Covid-19: Winds of Change

 How things change in one year!

At the beginning of 2021 everybody seemed perplexed that the much anticipated first wave of Covid-19 had somehow swept past India without causing much damage. 'The virus cannot survive the pollution levels here!', sniggered the wags and carried on with their lives. 

People were just beginning to take it easy when the second wave - the Delta variant - blindsided us in March 2021. Suddenly all the hospitals were struggling to cope with a deluge of patients and distraught families. Just about everybody seemed to be desperately looking for oxygen cylinders, medicines, oxygen concentrators and reliable test kits. By July, nearly half a million people had died on the official records with speculation rife on the scale of unreported deaths.

When Delta gave way to Omicron there was much talk on how the healthcare system had been geared up to meet the challenge. Skeptical as always, I thought this was bluster - just the sort of pep-talk expected from politicians to keep a lid on panic levels. It took a first-hand experience for me to realise how wrong I was!

We started 2022 on a positive note from our RTPCR test labs. It had started with a throat irritation and telltale signs of a fever. When a number of friends who attended a Christmas party started testing Covid-positive, we knew that ours was not the winter usual viral. The tests only confirmed this but what surprised me is the way in which the healthcare system had actually been geared up to cope with this new wave.

Within an hour of calling a private testing lab (SRL), a sample collector was at our doorstep (~INR 900 / ~USD 12 per test). The RTPCR reports arrived online a day later, on a Saturday. It is mandatory for the private labs to send a copy of the reports to the state health department also gone to the UP government health department, and we were pleasantly surprised to see how the SoPs clicked into place. 

On Monday morning a young government doctor visited us to collect first-hand data, to check if home-isolation was being strictly followed, and to hand over free kits of medicines. A team was sent across to spray and disinfect the apartment tower and, for the next week, we got at least one call a day from the 'Central Covid Control Room' to check if the infection had aggravated in any way. Thankfully, it did not. The infection was as mild as it could be - fever for a day, a sore-throat for two.

As per the new guidelines, at the end of a seven-day isolation period, it is no longer mandatory to take another RTPCR test but we  got tests done anyway using the new Rapid Antigen Tests that were now easily available on Amazon. Interestingly, these tests were no longer being imported from Germany, South Korea or China but made locally by a company called MyLab and sold for just INR 250 (~ USD 3.5) each. Clearly a lot of thought has gone into the design and production of these kits, each of which contains a sterile swab, a pre-filled extraction tube, test-card, instruction manual (English/Hindi) and a disposal pouch. 

One of these days I hope to understand more about the kind of technology and production systems that it takes to prototype and scale up production of these kits ("with immunochromatographic nitrocellulose assay...which uses highly sensitive antibodies to detect Covid-19 nucleocapsid proteins.."), to the current levels of 10 million sets per week!

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REFERENCES & LINKS

* https://www.cnbc.com/2021/07/23/coronavirus-how-india-is-doing-now-after-delta-variant-spread.html

* MyLab - wiki - https://en.wikipedia.org/wiki/Mylab_Discovery_Solutions#cite_note-1

* Pune start-up makes affordable, accessible Covid-19 test kit (March 2020) - https://www.financialexpress.com/lifestyle/health/pune-start-up-makes-affordable-accessible-covid-19-test-kit/1908524/

* Producing 10 million kits per week - https://www.reuters.com/business/healthcare-pharmaceuticals/indias-mylab-can-ramp-up-covid-19-test-production-100-mln-units-per-week-ceo-2021-05-21/

R-Value and it's Covid Travails

SARS-Cov-2 aka Covid-19, the virus behind the current pandemic continues to be a nightmare for everybody - especially for statisticians. 

It was bad enough to have the Chinese obfuscating the truth about the original 'Wuhan virus' last year, but now we have a range of mutants (and double-mutants) that seem to be spreading in ways that are difficult to predict. This is is making the work of those who prepare statistical models much more difficult, and this in turn is affecting the quality of decisions being taken by policymakers.

Take for instance, the reproductive-value or R-Value for Covid-19. R is the number of people that one infected person will pass on a virus. 

The lowest possible R-Value is R-naught or R0. Also referred to as the Basic Reproduction Number, it is the R-value of a population that is assumed to have zero immunity against a new infection. R0 is the division of the number of new infections by the number of existing infections, or the average number of new infections over an infectious period (R0= new infections/existing infections).

Measles has an R number of 15 in populations without immunity. It means that, on average, every 10 people with Measles will infect 15 other people. For Covid-19, the latest R-value estimate for India, is around 1.30. This number is showing wide variations across states with Uttar Pradesh recording the highest infection value at 1.62, followed by Andhra Pradesh at 1.61.

