I should be qualified to comment on the covid-19 pandemic. I'm a computational/system biologist working on infectious diseases and have spent five years in a world class 'pandemic response modelling' unit. In this thread, I will summarise what I believe I (don't) know. (1/12)
After having spent considerable time thinking how to mitigate and manage this pandemic, and analysing the available data. I failed to identify the best course of action. Even worse, I'm not sure there is such a thing as an acceptable solution to the problem we are facing. (2/12)
I believe that the covid-19 pandemic is the most serious global public health threat humanity faced since the 1918/19 influenza pandemic. There are major differences between the two events but I suspect there will also be similarities that may emerge once we look back. (3/12)
The most plausible scenario to me is for the covid-19 pandemic to wane in the late spring (in the Northern hemisphere), and come back as a second wave in the winter, which I expect could be even worse than what we're facing now. Pic below is what happened in 1918/19. (4/12)
Predictions from any model are only as good as the data that parametrised it. There are two major unknowns at this stage. (1) We don't know to what extent covid-19 transmission will be seasonal. (2) We don’t know if covid-19 infection induces long-lasting immunity. (5/12)
Seasonality is difficult to predict without time-series. Comparison between regions for the covid-19 pandemic suggests some seasonality, but likely less than for influenza. This would be roughly in line with other Coronaviridae (common cold and MERS). (6/12)
How long immunity lasts for following covid-19 infection is the biggest unknown. Comparison with other Coronaviridae suggests it may be relatively short-lived (i.e. months). If this were to be confirmed, it would add to the challenge of managing the pandemic. (7/12)
Short-lived immunisation would defeat both ‘flattening the curve’ and ‘herd immunity’ approaches. Devising an effective strategy would be even more challenging under low seasonal forcing. It would also considerably complicate effective vaccination campaigns. (8/12)
The covid-19 pandemic is an extremely challenging problem and there are still many unknowns. There is no simple fix, and poorly thought-out interventions could make the situation even worse, massively so. (10/12)
The covid-19 pandemic is not just an epidemiological problem. It is a ‘Global Health’ problem, that can only be tackled with an integrated and global approach. For example, there is no such thing as a choice between managing the pandemic vs. protecting the economy. (11/12)
Health and the economy are closely linked. The correlation between per-capita GDP and health (life expectancy) is essentially perfect. If the covid-19 pandemic leads to a global economy collapse, many more lives will be lost than covid-19 would ever be able to claim. (12/12)

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More from @BallouxFrancois

Feb 17
I've been thinking about the Covid surveillance measures that should be kept in place. I believe that mass Covid testing / sequencing and national dashboards should be scrapped fairly soon for the benefit of everyone's sanity, including mine.
Though, it would be ideal to keep some 'flu+' genomic sequencing measures in place. This could take various forms ranging from ONS-type surveillance + sequencing, to more opportunistic sequencing of strains from hospitalised patients and (symptomatic) incoming travellers.
There probably is an optimum (non-maximum) level for Covid genomic surveillance. The extraordinary amount of SARSCoV2 sequencing (8.3M genomes on Gisaid and counting) has not been that useful to date, epidemiologically so. Yet, this data has fuelled fear and conspiracies.
Read 6 tweets
Feb 12
Denmark/Finland/Norway have navigated the Covid19 pandemic well. They had inbuilt advantages, but their hybrid - centrist - strategy of balancing mitigation measures with other considerations such as keeping schools open and protecting individual rights has been a success.
All three countries are now lifting all (or most) pandemic restrictions. This may be considered as a bold move as case numbers are still very high, but given their vaccination coverage, this is not the 'unethical eugenist experiment' some claim it to be.
Few countries have been as successful at keeping Covid19 morbidity and mortality in check over the last two years, but an imminent lifting of all pandemic restrictions and a return to a pre-pandemic 'normal' is the future, theirs, and anyone else's fairly soon.
Read 4 tweets
Jan 29
Spillover events of SARSCoV2 from humans to animals have been reported for many species, including mink, white-tailed deer, dogs, as well as small and big cats (lions, tigers). We looked for SARSCoV2 genomic adaptations to transmission in animals.
Essentially any SARSCoV2 lineage seems equally likely to infect dogs, cats, lions/tigers, mink and deer. Host jumps into cats and dogs are dead ends. Dogs do not transmit well and domestic cats don't have much opportunity to infect other cats, and zoo animals are a bit stuck.
We found a minimum of 24 and 20 distinct clusters of SARSCoV2 in mink and deer caused by independent spillover events of viral strains circulating in humans. Subsequent animal-to-animal transmission may lead the virus to adapt to its new host.
Read 12 tweets
Jan 24
By far my biggest regret during the pandemic is that Covid vaccines were sold to the public as transmission-blocking, which, everyone should have known from the beginning wouldn't likely be the case.
This messaging has led to immense disappointment and confusion, and has fuelled - some largely understandable - vaccine hesitancy. This has been a public health fiasco given how effective Covid vaccines are at protecting against serious disease and death.
Spreading untruths, however well-intended, tends to backfire in public health, and in life more generally. It is particularly problematic when untruths are spread by those in a position of authority.
Read 6 tweets
Jan 15
The account below got suspended overnight. They stated they were badly struggling with their mental health, and admitted to having sent emails to public health professionals that having to wear a mask made them feel suicidal (which may be unwelcome but is not an offence).
1/ Image
I cursorily checked their account before replying and didn't find anything obnoxious or reprehensible in their timeline. I felt sorry and worried about them. I appreciate they may have posted something unacceptable since as they seem in a really bad state.
Though, if they had been mass-reported and suspended from twitter for their reply to me, I suggest to anyone involved to seriously reflect on their values and compassion levels.
Read 7 tweets
Jan 5
The next SARSCoV2 variant, and any after it, could be intrinsically less, as, or more virulent than Omicron. Though, the associated morbidity and mortality will further decrease over time, with more people having acquired immunity through vaccination and prior exposure.
No variant can become "totally impervious to vaccines and boosters" and protection from prior infection. A variant can largely escape 'neutralising antibodies' as Omicron does, and thus be more prone to (re-)infect immunised hosts.
Though, no variant will ever be able to bypass our cellular immunity (T-cell) response that controls the disease upon infection, and hence protects against the most severe symptoms. This stems from the myriad targets of T-cells (epitopes) in the viral genome.
Read 6 tweets

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