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 qualified healthcare experts over some person on Facebook.
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Travel matters. ""Spread of a #SARSCoV2 variant through Europe in the summer of 2020"
(aka The Tale of Europe, Summer Travel, & EU1)
But why should we care about summer 2020 now? Let's take a look...
Last Sept, while looking for #SARSCoV2 sequences that could help us understand transmission across #Switzerland, I noticed a cluster that was present not just across Switzerland, but also the UK & Spain. This is the cluster that eventually came to be known as 20E (EU1).
EU1 had a mutation at position 222 in spike - this caught my eye.
From mid-summer 2020, EU1 (orange) expanded across Europe - becoming the most prevalent variant in most of Western Europe, & accounting for >30% of sequences in Europe by the end of 2020.
We can see how EU1 rose over summer 2020 by looking at % of sequences each week that fell into EU1.
From initially expanding in Spain πͺπΈ, it quickly started being detected in other countries soon after EU borders opened in mid-June. βοΈπ
We see a general pattern of a rise, then a plateau in proportion, & a wide variation in how much EU1 dominated in different countries: in Spain, Ireland, & UK it was >60% sequences - in Norway & France it was <=20% by end of 2020, with other countries in between.
We were able to confirm Spain as the origin of expansion through phylogenetics - a collapsed phylogeny of seqs up to 30 Sept shows countries with shared genotypes as pie charts.
The earliest diversity is found in Spain (red) & shared with many other countries.
My initial concern was that EU1 was what we were all fearing in 2020: a more transmissible variant. π±
But laboratory work showed no difference in antibody binding (pic 1) or pseudoviral titers (pic 2).
So how did it spread so successfully?π€
The summer of 2020 followed on from one of the hardest springs in memory.
On heels of lockdowns, economic hurt, hospitalizations & death, it was defined by hopeful restriction loosening & a longing to regain normality.
Could travel have played a role in EU1's success? π§³π«
We were able to look closely at #SARSCoV2 cases across Europe over the summer (pic 1), including cases by Spanish province.
In addition, we looked at travel (pic 2). We usedπ±roaming data from across Europe to see when & where in Spain visitors went.
By combining the case numbers per province over timeπ·, with the location data πΊοΈ, plus info on their home country epidemic, we knew (generally) where people came from, where they went in Spain, & when.
We could use this in a simple model to predict how EU1 spread:π
While this matches the dynamics fairly well, our model was underestimating the proportion of EU1 cases.
In some countries we did well (France), in others off by 2-4x (pic 1). But in others we were off between 7-11x (pic 2)!
What wasn't our model capturing? π€
When we compared our estimated travel-related cases with those reported by the German & Swiss govts (only German shown), we confirmed that our model was underestimating the likelihood of bringing EU1 home.
Our model really was simple: there's plenty it doesn't capture...
For example: people don't go to the same places in Spain on holiday! French visitors stay north π, whereas UK holidaymakers head south & to islands ποΈ (pic 1).
Countries have similar & differing travel patterns (pic 2).
See the paper for full discussion, but what our model's underestimation suggests is that travel related activities are associated with more cases than expected:
Demographics, behaviour, & variation in incidence (city vs province-level) likely play a role.
πΆπ»ββοΈπ½οΈππ»ββοΈπΊπ»ππ»π¨βπ§
But this was last summer... & EU1 isn't even more transmissible. So why should we care about it now?! π€¨
As we head once again into summer & the balance of travel & transmission, while hearing about new variants -
I think EU1 can still tell us some very important things!
EU1 underscores the potential impact of travel.
Last summer in Europe travel persisted as cases rose in Spain. There was essentially no testing, & quarantine may not have worked as well as we wished. Test&Trace didn't stop transmission chains.
Differing travel volumes, locations & behaviours likely played a role.
Similarly, when we look at the spread of the Delta variant now in the UK vs other European countries, closer ties to India likely meant the UK has had many more introductions.
EU1 also highlights that bans to just one country probably aren't enough on their own:
By end-Sept 2020, there was more EU1 in Europe outside of Spain than inside of Spain.
It wasn't about Spain anymore: other Europe countries were transmitting after failing to control it.
But perhaps most importantly of all, EU1 shows us that not all rising frequencies are due to viral change.
EU1 rose in frequency when cases were rising, & had a spike mutation - an alarming combination. But it was not a variant of concern - rather a travel opportunist.
As we identify new variants, the critical question is to what degree viral changes are influencing transmission & cases, & how much might be changes in restrictions, behaviour, introductions & more.
EU1 reminds us how important it is not to underestimate the latter!
EU1:
- Underscores the potential impact of travel particularly when incidence differs between countries π«π§³
- Highlights what didn't work last summer π·ποΈ
- Reminds us that not all rising frequencies are due to viral change! ππ¦ "
Source:
Commentary: If you're planning travel away from home in the next few months, one thing to seriously consider - especially if anyone in your household is unvaccinated or at greater risk (immunocompromised) - is where you go. I would strongly suggest that you check vaccination levels in the locale you're traveling to - ideally at the city level, if not state/province level - and choose destinations with very high - 70% or more - vaccination levels in the overall population. I would also avoid places with lots of kids, especially kids under 12, because that entire population hasn't been vaccinated yet.
