The development of vaccines may well go down as the finest demonstration of the power of our understanding of bio-science to date. Its not just the speed of development , its the basis in molecular biology. 

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Vaccine decision  - extract of an NY Times opinion piece by  Natalie Dean is an assistant professor of biostatistics at the University of Florida.

Coronavirus vaccines are rapidly advancing through the development pipeline. The University of Oxford’s vaccine is in large trials in Britain, Brazil and South Africa. In the United States, researchers just began enrolling around 30,000
volunteers to test Moderna’s vaccine, and more trials are starting every day. Operation Warp Speed has set an
ambitious goal of delivering 300 million doses of a safe, effective vaccine by January.

While there is promising data from smaller trials that measured the antibody response in people who got a vaccine, it’s not enough to approve a vaccine. We don’t know the level of antibodies needed to prevent infection from this virus. There is a history of vaccines with promising immune response data that did not pan out in the field.

How many people need to be protected by a vaccine before it’s recommended for widespread use? Ideally, rates of
disease will be 70 percent lower in vaccinated people than in unvaccinated people. The World Health Organization says a vaccine should be at minimum 50 percent effective, averaged across age groups. (We know from influenza that vaccines don’t always work as well on older adults whose immune systems have declined.)

This benchmark is crucial because a weak vaccine might be worse than no vaccine at all. We do not want people who are only slightly protected to behave as if they are invulnerable, which could exacerbate transmission. It is also costly to roll out a vaccine, diverting attention away from other efforts that we know work, like mask-wearing, and from testing better vaccines.

The last thing Phase III trials do is examine safety. Earlier trials do this, too, but larger trials allow us to detect rarer side effects. One of those rare effects researchers are paying attention to is a paradoxical phenomenon known as immune enhancement, in which a vaccinated person’s immune system overreacts to infection. Researchers can test for this by comparing the rates of disease severe enough to require hospitalization across the two groups. A clear signal that hospitalization is higher among vaccinated participants would mark the end of a vaccine.

A key to getting a quick result is placing the trial in outbreak hot spots where people are most likely to be infected. We can even target the highest-risk people within those areas, using mobile teams to travel to neighborhoods, bringing the trial directly to the people. Some trials explicitly prioritize essential workers like health care workers or grocery employees. Others are simply focused on enrolling large numbers of participants as fast as possible. Combining those efforts, it could take as little as three to six months to generate enough convincing safety and efficacy data for companies to apply for expedited review by the Food and Drug Administration.

I worry nonetheless that public pressure may mount to approve a product that doesn’t meet our standards. Other
countries may decide to approve vaccines based on weaker evidence. Russia, for example, claims to be on track to
approve a vaccine in just a few weeks.

Waiting for a better vaccine to come along may feel like torture, but it is the right move. With so many potential shots on goal, scientists are optimistic that a safe and effective vaccine is out there. We can’t afford to jeopardize the public’s health and hard-earned trust by approving anything short of that."

Vaccine testing

Now that vaccine hype is off and running, I wondered what should be a realistic expectation.? According to https://www. healthline.com/health/clinical-trial-phases…“Phase III of a clinical trial usually involves up to 3,000 participants who have the condition that the new medication is meant to treat. Trials in this phase can last for several years.” Randomly, half get the placebo and half the test medication. In the case of a vaccine, the phase 3 trial involves 30,000 volunteers, started in August, with initial results by beginning of Dec after 4 months.

The current infection rate in the US is around 100 per day per million, on the average in the placebo half of the trial
population, 1.5 per day will get infected. Over the 4 months trial , about 200 will get develop symptoms, about 40 will go to hospital, and about 2 will die. Meanwhile, there will be a background level of hospitalizations and deaths that happen all the time, on the average over the 4 month in a random sample of 15,000, around 40 will end up in hospital.

My simple minded conclusion, is that at the end of the 4 month trial, we should know if the vaccine produced antibodies as they will be testing everyone. We might know something about reducing symptoms based on a sample size of 200, not much about hospitalizations based on a placebo sample size of 40 on a background of 40 and nothing about fatalities based on a sample size of 2 on a background of 50. To get to the trial population for a typical medication, we need to wait roughly a year and a half for 3000 placebo trial participants to show symptoms.

