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.
This is also available as an email newsletter at https://lunchtimepandemic.substack.com if you prefer the update in your inbox.
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I thought this newsletter would have gone away by now. At least I named it Lunchtime Pandemic and not Lunchtime COVID, since it looks like monkeypox is on a trajectory towards being a pandemic.
A reminder: good masks + good hygiene stops monkeypox too.
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Monkeypox on the move. "Monkeypox is mutating up to 12 times faster than expected, a study says, amid warnings the UK could see as many as 60,000 new cases a day by the end of the year.
As of Sunday 26 June, there were 1,076 cases across the UK, up by 166 on the previously Friday with health experts stating the outbreak is likely to spread further over the coming weeks.
While a surge to tens of thousands of daily cases in six months might seem exteme, scientists have found the virus appears to be mutating at an unusual rate.
In a study published in journal Nature Medicine, Portuguese researchers found samples of the virus had 50 mutations in its DNA compared to 2018. That’s between six and 12 times the number scientists would normally expect over the same time period."
Source: https://www.independent.co.uk/news/health/monkeypox-virus-uk-cases-mutating-b2111814.html
"Statement by WHO Regional Director for Europe, Dr Hans Henri P. Kluge
Today, I am intensifying my call for governments and civil society to scale up efforts in the coming weeks and months to prevent monkeypox from establishing itself across a growing geographical area. Urgent and coordinated action is imperative if we are to turn a corner in the race to reverse the ongoing spread of this disease."
Source: https://www.who.int/europe/news/item/01-07-2022-statement---no-room-for-complacency
Commentary: Monkeypox is on the verge of being declared a public health emergency.
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A great threaded read on BA.5. "The die is now cast: BA.5 is destined to be our dominant virus. In today’s 🧵I discuss the implications on the course of the pandemic, and how to think about responding. (I use “BA.5” & not “BA.4/5” since BA.5 is poised to outrun BA.4.). (1/25)
We’ve now gotten used to Omicron sub-variants – each about 20% more infectious than the prior one – and so it’s easy to be lulled into thinking… (2/25)
… that BA.5 is just another one. But, as Topol describes, BA.5 is a different beast, with a new superpower: enough alteration in the spike protein that immunity from either prior vax or prior Omicron infection (incl. recent infection) doesn’t offer much protection. Drat. (3/25)
As we did w/ original Omicron, we need to determine 3 things w/ each variant: infectivity, immune escape, & severity. We know BA.5 is worse on #1 and #2. Severity is still unclear, but we're seeing worrisome upticks in U.S. hospitalizations (though not yet deaths). (Fig). 4/25)
As BA.5 becomes the dominant U.S. variant (Fig), its behavior will determine our fate for the next few months, until it either burns itself out by infecting so many people or is replaced by a variant that’s even better at infecting people. Neither is a joyful scenario. (5/25)
BA.5’s ascendency comes against background of a high case # plateau & fair # of hospitalizations. Current US case rate is ~ 1/7 of January’s peak (115K cases/d vs ~800K/d). But since we’re missing ~80% of cases due to home tests, today’s true case-rate isn't far from Jan’s.(6/25)
What else has changed? Mandates are gone – likely forever in most of the U.S. And most people have ditched their masks & are unlikely to put them back on, no matter how large the surge. So it’s up to each of us to determine our own risk tolerance, and then own behavior. (7/25)
Before I get return to the implications of the BA.5 wave, let’s review the local data . In SF, we’re averaging 427 cases/day (51/100K/d; Fig). (Due to home testing multiply this by ~5 to get an apples-to-apples comparison w/ earlier eras.) SF hospitalizations are 114, up…(8/25)
… 6-fold since April, well above the U.S. trend (Fig L). @UCSFHospitals, our hospital numbers have been plateaued for 2 months. We currently have 42 patients in the hospital, still only ~1/3 of our January peak. And only 4 are in the ICU, a very low ICU:hosp ratio (Fig R).(9/25)
@mentions , the fraction of pts admitted “for” (vs “with”) Covid is now 50%. In Jan, it was 2/3 "for", 1/3 "with". This drop in “for Covid” admits, & particularly the fall in ICU #'s, are the silver-est linings of current phase. Let’s hope they stick.(10/25)
