Lunchtime pandemic reading.
Standard disclaimer: this is a roundup of informative pieces I've read that interest me on the severity of the crisis and how to manage it. I am not a qualified medical expert in ANY sense; at best I am reasonably well-read laity. ALWAYS prioritize advice from a qualified healthcare provider who knows your specific medical situation over advice from people on the Internet.
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Why won't we have answers about Omicron sooner? We need lab tests. "At 7:30 a.m. on 24 November, Kristian Andersen, an infectious disease researcher at Scripps Research, received a message on Slack: “This variant is completely insane.” Andrew Rambaut of the University of Edinburgh was reacting to a new SARS-CoV-2 genome sequence found in three samples collected in Botswana on 11 November and one picked up a week later in a traveler from South Africa to Hong Kong.
Andersen looked at the data and then replied: “Holy shit—that is quite something. The length of that branch …” A few minutes later he added: “Just had a look at the list of mutations—so nuts.”
They were talking about what is now called Omicron, a new variant of concern, and the long branch Andersen noticed refers to its distance to every other known virus on SARS-CoV-2’s evolutionary tree. The variant seemed to have picked up dozens of mutations, many of them known to be important in evading immunity or increasing transmissibility, with no intermediate sequences in the database of millions of viral genomes. On 23 November, after spotting the odd sequences in a global database, Tom Peacock, a virologist at Imperial College London, had already posted his own verdict on GitHub: “This could be of real concern.”
Now, once again, the world is watching as researchers work nights and weekends to learn what a new variant has in store for humanity. Is Omicron more infectious? More deadly? Is it better at reinfecting recovered people? How well does it evade vaccine-induced immunity? And where did it come from? Finding out will take time, warns Jeremy Farrar, head of the Wellcome Trust: “I’m afraid patience is crucial.”
Researchers in South Africa were already on the trail of this new variant. Several teams were independently trying to figure out why cases were spiking in Gauteng, a northern province that includes Johannesburg and Pretoria. And a private lab called Lancet had noticed that routine polymerase chain reaction (PCR) tests for SARS-CoV-2 were failing to detect a key target, the S gene, in many samples, a phenomenon previously seen with Alpha, another variant of concern. When Lancet sequenced eight of these viruses, they found out why: The genome was so heavily mutated that the test missed the gene."
Source: https://www.science.org/content/article/patience-crucial-why-we-won-t-know-weeks-how-dangerous-omicron
Commentary: What you can do is threefold. First, get fully vaccinated including boosters if available. Second, wear a mask at all times indoors any place that isn't your home and avoid large gatherings. Third, if you have ANY symptoms of cold, flu, or COVID - because Omicron appears to be representing differently - get tested. Many nations are doing a great job of genome sequencing tests, and knowing what's out there helps everyone.
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Early modeled estimates of Omicron now looking at 3x Delta's spread rate. "Following up here with speculative estimates of the rate of spread of Omicron and a stab at how to apportion this rapid rate of spread between intrinsic transmissibility and immune escape. 1/18
Monday's post was mainly meant to emphasize that observed rapid spread of Omicron can be influenced by both intrinsic transmissibility and immune escape. Here, I'll try to put (speculative) numbers on this rate of spread. 2/18
Key datapoints include rapid displacement of existing Delta viruses by Omicron in Gauteng and South Africa. Estimates of logistic growth rate here by @TWenseleers imply Omicron has ~5X current transmission rate of Delta. 3/18
But as stated previously, I believe this estimate is likely to drop somewhat as more data comes in. But I wouldn't be surprised if this drops to something still significant, say 3X or 4X the transmission rate of Delta in South Africa. 4/18
In addition to changes in relative frequency, we can look at what's happening with case counts, which have been rising rapidly in Gauteng and South Africa. We can measure the exponential growth in cases via Rt (the number of secondary cases caused by an index case). 5/18
In work from @lrossouw we get a rapid rise in Rt in Gauteng from ~0.8 to ~2.5 over the course of Nov corresponding to the take off of Omicron (unsupervised.online/static/covid-1…). 6/18 Image
Work from @seabbs and colleagues gives a similar result of Rt increasing from ~0.8 to above 2 over the course of November in Gauteng (epiforecasts.io/covid/posts/su…). 7/18 Image
I've revised my own phylodynamic estimates of rate of spread with a couple improvements. First off, I'm now using 206 Omicron genomes generously shared by researchers through @GISAID. 8/18
Secondly, I'm now masking spike which has issues of spurious within-Omicron diversity due to amplicon dropout during sequencing. I've adjusted molecular clock rate from 8×10^-4 to 5.5×10^-4 to compensate (determined from sequences taken over the course of the pandemic). 9/18
This updated analysis gives a median estimate of the common ancestor to Omicron viruses of Sep 30 with a 95% credible interval of between Sep 9 and Oct 13. 10/18 Image
This also gives a median estimate of doubling time of 4.9 days, which we can convert to an estimate of Rt assuming a generation interval of 5.1 days (eurosurveillance.org/content/10.280…). Doing so gives a median estimate of Rt of 2.0 with a 95% credible interval of 1.6 to 2.6. 11/18 Image
Having two very different methods give Rt estimates of between 2.0 and 2.5 gives me some (small) degree of confidence. We can triangulate relative fitness with Rt so that Delta in South Africa is at Rt of ~0.8 and Omicron is at about three times this with Rt of ~2.5. 12/18
We can then use the approach here to factor possible scenarios of intrinsic transmission vs immune escape that would give Omicron Rt of 2.5. 13/18
Under a scenario of 90% population immunity against previous variants, we get the following picture where Omicron could lie anywhere along the dashed line ranging from an intrinsic R0 of 3 and 83% immune escape to an intrinsic R0 of 9 and 20% immune escape. 14/18 Image
Note the these estimates are sensitive to assumed population immunity. Under a scenario of 85% population immunity, we get the following picture instead that shifts the required level of immune escape upwards for a particular R0 value. 15/18 Image
Again, based on wildly divergent spike protein, I'm guessing that immune escape will be substantial and so I still suspect that it's quite possible that Omicron will show lower intrinsic transmissibility than Delta. My updated diagram. 16/18 Image
Note also that high immune escape, lower intrinsic transmissibility is not necessarily a good thing. Higher immune escape places previously infected and vaccinated individuals more at risk. 17/18
We'll know much more about this level of risk in ~2 weeks when we get neutralization results. I'm particularly interested in neutralization titers of individuals with two doses of vaccine vs individuals with three doses of vaccine. 18/18"
Source:
Commentary: Bedford Lab has done a tremendous amount of excellent work throughout this pandemic. Their previous work in many cases has been spot on. A spread rate that high for Omicron effectively - three times Delta's capabilities - means that we are in for a rougher winter than expected.