Fishing boat study shows antibodies protecting against infection - small study  8/2020

Three crew of a Seattle fishing boat who were found to have antibodies able to neutralise the new coronavirus remained uninfected in an outbreak that swept through the ship, sickening most people on board, researchers have reported. Researchers  screened 120 of 122 people before they boarded the fishing vessel in May, testing both for active virus and for antibodies in the blood that would indicate a previous or ongoing infection. None of the crew tested positive for the virus, but six had some antibodies and of those, three had evidence of
neutralising antibodies. More than two weeks after the boat set sail, it returned to shore with an infected crew member who needed hospital treatment. They found that 85 percent—104 crew members—were infected. But none of the three with neutralising antibodies tested positive, nor did they report any symptoms during the outbreak.

"Therefore, the presence of neutralising antibodies from prior infection was significantly associated with protection
against re-infection," the authors of the study said.

Mild Covid gives immunity  5/2020

Even people with minor illness from the coronavirus can develop antibodies that could leave them immunised for several weeks or more, according to an early French study that tested hospital staff with mild infections. The study was carried out on 160 members of staff at two hospital sites in Strasbourg who had all tested positive for
COVID-19 and suffered mild forms of the disease. Two types of serological tests, which aim to look for a previous
infection, indicated that almost all health workers—153 out of 160 in one case, 159 out of 160 in the other—had
developed antibodies within 15 days after the onset of infection. Using a separate test to determine if the antibody could neutralise the virus, the study found some 98 percent of the volunteers had these antibodies between 28 and 41 days after the first signs of infection.

The researchers said in a statement on Tuesday that the neutralising activity of the antibodies appeared to increase
over time.

Vaccine trial status 10/29/20

The experts (see the links below) are making it clear what is expected from the current  vaccine trials - information on whether the vaccine reduces infections, but nothing about reduction of hospitalizations or deaths, the sample size is just to small.   The Pfizer vaccine trial started July 28 and involved 44,000 volunteers. By October 27, they announced that they were almost fully enrolled and had not yet reached 32 infections. Apparently, once they reach 32 infections, an independent panel reviews the data to make a first assessment of the vaccine, with a final goal of 100 infections to analyze. A cold and a positive test qualifies as an infection.

The trial has started 3 month ago, and is only just fully populated so lets assume they have had an average of 22,000 volunteers for the test period up till now. The current infection rate in the US is around 100 per day per million. In the 3 months of the trial, if the vaccine is working there should have been around 100 infections in the placebo group. So either the average number of volunteers is lower, or they are being more careful and not getting infected. Either way, we still have to wait before any conclusions can be made.

It is probably worth noting that 32 infections is a pretty small number to base any conclusions.  In an article an editor at BMJ stated “Like Pfizer and Johnson and Johnson, Moderna has designed its study to detect a relative risk reduction of at least 30% in participants developing lab-confirmed COVID-19, consistent with FDA and international guidance.” In addition "None of the trials currently underway are designed to detect a reduction in any serious outcome such as hospitalisations, intensive care use, or deaths. Nor are the vaccines being studied to determine whether they can interrupt transmission of the virus,"

This makes sense, because we have a Case Fatality Rate of about 2% at the moment so no one should have died in
either group, and so they cannot tell if the vaccine is safer than getting Covid based on this sample size. The test would need to be at least much longer or larger to draw any safety conclusions. Ironically. the more effective the vaccine, the more difficult it is to know if the vaccine makes the results of infection better or worse. When you plan to vaccinate 300M people, it is a critical question.

https://www.cnn.com/2020/07/28/health/pfizer-coronavirus-vaccine-trial-begins-biontech/index.html
https://www.yahoo.com/news/pfizer-not-yet-ready-release-115316798.html
https://medicalxpress.com/news/2020-10-covid-vaccine-trials.html



