Forever Covid

Is the pandemic over? Not yet, but now we know how it will end!

Nilotpal Chakravarti
15 min readSep 28, 2021

Vietnam’s Vaccines

Is the pandemic over?

The question will seem absurd if you are a resident of Ho Chi Minh City, undergoing a harsh lockdown, virtually confined to your home.

A man living in an area under lockdown receives food through a barricade during the COVID-19 pandemic in Ho Chi Minh City, Vietnam July 20, 2021 [File: Reuters]

Vietnam fought and defeated three great powers (France, United States and China) in the twentieth century. In the twenty-first it fought Covid-19 with the same fierce determination. Its low tech but very effective contact tracing, strict border controls and localized lockdowns kept cases down and the economy open. In fact, Vietnam was among the very few countries whose economies grew in 2020.

How did Vietnam, get from being a Covid-19 success story, to an epicentre of the pandemic?

A Facebook page that I deliberately refrain from referencing, points out that Covid-19 deaths have gone up in Vietnam, in lockstep with vaccinations. Without quite saying so explicitly, it implies that vaccination has proved useless in preventing Covid-19 deaths or — even worse — may actually be causing the deaths in Vietnam.

Like most vaccine misinformation this post is based on ignorance of basic statistics.

Vietanam: Daily Number of Confirmed Covid-19 Deaths & Share of Population Fully Vaccinated Against Covid-19

The above graphs do indeed suggest that Covid-19 deaths and vaccinations in Vietnam are correlated. However, as anybody who took a first course in statistics has been told, correlation does not imply causation. And even if there is a causal connection, we can’t infer the direction of causation from the correlation.

In fact, the Facebook post has got the story backwards. The increase in Vietnam’s Covid-19 deaths is the cause and not effect of increasing vaccination.

Vietnam had not placed any orders for Covid-19 vaccines, having decided to develop its own and keep a lid on infections till they were available.

Vietnam’s Indigenous Covid-19 Vaccine Nanocovax is Nearly Ready (Photo Credit: https://nanopharma.com)

Unfortunately, the more infectious Delta variant upended Vietnam’s plans. Cases and deaths shot up sending Vietnam into an exceptionally hard lockdown. Vietnam began scrambling desperately for vaccines.

Vaccinations have probably had no significant impact on death rates in Vietnam — yet. Too few — still just over 8% of the population — have been fully vaccinated for that to happen. Vietnam’s deaths are beginning to trend down but that is more likely due to strict lockdowns.

The Hinge of the Pandemic

The fate of a battle often turns on a hinge, a decisive action taken or not taken. That’s true of pandemics too!

The variant of the SARS-CoV-2 virus, which would later come to be known as the Delta, had been first detected in India in October 2020. However, it really took off in late February 2021. India’s Second Covid Wave had arrived. It would leave hundreds of thousands dead in its wake, according to official figures; more probably millions perished.

INSACOG, (Indian SARS-CoV-2 Consortium on Genomics), a body set up by the Government of India for the express purpose of studying and monitoring genome sequences and virus variation of circulating strains of COVID-19 in India, warned about the Delta variant in early March 2021.

A brilliant paper by Bhramar Mukherjee, Professor of Epidemiology at the University of Michigan, and others, addresses the counterfactual: what would have happened if India had acted soon enough against the Second Covid Wave?

Their model gives a clear and convincing answer. Over 90% of the lives lost could have been saved if a “light lockdown” had been implemented in mid-March.

There was a moment in March when the Delta could have been stopped in its tracks by restrictions on travel and public gatherings. However, the Indian government ignored INSACOG’s warning and the moment passed. The highly transmissible Delta variant spread like wildfire, fuelled by large public gatherings including electoral rallies, public protests and above all the Kumbh Mela, a once-in-twelve-years religious festival at which millions of pilgrims gathered.

The Second Covid Wave travelled from west to east across India and also spread from large cities to India’s rural hinterland. Cases kept going up in March. Still the government introduced no serious restrictions on large gatherings and citizens also appeared unconcerned. Piecemeal restrictions of varying severity and duration were only put in place by various Indian states around the middle of April. The wave had by then become an unstoppable tsunami.

