The new Imperial report

The new Imperial report

As the UK went through 100k daily cases, there is something for everyone in the data coming from UKHSA this week, and no doubt different people will interpret it in different ways. Lockdown sceptics will argue the confirmation of the milder disease means ministers should resist further restrictions. One government insider says: “This is why it was right for us to wait for more data.” Others in Whitehall stress that people should not read too much into the conclusion that Omicron is milder, as its higher transmissibility means it could still lead to a large wave of hospitalisations. In other words, once again the data does not exactly pave the way for a clear-cut decision for ministers. There is some speculation among scientists that Omicron infections are plateauing. In a Times piece by Rhys Blakely and Chris Smyth, the WHO’s Paul Hunter backed Johnson’s “wait and see” approach, noting that reported cases were forecast to be at 200,000 per day by Monday but are ~90-100k. “Where have all those cases gone? It’s possible that something is changing with the epidemiology of Omicron — it’s possible that it’s not growing at the rate that it was,” they speculate. They also suggest that cases in London could be calming down. “Analysis by the UK Health Security Agency showed that, following a rapid rise in the past fortnight, the increase in cases and suspected cases of Omicron is slowing in the capital. Sir Jeremy Farrar, director of the Wellcome Trust said yesterday ministers now face the most “difficult and uncertain” period of the pandemic since the coronavirus made its first march towards Britain nearly two years ago. He urged them to wait a day or two before introducing new regulations. Transmission of the Omicron variant is “eye-wateringly high”, he added, but it is not yet clear what that will mean for the NHS. The coming days will provide more data, but what are the most important questions and when will we have answers?

https://www.thetimes.co.uk/article/clues-to-solve-the-omicron-puzzle-emerging-slowly-f98hr5t3d?

I note the FDA has authorised Pfizer’s pill, but pretty supply constrained. Merck’s still pending; Pfizer have upped their 2022 production target to 120mn courses.

This is pretty remarkable data here – we’d know with our age structure if something was amiss with Omicron by now:

Here is London data:

 

This is pretty conclusive:

A WHO official has said it is too soon to say whether the new variant is more transmissible than the Delta variant, almost a month after South Africa first raised the alarm about its emergence. “We do have some data suggesting that rates of hospitalisation are lower,” WHO’s technical lead on Covid-19, Maria van Kerkhove, said. But she warned against drawing conclusions from early data because “we have not seen this variant circulate long enough in populations around the world, certainly in vulnerable populations”. She said the data on the new variant was still “messy” as countries reported its arrival and spread.

But now we have a new Imperial report: “To assess differences in the risk of hospitalisation between the Omicron variant of concern (1) and the Delta variant, we analysed data from all PCR-confirmed SARS-CoV-2 cases in England with last test specimen dates between 1st and 14th December inclusive. Variant was defined using a combination of S-gene Target Failure (SGTF) and genetic data. Case data were linked by National Health service (NHS) number to the National Immunisation Management System (NIMS) database, the NHS Emergency Care (ECDS) and Secondary Use Services (SUS) hospital episode datasets. Hospital attendance was defined as any record of attendance at a hospital by a case in the 14 days following their last positive PCR test, up to and including the day of attendance. A secondary analysis examined the subset of attendances with a length of stay of one or more days. We used stratified conditional Poisson regression to predict hospitalisation status, with demographic strata defined by age, sex, ethnicity, region, specimen date, index of multiple deprivation and in some analyses, vaccination status. Predictor variables were variant (Omicron or Delta), reinfection status and vaccination status.

Overall, we find evidence of a reduction in the risk of hospitalisation for Omicron relative to Delta infections, averaging over all cases in the study period. The extent of reduction is sensitive to the inclusion criteria used for cases and hospitalisation, being in the range 20-25% when using any attendance at hospital as the endpoint, and 40-45% when using hospitalisation lasting 1 day or longer or hospitalisations with the ECDS discharge field recorded as “admitted” as the endpoint. These reductions must be balanced against the larger risk of infection with Omicron, due to the reduction in protection provided by both vaccination and natural infection. A previous infection reduces the risk of any hospitalisation by approximately 50% (Table) and the risk of a hospital stay of 1+ days by 61% (95%CI:55-65%) (before adjustments for under ascertainment of reinfections).