Vaccine update 11/11/20

Terrific news on the vaccine front, Pfitzer reports that their vaccine was “at least  90% effective”, based on 98 infections in the Phase 3 trial. A political opinion poll is based on around 1000 interviews, and as we know, are not very accurate. We should be encouraged but cautious in drawing conclusions from a sample 1/10 of an opinion poll.  The data is not   yet public , assuming that Pfitzer have been appropriately conservative in their announcement, “at least  90% effectivity” based on a sample of 98 means that at most 1 or 2 people in the treatment group became infected. As a result we knownothing about any possible side effects of being vaccinated and then getting infected.
Very encouraging early results.

https://www.vox.com/21556359/pfizer-vaccine-covid-19-biontech-trial-results-coronavirus

Vaccine update 11/18/20 

The Moderna and the Oxford vaccine show similar success, suggesting that Covid is  an infection that can be blocked by vaccination. It sounds like Q1 is a realsitic target for wide availability. 

There is more data on the Pfitzer, the high lights from their press release (not a paper !) are;

  • Primary efficacy analysis demonstrates BNT162b2 to be 95% effective against COVID-19 beginning 28 days after the first dose;170 confirmed cases of COVID-19 were evaluated, with 162 observed in the placebo group versus 8 in the vaccine group

  • Efficacy was consistent across age, gender, race and ethnicity demographics; observed efficacy in adults over 65 years of age was over 94%

  • Safety data milestone required by U.S. Food and Drug Administration (FDA) for Emergency Use Authorization (EUA) has been achieved

  • Data demonstrate vaccine was well tolerated across all populations with over 43,000 participants enrolled; no serious safety concerns observed; the only Grade 3 adverse event greater than 2% in frequency was fatigue at 3.8% and headache at 2.0%

  • Companies plan to submit within days to the FDA for EUA and share data with other regulatory agencies around the globe

  • The companies expect to produce globally up to 50 million vaccine doses in 2020 and up to 1.3 billion doses by the end of 2021

Really good news, but please note that a sample of 162 infected persons is 10x lower than a typical opinion poll ! These numbers will change and who knows in which direction. 

https://www.pfizer.com/news/press-release/press-release-detail/pfizer-and-biontech-conclude-phase-3-study-covid-19-vaccine

11/30/2020 Vaccine update

Moderna has gone public with their data and have applied for emergency use. The results were;

            11 of 15,000, none became seriously ill.  

            185 out of 15,000 in placebo.

            94.1% effective 

Very similar results  to Pfitzer, which is encouraging as Moderna and Pfitzer use the same approach. 

12/14/20 EUA submission and approval  for Pfitzer

The submissions to the FDA for EUA are public documents. Here are a few extracts from an analysis of those docs

"The FDA briefing docs also highlighted how important it will be for patients to come back for a second dose. The phase 3 trial revealed that the vaccine was only 52% effective in the three weeks between the first and second dose, the analysts noted. Efficacy skyrocketed to nearly 95% a week after the second dose.

One major point of discussion at the meeting—where vaccine experts will offer their approval advice to the FDA—will be side effects that cropped up in the phase 3 trial, analysts predicted. The side effects were rare but inflammatory in nature. For example, there were more cases of appendicitis and Bell’s palsy among those who received the vaccine than in the placebo group.

Pfizer is planning three post-authorization surveillance studies, according to the briefing package (PDF). And the FDA will also have access to data gathered from a new Centers for Disease Control smartphone app called v-safe. Vaccine recipients will be able to opt-in to v-safe and use it to report any side effects.

J.P. Morgan analysts concluded that side effects reported in the trial wouldn't scuttle Pfizer’s emergency use authorization (EUA), because the stats lined up with numbers typical in the general population. The incidence of Bell's palsy, a type of facial paralysis, matched up with typical experience, the FDA said, though there were no cases reported in the trial's placebo group.

SVB Leerink analysts picked out another detail in the Pfizer briefing document: The previous infection offered just 37% protection against re-infections with symptomatic COVID-19. Granted, only seven cases of re-infection were reported in the trial, but the revelation that getting sick with COVID might not protect people from catching the virus again could be significant, the analysts said."