The problem with the R-Value is that it gives us a picture of the past - by the time you calculate it, the number is already outdated. This is because it is based on data recorded on hospitalisations and death figures to get a sense of how many people have the virus – but the problem with this is that, since the virus’s incubation period is so long, it only gives an accurate picture of a few weeks ago.

Add to this the complications coming from recent mutations of the virus in different parts of the world, each with its own incubation period - the "UK" B.1.1.7; the "South Africa" B.1.351; "Brazil" P1, "India" variants B.1.36 (Bangalore) / B.1.1.7 (Punjab) and B.1.617 which contains two specific mutations - E484Q and L452R which is capable of 'immune escape', and infecting those who have already been vaccinated. 

Add to all this other newer emerging variants of concern (VoCs) and we have all ingredients for a statisticians' perfect nightmare. 

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LINKS & REFERENCES

* https://www.bbc.com/news/health-52473523

* https://theprint.in/health/indias-covid-r-value-increases-to-1-30-this-week-the-highest-since-april-2020/633783/

* https://www.weforum.org/agenda/2020/05/covid-19-what-is-the-r-number/

* https://www.statista.com/statistics/1101713/india-covid-19-cases-by-type/

* R0 Explained - https://indianexpress.com/article/explained/coronavirus-r0-reproduction-number-explained-6354339/

Covid Shielded

The lady who helps us with the housework is from a remote coastal village in West Bengal. Yesterday she got a call from her parents and the news was that they were both suffering from fever. A few thousand kilometres away, near the capital city, we too were afflicted by the same symptoms - the expected after-effects of a vaccination national drive against Covid-19. 

We were among the four million+ people who got vaccinated in India today. While the fever and the dull pain of an intramuscular injection abates, it is quite amazing to think of superlative effort that has gone into creating, testing and delivering these vaccines all over the world.

The vaccination program started its rollout in India couple of months ago. First for those over 65 years of age, and for those who were vulnerable due to 'co-morbidities'. At first people were wary, and senior citizens had to be coaxed and cajoled to the vaccination centres. This changed on 1 April 2021 when the government decided to expand the coverage to those over 45 years of age.

The sheer scale of this effort does not hit you until you participate in it. It is a four step process is driven by information technology in which each dose can be traced back to a specific vial at a specific vaccination centre:

(1) Registration at CoWIN site - a single phone can be used to make four bookings at either government 

(2) Selecting a vaccination centre - Based on your postal PIN code you can opt for either the nearest government centres (free of charge) or private hospitals / clinics (fixed at INR 250) 

(3) Vaccination - At the hospitals a queuing system ensures that people maintain social distance. Each vaccine station has three staff  - two for writing out the registration details, one  for preparing the vaccination card, one for checking the CoWIN id, uploading the confirmations online, and a nurse who administers the vaccine. The whole process takes about 8 minutes. After the jabs people are expected to wait for 30 minutes of observation before returning home. 

(4) Certificate - within a few minutes of getting vaccinated an SMS message leads you to an online certificate (PDF) which can be used as proof while travelling.

(4) Follow-up - each vaccinated person is given a card which specifies the vaccine type (Covidshield / Covaxin), the date for the second dose (min. 28 days), emergency helpline numbers and a list of five possible after effects (mild fever, pain and swelling, etc.,)

One thing I have learnt along the way is that the government machinery seems to be far more efficient than the private sector. In my immediate neighbourhood all the hospitals were booked until 14 April, so I expanded the generic Noida PIN code and booked two slots on 1 April at Metro Hospital from a list of about 10 hospitals. 

However my experience at Metro Hospital left me quite disappointed. It is a large hospital in Sector-11 Noida. When I found my way to the entrance the staff seemed paralysed by chaos - there were over a 100 angry, impatient people already crowding inside, with the guards telling the newcomers that they would need to wait for three hours!

I went back to the CoWIN site and got my appointment rescheduled to the  next day at the District Combined Hospital, a government facility in Sector 30. Over here the whole process was a breeze. There was ample parking outside; masks, hand sanitisers and social distancing was compulsory; tokens were being distributed at the main gate and security guards were systematically guiding people through waiting halls while giving priority to the elderly and infirm.

Millions of tiny vials from Oxford-AstraZeneca / Serum Institute of India, Sputnik and J&J have now set out to deal with a virus from China that had the world paralysed for more than a year. Hope is in the air, and in our blood streams.

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LINKS & REFERENCES:

https://www.livemint.com/news/india/covid19-vaccination-over-36-lakh-people-get-the-jab-on-april-1-the-highest-so-far-11617335903675.html

https://www.bbc.com/news/world-asia-india-55748124 - Covishield and Covaxin: What we know about India's Covid-19 vaccines

On the remarkable role being played by Co-WIN and its developers (19 April 2020, Indian Express) - https://indianexpress.com/article/india/co-win-platform-coromnavirus-vaccine-india-modi-govt-7279432/