Ernie Dainow's Blog

There is a lot of news about the coronavirus pandemic especially now that cases are on the rise in Canada and Europe. A lot of the news focuses on one particular aspect. It is quite difficult to get a high level overview not only about what is happening but what is the likely progression.

Here is my analysis based on reading a lot of these news items and integrating them with a little thought.

Case counts have been on a steady increase in Canada since the beginning of September.

In the U.S. case counts have declined from the peak at the end of July, but they are still very high and are starting to rise again.

In Europe, case counts started to rise in early August.

News reports, presumably based on public health information and government policies would have you believe that these increases are due primarily to group gatherings exceeding social distancing rules. Videos to prove this point show groups of young people dancing, but in most of these videos the people are outside and not in exceedingly large crowds. These are not conditions for rapid virus spread.

A big part of the problem is that contact tracing has failed, especially in the U.S.
https://www.nytimes.com/2020/07/31/health/covid-contact-tracing-tests.html?s=09#click=https://t.co/IuIOrWkNoq

In Canada with lower case counts, some contact tracing is being done successfully. But about 33% of the new cases do not get traced. This means that the sources of infection for a lot of new cases are not discovered and these cases lead to further spread of the virus.

It’s easy to trace cases in outbreaks that are all from the same place such as a bar or a public or private gathering. But most of the new cases that are not being identified are likely from the increased interactions that have been occurring as restrictions have been relaxed. A number of people have reported that their employers have requested that they return to work, at least part-time. After six months of working from home, many employers are getting nervous that their employees are not working a full week and they want to be able to monitor them more closely. Many of these people returning to work are taking public transit which can be quite crowded.

At lunch time many people probably go out to eat in restaurants and go shopping. All of these activities lead to increased contact and increased transmission. Even if they are following guidelines and wearing masks, masks are not 100% effective. They leak and are often handled improperly. When people adjust the mask or take it off they often touch the outside of the mask. If the mask is working and protecting them from virus then the mask exterior may have virus droplets. When they take the mask off they are transferring the virus to their hands which will often then be transferred to their face.

These strong trends in rising virus case counts mean we are in the second wave and will require a full lockdown scenario. Lockdown will be lifted in early December, just in time for Christmas shopping. But a third wave will start around March 2021 and require another lockdown, as explained and predicted in this blog on May 9, 2020

Opening up the economy

As far as vaccine research progress goes, there are daily reports differing on when a vaccine will be ready. None of them explain the reasons for their dates. Here is the optimistic scenario.

Several leading vaccines will complete their phase III clinical trials by the end of December 2020. The ones that are safe and effective will get fast track approval from the FDA. It is reasonable to expect that one or more vaccines will be available for use by April 2021.

Once people start getting vaccinated it will take some time before enough people are immune to decrease the spread of the virus. If 6% of the population can be vaccinated per month, the virus will continue spreading through the summer and there may be a fourth wave that requires lockdown.

It won’t be until November 2022 that there will be sufficient immunity to slow down the spread of the virus. This is when 50% of the population has immunity from either a vaccination or from having been infected and recovered from the virus. This is the “herd immunity” that will finally stop the epidemic spread of the virus.

You don’t need a complicated epidemiological model to predict this, other than to account for some of the more subtle variatons due to lockdown periods. This is just simple math — if a country can vaccinate 6% of its population per month, it can achieve 50% herd immunity in 8 months.

Canada, Europe, the U.S. and Australia can likely achieve this timeline. For the rest of the world it will likely take longer.

The original source of the Covid-19 virus was one of the important unanswered questions that was summarized in a Nature article summarized in an earlier blog.
https://anydaynow.blog/waiting-for-answers-to-key-questions/

The conclusion was that it had likely originated from a bat, as did SARS, and was transmitted to another animal before jumping to a human. Despite many investigations, the intermediate species has not been identified. The following article provides more details, a story of scientific detective work.
https://time.com/5870481/coronavirus-origins

There was another claim made repeatedly by Donald Trump that the virus had come from a Chinese lab and that China was responsible for leashing the pandemic on the world. Trump and Secretary of State Mike Pompeo stated on numerous occasions that they had intelligence reports to back this up. Neither of them ever gave any details of these reports and they eventually backed off from this claim.
https://www.theguardian.com/world/2020/may/03/mike-pompeo-donald-trump-coronavirus-chinese-laboratory