The conclusion is that there may be subtle differences in side effect between vaccines.... and of course the sample size is really small, but will get bigger quickly. 

8/16/21 Breakthrough infections

Lots of noise about breakthroughs. "As of July 2021, nearly half of the vaccinated people hospitalized with breakthrough COVID-19 infections were immunocompromised – despite making up only 2.7% of the U.S. adult population. In comparison, the rate of breakthrough cases among vaccinated people who are not immunocompromised was less than 1%."

 

https://www.yahoo.com/.../immunocompromised-people-nearly...

The Israel Health Ministry’s data analysis has produced some new estimates about the effectiveness of Pfizer vaccines, according to The Washington Post:

  • In protecting against infection, Pfizer vaccines are 95% effective for the alpha variant but only 64% effective for the delta variant.

  • In preventing symptomatic COVID-19 cases, Pfizer vaccines are 97% effective for the alpha variant but only 64% effective for the delta variant.

  • In preventing hospitalization and serious disease, Pfizer vaccines are 97.5% effective for the alpha variant and still 93% effective for the delta variant.

https://www.deseret.com/coronavirus/2021/7/20/22584134/whats-going-on-in-israels-outbreak-among-vaccinated-people

8/23/21  Full approval for Pfitzer 

I was interested in what is required for full vaccine approval, I found this summary - it takes over 6 months because it requires 6 month of tracking of the original test individuals. They had around 100 infections in the test and placebo  populations  for the emergency authorization, they have nearly 1000 infections as a basis for the full authorization. 

"It is important to note that the number of people who participated in the initial COVID-19 safety studies was similar to that in the safety studies of other commonly used vaccines, including vaccines for tetanus, diphtheria, whooping cough and meningitis. Over 43,000 adults participated in the early phases of the Pfizer-BioNTech clinical trial, over 30,400 in Moderna’s and over 44,000 in Johnson and Johnson’s. Half the participants in each study were given a vaccine, while the other half were given a placebo.

Full FDA approval, (on the other hand), requires participants in the original studies to be followed for at least six months. Reviewers look at data from the same study participants but collected over a longer period of time. All adverse events are examined. The manufacturer must also provide more detailed manufacturing plans and processes, as well as a higher level of oversight and inspections. All of this adds significantly more time to the review process."

https://news.yahoo.com/does-full-fda-approval-vaccine-192125978.html?fr=sycsrp_catchall

An analysis of 927 confirmed cases in the trial of approximately 44,000 individuals -- who were randomized 1:1 to vaccine or placebo -- found that starting a week after the second dose, the vaccine had a 91.3% efficacy against symptomatic COVID-19 through 6 months.

https://www.medpagetoday.com/infectiousdisease/covid19vaccine/94167?xid=nl_covidupdate_2021-08-23&eun=g1389549d0r&utm_source=Sailthru&utm_medium=email&utm_campaign=DailyUpdate_082321&utm_term=NL_Gen_Int_Daily_News_Update_active

8/24/21 Effectiveness against Delta variant

https://www.businessinsider.com/how-well-vaccines-work-against-delta-variant-chart-2021-8

                                                      BOOSTERS

9/10/21 The need for boosters 

 A comprehensive paper on Pfitzer vaccine aging and boosters based on Israel  data on a population of 5000 cases of  65 years or older.   For the over 65 year olds, from 5 to 6 months after vaccination,  the  "breakthrough" cases per million increased by 1.2x. However a booster decreased the case rate by 10x.   The vaccine efficiency was estimated to have decreased to around 50%. This is all consistent with an initial efficiency of 95%, that can be re-achieved using the booster.  The data showed the immunity being achieved 20 days after Booster. Without booster, sever illness rates were at least 10x lower than confirmed cases rates, but they did increase from 5 to 6 months. 

https://www.nejm.org/doi/pdf/10.1056/NEJMoa2114255?articleTools=true

This provides strong support for a booster for the over 65 crowd after 5 months from the initial vaccination.   Its worth noting that  the infection rate for >65 is comparable to the general population, but 60% get hospitalized and 18% die compared to 20% and 1% die-ing in the general population. 

