7 August, 2020

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The Evolution Of The Covid-19 In Sri Lanka & Prospects For Relaxing Many Constraints

By Chandre Dharmawardana

Dr. Chandre Dharmawardana

[This is a shortened version of a more technical paper, 15-04-2020]

An outbreak of a new type of  pneumonia like disease was first reported on 31st December 2019 from Wuhan City in the Hubei Province of China. It was identifies as caused by  a ‘Novel Corona Virus’ on 7th January 2020, and renamed Covid-19 on 11th February 2020. The WHO  upgraded  the disease to a pandemic on the 11th of March 2020.

From then on, many countries all over the world rushed to impose social distancing, lockdowns and curfews to prevent the spread of the disease. Sri Lanka’s initial official  response to Covid-19 began on January 27 when quarantine measures were imposed on incoming air passengers. The first local case, a guide working with Italian tourists, was detected on 10th March, and the importance of methodically identifying transmission chains became clear. This can be more important than blindly testing populations looking for Covid-19 positive cases (see my article in the Island, 1st April).

The government at first attempted to contain the people in their homes by declaring public holidays and extending them. However, from March 18th  the government began to impose curfews in Covid-19 hot spots, many being in areas to which returnees from abroad, travelers or religious teachers had arrived and irresponsibly ignored social distancing and quarantine requirements.  Other who hold irrational beliefs (e.g., that the disease is caused by non-humans working in consort with “Naga beings”) also ignored social distancing, wearing masks etc., and proposed inhaling herbal smoke and consuming broth made from “traditional rice” for fighting  the disease!

In Western countries too,  patterns of transmission through human chains proved important. Also, support workers who worked in multiple nursing homes were potential carriers for spreading the disease. Nearly half of the dead in Canada from Covid-19 are in nursing homes. Such transmission chains are not normally implemented in  simulation models that are used in epidemiology. Furthermore, some countries, when releasing daily data of “new cases” do not separate out cases that appear in quarantined populations from cases that appear from within the general public. New cases detected in quarantined locations do not add to the growth of the epidemic and should be treated differently in epidemiological modeling. What are labeled as “Covid-19 cases” in one country may not conform to the same labeling in another country.

Many of the epidemiological simulation models in current use are well known in the physical sciences and in ecological studies (see Bolker, Ecological models and data. Princeton University Press). They are applied to competing chemical reactions, polymerization processes, competing plant growth etc. Most  of these processes begin with a period of exponential growth which gets gradually dampened and  “flattens out”. That is, many growth processes that are very different at the “individual level” all display growth and saturation characteristics having a universal shape. The so called logistic model is one of the simplest models belonging to this class. Here we exploit this universality and use a more sophisticated version of such a model to study Sri Lanka’s Covid-19 data.   

Data analysis and modeling

The Epidemiology unit of Sri Lanka’s ministry of Health (EU-SLH) has provided authoritative documentation in monitoring the evolution of Covid-19 via its daily bulletins. The cumulative numbers, i.e., the “total confirmed cases” reported by EU-SLH  data are displayed in Figure 1 (curve with squares). 

The data from 10th of March to 15th April have been used in constructing our epidemiological model which can be constantly updated as new data comes in. It is clear that the trend in the data changes  from 25th to 30th March, and then resumes its upward trend though with a different rate. This bi-modal characteristic is seen in the daily-change figures as well, in spite of the  noisy nature of the data. This suggests two independent loci of infection, or the effect of government interventions to control the epidemic, occurring with a time lag. 

Efforts have been made to  account for the fact that the “confirmed cases” reported  daily by the EU-SLH includes new cases that appear among quarantined  people. If the quarantining is effective, such new cases should not “push the curve upwards” and change the final flattening trend of the curves. For instance, on the 13th of April 15 new cases were reported, when the cumulative number of confirmed cases jumped from 218 to 233. However, all 15 new cases were from those already confined in quarantine centers, and hence cannot be included as infection loci for the public. A data curve corrected for such cases is given (with triangles) in the figure, and labeled “confirmed public cases”. Using these sets of data, we give our model results, and predict the long-term behaviour (asymptotic behavior) and the number of cases to expect when the curve “flattens”, in each scenario.

Figure 1. Models for the time evolution of the total number of Covid-19 cases, showing projected long-term behaviour for three types of data treatment.