Our asymptomatic test + rate, which has been 5-6% for a couple of months, has inched up – today it's 6.5% (Fig). Again, this is my go-to number to get a feel for the risk of maskless indoor gatherings. If 1 in 16 people who feel fine actually has Covid, spend enough time…(11/25)
… maskless indoors & it’s near-certain that you’ll get it. (If 6.5% of an asymptomatic population has Covid, in a crowd of 50 people, there’s a 96.% probability that someone there is pos.) This is particularly true since vax (even w/ 2 boosters) and/or prior infection… (12/25)
… now offer relatively little protection against infection, although they still remain enormously protective against severe infection & death. In fact, this is one of the biggest implications of BA.5: a prior infection – including an Omicron infection as recent… (13/25)
…as last month – no longer provides robust protection from reinfection. And that old saw about hybrid immunity (vax plus infection) providing “immunity superpower” (& thus no need to be careful) is no longer true – we’re seeing such folks get reinfected within 1-2 months.(14/25)
Analogously, booster #1 offers relatively little protection vs infection. In fact, your 2nd booster (I got mine 10 weeks ago) is also not protecting you much against infection – its protective effect vs. infection seems to wane in about 2 months. nejm.org/doi/full/10.10… (15/25)
Does this mean you shouldn’t get boost #2? Absolutely not! In fact, I’ve been on the fence about boost 2 for folks not at very high risk (ie, below age 70). But recent data shows a powerful ⬆in protection from boost #2 (4-fold mortality reduction in people >age 50; Fig). (16/25)
Many ask: “Shouldn’t I wait on boost #2 until fall, when a new bivalent (combo of original & Omicron-specific boost) is available? For those over 50, I’d say no – there's too much Covid around and evidence of benefit from boost #2 is persuasive. Pfizer/Moderna are now…(17/25)
…developing a booster targeting BA.4/5 (the one they’ve built vs the original Omicron will have limited utility against BA.5). If the new booster is highly effective (not guaranteed), I doubt that getting a 2nd boost now will block you from getting bivalent boost in fall.(18/25)
Given all of this, what should individuals do today? As always, it depends on how you feel about getting Covid. As I discussed last week @washingtonpost (below), I’m still trying to avoid getting Covid, largely because of risks of Long Covid. washingtonpost.com/outlook/2022/0… (19/25)
So I still avoid indoor dining & will continue to wear an N95 in crowded indoor spaces until cases come way down. (If you’re in the “I already had Covid so I’m not worried” camp, realize there’s no evidence that Long Covid risk from a 2nd or 3rd case is <that of case #1.)(20/25)
We need to change our thinking about the value of vax/boosting. Vax/boost remains hugely valuable in preventing a severe case that might lead to hospital/death. But its value in preventing a case of Covid, or preventing transmission, is now far less than it once was. (21/25)
This means that to gather indoors safely, a vax/booster requirement – while better than nothing – isn't very reassuring. To do indoor gatherings safely, it’s really about good masking (& no indoor eating) and ventilation; adding pre-event rapid testing offers additional…(22/25)
… protection. At a policy level, I can’t see mask mandates returning just because BA.5 case rates go way up. But if hospitals still filling up, particularly if we also have staff shortages, I think we’ll see mandates return in Blue states. It would be the right call. (23/25)
It seems clear that BA.5 will lead to an ongoing plateau, if not a moderate surge, lasting through summer & into fall. Beyond that, much depends on whether a new variant emerges to supplant it. Given the pattern of the past year, it would be foolish to bet against that.(24/25)
I wish I had a happier analysis of our current Covid state. But BA.5 is yet another Covid curveball to be dealt with, and it's not great news. (And I wish that BA.5 was the only bad news in the U.S. these days.) Despite all of it, I hope you have a happy & healthy 4th! (25/end) "
Source:
Commentary: This long and informative thread essentially says that BA.5 is the new dominant strain in many places - and our existing pharmaceutical countermeasures are losing effectiveness at stopping spread. They still do stop severe outcomes, which is why they're important to maintain. The key takeaway is that BA.5 is HIGHLY immune evasive, so vaccines by themselves will not stop spread or even slow it down much.