There is no evidence that the virus was manmade. A director at the Wuhan Institute of Virology, a highly respected virologist, checked the inventory of all virus samples in the lab and determined that none were close to Covid-19 when the virus was first discovered in Wuhan and that everyone in the lab tested negative for Covid-19.
https://www.sciencemag.org/news/2020/07/trump-owes-us-apology-chinese-scientist-center-covid-19-origin-theories-speaks-out?utm_source=Nature+Briefing&utm_campaign=42390640f2-briefing-dy-20200727&utm_medium=email&utm_term=0_c9dfd39373-42390640f2-45132230

An important question besides where has the virus has come from is where is the virus going?

The Time article has a very interesting section on how molecular biologists are able to determine the genetic sequence of viruses. There have been many mutations since the first case of Covid-19 was identified and they have been put into an international database. The particular strain of the virus has been used to identify virus outbreaks that have occurred in different countries in the world. This chart is a stunning visual and information display of this information.

There is some thought that Covid-19 mutations have become less virulent. In Europe people are less likely to die if they get Covid-19 now compared with earlier in the pandemic. There is one mutation D614G that has become more predominant than others, but there is no confirmation that this or any other variant has actually become more dangerous.

https://www.newscientist.com/article/2252699-covid-19-is-becoming-less-deadly-in-europe-but-we-dont-know-why/?utm_medium=social&utm_campaign=echobox&utm_source=Facebook#Echobox=1598284086

https://www.nytimes.com/2020/09/11/opinion/coronavirus-mutation-reinfection.html

States with the huge surges have reversed some reopening policies and mandated the use of masks. However, many of these states continue to have more new case counts per million than many countries with the worst outbreaks.

This article shows background graphs to demonstrate several case comparisons.
https://www.nytimes.com/interactive/2020/08/24/us/coronavirus-cases-decreasing.html

Two major Covid-19 vaccines have started phase 3 clinical trials and are expected to complete by the end of 2020. If the results prove to be significant and safe and receive fast track FDA approval, there should be vaccines available in the first half of 2021.

The University of Oxford trial is recruiting 50,000 volunteers and the Moderna trial is enrolling 30,000 subjects. Both companies are proceeding with parallel plans to manufacture the vaccine so that if approved there will be minimal delay before the vaccines are available.

There is also recent news of a Covid-19 vaccine developed by Russia.  Under revised Russian law, the vaccine has been released before a phase 3 clinical trial has been completed. This has received widespread condemnation for being unsafe.
https://www.cnn.com/2020/08/11/europe/russia-coronavirus-vaccine-putin-intl/index.html

In fact what the Russians are doing may not be that different. The Moderna and Oxford trials are trying a drug on an experimental basis on 80,000 people, before any phase 3 trial results are known. If the Russians review the results of their vaccine after it has been given to 50,000 patients, they may determine that the vaccine is not safe and/or not effective and may withdraw it. This is not very different from the Oxford trial.

What really irks the U.S. and U.K. is that Russia, like Oxford and Moderna is proceeding with manufacturing the vaccine, but has jumped ahead of them by making deals with 20 countries to sell them more than one billion doses of their vaccine.

So what is the impact of having a Covid-19 vaccine in early 2021?

We ran a model simulation for Canada. If 100,000 people per day can be vaccinated starting in April 2021, then by the end of Oct 2021, daily coronavirus cases decline to 0. At that point population immunity is 60%. This would be “herd” immunity.

This result is generic and can be applied to any country. If a country can vaccinate 0.25% of its population per day, it can achieve herd immunity in 8 months.

When Covid-19 cases began to rise in the U.S. in March, testing was a major point of contention. There were differing opinions as to whether enough testing was or could be done. A lot of testing was delayed after it became clear that the tests developed by the CDC were faulty. In an effort to counteract this shortage of tests, the FDA allowed many test kits to be sold without any validation. This led to perhaps an even worse situation. A detailed report by 60 Minutes shows what a disaster this was.
https://www.cbsnews.com/video/coronavirus-antibody-testing-inaccurate-data-60-minutes-2020-06-28/

With the pandemic in the U.S. spreading so rapidly since June, many people do not believe it is possible to test enough people and get results fast enough to control the virus. Most states are far below the minimum testing target.
https://www.nytimes.com/interactive/2020/us/coronavirus-testing.html

However, this conclusion is based on the testing technology that is currently in widespread use, namely a molecular diagnostic test of a nasal or throat swab. There are other techniques that are much more efficient, faster and cheaper. These may be able to close the current testing gap so that testing can be used to get better control of the virus and reduce how fast it is spreading.