If we consider the data set labeled as “confirmed public cases”, where Covid-19 cases arising among quarantined people are not considered relevant to the spread of the epidemic, then the long-time asymptote  is about 206, and definitely below 210. If all cases (the cumulative daily totals reported by the EU-SLHD) are included in fitting the model, then the projection is 298, and certainly below 310. On the other and, if only the initial data set (prior to the imposition of social distancing and curfews) were used, the asymptote is ~325, but alternative parameter choices giving even 600 are possible. This shows that social distancing and curfews were effective in constraining the evolution of the epidemic.

Figure 2. A comparison of daily “new” numbers of the model

The model can now be used to predict the daily “new” numbers from

10th March onwards, and examine how well they agree with the observed data. Note that what was fitted was the cumulative daily totals, and not this differential quantity. Hence good agreement with

the general trends in the daily “new” numbers is a useful test of the quality of the model. Our model reproduces the rough bi-modal character of the observed data and the general trends (Fig. 2).

Conclusion

Assuming that that the hospital resources are able to handle even 500 cases, these studies suggest that Sri Lanka  should be able to resume nearly normal economic and civic activity by the end of the first week of May, assuming that the epidemic retains the characteristics shown in the current data. The confirmed new cases are arising mainly in hotspots in six districts, while the other districts seem  close to normal. Hence a graduated approach to opening the economy should be followed. Important civic activities like elections can be held while still imposing physical distancing. Sri Lanka’s economic rekindling is linked to domestic needs as well as those of  its foreign trading  partners. 

The Covid-19 epidemic has created a situation where working online is becoming permanently  institutionalized, and this is environmentally very desirable  in reducing travel stress, particulate dust and combustion of fossil fuels. The re-opening should make all such desirable features a permanent characteristic of the economy.

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Latest comments

  • 5
    1

    We presume Glyphosate would be the treatment.
    /
    But where to find it professor? Monsanto doesn’t even exist anymore.
    /
    Please help with your expertise on human health.

    • 3
      1

      Yes, going by his record on kidney disease of Rajarata farmers, Dr Chndare will be a good source of advice on human health.
      =
      Vaguely remember him recommending Arsenic to balance Cadmium toxicity coming from rice.
      =\
      How good id that!
      =
      Please help us.

    • 3
      0

      This is BS.
      .
      This man as an Monsanto company supporter, may thinking that he could score more if he could come with that in this backdrop.

      Nobody in the world – not even the pioneers in CORONA virus research are aware how dangerous COVID19 SARS COV2 WOULD be.
      Some believe, also today, in Europe, if they have to get ready for the second wave … our Musalayas make every overestimations about our country – whoser percapita is much muc lower than that of the lowerst country in Europe.

      Not even 2 bed ICU capcity/ 100 000 according to world statistics, how would SRILANKA face if the spread would turn out to be SUPER spreading ?

      I wonder why the KIND of men with some ACADEMIC titles make every effor to be in good books of this BPs’s led govt ?
      :
      Glyphosat ban – was against to this man ‘s research outcome. He never supported anyone in SL, in that regard even if unprecedented numbers of patients in farming communtiy were caught by NOT COMMON KIND OF renal diseases. That was based ont he AGROCHEMICALS being used in the country, over the decades. Those agro chemicals, were made compound with GLYPHOSAT which is a herbicide being used in EUROPE, America and ASIA above all in developing countries.
      THree are two groups of researchers working on finding the etiology of the disease – but this writer and their groups work on PRO- american manufaturing company-MONSANTO.

    • 2
      0

      Hai Dhane,
      \
      Long time, No hear!
      \
      How are things in Quebec.
      Are you still in touch with your alter ego Dr Chandare?
      \
      Please write.

  • 1
    0

    All good stuff Doctor! So looks like life will be back to normal with a vengeance come May. The bast bit is in the last para, and if we change our working habits, then there will much relief for the hard pressed working people in the city who will at last have cleaner air to breathe.

    Our people have been suffering these past few weeks; we Sri Lankans like to be free birds. We will make up for what we missed with a glorious Wesak, some overdue cricket, a lot of local tourism, and a belated Bak Maha Ullela, and the elections.

    But . . but . . . we could be jumping in the gun in our enthusiasm and up with a second surge that will send us all back into lock-down again. Only time will tell.