Mask up. Ventilate. Avoid indoor dining in places that aren't your home. If we don't update our vaccines, chances are the fall and winter of 2022 will be quite ugly.
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Omicron leaves you infectious for 8 days. "The characteristics of the participants were similar in the two variant groups except that more participants with omicron infection had received a booster vaccine than had those with delta infection (35% vs. 3%) (Tables S1 and S2 in the Supplementary Appendix, available with the full text of this letter at NEJM.org). In an analysis in which a Cox proportional-hazards model that adjusted for age, sex, and vaccination status was used, the number of days from an initial positive polymerase-chain-reaction (PCR) assay to a negative PCR assay (adjusted hazard ratio, 0.61; 95% confidence interval [CI], 0.33 to 1.15) and the number of days from an initial positive PCR assay to culture conversion (adjusted hazard ratio, 0.77; 95% CI, 0.44 to 1.37) were similar in the two variant groups (Figure 1A through 1C and S1 through S3, and Tables S3 through S5). The median time from the initial positive PCR assay to culture conversion was 4 days (interquartile range, 3 to 5) in the delta group and 5 days (interquartile range, 3 to 9) in the omicron group; the median time from symptom onset or the initial positive PCR assay, whichever was earlier, to culture conversion was 6 days (interquartile range, 4 to 7) and 8 days (interquartile range, 5 to 10), respectively. There were no appreciable between-group differences in the time to PCR conversion or culture conversion according to vaccination status, although the sample size was quite small, which led to imprecision in the estimates"
Source: https://www.nejm.org/doi/full/10.1056/NEJMc2202092?query=featured_home
Commentary: this is a critically important piece of research. COVID doesn't obey time limits; the current recommendation that you can stop isolating after 5 days is based on old strains of COVID. The omicron strains have a median of 8 days of infectiousness, which means you need to test each day until you test negative. Once you test negative, only then are you no longer infectious. 5 days is not enough.
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COVID may cause bone loss. "Extrapulmonary complications of different organ systems have been increasingly recognized in patients with severe or chronic Coronavirus Disease 2019 (COVID-19). However, limited information on the skeletal complications of COVID-19 is known, even though inflammatory diseases of the respiratory tract have been known to perturb bone metabolism and cause pathological bone loss. In this study, we characterize the effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on bone metabolism in an established golden Syrian hamster model for COVID-19. SARS-CoV-2 causes significant multifocal loss of bone trabeculae in the long bones and lumbar vertebrae of all infected hamsters. Moreover, we show that the bone loss is associated with SARS-CoV-2-induced cytokine dysregulation, as the circulating pro-inflammatory cytokines not only upregulate osteoclastic differentiation in bone tissues, but also trigger an amplified pro-inflammatory cascade in the skeletal tissues to augment their pro-osteoclastogenesis effect. Our findings suggest that pathological bone loss may be a neglected complication which warrants more extensive investigations during the long-term follow-up of COVID-19 patients. The benefits of potential prophylactic and therapeutic interventions against pathological bone loss should be further evaluated."
Source: https://www.nature.com/articles/s41467-022-30195-w
Commentary: If you've had COVID and there's a history of things like osteoporosis or other bone diseases in your family, talk to your healthcare provider about more rigorous screening to make sure COVID didn't impact your bone density.
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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. P100 respirators are back in stock at online retailers, too and start around US$40 for a reusable respirator. 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, including boosters. 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 available. If it's available, choose Moderna as your first choice for both vaccine and booster, Pfizer as your second choice. However, remember than any vaccine is better than no vaccine.
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, or you know, a global war breaks out.
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 several rapid antigen tests and/or acquire them from your healthcare provider or government. 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.