High historical infection attack rates and observed reinfection rates with Omicron mean it is necessary to correct hazard ratio estimates to accurately quantify intrinsic differences in severity between Omicron and Delta and to assess the protection afforded by past infection. The resulting adjustments are moderate (typically less than an increase of 0.2 in the hazard ratio for Omicron vs Delta and a reduction of approximately 0.1 in the hazard ratio for reinfections vs primary infections) but significant for evaluating severity overall. Using a hospital stay of 1+ days as the endpoint, the adjusted estimate of the relative risk of reinfections versus primary cases is 0.31, a 69% reduction in hospitalisation risk (Table)”:

https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-50-severity-omicron/

Labour leader Keir Starmer was asked why he isn’t calling for a circuit-breaker, as he did in autumn 2020. It’s worth reading Starmer’s answer in full: “Because if we look at the new variants, the numbers are a cause for concern. The hospitalisations are different than they were last autumn when we call for the circuit break. Sorry, the autumn before when we called for the circuit break. We’ve asked ourselves a quite difficult question, which is: ‘What does a responsible opposition acting in the public interest do at a moment like this?’ And the answer is we act in the public interest, and we act to protect public health and therefore the government needs to get a grip, needs to come up with a plan, we will look at it just as we did last week with Plan B, if we think it’s the right measures then we will then support it. And that’s very important. Now, this is different to the position we were in earlier this year, or even last year, because now it’s clear the government can’t get through public health measures on its own votes. So we only have Plan B because the Labour Party acted in the public interest to support the plan that the government put before parliament. So we’ve entered a new phase, if you like of the virus now, where it falls to the opposition to provide the leadership that the prime minister can’t show.” This means that means Starmer is backing the government’s current COVID policy. He certainly isn’t calling for anything tougher right now. Shadow Health Secretary Wes Streeting said Tuesday: “We’re all breathing a sigh of relief that Christmas is going ahead as planned, but the country also deserves some certainty about what comes after Christmas so that families and businesses can plan ahead.” Joe Biden has now told Americans they can enjoy Christmas without new restrictions, instead expanding testing and vowing to reinforce hospitals. The comparison between the U.S. and U.K. situation is very interesting. Biden claimed overnight: “This is not March 2020. 200 million people are fully vaccinated. We’re prepared. We know more.” But the U.K. government is suggesting that two jabs — Biden’s definition of “fully vaccinated” — do not offer sufficient protection against Omicron. Only around 30% of Americans are boosted. More than 50% of Brits have had three jabs.

In the near-term, increasing the penetration of boosters appears to be the best way to increase protection against symptomatic infection, but given the speed of the Omicron wave and limited penetration of boosters, I do not expect a significant portion of the US population to be protected (less than 30%). China and much of Asia is in a worse state due to lack of previous immunity + crappy vaccines. Preliminary data from the UK and SA support the view that 2 doses have limited efficacy against infection (~30%) while 2 doses do provide efficacy against hospitalisation (~70%). Three doses or two doses and prior natural infection provide decent protection against infection (~75%). One should expect the Omicron wave to feature a high absolute number of cases, but because of its significant transmissibility to also reach peak rapidly. It remains unclear given the much greater proportion of the population that is susceptible to Omicron if the peak will plateau or resolve quickly because infection saturation occurs rapidly. I expect the US Omicron wave to be in the steep part of its growth in 1-2 weeks. In the UK, Omicron became the dominant variant on 14/12 and peak absolute cases from an Omicron wave could occur at 2-3x the number of daily cases versus the prior delta wave. UK cases confirmed using Taqpath PCR assay. S-gene target failure (SGTF) in purple is a surrogate for Omicron:

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1043098/20211221_OS_Daily_Omicron_Overview.pdf

I note AZN developing a Omicron specific version:

https://www.ft.com/content/e61faf47-d563-4a87-8f0c-dcf7b8b28b43

Obviously it’s coming to the USA and statnews has some interesting data visualisation:

It is important to note that the numbers for the last two weeks are forecasts based on models and these numbers come with fairly large error margins. As is always the case with any kind of forecast, the real numbers that come in over the next few weeks will differ from these estimates. Still, comparing these forecasts with the limited real world data thus far collected in countries where Omicron was discovered earlier shows that the CDC estimates are at least comparable:

https://covariants.org/per-country

Broadly speaking, there are two different emerging stories in new case data. Here is a heat map visualizing the history of the pandemic so far. Each row is one state or territory (plus New York City). Each block represents a two-week chunk of time. The color represents how many new cases were reported over two weeks in that area. At the top is the national total. The rows are sorted by geography, roughly west to east, to make regional trends easier to see:

Looking at cases this way makes it easier to see where different waves occurred and how they spread and varied over time. At the right is the most recent data; they show that cases have been on the rise for several weeks now in New England and in parts of the Midwest. These increases significantly predate the discovery of the Omicron variant and so are likely driven by Delta. Meanwhile, in the last two weeks there has been a sharp increase in cases in and around New York, likely driven by Omicron. The speed of these increases has been stunning. Cases in New York are now accelerating faster than at any point since the start of the pandemic. For context, this kind of case acceleration is comparable to the peaks set by states like Louisiana and Florida when they were hard hit by the Delta wave in late summer/early autumn:

Since August of this year there has been a pretty stable relationship between case rates and vaccination rates, with the most highly vaccinated states tending to have the lowest new case counts. Starting in December this correlation has become much weaker:

This may reflect waning immunity from older vaccinations, increasing spread of the Omicron variant, or perhaps simply vaccine data collection problems. Importantly, the definition of “fully vaccinated” used here does not include booster shots. Similar to the visualisation above, here is the history of hospitalisation rates by state or territory since last autumn:

What is promising here, at least so far, is that recent increases in hospitalisation rates, especially in the Northeast, have been more modest than corresponding case increases. It is important to note here that hospitalisations tend to lag behind new case reports, so this picture could change. It could be the case that high vaccination rates in the Northeast may be contributing to lower rates of hospitalisations, which is consistent with copious data showing hospitalisations are higher for the unvaccinated:

A paper from SA shows that on multivariable analysis, after controlling for factors associated with hospitalisation, individuals with SGTF infection had lower odds of being admitted to hospital compared to non-SGTF infections (adjusted odds ratio (aOR) 0.2, 95% confidence interval (CI) 0.1-0.3). Among hospitalised individuals, after controlling for factors associated with severe disease, the odds of severe disease did not differ between SGTF-infected individuals compared to non-SGTF individuals diagnosed during the same time period (aOR 0.7, 95% CI 0.3-1.4). Compared to earlier Delta infections, after controlling for factors associated with severe disease, SGTF-infected individuals had a lower odds of severe disease (aOR 0.3, 95% CI 0.2-0.6). Conclusion Early analyses suggest a reduced risk of hospitalisation among SGTF-infected individuals when compared to non-SGTF infected individuals in the same time period, and a reduced risk of severe disease when compared to earlier Delta-infected individuals. Some of this reduction is likely a result of high population immunity:

https://www.medrxiv.org/content/10.1101/2021.12.21.21268116v1

The US Department of Defence (DOD) is just weeks away from announcing a vaccine that can fight against Covid-19, including the Omicron and Delta variants, lots of tweets say. The Walter Reed Army Institute of Research, the largest biomedical research facility of the DOD, is close to a breakthrough after two years of work into a vaccine that would work not only against the existing strains and variants but also other potential ones, reported Defense One. Walter Reed’s vaccine, named Spike Ferritin Nanoparticle Covid-19 vaccine, or SpFN, completed animal trials earlier this year with positive results. Phase 1 of human trials have also been conducted this year with positive results, Kayvon Modjarrad, the director of Walter Reed’s infectious diseases branch, said. The vaccine is yet to undergo phase 2 and phase 3 trials while results of phase 1 are under review. “It’s very exciting to get to this point for our entire team and I think for the entire Army as well,” Dr Modjarrad said. The institute said it took longer than expected for human trials because the vaccine had to be tested on people who had neither been inoculated nor infected with Covid to know its efficacy. “With Omicron, there’s no way really to escape this virus. You’re not going to be able to avoid it. So I think pretty soon either the whole world will be vaccinated or have been infected,” Dr Modjarrad said. “We need to evaluate it in the real-world setting and try to understand how does the vaccine performs in much larger numbers of individuals who have already been vaccinated with something else initially…or already been sick,” he added. Walter Reed has not yet revealed the name of its industry partner, who would undertake the wider rollout of the vaccine. The research institute said it was focused on the “longer game” to understand how the viruses mutate and not only the original emergence of SARS.

Among the possible treatments for people just developing COVID-19 symptoms, antibody-rich plasma donated by recovered patients has taken a backseat to options such as monoclonal antibodies and antiviral pills. But a new clinical trial suggests it may deserve a bigger role. The trial results, posted today as a preprint, showed a transfusion of convalescent plasma cut rates of hospitalisation roughly in half—from 6.3% to 2.9%—in people treated early in the course of their infection with SARS-CoV-2. The treatment is currently authorized in the United States only for emergency use in certain hospitalized patients, but the researchers behind the study now say its use should be expanded. And they hope convalescent plasma will take a more prominent role in the fight against COVID-19 as the Omicron variant, shown to reduce the effectiveness of some monoclonal antibodies, becomes dominant. They argue it may be particularly useful in lower income countries that can’t afford or don’t have access to other treatments:

https://www.medrxiv.org/content/10.1101/2021.12.10.21267485v1

A paper reports on safety incidents in laboratories in China. The deaths of two people following a laboratory explosion at a Chinese university in October have raised alarm among researchers. The full circumstances that led to the deaths at the Nanjing University of Aeronautics and Astronautics (NUAA), in Jiangsu province, are not yet known — but they come amid wider concerns about safety in university teaching labs in China. The deaths are the latest in a series of fatalities caused by explosions in academic laboratories in China, often involving students in chemistry departments, that have been reported in recent years. Some researchers are optimistic that the situation is improving. But others say China’s government needs to do more to improve safety. In the recent incident, nine people were injured and two died as a result of an explosion just before 4 p.m. in the NUAA’s College of Materials Science and Technology, according to a Weibo post. Earlier this year, on 31 March, a graduate student was killed following an explosion at the Institute of Chemistry of the Chinese Academy of Sciences in Beijing. Previous lab blasts led to deaths of three students conducting a sewage-treatment experiment at Beijing Jiaotong University in December 2018; one death in the chemistry dept at Tsinghua University in Beijing in December 2015; and one death in a chemistry lab at the China University of Mining and Technology in Xuzhou in April 2015. It’s not possible to say what the cause was of any individual explosion and death without a full investigation report, none of which have been made public except for the incident at Beijing Jiaotong University, and some may not have been caused by negligence or lack of safety procedures. However, China has far more students than many other countries, so it's difficult to say if it has a larger number of lab-related deaths per capita and researchers note that lab safety is an issue in many countries. Some also question the idea that incidents are becoming more frequent in China and argue that serious accidents were probably happening 15–20 years ago as well, but they just weren’t reported publicly before the rise of social media:

https://www.sciencedirect.com/science/article/abs/pii/S0950423021002771?via%3Dihub