  • 1
    0

    “Important civic activities like elections can be held while still imposing physical distancing. “
    Yes, it’s easy to win and election under the present environment, and that is all you power hungry, spineless murderers expect to achieve.

    Rubbish from another ‘Permanantly Head Damaged’ (Phd) ‘Jarapassa’ boot licker?
    Your Phd. clans research, opinions and conclusions have already ruined the mother nature’s natural environment and it’s life cycle.

    • 0
      1

      If the social lockdowns are continued, and if the military goes on running the show, the military control becomes a fait accompli.

      So it is important to hold the elections. It is likely that the UNP and even the TNA will get reduced to a few seats, like what happened in the 1970s, with the UNP and the Tamil Congress. But the UNP came back later, with more power, and the TC got replaced by the ITAK.

      Sri lanka is set to see a similar event once again, and I think it will be a good thing for minority politics, because it has reached a cul de sac with the TNA and the UNP cohabitation whose balance sheet was to allow people like Ravi kaynanayaka to live in penthouses and Sampanthan to get himself a retirement villa, while Sumanthran can bask in US approval.

      It required a Nixon to go to China and fix the USA and China problem in the 1970s. It is possible that Gotabhaya is the only Sinhala politician who can redress the problems of minority-majority politics. But will the minority leaders work with him, and will Gotabhaya be man enough to work with them?

      What ever it is, this can be known only after an election.

  • 3
    1

    What is the scientific basis for the hypothetical curve and the extrapolated curve fits?

    • 2
      5

      What is the scientific basis for the hypothetical curve and the extrapolated curve fits?
      What is the scientific basis for believing that the sun will rise tomorrow morning? The fact that the sun rose during the last 1000 days past, nay the last 100,000 days past, nay the last billion days past, is no proof that it will rise tomorrow morning!
      It doesn’t even make it more probable.
      But that is how science works. Science makes a model and assumes that the model holds for the future.
      If it doesn’t work make a new model!
      Or, if you don’t like that approach, turn to the scriptures and divine revelation!
      Or Astrology, or, like our politicians, go various shrines in South India

      • 1
        0

        R
        What bothers you about my question?
        Do you think that any b***s*** graph can pass without challenge!
        A scientific model has to be based on reliable data and theory. The random nature of daily data (Fig 2) itself is an obstacle to reliable interpretation.
        To create models with no scientific basis is either daft or downright dishonest..

  • 1
    0

    Professor Kumar David has also proposed that the curfew should be removed and normalcy should prevail as soon as possible.
    This Prof. has also concluded that that the restraints should be lifted, but not as speedily as suggested by Prof. KD.
    He is suggesting the re4lease after the first week of May.
    Before they release these restraints, they should also see if the hospitals aere ready to deal with a possible re-surg of the epidemic.

  • 0
    1

    I did not read your whole article. but, looking at the graph, the total no of infected is a third order regression. It is because of Asymptomatic infections. Other than it, as the govt had very good isolating physical distancing mechanisms, all other curves become second order regression. SO, in the second order curve only the physical distancing (one variable) did not aggravate disease spread while because of the asymptomatic cases, there were two variables affecting the total numbers..

    • 2
      0

      I think this JD fellow is talking thorugh his hat.
      He says he didn’t read the article. If he did, he wi9ll see that the author says he used something more sophisticated than a “logistic” epidemics model. I googled it and find that it has an exponential growth and other effects and is fully non-linear, and not linear, second order or third order. exponential growth alone requires a minimum of two parameters.

      • 1
        0

        DJ
        Thanks.
        What seem the relevant parameters used?
        How does one accommodate the random component of the daily data?
        I suspect a b******t component entering the analysis somewhere.

  • 0
    1

    20 days ago, world’s rate of new COVID-19 cases reached the peak then almost all of the countries went on a lock down mode. Because of it, in the last 20 days, the rates of new cases in the world have been coming back to the level that we saw about 2 months ago.
    .
    The cooling rate might be related to the policy of promoting social distancing by WHO. Now, all countries are gradually going to relax the lock down mode in coming weeks and still keep up the social distancing regulations. It seems social distancing is the only reliable protection that we all have now while gradually spreading the cases to the local populations.
    .
    It’s interesting to see the peaking of new cases in Japan and Singapore over the last 20 days. Now sure, the reason behind those 2 countries’ heating and cooling rate of new cases that are cycling in every 10 days. Perhaps they are already spreading the cases to the local population in a control manner.
    .
    SL is the only country now keeps the total cases in 200+ ranges with lowest spreading rate 22 days after confirming the 100th case. We should kudos all for achieving that target in short time.
    .
    Next challenge will be keeping the rate of new cases low while gradually spreading the cases to the local populations. In this phase, seniors and people with underline medical conditions are taking a direct hit in high income countries now. Hope SL will successfully pull this phase too in coming months.