The average of 5 studies was less clear cut, showing vaccination case efficiency dropping from 90 to 80%, efficiency against sever illness declined slightly from 95% to 93%. This has lead to reluctance to support boosters for all ages and all vaccines. 

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)02046-8/fulltext

Side effects studies on 1M vaccinated and 200K Covid infections, suggest that the worst vaccine side effects occurred at around 0.1% rate for arrythmias, acute kidney injury, and pulmonary embolism. These would seem to compare favorably to an average CFR of 2%. For the 16-44 crowd the CFR is around 0.1% so side effects are starting to be significant, and probably accounts for the care being taken with the under 16's. 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8427535/

9/17/21  CDC on need for boosters  major vaccines

 

CDC looked at hospitalization rates for the different vaccines in a retrospective "case control analysis" as compared to a gold standard - time based double blind randomized study . They sampled 3600 from all age groups who were in hospital for Covid-like symptoms, and then looked as how many actually tested positive. Therefore the control group were individuals who were in hospital for Covid like symptoms, but were not actually Covid infected. This is a different control group than is used for most vaccine efficiency estimates (such as the Israel study above) which is random individuals in the general population.  Obviously sick but not infected is a much more select control group.

Over 4 months from vaccination, protection from getting sick from Covid as compared to just randomly getting sick, for  Pfitzer dropped from 88 to 77%. Moderna dropped from 93 to 92%. J&J dropped from 71-68%. 

 

The relative prevalence of the different vaccine types in the "just sick control group" seems to track the prevalence in the general population, suggesting that the odds of getting hospitalized without being infected by Covid is independent of vaccine status, Moderna appears to perform best with no evidence of aging and/or Delta variant sensitivity, very few people in hospital who were sick and had Moderna actually had measurable virus. The data on effect of time from vaccination for Pfitzer seems reasonably consistent with the Israel data with significant loss of effectiveness.  Its worth noting that Moderna’s shot contains 100 micrograms of vaccine, more than three times the 30 micrograms in the Pfizer shot. And Pfizer’s two doses are given three weeks apart, while Moderna’s two-shot regimen is administered with a four-week gap.

https://www.cdc.gov/mmwr/volumes/70/wr/mm7038e1.htm

 

There are now 4 studies, including the one above,  that show that Moderna has maintained its effectiveness better that Pfitzer,  The declines seem  to be focused on the >65 crowd. 

https://www.businessinsider.com/moderna-vaccines-might-not-need-boosters-like-pfizer-2021-9

Based on a summary of the Moderna filings for boosters, after 8 and 13 months post vaccination, and using a nominal 500 cases/M/day for the unvaccinated infection rate, the vaccine efficiency (VE) declines from 91% to 86%. This is consistent with previous data that showed initial VE of 93% declining to 92% after 4 months. All round it would suggest that boosters for Moderna after a year might be worth considering. 

https://www.medscape.com/viewarticle/958808

10/15/21 CDC update

CDC published April - Sept 2021 summary for incidence rates for cases and deaths by age and vaccine type comparing fully vaccinated to unvaccinated covering 30% of the US population, so its a very large data base. I calculated vaccine efficiency  (VE) and Case Fatality Rates  (CFR) .  No question that Moderna is better than Pfitzer which is better than J&J. Once fully vaccinated  population is  established, from May onwards, in 4 months there is a small but noticeable  decline in VE for Moderna and Pfitzer, worse in the 80+ community. These data are consistent with Israeli data for 65+ and Pfitzer detailed above.

                      Moderna  = 91 to 87%

                       Pfitzer      = 89 to 82%

                       J&J             =76%

            All vaccines 80+ =84 to 68% 

The CFR can also be calculated.  The CFR's  for the unvaccinated are in line with early data, as high as 20% for the 80+. The CFR's for the vaccinated are roughly half, showing that vaccination really does reduce the severity of the infection. 

The basis for boosters for all oldies is pretty clear cut.  