Now an India comment: India’s daily COVID-19 case counts remain in check despite some recent Omicron variant cases being detected. The risk of a third wave remains as there are few activity constraints currently. Going by the experience of the second wave, there are some points:

  • India’s COVID-19 infections still in check: India’s daily COVID-19 case count remains in check (7DMA under 6k cases; from highs of more than 400k in May) even though several Omicron variant infections have been detected recently. It is still too early to form conclusions: the first delta variant infection was first detected in India in Oct 2020, but cases started to move up only in February 2021. There are few restrictions to domestic activity (most mobility indicators have recovered); the risk of a third wave in India cannot be ignored.
  • State-wise trends in India: Daily case counts (7DMA) have started to increase in a few parts of the country (Maharashtra / Mumbai, UP, Gujarat, Bihar), but the numbers are still very small. In some other states, cases had started to increase in December, but have recently declined again (Karnataka, Chhattisgarh, Telangana, Jharkhand). India’s total case counts benefit from continued declines in infections in Kerala – where cases peaked only around end August. The state still accounts for around half of daily cases in the country.
  • The evidence from other countries is still unclear. While it seems evident that vaccinations do not necessarily avert new infections, a few highly vaccinated countries have also recently seen fatality counts increase (South Korea, Germany). In some others (UK, South Africa), fatality counts have not increased in line with infections. This divergent behaviour cannot be blamed on ‘herd immunity’. Updated sero-prevalence data is not readily available. In many countries, there seems to be little correlation between historical reported cases and herd-immunity. India has reported cumulative cases at c.3% of population, but regional sample surveys have found COVID-19 antibodies in 70-90% of people.
  • Vaccination progress on track: India has administered c.1.39 billion doses of vaccines (as of Dec 21). Of c.900 million adults in the country, 829 million have received at least one shot and 557 million (62%) have received both doses (India has not opened vaccination for people aged below 18 yet). The vaccine dose to population ratio for Indians above 45 years of age crossed 80% in August, but no booster shot program has been proposed in the country yet. This is aggregate cases and deaths:

No epidemiological model can transform you from a wallflower into a risktaker, or tell you whether something is “worth it.” It’s the first variable, the dangers of infection, that science is best positioned to illuminate. And yet those risks sometimes seem to change by the month, if not the week. Immunity ebbs, variants emerge, and the virus surges and fades. Right now, with the rise of the Omicron thingy, the pandemic is shifting. Although the risk calculus remains largely unchanged for some people, others, especially those whom doctors describe as “vulnerable” to COVID-19 may be entering a newly dangerous phase of the pandemic. Who is vulnerable? How concerned should they be? And for how long will they need to remain on high alert?

Vulnerability is at the centre of how doctors think. When we describe our patients to one another, we use “one-liners”, succinct, sentence-long summaries of who patients are and why they are seeking care. One-liners centre on age and pre-existing conditions. The goal is the division of patients into categories of risk, that is, risk stratification. A healthy thirty-five-old man coming in with chest pain? We think of a muscle strain, not a heart attack. A sixty-five-year-old woman with two recent cardiac stents? Now a heart attack leaps to the fore. There can be surprises: the young man might have an unappreciated family history of early cardiac disease, and the older woman might just have finished a half-marathon. Still, the odds are the odds.