    • 2
      0

      “SL is the only country now keeps the total cases in 200+ ranges…”
      Have you heard of a country called Venezuela that, despite suffering heavily from US embargoes and threats, has a lower infection rate than Sri Lanka.
      It has the best per capita performance in the whole of Latin America and the Caribbean, despite adjoining countries performing poorly.
      Globally, Vietnam has the most impressive record.
      *
      Myanmar has a better record than us.
      Sri Lanka, with just one entry point, had no reason for any infection after the Chinese patient was identified and cured.

      • 0
        1

        Here is Vietnam and SL’s COVID-19 stats.
        .
        Vietnam: 276 cases after 26th day from confirming 100th COVID-19 case.
        .
        SL: 244 cases after 24th day from confirming 100th COVID-19 case.
        .
        Do you believe any stats from countries like of Venezuela, Myanmar and North- Korea?
        According to Reuters, “Venezuela is least equipped for virus.
        Recent reports show that there are only 84 intensive care unit beds serving the whole country and about two-thirds of healthcare workers reported not having access to gloves, soap and other disinfectants. The problem is worse still in public hospitals, where water shortages are common and can last for weeks. In addition, responding to Covid-19 is complicated by a lack of functioning X-rays, access to laboratory tests and respirators.”

  • 0
    2

    The TNA has asked the EC to not to hold elections.
    How much public support does the TNA have today? less than 6% of the 22 million
    The JVP has asked the EC to not to hold elections.
    How much public support does the JVP have today? less than 2.5% of the 22 million
    The SLMC has asked the EC to not to hold elections.
    How much public support does the JVP have today? less than 2.5% of the 22 million.

    If an election is held, they may be further wiped out!!!
    That is the democratic process.

    HOLDING ELECTIONS is the very basis of democracy.

    How should we determine if we should hold elections?
    If the number of Covid-19 cases does not increase (increases in quarantine centers do not matter, as said by this writer ), then the EC must give at least two weeks for
    electioneering and fix a date, possibly very late May 2020?

    • 1
      0

      VG
      The case for delaying the elections cannot be rejected based on what the TNA intends to achieve.
      Elections should be held on a level playing field. The country has to return to a degree of normalcy for a fair opportunity for the rival parties to campaign.
      The country has been traumatized by the curfew overkill. A few month delay to stabilize things will benefit democracy.

  • 0
    2

    In the US, when they give statistics, they give the number of “Black People infected”, the number of Hispanics etc., and this is very helpful in making a sociological understanding of how the Covid-19 strikes.
    A majority of the infected or locked down villages in Sri lanka are Muslim villages, due to the follow of some my own people and their uneducated “religious teachers” who have tried to hold prayer gatherings etc. Then there was this stuff about burials and cremations. I am ashamed of the lack of education of our people because the Muslim leaders merely concentrate in making profits for a few business tycoons, and
    make most of the people mere Madrases trainees having no modern knowledge. They want to teach the Sharia and not science, engineering and medicine because politicians can better control ignorant people

    The government should Covid-19 release data analyzed an Ethnic basis to better comprehend the way in which the disease is being propagated.
    I thank the author for a useful discussion, and I hope this write is able to get data based on ethnicity and plot the graphs for our information and post them in the electronic media.

    • 2
      0

      Bodin
      This is not the cleverest stunt I have seen to push an anti-Muslim agenda.
      Are most of our clergy, regardless of religion, capable of any modern thought let alone receiving modern education?
      What do we do with the COVID19 ethnic statistics? Add to the misinformation against Muslims?
      The US is the most racist government in the West. It is decades of pressure from below that led to statistics. But life goes on the same old racist track regardless of statistics.
      *
      It may help if our government will also educate the public on ethnic distribution in matters like pupils per school, employment by category, poverty level etc. A historic data record will be very informative.

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