Funeral Pyres Built in Parks and Other Empty Spaces after Delhi’s Crematoriums Reached Capacity

Images of the holocaust that followed have been seared into the world’s consciousness. Funeral pyres burning non-stop; dozens of corpses floating in the River Ganga (Ganges) that Hindus hold sacred; people dying while waiting for hospital beds to become available; friends and relatives searching desperately for oxygen while a patient’s supplies ran low.

How the Delta Changed the Pandemic

The Delta wave spread to other countries in Asia and beyond.

The linchpin of Vietnam’s Covid-19 strategy was contact tracing. Vietnam would trace the contacts of suspected or confirmed Covid-19 cases, the contact of contacts and so on till the third or fourth degree.

Vietnam wasn’t alone. In 2020, when Covid-19 devastated many “developed” countries in Europe and the Americas, lower-and-middle-income countries like Rwanda and Sri Lanka managed to keep cases and deaths down through effective contact tracing, isolation and border controls.

Unfortunately the Delta variant is much more transmissible than the original “wild” (Wuhan) strain, (though probably not as infectious as chicken pox as a leaked report from CDC had claimed). Delta viral loads are higher and even a fleeting contact lasting seconds can result in infection. Its incubation period is also shorter. This means that there are many more contacts to trace and a contact much likelier to begin spreading the disease before being isolated. All this makes contact tracing a much less effective tool against Delta.

Now it was the turn of countries such as Vietnam, Sri Lanka and Rwanda to be hit by vicious Delta waves.

Selected Countries (Rwanda, Sri Lanka, UK, US, Vietnam): Daily Number of Confirmed Covid-19 Deaths per Million Before and After 5 May 2021

Of course that didn’t mean that Delta was irresistible. The Delta, like other variants of Covid-19, is spread by human-to-human contact and can be controlled through lockdowns and other strict restrictions on travel and public gatherings provided these are applied early and stringently enough.

New Zealand announced a nationwide lockdown on 17 Aug when a single case of the Delta variant was detected. Since then it has had only one confirmed Covid-19 death.

Taiwan too has managed to contain the Delta variant so far with strict restrictions on public gatherings and social distancing but without a total lockdown. Its confirmed Covid-19 death rate, though higher than New Zealand’s is, at 35 per million, still one of the lowest in the world.

Taiwan: Cumulative Covid-19 Confirmed Deaths Per Million

Indonesia dithered and paid a terrible price. The government first allowed the mudik, the annual homecoming of millions of Indonesians over the Idul Fitri holidays and then belatedly banned it. In any case the ban was not strictly enforced and was skirted by millions letting the virus spread outward from the densely populated islands of Java and Bali to Sumatra, Kalimantan and Nusa Tenggara.

George Santayana (Wikipedia)

Indonesia’s second Covid wave was an eerie replay of India’s, proving once again the truth of Spanish-American philosopher George Santayana’s dictum “those who do not remember the past are condemned to repeat it.”

Masks, thermometers, hand sanitizers out of stock at Indonesian pharmacy. Image credit: SiberianCat on ikimedia Commons (CC BY-SA 4.0)

The healthcare system collapsed as cases and deaths surged. Hospitals ran out of beds and oxygen and people died while waiting to be admitted just as they had in India. Pharmacies ran out of thermometers, masks and hand sanitizers. Graveyards ran out of space. When Indonesia’s Second Covid Wave receded at last, it left behind a toll worse than India’s on a per-capita basis.

Death by Bad Data

We now know how the pandemic will not end. Thanks to Delta it will not be through the world achieving herd immunity.

Ever since the beginning of the pandemic a number of experts, including the Great Barrington trio of Jay Bhattacharya, Sunetra Gupta and Martin Kulldorf, have insisted that the quickest and most humane way to end the pandemic is to let the virus rip through the population while taking unspecified steps to offer “focussed protection” to the more vulnerable. When a sufficiently large fraction of the population — known as the herd immunity threshold (HIT)- is infected, the pandemic begins to die down because it becomes harder and harder for the virus to find susceptible people to infect.