Omicron is thought to be at least twice as transmissible as Delta, which itself is twice as contagious as the original – all depending on how one counts it; it may be more than three times as effective at reinfecting those who’ve already contracted the coronavirus. But it doesn’t transform our risk stratification. Those who were most vulnerable to Alpha or Delta are still the people who are most susceptible to the new variant. There will be exceptions—a young vaccinated person who ends up in the I.C.U., or an elderly smoker with nothing but a stuffy nose but, for the most part, the established logic of COVID risk still serves as a reliable guide. There’s one category of vulnerability from which it’s possible to escape. recent analysis examined hospitalisations between June and September—the post-Delta, pre-Omicron period. It found that eighty-five per cent of hospitalized people were unvaccinated. How will Omicron change this picture? It’s too early to say for certain, but, as the new variant starts to displace Delta, a rule of thumb is emerging: to maintain a similar level of protection, you need one more dose than you did before. If two doses of an mRNA vaccine were enough to prevent a Delta infection, then three are needed for Omicron; if you’ve received two shots and you get a breakthrough Omicron infection, you’ll be reasonably protected against severe disease, but you’ll be safer if you’ve received three:

https://www.healthsystemtracker.org/brief/characteristics-of-vaccinated-patients-hospitalized-with-covid-19-breakthrough-infections/?

People with chronic medical problems make up a second vulnerable group. In general, the chance of having a bad coronavirus infection increases with the number and severity of medical conditions from which you suffer. One study of hospitalized COVID patients found that ninety-five per cent of them had at least one underlying medical condition; some 60% of U.S. adults have a chronic health problem:

https://www.cdc.gov/pcd/issues/2021/21_0123.htm

Still, not all problems are equally concerning. The Centres for Disease Control and Prevention has identified more than a dozen conditions that place individuals at higher risk for severe disease. People with illnesses affecting the respiratory or immune system—emphysema, heart problems, cancers, and certain autoimmune diseases that necessitate immunosuppressant drugs—will remain vulnerable, even after immunisation. Finally, it’s impossible to talk about  risk without focussing on the role of age. Older people make up the third category of vulnerability. The risks start climbing earlier in life than we’d like. The  mortality rate for Europeans and Americans over the age of sixty-five is more than 80x higher than for those in their late teens and twenties, and over-sixty-fives have accounted for more than 75% of the deaths. The coronavirus has now claimed the lives of at least one in every hundred older Europeans or Americans. The risk is greatest for those living in nursing homes and long-term-care facilities; during the pandemic’s first year, they constituted less than one per cent of the U.S. population but 35% deaths. That’s not to say that younger people should ignore it; in September, it was the leading cause of death among middle-aged Americans—but the risks of infection are, and will remain, highest for those in their sixties, seventies, and beyond. All of this was true before Omicron, and remains true now.

Good risk calculations are often local. People with similar medical circumstances face vastly different risks depending on where they live; it’s important to review the infection and immunisation rates in one’s particular community. And yet it’s possible that such conscientious risk assessments are being rendered irrelevant by the sheer contagiousness of Omicron. Last month, around a hundred and twenty fully vaccinated people went to a holiday party in Norway. They said that they’d tested negative before the event, but at least eighty of them emerged with Covid. Outbreaks like this will become commonplace as Omicron spreads across the globe:

https://sciencenorway.no/covid19/at-least-140-people-were-infected-with-covid-19-after-christmas-party-in-oslo/1949790

Vaccinated people, moreover, may come to present a greater threat to vulnerable individuals than they did just a few months ago. Immunized individuals are still less likely to contract the virus—if you don’t get it, you can’t spread it—and, even if they get infected, their immune systems lower the levels of virus circulating in their bodies. But Omicron likely weakens both defences. Compared to Delta, it is much better at evading vaccine-generated antibodies, and it replicates much faster inside our airways, allowing us to spread it before our immune systems step in. Vaccinated people were more likely to transmit Delta than prior variants, so there’s reason to believe they’re even likelier to transmit Omicron. All of this is cold comfort for people who are both vaccinated and vulnerable. Vaccine effectiveness is usually reported in the aggregate—for people of all ages, backgrounds, and levels of medical vulnerability—and yet, at the end of the day, a lot depends on your one-liner. The extent to which Omicron cases will result in mass death—as happened last winter, when nearly a quarter million Americans lost their lives to Covid is not yet clear. In South Africa, where Omicron first started to spread, Covid deaths have not risen in tandem with cases. It’s too early to draw definitive conclusions—deaths can lag infections by a period of weeks, and no country has enough experience with the new variant to feel reassured. But there is some evidence that Omicron may deliver a less punishing illness to those it infects. Moreover, reinfections and breakthrough cases tend to be less severe than infections in people with no immunity. It’s possible that Omicron could be bringing us closer to the long-awaited “decoupling” of coronavirus cases and deaths.

