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.
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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A useful thread to understand aspects of vaccine efficacy. "VACCINE EFFICACY 101: A biostatistician's primer
- How is vaccine efficacy calculated?
- Distinguishing between infection, disease, & severe disease.
- Measuring reduced infectiousness.
- Vaccine efficacy vs. effectiveness!
2) Vaccine efficacy (VE) measures the relative reduction in infection/disease for the vaccinated arm versus the unvaccinated arm. A perfect vaccine would eliminate risk entirely, so VE = 1 or 100%. This can be calculated from the risk ratio, incidence rate ratio, or hazard ratio.
3) Vaccine efficacy of 50% roughly means you have a 50% reduced risk of becoming sick compared to an otherwise similar unvaccinated person. Or you have a 50% chance of becoming sick given that you were exposed to enough infectious virus to make an unvaccinated person sick.
4) Though we talk about vaccine efficacy as a single number, there are actually several different types of vaccine efficacy, such as:
- Efficacy to prevent infection (sterilizing immunity)
- Efficacy to prevent disease
- Efficacy to prevent severe disease
5) Most Phase 3 trials are measuring efficacy to prevent disease as the primary analysis, with efficacy against infection and against severe disease as secondary analyses.
6) Preventing infection entirely is the hardest to achieve. And of course a vaccine that prevents infection will also prevent disease and severe disease. But we can have vaccines where people are still infected but their disease severity is lessened.
7) So far I have talked about how well a vaccine directly protects the vaccinated individual. Another important type of vaccine effect is the ability of a vaccine to reduce infectiousness to others. This is known as indirect protection, and is related to herd immunity.
8) A vaccine that prevents infection entirely provides indirect protection to others. If I can't get infected, I can't infect you. But it is possible to have a vaccine that prevents disease but individuals can still be infectious.
9) Household studies can be very useful here, where we follow the household contacts of infected vaccinated individuals and infected unvaccinated individuals, and compare how frequently they are infected. Pioneering work from my mentor @betzhallo.
10) Finally, vaccine efficacy vs. effectiveness? We like to reserve "efficacy" for estimates from randomized trials, where everyone receives the vaccine as intended (proper cold chain, no missed doses). We distinguish this idealized measure from real-world "effectiveness." END"
Source:
Commentary: What we're aiming for is efficacy against the disease and preventing the spread of infection. That's going to be the hardest part. And there's no guarantee any of the vaccine candidates will accomplish these goals. What that means for all of us is that the new normal is just normal now. Expect to be wearing a mask in public at least for another year, if not longer, and for things like conferences, concerts, and big events to still be high risk.
We have to plan for a scenario where a vaccine is only somewhat effective and may not prevent infection of others.
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Conflicting evidence on antibody decay. "The results reported in the letter by Ibarrondo et al. (Sept. 10)1 regarding the rapid decay of anti–severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in patients who had recovered from Covid-19 are in contrast to our findings and those of other research groups, such as Wang et al. from China.2 In their study, Wang et al. showed that IgG responses were detected in most patients with either severe disease or mild disease at 9 days after the onset of infection, and the IgG levels remained high throughout the study (35 to 40 days). These findings are in accordance with those from our investigation of the longitudinal profile of IgA and IgG antibodies against SARS-CoV-2 in samples of convalescent plasma obtained from 151 donors. We found that the IgA levels remained high until 50 to 60 days after the onset of symptoms and that the IgG levels remained elevated, with only a slight decrease, at 120 days after the onset of symptoms. Therefore, we need more data regarding the kinetics of SARS-CoV-2 antibodies from different research groups to understand the human antibody response against this disease."
Source: https://www.nejm.org/doi/full/10.1056/NEJMc2027051
Commentary: Don't count out antibodies yet. More research is needed to find out just how fast COVID-19 antibodies actually last. The science is still uncertain.
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Seroprevalence from dialysis. "We tested the remainder plasma of 28 503 patients receiving dialysis throughout the USA, using a chemiluminescence assay with high sensitivity and specificity. To our knowledge, we provide the first nationally representative estimate of SARS-CoV-2 seroprevalence in the US dialysis and US adult population, and estimates for differences in seroprevalence by neighbourhood race and ethnicity, poverty, population density, and mobility restriction. We also evaluate which of the existing measures of COVID-19 incidence most closely correlate with seroprevalence. Most importantly, we show that as patients receiving dialysis have monthly blood draws, without fail and without bias, and are a population with increased representation of racial and ethnic minorities, repeated cross-sectional analyses of seroprevalence within this sentinel population can be implemented as a practical and unbiased surveillance strategy in the USA.