And almost since the beginning of the pandemic the Great Barrington trio and others have claimed that herd immunity was around the corner. Sunetra Gupta had claimed in July 2020 that the UK had reached herd immunity. A winter wave of Covid-19 and 100,000 deaths would prove her wrong. She may be held personally responsible for some of these deaths as she & Anders Tegnell, the Swedish epidemiologist, had successfully persuaded the Prime Minister Boris Johnson to delay a lockdown in September 2020, possibly resulting in 1.3 million extra coronavius cases.

The proponents of herd immunity often cherry-pick data to support their arguments. In January 2021, an article by Sanjiv Agarwal & Jay Bhattacharya claimed that “more than 50 per cent of the Indian population may have developed natural immunity to the virus.” In support of the claim it cited data from Thyrocare, which runs a chain of diagnostic centres and clinics in India. “This fact is corroborated by serological tests for Covid antibodies carried out commercially on a large scale by Thyrocare. The founder of Thyrocare, Dr A. Velumani, says that “nature… already has immunised, freely, silently 70% Indians”.

Extract from article by Sanjiv Agarwal & Jay Bhattacharya

The Thyrocare data was of course not representative of India. In fact, it provides an almost textbook example of a biased sample. Most of the people tested at Thyrocare were tested precisely because there was some a priori reason to believe that they had been infected. How could Jay Bhattacharya, a Professor at Stanford University, miss that? I can only attribute it to confirmation bias.

Gautam Menon, the well-known Indian epidemiologist, has pointed out how theories claiming that most Indians were immune to Covid-19 circulated widely in early 2021. A sero-positivity survey in January showed that just a little over 20% of the population had been infected and therefore many remained susceptible. It was largely ignored. The effect was to induce a sense of complacency among both Indian citizens & the government and slow the response to the second wave.

Misinformation: the fifth horseman of the Covid apocalypse (Credit: Bill Bramhall’s editorial cartoon for Monday, Aug. 16, 2021 — New York Daily News)

Bad data and confirmation bias continued to kill during India’s second wave. Sanjay Gunjyal, a senior police official in charge of Kumbh Mela security arrangments, kept on insisting till the end of May that the Kumbh was not a super-spreader event as only 0.2% of the Covid-19 tests conducted at the mela site between 1 Jan and 30 April were positive. This was unbelievably low given that during this period the test positivity rates in both India and Uttarakhand (the state where the Kumbh was being held) had risen from 2 to nearly 20%.

In fact, a dubious private lab had simply faked at least 100,000 (and quite possibly more) of the results and charged for the tests. Since positive test results would need follow-up almost all fake results were negative, accounting for the low test positivity rate. The low rate should have set alarm bells ringing and led to careful scrutiny of the data, but it didn’t and the Kumbh was allowed to continue.

The Silver Bullet

The Delta variant has changed the nature of the Covid war. But so have vaccines. They have tilted the scales in favour of humanity.

Consistent data from many countries have established beyond any reasonable doubt that Covid-19 vaccines greatly reduce the chance of severe disease and death. Only 0.09% of vaccinated cases in Singapore between May 1 to Sept. 16, needed intensive care or died; the rate for the unvaccinated was 1.7%. Among people 80 or older the respective figures were 1.79% and 15%. Data from the UK, India, and elsewhere support the same conclusion.

Share of Delta Variant among SARS-CoV-2 sequences Aug 9, 2021

In all these countries, and in fact in most from which we have data, Delta is now the dominant variant. So, vaccines seem to be holding their own against Delta, at least as far as severe disease and death are concerned.

A person can become immune to Covid-19 either by becoming infected and surviving or by being vaccinated. Being vaccinated is clearly the better option because it avoids the risk of death or severe disease from Covid-19.

So, can we achieve herd immunity while reducing the risk to lives by vaccinating enough people?

