Analysis and Musings on the Covid-19 Pandemic

As a retired epidemiologist I have been closely following the Covid-19 Pandemic since mid-February.  I initially read all the WHO Situation Reports then started analysing and compiling the public available data for some of the countries I had a special interest.  I have also been compulsively reading news articles on the pandemic.  

My analysis is rudimentary and limited to a few spreadsheets but it is all helping me understand the Pandemic and satisfying my basic nerdy tendencies.  I suppose this is my way of coping while under lockdown on a small sailboat in Marigot Bay, St Martin in the Caribbean, trying not to worrying about when we can go somewhere out of the hurricane zone all the while looking onshore at the still very visible damage from the last hurricane in 2017.  

What follows are two write ups that I have done in trying to make sense of the world situation.  Initially I was not intending to put these words in a blog but now I will share them for what they are worth.  The first half of the blog was written the end of March when the world had about 750,000 cases and the US reported about 100,000 cases and less than 2000 deaths.  The second half of this entry was written on 1 May when in less than 5 weeks the number of world cases increased to more than 3.3 million and the US has recorded more deaths (>65,000) than it sustained from 10+ years of fighting the Vietnam War.

29 March 2020

For the purposes of the first half of this discussion the following definitions will be used.  Start of the epidemic in a country:  cumulative 100 cases, Epidemic ‘under control’ or incidence curve flattened: consistently less than 200 cases per day.  To date, 29 March 2020, only China and South Korea have managed to get the outbreaks in their countries under control.  It is still early days and there could be another flare up in these countries but hopefully with continued good public health infection control measures the worst is over for these countries.

China has taken about 45 days to get the worst of the epidemic under control.  At that point China had about 80,000 cases and nearly 3000 deaths (about a 4% death rate at this time but data is not complete).  It is now (29 March) day 70 of the epidemic and China’s daily new cases are around 100 and deaths are in single digits. 

Korea, who has achieved the highest per capita testing rate of any country, got the epidemic under control by day 20.  At that point Korea had just under 8000 cases and 66 deaths (less than 1% mortality rate – with caveats as data is not complete).  It is now in day 37 of their epidemic and like China, Korea’s daily new cases are around 100 and daily deaths are in single digits.  The mortality rate is 1.6% as of 29 March.  Since Korea has done such a high rate of testing (ie screened the greatest proportion of the population) this mortality rate may prove to be the most accurate for the true mortality rate for this virus.

Early Timeline

A bit more detail on the timeline of the epidemic in each of these countries.  China first reported cases of a novel pneumonia to the WHO on 31 December 2019.  At this time it had identified just over 30 cases.  In less than 2 weeks China had isolated, identified and sequenced the new coronavirus.  It made the genetic sequence available to other countries so they could start developing diagnostic testing kits.

By mid to late January other countries around the world were reporting cases. Japan and Korea reported their first cases on the 15^th and 20^th January, respectively.  At the time of Korea’s first case China had 278 confirmed cases.  By the end of January there were just under 10,000 confirmed cases worldwide with just over 100 cases in 19 countries outside China. (90% of the world cases were still in China.)

By the 15^th of February, China still had 90% of the world’s cases and reported over 50,000 cases.  In all, cases of the coronavirus were identified in 25 countries: Korea 28 cases, Australia 15 cases and the US 15 cases.  All but 3 and 2 of these cases respectively had a history of travel to China for Australia and the US.  Thus evidence of community transmission was clear by mid February for the US and Australia.  At this point when community transmission is noted, good outbreak control would demand decisive public health measures: test, isolate, trace, and more test, isolate, trace.

By the 1^st of March, 19 of the 58 (33%) countries outside of China who reported coronavirus infection were reporting local transmission of the virus.  On the 11^th of March the WHO declared Covid-19 a pandemic.  There were now over 100,000 cases worldwide.  Thirty percent of those cases were now outside China in 113 countries and territories; 63% of these countries were reporting local transmission.  

The data for the US cases is sketchy from the late January to mid-March.  From my reading of the publically available data, the CDC only reported to the WHO 4-5 days per week and the testing kits at this time were faulty.  No centralised reporting or response seemed to be occurring.  Private labs were charging for tests and public labs were given faulty kits.  

By 16 March Johns Hopkins started publishing a dashboard of world cases (https://www.medpagetoday.com/infectiousdisease/publichealth/84698 ) compiling data from multiple sources.  This data is now more consistent and published in real time.  The WHO situation reports continue to publish case numbers and deaths by country.  These numbers are slightly different from the JH dashboard but in the same ballpark.  Generally there seems to be a reporting delay with the WHO data and the data is a day or two behind the JH dashboard reports.

Europe and the USA are now the epicentres of the pandemic.  Italy, Spain, Germany and France are hardest hit in Europe.  Italy and Spain instituted mandatory self-isolation and shut down of all non-essential business on the 11^th and 13^th of March and France enacted restrictions on the 17^th.  The extent of the restrictions in Europe vary and were often incrementally introduced, starting with suggestions of working from home and self-isolating to closing schools and all businesses except groceries, pharmacies and a few others deemed to be essential.  I believe now Italy and Spain are enlisting the military and police to enforce these restrictions and streets are basically empty.