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Durability of antibodies may be better than initially thought. "COVID-19 caused by SARS-CoV-2 infection has caused substantial morbidity and mortality worldwide and paralyzed the international economy. Understanding the magnitude and duration of the antibody response to SARS-CoV-2 is important to achieve a balance between curbing the pandemic and minimizing adverse effects on society.1 Although the antibody response to SARS-CoV-2 within 9 months has been extensively studied,2,3,4,5,6 little is known about the magnitude and kinetics of antibody responses for over 9 months. Moreover, with limited observations over 9 months (nβ<β100),2,7,8 several studies have produced inconsistent conclusions about antibody dynamics, suggesting different rates of antiviral antibody positivity at the last follow-up.2,7,8 These studies have been limited by a lack of measurement of neutralizing antibodies (NAbs),7 of inclusion of mild or asymptomatic cases,2,8 and of further exploration of potential predisposing factors for antibody dynamics.2,7 Considering the individual heterogeneity (such as disease severity)8 and time-dependent nature1 of the immune response, in-depth characterization of SARS-CoV-2 antibody kinetics across disease severity groups over a long period is urgently needed. Therefore, we repeatedly tested IgM, IgG, viral spike protein receptor-binding dom (anti-RBD) IgG, and NAb titers in COVID-19 patients during a follow-up period of up to 10 months and explored potential predisposing factors of antibody titers during follow-up.
The positivity rates for IgM, IgG, anti-RBD IgG, and NAb fell to 20.4% (39/191), 97.9% (187/191), 97.4% (186/191), and 95.8% (183/191), respectively, during 9β10 months post symptom onset (Fig. 1A). As shown in Fig. 1B and Fig. S1, a rapid decline in IgM titers was observed from 1 to 6 months post symptom onset, with median (IQR) optical density (OD) values at 1β2, 3β4, and 5β6 months post symptom onset of 0.65 (0.15β1.24), 0.18 (0.05β0.51), and 0.06 (0.02β0.21), respectively. Afterwards, IgM titers remained relatively stable for 6β10 months. In addition, progressive declines in IgG and anti-RBD IgG were observed during 1β10 months after symptom onset, with median OD (IQR) values from 2.61 (2.20β3.00) and 3.11 (2.69β3.51) at 1β2 months to 2.08 (1.74β2.64) and 2.29 (1.95β2.67) at 9β10 months post symptom onset. Similarly, a significant decrease in NAbs was identified during the whole observation period. The median (IQR) NT50 was 1096 (430β3222) during 1β2 and decreased to 249 (105β501) during months 9β10."
Source: https://www.nature.com/articles/s41423-021-00708-6
Commentary: Overall, this is excellent news for both the vaccines as well as anyone who had COVID-19; antibody durability for 3 of the 4 categories remains high even 10 months after infection. Absent a new strain that radically changes the immunity calculus, it would seem that we'll be able to rely on booster shots probably annually, like flu shots.
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Fomites pretty much ruled out. "Background: Coronavirus disease 2019 (COVID-19) is primarily a respiratory disease that has become a global pandemic. Close contact plays an important role in infection spread, while fomite may also be a possible transmission route. Research during the COVID-19 pandemic has identified long-range airborne transmission as one of the important transmission routes although lack solid evidence.
Methods: We examined video data related to a restaurant associated COVID-19 outbreak in Guangzhou. We observed more than 40,000 surface touches and 13,000 episodes of close contacts in the restaurant during the entire lunch duration. These data allowed us to analyse infection risk via both the fomite and close contact routes.
Results: There is no significant correlation between the infection risk via both fomite and close contact routes among those who were not family members of the index case. We can thus rule out virus transmission via fomite contact and interpersonal close contact routes in the Guangzhou restaurant outbreak. The absence of a fomite route agrees with the COVID-19 literature.
Conclusions: These results provide indirect evidence for the long-range airborne route dominating SARS-CoV-2 transmission in the restaurant. We note that the restaurant was poorly ventilated, allowing for increasing airborne SARS-CoV-2 concentration."
Source: https://www.journalofinfection.com/article/S0163-4453(21)00273-5/fulltext
Commentary: The absence of fomite transmission - meaning big droplets and surface contact - is becoming more and more clear. COVID-19 is an airborne disease, period. It spreads through the air, which means that ventilation and masks will continue to be needed until all populations are sufficiently vaccinated.
That said, the habits of routinely cleaning surfaces are beneficial for more reasons than just COVID-19, so if you've gotten in the habit of washing/sanitizing your hands and common work surfaces, don't stop.
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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 other people, 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. 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.
3. Wash/sanitize your hands every time you are in or out of your home.
4. Stay home 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.
5. Get your personal finances in order now. Cut all unnecessary costs.
6. Replenish your supplies as you use them. Avoid reducing your stores to pre-pandemic levels in case an outbreak causes unexpected supply chain disruptions.
7. 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).
8. Masks must fit properly to work. Here's how to properly fit a mask:
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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/
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
To be clear, 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.