Pooled sampling combines samples from several people and tests them in a single test. If the test is negative, it saves testing each of the samples. If the test is positive, then each sample does need to be tested. This technique was actually developed during World War II. Basic pooled testing was given “emergency use authorization” for Covid-19 testing by the FDA on July 18, 2020.

But there are newer more efficient pooled testing techniques. Using a mathematical model based on a “hypercube” can minimize the number of tests needed to isolate the positive cases and so can use larger sample sizes. This approach has been successfully used in Rwanda.
https://theconversation.com/rwandas-covid-19-pool-testing-a-savvy-option-where-theres-low-viral-prevalence-141704

Another very promising direction is cheap at home tests. This will allow very large scale testing without the detrimental time delays of waiting for a lab to process the sample. The following reports a really simple and fast test that is in late development. You simply spit into a test tube and insert a paper strip that will change color in 15 minutes if the virus is detected.
https://www.nytimes.com/2020/07/03/opinion/coronavirus-tests.html

New testing techniques such as these are potential “game-changers” in controlling the spread of the coronavirus.

There is a growing sense in the U.S. that the epidemic is now unstoppable. Each state, city and rural area has their own crisis. Hot spots can suddenly turn up anywhere. A small outbreak in Alaska has been one of the country’s fastest-spreading for three weeks, while transmission in Texas and Arizona has slowed.

Perhaps 10% of the infected account for 80% of new cases. Unpredictable super spreading events in nursing homes, meatpacking plants, churches and bars are major drivers of the epidemic.

Contact tracing is moot, there are too many cases to track.

None of the medicines for which hopes were once high (AIDS drugs, antivirals and malaria drugs) have proved to be cures. Experts familiar with vaccine and drug manufacturing are disappointed that, thus far, only dexamethasone and remdesivir have proved to be effective treatments, and they are limited to special circumstances.

Read more at
https://www.nytimes.com/2020/07/29/health/coronavirus-future-america.html

Six months of a global pandemic have stirred an unprecedented amount of research. While many things about Covid-19 have been discovered, a lot of research has produced incomplete and sometimes contradictory results.

These are the pressing questions that do not have answers yet.

1. Why do people respond so differently?

Some people have mild symptoms or even no symptoms and don’t know they are infected. While most reactions are respiratory there are also cases of heart and blood vessel damage and kidney failure. Many people require hospitalization, some end up in an Intensive Care Unit (ICU) and many people die from Covid-19.

2. What’s the nature of immunity and how long does it last?

Studies have found that the level of antibodies produced by the immune system when someone has been infected with Covid-19 can vary quite a lot. It is not known what level of antibodies are necessary to provide immunity or how long it lasts.

3. Has the virus developed more dangerous new mutations?

Molecular biologists can determine the genetic mutations in Covid-19 and use this information to track how the virus has spread from one region to another around the world. But it is not known if any of these mutations are more virulent or transmissible than others.

4. How well will vaccines work?

Some vaccines might work well at preventing lung infections but not infections elsewhere in the body. Some vaccines may produce enough antibodies to work for some people but not enough to protect others from infection.

5. What is the origin of virus?

There is general agreement that the virus originated in bats. Scientist are able to compare the Covid-19 genome to the genomes of coronaviruses found in different bats and other animals. So far, there are genetic differences that are too large to conclude what the original source might be.

For a more complete report on these questions and the research that has been done see
https://www.nature.com/articles/d41586-020-01989-z

Television news loves to show pictures of crowded beaches as examples of how people are ignoring social distancing guidelines. In some cases this may be true, but in many cases they have just lost perspective.

Here’s a photo of a beach that looks overcrowded.

But that’s because you are looking at a long stretch of beach along the shore line.

When you look at the same beach, looking towards the water, you can clearly see that there is easily more than 6 feet between groups of people.

The responsible way for television to report overcrowding at a beach would be with an aerial view.