Although the USA restricted travel of foreign nationals from China on 23 January, it did not follow through with further restrictions on travel.  US citizens and permanent residents who had travelled in China were not restricted or monitored.  There also were only token restrictions and follow-up for travellers from Europe.  Nor was there a co-ordinated approach to testing and monitoring until mid-March.  Indeed, from all reports the outbreak control efforts are still fragmentary and vary substantially from state to state.  As of 29 March the USA is in the 26^th day of its outbreak and has over 125,000 cases.  On day 26 of China’s outbreak 64,000 cases were reported, half the number of cases even though China has four times the population of the USA.  In the last week cases of coronavirus infection in the US have increased four-fold, from 33,000 to 130,000.

1 May 2020

How rapidly things have changed!  In the 100 days since China reported about 100 cases, the virus is fully entrenched around the world in the worst pandemic since Spanish Flu in 1918-19.  The world is in lockdown and a long economic recession/depression is upon us.  There are now over 3.3 million confirmed cases and over 230,000 deaths worldwide.  Europe and the US are currently the epicentres of the pandemic.  The US has more than 1.1 million cases and 65,000 deaths while Spain, Italy, UK and France each have around one quarter of a million confirmed cases and more than one tenth of them have died – death rates that are 400-500 per million population.  Germany is fairing much better with a death rate of around 80/million.  Australia and New Zealand have done very well and basically the virus in those countries is under control.  Their infection trajectory curves have flattened.

European countries, the US, New Zealand and Australia are cautiously taking steps to open up and start the economy again.  This of course is quite a reasonable action provided the testing, tracing and health care infrastructure is in place to support any hot spots that may occur.  I am not convinced the infrastructure is adequate for all these places, especially in the US which has had by far, the worst response to the Pandemic within the developed world.  Many of the countries opening up still have several thousand new cases every day and several hundred daily deaths.  Time will tell how well this opening up goes.  

For my own interest, I am monitoring the data as best I can to see if we see a surge in cases.  Obviously the epidemiologists and policy makers around the world are also monitoring the situation using much more sophisticated tools and more complete data than I have at my disposal sitting on a small sailboat in the Caribbean. (I would love to be able to analyse some of this data using SPSS or STATA but those analysis skills and software are long gone for me.)

Learning Lessons

The Guardian published an article on the 10 lessons learned so far from the Pandemic, (https://www.theguardian.com/world/2020/may/01/10-key-lessons-for-future-learned-fighting-covid-19-coronavirus-society) which deserves further consideration.  A big question about this pandemic is why some countries seem to, so far, have come through with relatively few deaths and minimal economic disruption.  What are the factors and behaviours that have contributed to this?  The above article explores these issues. I would like to add some comment to these issues to make sense of it all for myself.  

One of the major, if not the major, factor that seems to affect the impact of the epidemic within a country is the speed in which that country responded to the virus threat.  The tools and knowledge of how to respond to an epidemic threat are well established and readily available and have been for decades, but the political will and ability to take up and act on the knowledge varied greatly.  To my mind, this current world crisis can be seen as the great verdict on the coalescence of science and politics.  

As mentioned at the beginning of this article, written over a month ago, China reported to the WHO on 31 December the occurrence of a novel pneumonia infection in the Wuhan province.  At this time it had identified about 30 cases.  By the mid-January 2020, there were 282 laboratory confirmed cases in the world.  All but four of these cases were in China.  At this time in the epidemic, only laboratory confirmed cases were being counted.  The actual number of cases would have been much higher as accurate and wide spread testing and identification of asymptomatic cases was not yet occurring.  By the third week of January China locked down Wuhan province, a province of more than 11 million people.

Much has been made by Trump and his ilk that China wilfully failed to contain the virus and that the three week delay in locking down Wuhan lead to the Pandemic.  I do not make apologies for China as it certainly made mistakes and this delay has had very dire consequences.  Nevertheless this was a new disease with unknown pathogenesis and infectivity.  It would be a rare country that would recognise the significance and world import of a cluster of new pneumonia cases to the extent that it would think it necessary to quarantine 11 million people within days of recognising cases.  China did lock down in January and now 14 weeks later the virus is contained in that country and there have been only a handful of deaths and cases in the last fortnight.  Sadly 14 weeks ago Pandora’s Box was already well and truly opened.  

However by the third week of January the world was made aware that there was a new infectious disease that should be taken seriously.  Every country that confirmed the arrival of this new disease within their borders and failed to act quickly and decisively contributed to the spread of the Covid-19 virus.  To my mind they are even more ‘guilty’ (if guilt can or even should be ascribed for a pandemic) as they were warned but failed to act.  With the proper actions the virus could have and should have been contained within each country.  South Korea, Thailand, Taiwan, Iceland, Norway, Greece, New Zealand, and Australia are some of the countries that have so far managed to do this and their infection trajectory has flattened with minimal cases and death.  

As we enter a new phase of the Pandemic in which countries will begin to lift their quarantine, we will see how well science and politics coalesce.  

Marigot Bay, St Martin