If Omicron really is 3x as good at spreading as Delta, hospitals and healthcare systems will be overloaded again in relatively short order. Do your best to keep yourself healthy over the holidays so you don't need to consume services that might not be available.
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A reminder of the simple daily habits we should all be taking.
1. Wear the best mask available to you when you'll be around people you don't live with, even after you've been vaccinated. Respirators are back in stock at online retailers, too. Wear an N95/FFP2/KN95 that's NIOSH-approved or better mask if you can obtain it. If you can't get an N95 mask, wear a surgical mask with a cloth mask over it.
2. Verify your mask's NIOSH certification here: https://www.cdc.gov/niosh/npptl/usernotices/counterfeitResp.html
3. Get vaccinated as soon as you're able to, and fulfill the full vaccine regimen. Remember that you are not vaccinated until everyone you live with is vaccinated. If you received an adenovirus vaccine (J&J/AstraZeneca), consider getting an mRNA single shot booster (Pfizer/Moderna) if permitted.
4. Wash/sanitize your hands every time you are in or out of your home.
5. Stay out of indoor spaces that aren't your home and away from people you don't live with as much as practical. Minimize your contact with others and avoid indoor places as much as you can; indoor spaces spread the disease through aerosols and distance is less effective at mitigating your risks.
6. Aim to have 3-6 months of living expenses on hand in case the pandemic gives another crazy plot twist to the economy.
7. Replenish your supplies as you use them. Avoid reducing your stores to pre-pandemic levels in case an outbreak causes unexpected supply chain disruptions.
8. Ventilate your home as frequently as weather and circumstances permit, except when you share close airspaces with other residences (like a window less than a meter away from a neighboring window).
9. Masks must fit properly to work. Here's how to properly fit a mask:
10. If you think you may have been exposed to COVID-19, purchase a rapid antigen test. This will detect COVID-19 only when you're contagious, so follow the directions clearly. https://amzn.to/3fLAoor
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Common misinformation debunked!
There is no basis in fact that COVID-19 vaccines can shed or otherwise harm people around you.
Source: https://www.reuters.com/article/factcheck-covid19vaccine-reproductivepro-idUSL1N2MG256
There is no mercury or other heavy metals in the Pfizer mRNA vaccine.
Source: https://www.technologyreview.com/2020/12/09/1013538/what-are-the-ingredients-of-pfizers-covid-19-vaccine/
There is no basis in fact that COVID-19 vaccines pose additional risks to pregnant women.
Source: https://www.nejm.org/doi/full/10.1056/NEJMoa2104983
There is no genomic evidence at all that COVID-19 arrived before 2020 in the United States and therefore no hidden herd immunity:
Source:
There is no evidence SARS-CoV-2 was engineered, nor that it escaped a lab somewhere.
Source: https://www.washingtonpost.com/world/2020/01/29/experts-debunk-fringe-theory-linking-chinas-coronavirus-weapons-research/
Source: https://www.nature.com/articles/s41591-020-0820-9
Source: https://www.nationalgeographic.com/science/2020/05/anthony-fauci-no-scientific-evidence-the-coronavirus-was-made-in-a-chinese-lab-cvd/
Source: https://www.smh.com.au/national/are-we-ignoring-the-hard-truths-about-the-most-likely-cause-of-covid-19-20210601-p57x4r.html
There is no evidence a flu shot increases your COVID-19 risk.
Source: https://www.factcheck.org/2020/04/no-evidence-that-flu-shot-increases-risk-of-covid-19/
Source: https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa626/5842161
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Disclosures and Disclaimers
I declare no competing interests on anything I share related to COVID-19. I am employed by and am a co-owner in TrustInsights.ai, an analytics and management consulting firm. I have no clients and no business interests in anything related to COVID-19, nor do I financially benefit in any way from sharing information about COVID-19.
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A common request I'm asked is who I follow. Here's a public Twitter list of many of the sources I read.
https://twitter.com/i/lists/1260956929205112834
This list is biased by design. It is limited to authors who predominantly post in the English language. It is heavily biased towards individual researchers and away from institutions. It is biased towards those who publish or share research, data, papers, etc. I have made an attempt to follow researchers from different countries, and also to make the list reasonably gender-balanced, because multiple, diverse perspectives on research data are essential.
This is also available as an email newsletter at https://lunchtimepandemic.substack.com if you prefer the update in your inbox.