted by a krypton-chlorine (Kr-Cl) excimer lamp. Brenner's group started with the 207 nm lamp, publishing results on sterilization of bacteria in 2013;1 in 2017, the results at 222 nm for bacteria were reported.2 The latest results, on sterilization of the influenza virus, were published this month (Feb. 2018) in Scientific Reports.3

1. Manuela Buonanno et al., PLOS One (2013); freely available online at
2. Manuela Buonanno et al., Radiation Research (2017);
3. David Welch et al., Scientific Reports (2018); doi:10.1038/s41598-018-21058-w

Saturday 11 April 2020

Stating the Obvious about surgical masks.

It's not just nice to have, but essential that "what everybody knows" has some decent  evidence behind it though.

 Leung, N.H.L., Chu, D.K.W., Shiu, E.Y.C. et al. Respiratory virus shedding in exhaled breath and efficacy of face masks. Nat Med (2020).

We identified seasonal human coronaviruses, influenza viruses and rhinoviruses in exhaled breath and coughs of children and adults with acute respiratory illness. Surgical face masks significantly reduced detection of influenza virus RNA in respiratory droplets and coronavirus RNA in aerosols, with a trend toward reduced detection of coronavirus RNA in respiratory droplets. Our results indicate that surgical face masks could prevent transmission of human coronaviruses and influenza viruses from symptomatic individuals.

Thursday 9 April 2020

Coronavirus Pandemic Update 52: Ivermectin Treatment; Does COVID-19 Atta...

Sheep Dip.

Seriously, that's this drug's main use. Also as a head lice treatment.

Wednesday 8 April 2020

No Clinical Benefit evidenced.

No Evidence of Rapid Antiviral Clearance or Clinical Benefit with the Combination of Hydroxychloroquine and Azithromycin in Patients with Severe COVID-19 Infection, Molina et al, M├ędecine et Maladies Infectieuses, pre publication March 2020.

These virologic results stand in contrast with those reported by Gautret et al. and cast doubts about the strong antiviral efficacy of this combination. Furthermore, in their report Gautret et al also reported one death and three transfers to the ICU among the 26 patients who received hydroxychloroquine, also underlining the poor clinical outcome with this combination. 

In addition, a recent study from China in individuals with COVID-19 found no difference in the rate  of  virologic  clearance  at  7  days  with  or  without  5  days  of  hydroxychloroquine,  and  no difference  in  clinical  outcomes  (duration  of  hospitalization, temperature  normalization, radiological progression) (4). These results are consistent with the lack of virologic or clinical benefit of chloroquine in a number of viral infections where it was assessed for treatment or prophylaxis with sometimes a deleterious effect on viral replication (5-8). 

In summary, despite a reported antiviral activity of chloroquine against COVID-19 in vitro, we found  no  evidence  of  a  strong  antiviral  activity  or  clinical  benefit  of  the  combination  of hydroxychloroquine  and  azithromycin  for  the  treatment  of  our  hospitalized  patients  with severe COVID-19. Ongoing randomized clinical trials with hydroxychloroquine should provide a definitive answer regarding the alleged efficacy of this combination and will assess its safety's not a Double Blind study. There may be some benefit in less severe cases, though there's no good or even fair  evidence of that either. It may be harmful, rather than beneficial, though again, no Double Blind studies have been done.

We can't absolutely exclude the possibility that there may be some benefit at this point. It just seems increasingly unlikely that any benefit, if any exists, is large.

Saturday 4 April 2020

Coronavirus Pandemic Update 49: New Data on COVID-19 vs Other Viral Infe...

In the UK, 1 in 4 cases of viral pneumonia that require ventilation do not survive. With COVID-19, mortality is double that, 1 in 2.

Friday 3 April 2020

The End of the Beginning in Canberra?


The ACT will begin "actively looking" for community transmission of coronavirus in Canberra, allowing a random sample of ineligible people to be tested for COVID-19 each day.

Key points:

  • There are now 91 confirmed cases of COVID-19 in Canberra, after four more were added to the tally
  • A random selection of people who do not meet testing criteria will be tested at two Canberra locations
  • One confirmed case remains under investigation due to its unknown origin

Announcing four more cases of COVID-19 in the ACT, chief health officer Kerryn Coleman said testing would be expanded, as fewer returning overseas travellers and close contacts were being tested each day.
From Monday, a random selection of people who present at Weston Creek Walk-In Centre and the drive-through facility set up at EPIC, but do not meet the testing criteria, will be tested anyway.
"We are able to do this because there is a decrease in demand for testing from returning travellers and known contacts of confirmed cases," Dr Coleman said.
"We are actively looking for evidence of community transmission in Canberra."
More than 5,000 tests have been conducted in Canberra so far

Canberra has a population of 400,000, so this is a rate of 1 in 80. When we get a rate of 1 in 10, with retesting, we may have a handle on the situation, so can be more confident in what we're doing.