Unfortunately, Delta is more infectious than the original Covid-19 strain. Much more. Remember R0 (R nought)? The average number of persons in a completely susceptible population infected by a disease carrier. R0 is between 2–3 for the original strain and 6–7 for Delta.

To reach herd immunity we need to vaccinate a fraction 1–1/R0 of the population. So the required the Herd Immunity Threshold (HIT) against Delta is between 80 and 90%.

This calculation assumes that an immunized person is a perfect shield. She can’t become infected again and transmit the virus to someone else.

But of course that is not true. No vaccine is perfect. A vaccinated person can also be infected; this is called a breakthrough infection. And unfortunately although the vast majority of breakthrough infections are mild, people with such infections can also transmit Delta though viral loads decrease faster in vaccinated patients.

Suppose that p% of the immunized population can become infected and transmit the infection in turn. Then the HIT is (1–1/R0)/(1-p). If p is a fairly low 10% this would take the HIT to nearly 100%. We need vaccines that are nearly perfect at preventing not only disease but virus transmission to achieve herd immunity. If p is a bit larger the HIT goes above 100%.

And that’s not all. Vaccine immunity is not permanent. Data from Israel suggests that immunity from the Pfizer-Biontech vaccine wanes quite a bit in 6 months. That is also true of Astra-Zenaca and probably other vaccines as well.

So herd immunity against Delta seems impossible with the present generation of vaccines.

Even less plausible is the hope that Covid-19 may be eradicated the way smallpox has been and polio may be in the not-too-distant future. It is far too widespread for that.

Sorry New Zealand. You did everything right. You eliminated the virus twice and seem all set to do it a third time. But we — the rest of the world — let you down. The moment you relax border controls the virus will sneak in again.

Our best hope at this point is that Covid-19 will transform from pandemic to endemic. When a disease is endemic it persists in the community at a low, stable, manageable level. Eventually more or less everybody in the community is exposed to it.

The Singapore Experiment

Singapore, my home, is a tiny, rich, technologically advanced, small island nation in South East Asia. It is tempting to assume that Singapore is rather unique and its experience not very relevant for the rest of the world. But in fact its current experiment is of enormous importance. That’s because Singapore is probably the first country to have opted for the goal of a managed transition to the endemic phase.

Singapore has had only one large outbreak in 2020, restricted to more than 1,200 small and 43 large migrant workers’ dormitories. It was contained by universal testing, isolation of dormitory residents and a lockdown that was particularly harsh for the migrant workers. Antibody tests showed that just under half the 323,000 workers were infected but only 2 died. The overwhelming majority of the community outside the dormitories remained virus free.

If you are in the UK you will certainly think that the pandemic is over. The British essentially vaccinated a large proportion of the population and then relaxed all restrictions to let the virus spread unchecked.

Crowds at an English Premier League match

That is not and can’t be Singapore’s way. The UK has had several Covid-19 waves. These have killed a large number of vulnerable people and probably immunized a considerable proportion of the unvaccinated. The same is true of Israel and most of the highly vaccinated countries of Europe and North America.

Singapore has fully vaccinated 82% of its population and partially vaccinated a few percent more. That still leaves close to a million unvaccinated, including about 87,000 seniors 60 years or older. Since Singapore has shielded its citizens well from Covid-19 they would be vulnerable if the SARS-CoV-2 was allowed spread unchecked. And daily death rates of the kind that UK and Israel face would not be tolerable for Singapore.

Selected Countries (Israel, Singapore, UK): Daily Number of Confirmed Covid-19 Deaths per Million

In Singapore, there was no big bang lifting of all restrictions together; no “Freedom Day” UK style. Masks remained (and remain) mandatory. Restrictions on public gatherings were relaxed gradually but not lifted altogether. For instance, only the fully vaccinated were allowed entry to gyms and dine-in restaurants and that too in groups of 5 at most.

