Virus Variants

The news has been full with reports of the coronavirus variants. These are several new versions of Covid-19 that have developed through mutation. In fact there have been many mutations of Covid-19 since it was first discovered. Here is a report of six strains from August 2020. https://www.sciencedaily.com/releases/2020/08/200803105246.htm

But more recently several new variants have appeared with changes in the spikes on their surface which helps them attach more easily to human cells than the original virus. These are the new variants of concern that have been identified in Canada.

UK Variant B.1.1.7 first emerged in the U.K. in September 2020. This variant spreads about 50% faster than the original strain and can be transmitted in less time.

South Africa Variant B.1.351 was first discovered in South Africa in December 2020. This variant is more efficient than others in targeting and infecting healthy cells. South Africa paused the rollout of the AstraZeneca vaccine after preliminary trial data showed it offered minimal protection against mild to moderate illness from this variant. 

Brazil Variant B.1.1.28 or P.1 was first identified in December 2020 when it caused one of the deadliest outbreaks in Manaus, Brazil. This variant may reduce the ability of antibodies developed from previous infections and vaccinations from killing the virus.

https://www.scientificamerican.com/article/the-most-worrying-mutations-in-five-emerging-coronavirus-variants/

Here are reports that show the rapid spread of the UK variant, in Ireland and Denmark.

• In Ireland less than 10% of positive tests at Christmas were caused by the UK variant, but rose to 45% by the middle of January.
• In Denmark the UK variant climbed from 0.3% of all samples sequenced in November to 2.9% in early January. The variant’s share of total cases is growing exponentially and is expected to be the dominant variant by mid-February. Denmark has been in lockdown since Dec. 11 and case numbers are dropping. The reproduction number is now at 0.9 but that is not particularly reassuring. “We think this is like the calm before the storm. We need to have a reproduction number below 0.7 if we want to avoid exponential growth in February and March.”
  https://www.spiegel.de/international/world/can-germany-stop-the-new-supervirus-a-e9ffc207-0015-4330-8361-b306f6053e15
   (Der Spiegel is the largest weekly news magazine in Europe)

This chart shows the percentage of all cases that are the UK variant in countries where it has been detected.

https://tomaspueyo.substack.com/p/variants-v-vaccines

The UK variant is the most prominent variant in Canada, with almost 400 identified as of February 11.
https://nationalpost.com/news/canada/the-state-of-covid-19-variants-in-canada-ontario-has-more-than-half-the-cases

On January 8, a single case of Covid-19 was detected at Roberta House, a long-term care home in Barrie, Ontario. The disease ripped through the facility with such speed that by January 25 more than 200 people had contracted the virus and 44 residents and one caregiver had died. The variant was also detected at another long-term care home in the area.
https://barrie.ctvnews.ca/more-than-100-cases-believed-to-be-u-k-covid-19-variant-linked-to-barrie-ont-care-home-1.5282898

Note that the UK variant spreads more quickly, estimated at 50%, but it is not currently known to be more virulent. That is, you are not more likely to die if you get the UK variant. It may be counter-intuitive but a virus that is more contagious will cause a lot more deaths than a virus that is deadlier, as shown in this graph.

The math for this is quite simple:

Suppose 10,000 people are infected, R=1.1, infection fatality risk=.8%, generation time=6 days. 

In a month there are 5 periods of 6 days, so transmission increases by 1.1⁵.
So 10,000 x 1.1^5 x 0.8% = 129 new fatalities after a month of spread.

If the fatality risk increases by 50%,
10,000 x 1.1^5 x (0.8% x 1.5) = 193 new fatalities.

But if transmissibility increases by 50%,
10,000 x (1.1 x 1.5)^5 x 0.8% = 978 new fatalities.

(You can verify the numeric result of a formula by copying and pasting it into a Google search bar, which can be used as a general calculator.)

So what are the implications of these new variants?

Since they are more transmissible, you should take extra precautions when you are in the vicinity of other people.

• Make sure to follow the social distancing rules, which have not changed from 2 meters ( 6 feet). 
• Try to reduce the time that you are in proximity to others.
• There is a new recommendation from the CDC to wear double masks. They can increase your protection from aerosol droplets by 90%.
  https://www.theguardian.com/world/2021/feb/10/mask-guidance-cdc-two-masks-close-fitting

Aside from a “third wave” spike in cases in March or April, there is not a lot being said about the full impact on the pandemic in Canada. While many epidemiologists have access to models that make predictions, I have not seen any graphs of them. Health authorities are pussy-footing around this, much as they did at the beginning of the pandemic in March 2020. 

Is it because the picture looks very grim?

This graph shows the pace of the UK variant in the United Kingdom. It peaked over a period of 2 months and increased the daily cases by a factor of 4. The UK entered lockdown on January 5, 2021, after which cases have declined.

https://ourworldindata.org/coronavirus-data-explorer?zoomToSelection=true&minPopulationFilter=1000000&time=2020-03-02..latest&country=CAN~GBR&region=World&casesMetric=true&interval=smoothed&smoothing=7&pickerMetric=location&pickerSort=asc

To see how a similar pattern would look in Canada, I returned to the spreadsheet model I used at the beginning of the pandemic. I “restarted” the model by entering the actual case counts for February 13, 2021 and modified the spreadsheet calculations to model the following assumptions.

– Used the Reproduction number R(t) of 1.1 reducing to .9 for lockdown periods.
https://epiforecasts.io/covid/posts/global/
– In March to April gradually Increased R(t) up to 50% to account for the increase in the UK variant.
– Added actual vaccinations that have been administered.
– Added the vaccine rollout assuming Canada hits its target that “everyone who wants a vaccination will get it by September 2021”. Since not everyone will want the vaccine, 70% of the population was used.
https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/covid-19-vaccine-treatment/vaccine-rollout.html#a4a

Here is the result, using relaxed lockdowns starting in February to reflect the fact that Ontario, Quebec, Alberta and Manitoba (but not B.C.) have begun easing restrictions.

This shows a large spike over a three month period with an increase of 4 times the number of daily cases, reaching almost 30,000 cases per day at the end of May before the vaccines start to take effect. This is very similar to what happened in the U.K.

This large increase in daily cases means that there will have to be another lockdown. 

Here is the result when a lockdown is applied for 7 weeks beginning mid-April.

This shows that by the end of the lockdown in mid-May when the percent of the population that is vaccinated reaches 33%, the number of cases stops increasing. By the end of August there are less than 100 cases per day and the percentage of the population that has been immunized (through vaccination or prior infection) is 70%. This is herd immunity. 

Life could return to normal within Canada in September 2021.