Still, barring new evidence, when it comes to taking risks during the Omicron surge, the right answer for vulnerable people might be to just wait. This sounds easy, but for many people it isn’t. “What happens if you worked your whole life and you saved your whole life, and the pandemic has stolen the couple of years where you were actually healthy enough to travel?” Aronson asked me. “That’s also a form of grief and loss.” Risk and vulnerability are puzzles we grapple with even in ordinary life. ​​At the beginning of Virginia Woolf’s “Mrs Dalloway,” Clarissa, the novel’s fifty-something protagonist, walks the bustling streets of London, gathering provisions for a dinner party. She pauses for a moment in the crowd, her mind wandering to a long-ago suitor and the unrealized dreams of her youth. She considers her own age and the ways in which her life might have gone wrong, and still might. “She felt very young; at the same time unspeakably aged,” Woolf writes. “She always had the feeling that it was very, very dangerous to live even one day.”

Aging involves confronting an ever-expanding set of risks; it means accepting that one’s days are growing more dangerous. A strain, a pain, a virus that in youth might have passed without notice—each new malady becomes saturated with a sense of foreboding. There is no escaping the bodily tax of time. And yet, in another sense, the dangers of aging rise and fall more generally. With the advent of cardiac stents, heart attacks became a little less deadly, and so aging became a little less dangerous. With advances in chemotherapy, some cancers are no longer lethal. Bit by bit, growing old has become safer.

During the pandemic—especially with the arrival of Omicron—the dangers of age have skyrocketed. But that won’t last forever. Being older will eventually return to being ordinarily risky; Covid will be one of many diseases to worry about as we age. Booster shots, pills, rapid tests, better masks, and upgraded ventilation systems could shift the balance. Meanwhile, the  risk for vulnerable Americans—and the rest of us—changes dramatically with the level of community spread. A period like the current one, during which the U.S. is tallying, on average, a hundred and thirty-three thousand new coronavirus cases a day, is far more threatening for a vulnerable person than one in which the country records a tenth as many daily cases, as it did at points this past summer. Because immunity isn’t binary but a matter of degree—and because each encounter with the virus or a vaccine makes our immunity broader and more robust—each wave brings us closer to a situation in which the coronavirus is endemic: a familiar, low-level threat to which we’ve all been exposed, along the lines of the flu, rather than an acute, novel emergency. Our one-liners are what they are; our risks will never go to zero. But those risks will ease with time and, eventually, stop dominating our lives.

We’re not there yet. For now, the risk is high. And the infectiousness of the coronavirus means that it’s not just your one-liner that matters. Many of us can use vaccines and boosters to protect ourselves against Omicron. But not everyone has that option. We live in a society with people who can’t escape vulnerability. We owe it to them to reduce their risk. For one more winter, we must make it safer to live each day.

Earlier this year, the Africa Centres for Disease Control and Prevention (Africa CDC) released results of a large survey across 15 African countries in which 79% of respondents said they would get vaccinated against Covid-19, with even greater rates of acceptance among people living in villages:

https://africacdc.org/download/covid-19-vaccine-perceptions-a-15-country-study/

In August, another 12 country study found acceptance rates ranging from 67% to 89% in Burkina Faso, Mozambique, Nigeria, Rwanda, Sierra Leone, and Uganda:

https://www.nature.com/articles/s41591-021-01454-y

For comparison, the same 12-country study found that only 65% of Americans planned to get vaccinated, a number consistent with current vaccination coverage levels. To be sure, these polls found pockets of vaccine hesitancy in all surveyed countries, an unsurprising finding anywhere, especially in communities still affected by colonialism, unethical clinical trials and dodgy global health practices. In Mbarara, community members regularly ask about vaccine safety and side effects, and people expect us to fully answer these before they request their shot. Effective vaccination campaigns anticipate, plan for, and respond to the concerns that people have, understanding that trust in vaccines is dynamic and achievable through sustained community engagement. Low- and middle-income nations have consistently shown the rest of the world how to achieve excellence in vaccine delivery, from Nigeria eliminating polio after partnering with religious leaders to promote immunisations, to Rwanda vaccinating 93% of girls against human papilloma virus (HPV) after enlisting local leaders in outreach.

Instead of acknowledging this remarkable vaccination track record, outsiders have taken reports of declined vaccine shipments in some African countries, likely the result of numerous factors, including poorly coordinated donations and the difficulty of moving doses to rural areas, as evidence of widespread distrust across the continent, overlooking the heterogeneity of 54 countries, more one billion people, and distinct local health, cultural, and political contexts that strongly influence vaccine uptake.

Hesitancy is a red herring when it comes to immunisation in Africa. Multiple challenges abound to reach World Health Organisation’s goal of vaccinating 70% of the world’s population by mid-2022. In addition to poorly coordinated donations, these include receipt of expiring doses, receipt of large numbers of different types of vaccines with unique storage and transport requirements, over-centralized vaccine production, profiteering in the pandemic, and more. At best, claims of widespread vaccine hesitancy across African nations are uninformed speculations, not supported by data. At worst, they are deliberate attempts to distract audiences from the injustice of unequal access to lifesaving Covid-19 vaccines.

Snippets:

Does a heterologous SARS-CoV-2 vaccination strategy with the vector vaccine Ad26COVS1 result in a higher rate of antibody response compared with a homologous third dose of mRNA vaccine (mRNA-1273 or BNT162b2) in kidney transplant recipients who did not develop SARS-CoV-2 antibodies after 2 doses of an mRNA vaccine? This randomized clinical trial found that a third dose of SARS-CoV-2 vaccine in 197 kidney transplant recipients without antibodies after 2 doses of an mRNA vaccine induced an antibody response in 35% of the homologous (mRNA) group vs 42% of the heterologous (vector) group, with no statistically significant difference. The findings of this randomized clinical trial show that homologous and heterologous vaccination strategies for a third SARS-CoV-2 vaccine dose in kidney transplant recipients are comparable, with both mRNA and vector vaccines achieving seroconversion in more than one-third of kidney transplant recipients. However, given the high rate of non-responders after the third dose, additional strategies to induce an immune response in kidney transplant recipients are urgently needed:

https://jamanetwork.com/journals/jamainternalmedicine/fullarticle/2787200

Is COVID-19 associated with severe gastrointestinal manifestations in children? In this multicentre cohort study of 685 Italian children with COVID-19, 10% showed severe gastrointestinal involvement characterized by diffuse adeno-mesenteritis, appendicitis, abdominal fluid collection, ileal intussusception, or pancreatitis. Children older than 5 years and those presenting with abdominal pain, leukopenia, or receiving a diagnosis of multisystem inflammatory syndrome were more likely to have severe gastrointestinal manifestations. Severe gastrointestinal involvement is not uncommon in children with COVID-19, and awareness about its frequency and presentation may help practitioners to appropriately manage children at risk of severe outcomes:

The above and the table below shows imaging findings:

https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2787258

Graphs:

Time series of primary series/booster vaccinations (top), new COVID cases (middle) and current hospitalisations due to COVID (bottom) in the US:

Emerging hot spots in the US. The x-axis is growth rate of new cases compared to last week, the y-axis is the new case per hundred, and z is the latitude. Each state is colour coded by vaccination rate:

Justin Stebbing

Managing Director

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