The transition was planned carefully. Testing was going to be a critical part of the transition and the new normal that would follow. This was ramped up and now includes:

  • Rostered testing of high-risk workers including those living in dormitories, teachers and staff in educational institutions and workers in healthcare, eldercare, spas and gyms, and F&B and construction sectors.
  • Encouraging individuals and small businesses to carry out self-tests using DIY (Do-It-Yourself) Antigen Rapid Test kits. These are widely available in retail stores and have been distributed freely by the government
  • Wastewater surveillance at several hundred locations across the island.
  • Mass testing of entire neighbourhoods whenever there is evidence of an emerging cluster

The role of contact tracing also changed. Singapore had laid great stress on establishing the chain of transmission, i.e., determining exactly who had infected each patient. A case would be considered linked if the source of infection could be established and unlinked otherwise. Statistics published everyday included the number of linked and unlinked cases. This strategy helped Singapore to identify super-spreaders and stop the spread of infection in the community.

Unfortunately with the rise of Delta establishing links became increasingly difficult. It also made less sense since Singapore is now no longer trying to identify and eliminate all community cases. Singapore has now abandoned it altogether and no longer reports linked and unlinked cases. It hasn’t however given up on contact tracing.

The Singapore government had hoped that the spread of Covid-19 would be slow and controlled. Unfortunately Delta refused to follow the script. The relaxation of restrictions led to an exponential rise in the number of cases.

Number of Confirmed Daily New Covid-19 Cases Per Million

This was not unexpected but the speed took everyone by surprise. Some restrictions were reimposed. Work-From-Home became the default option, whenever possible, once again.

Fortunately deaths rose much more slowly than cases. But rise they did. There were just 37 confirmed Covid-19 deaths from the beginning of the pandemic in January 2020 till the end of July 2021. There have been 43 since then.

Part of the Car Park at Tan Tock Seng’s Hospital has been Converted into a Temporary Covid-19 Screening Facility

The number of ICU admissions now stands at 27. This is nowhere close to overwhelming Singapore’s healthcare system. 300 ICU beds can be made available at short notice for Covid-19 patients without degradation of quality of healthcare and at a pinch that can go upto 1,000. Still, there are early signs of stress on the healthcare system. Supply chains have also been stressed; large clusters have resulted in closure of a market which handles most of Singapore’s fish imports and another that processes a large share of its vegetable imports.

Singapore’s vaccination rates seem to have reached a plateau and the country has begun offering booster shots to the elderly and the immuno-compromised.

The most dramatic change in Singapore’s Covid-19 strategy is in its Covid-19 recovery protocols. Till very recently, everybody who tested positive had to recover in either a hospital or a designated Covid Care Facility. While this isolated all Covid-19 cases from the community it resulted in many hospital beds being occupied by patients with no or very mild symptoms.

Singapore’s Covid Home Recovery Protocols

Now, patients who are fully vaccinated, young and with no serious underlying medical conditions and without serious symptoms, can recover at home.

Singapore’s decision to follow the endemic route has had immediate repercussions. Hong Kong reacted sharply and broke of all discussion on a possible travel bubble with Singapore, as it is constrained to follow China’s Zero Covid policy. On the other hand, Singapore’s experiment is surely being followed closely by Malaysia, South Korea and the Australian states of New South Wales and Victoria. They will all probably follow suit once they see Singapore’s experiment succeed.

Disclosure: I am the Director of Smart Consulting Solutions Pte Ltd, incorporated in Singapore and its subsidiary Radix Analytics Pvt Ltd, incorporated in India. I am also a Visiting Faculty Member at the Indian Institute of Management, Udaipur. However, the opinions expressed in this post are solely mine and not necessarily shared by any company or institution with which I am affiliated.

Some of the material that I used in this blog was shared on Prof Gautam Menon’s Facebook page and some provided by Ravi Dixit. They are not responsible for the content in any other way. I am grateful to my friend Dr. Ashish Kumar Dawn for his comments. Shamik Chakravarti corrected a few errors.

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Nilotpal Chakravarti

I have spent over 30 years in academia and industry exploring how to use mathematical methods to solve real world problems