The number of cases in unvaccinated as per M of unvaccinated tracks the  number of "breakthrough" cases in vaccinated as per M of vaccinated, which suggests breakthroughs are being infected by the unvaccinated. If and when breakthroughs are larger, we will have reached herd immunity in the unvaccinated. 

https://data.cdc.gov/dataset/Rates-of-COVID-19-Cases-or-Deaths-by-Age-Group-and/fwff-rpze

Updated on the 14th of each month, 1.5 months behind.

                                                BREAKTHROUGHS

At the start of the pandemic, the susceptible are the majority. By November 2021, in  US and UK, the susceptible are now  in the minority so infectious individuals will have most contacts with protected. This will reduce the apparent unvaccinated case rate/M.  When unvaccinated case rate/M matches breakthrough, infections will be uniform through the population, and  rates/M will reflect ratio of  vaccinated/unvaccinated.

 

UK Breakthrough data 

 In the Sept.(week 38)  issue of the Vaccine surviellance report, an analysis that showed after the July peak in cases infection in the unvaccinated dropping and infection in vaccinated stayed flat. This strongly suggests breakthrough infections are starting to dominate.  Also, around 50% of the Covid patients in the hospital are now vaccinated, and 98% of the blood donated has Covid antibodies, suggesting the nominally unvaccinated are protected to some degree by prior infection and because they are surrounded by protected people and the infection cannot propogate.  

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1029606/Vaccine-surveillance-report-week-38.pdf

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1018555/S1363_Hospital_Admission_for_COVID-19_and_impact_of_vaccination.pdf

The data for November (week 46) broken down by age shows that the vaccinated are the majority of cases, except for the under 18 who have just been allowed to vaccinate (on right), further evidence that the unvaccinated are now protected against infection to some degree.  Once infected, the Case Severity Ratio (CSR) the ratio of sever or hospitalization to cases, and CFR ratio of deaths to cases as a function of age measure outcomes.  The solid lines for CSR in vaccinated and unvaccinated are roughly parallel, as are CFR, with Vaccinated rates 10 x lower, so vaccines really do provide protection. However, comparing deaths to hospitalizations (solid and dashed lines), shows outcomes are exponentially worse with age. Unfortunately, at age 80 if you get seriously sick you will probably die. 

All suggests that  herd immunity to the primary infection has been achieved, breakthroughs are dominating in the UK.

US data on breakthroughs

Data on breakthroughs is much more fragmented in the US. There is now a monthly update, the data on the right shows vaccinated/M cases rising. relative to unvaccinated/M . The CDC is also reporting that in Sept, CFR for the vaccinated is 14x lower than unvaccinated, in line with the UK data. 

Post herd immunity dominated by breakthrough infections.

As the infection has progressed there has been an  increase in “breakthrough” infections of people who have been vaccinated as compared to the unvaccinated. This has been attributed to loss of vaccine effectiveness  and/or increasing domination of the vaccine population and/or Delta variant. There is a fourth possibility, many of the unvaccinated will have been infected, knowingly or unknowingly, so there will be increasing immunity in the unvaccinated. Eventually there will be 2 populations; vaccinated, and unvaccinated  ex-infected. 

Breakthrough infections can occur across the entire population both vaccinated and unvaccinated ex-infected, so it can be modelled very simply as a new infection that can attack the whole population with a much smaller Reproduction Number.  

Israel data on  breakthrough infections 

There is a new paper from Israel that claims natural protection in the unvaccinated 25x more effective in preventing infection. The define unvaccinated and unprotected as anyone unvaccinated who has not had a positive Covid prior to a cut off date.  This ignores asymptomatic and untested infections. Furthermore, there were 10x as many people in the data  base who were vaccinated compared to unvaccinated uninfected. As the minority, the chance that an infectious individual would meet another unvaccinated/unprotected individual was 10x smaller than at the beginning of the pandemic. The cases/M vaccinated and unvaccinated in the Israel study simply reflect the relative populations. 

https://ncrc.jhsph.edu/research/comparing-sars-cov-2-natural-immunity-to-vaccine-induced-immunity-reinfections-versus-breakthrough-infections/

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