Similar to data from other highly affected countries and regions (eg, Spain and Wuhan, China), despite the intense strain on resources and unprecedented excess mortality being experienced in the USA during the COVID-19 pandemic, fewer than 10% of US adults had formed antibodies to SARS-CoV-2 as of July, 2020. There was significant regional variation from less than 5% prevalence in the west to more than 25% in the northeast. Public health efforts to curb the spread of the virus need to continue, with focus on some of the highest-risk communities that we identified, such as majority Black and Hispanic neighbourhoods, poorer neighbourhoods, and densely populated metropolitan areas. A surveillance strategy relying on monthly testing of remainder plasma of patients receiving dialysis can produce unbiased estimates of SARS-CoV-2 spread inclusive of hard-to-reach, disadvantaged populations in the USA. Such surveillance can inform disease trends, resource allocation, and effectiveness of community interventions during the COVID-19 pandemic."
Source: https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)32009-2/fulltext
Commentary: This is such a smart idea, one of many innovations that have come out of this pandemic along with sewage monitoring. The reality is that we need as many eyes and ears monitoring for COVID-19 as possible, since our testing capacity remains limited planetwide. The more we can use these other medical practices as sensors to detect infection, the faster we can respond.
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A petition for the CDC as an independent federal agency separate from HHS. "Recent polling shows that Americans trust the US Centers for Disease Control and Prevention (CDC) more than the White House to handle coronavirus disease 2019 (COVID-19) and accurately report data on the pandemic.1 Despite this finding, the White House has frequently curbed the ability of the CDC to function at its full potential. Over the past 6 months, the administration has revised evidence-based CDC guidelines, blocked CDC officials from appearing on television, cut off CDC communication with a newly commissioned Department of Health and Human Services (DHHS) working group focused on reopening schools, and ordered hospitals to bypass the CDC and send information on patients with COVID-19 to a central database.
A relevant question is not whether the public trusts the CDC to make public health policy decisions, but whether the CDC can autonomously make these decisions in the first place. As it stands, the CDC, which falls under DHHS in the executive branch, is subject to political pressures that may influence its decision-making process. Furthermore, the composition of the CDC itself changes with each new administration, and its director does not require Senate confirmation. These characteristics risk dissolving public trust by enabling the CDC to be treated as a political arm of the party in power rather than as an apolitical agency. To carry out its mission effectively, the CDC must remain depoliticized, trusted, and able to respond to public health disasters swiftly, without restrictive political pressures. For these reasons, we believe the CDC should become an independent federal agency.
There are multiple examples of existing independent federal agencies, including the Federal Reserve System and the Federal Trade Commission, that can make decisions swiftly during national crises without Presidential or Congressional approval. A framework of essential attributes shared across these agencies has previously been described in a proposal to make the US Food and Drug Administration (FDA) independent,2 including the following key attributes: (1) a single director appointed by the President and confirmed by the Senate (akin to that of the Federal Reserve), (2) rule-making authority in accordance with Congressional enabling legislation and intent, (3) oversight by the Office of Management and Budget limited to significant regulations and policy development, and (4) independent litigation authority through the Department of Justice.
In 1994, the Social Security Administration was moved out of DHHS and reconfigured as an independent federal agency.3 A similar process should be applied to the CDC. As an independent federal agency, the CDC could be governed by a single director and include a governing board with diverse lifetime experiences in public health. Additionally, to prevent politicization of the board, each member could require Senate confirmation to be appointed, serve staggered terms that span multiple presidential and congressional terms, and receive protections from budgetary cuts. Many independent agencies are not subject to regular congressional appropriation and authorization processes for funding. Some agencies, including the Consumer Financial Protection Bureau, determine their own budgets, with some limitations enforced by Congress, and are not required to submit their request for review by the Office of Management and Budget.4 A similar degree of autonomy for the CDC could help ensure it maintains funding required to protect public health regardless of the political climate.
To ensure accountability, CDC board members could be removed for cause and reappointed via congressional approval. The CDC could also have some rule-making (eg, nationwide mandates, emergency declarations) supervised by the Office of Management and Budget. Importantly, to counterbalance federal oversight, the CDC could have independent litigation authority through the Department of Justice to challenge excessive oversight. This balancing of authority would safeguard against politicization from those acting in bad faith who belong to either entity."
Source: https://jamanetwork.com/channels/health-forum/fullarticle/2771202
Commentary: This is essential. If you're a US citizen or permanent resident, petition your elected officials TODAY to make the CDC an independent federal agency with the recommended oversight described in the article. This is far from the last pandemic we'll see.
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A reminder of the simple daily habits we should all be taking.
1. Wash/sanitize your hands every time you are in or out of your home for any reason. Consider also spraying the bottoms of your shoes with a general disinfectant (alcohol/bleach/peroxide) when you return home. Remember that cleaners are NEVER to be ingested or injected.
2. Always wear a mask when out of your home and if going to a high risk area, wear goggles. Respirators are back in stock at online retailers, too.
3. Stay home as much as possible. Minimize your contact with others and maintain physical distance of at LEAST 6 feet / 2 meters, preferably more. Avoid indoor places as much as you can; indoor spaces spread the disease through aerosols and distance is less effective at mitigating your risks.
4. Get your personal finances in order now. Cut all unnecessary costs.
5. Replenish your supplies as you use them. Avoid reducing your stores to pre-pandemic levels in case an outbreak causes unexpected supply chain disruptions.
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Common misinformation debunked!
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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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.