More Infectious Variant Of COVID-19 In Goa

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Nandkumar M Kamat

Goa does not have a scientific knowledge based pandemic exit strategy. There is no “second wave” attributable to the original Wuhan strain in Goa but it could be just an unrecognised “first wave” by a novel summer ready Covid-19 variant. What this means is something very dreadful- the expected seasonal behaviour of Covid-19 here shows that the “third wave” adapted to highly humid monsoon conditions would also follow from June and may last till October 2021. Then the “fourth” and “fifth” waves may follow- each representing a different consortium of highly infectious Covid-19 variants.

There is nothing to panic because despite rising infections the mortality hereafter would be less. Mass adult vaccination may aid in reducing the deaths. Almost one million people may get tested with RT PCR by the end of this year.

However, from purely the angle of molecular ecology and biology of Covid-19, I find that the present strategy of Goa government to contain and manage the pandemic is scientifically completely faulted. Would the government tell us whether the “second wave” in the state they are claiming is caused by the original virus from Wuhan (WIV 04-reference or hCoV-19/Wuhan/WIV04/2019) which was sequenced on January 10, 2020? Or is it some novel variant and if it is a novel variant then whether it is identical to similar ones found in other states in India?

The Government of India established in December 2020 a new country-wide consortium named INSACOG to identify new and circulating variants by genome sequencing across multiple states. One of the main goals of this consortium is to sequence 5 percent of all COVID-19 positive cases in the country. We would like to know what the Goa government has done to take help of INSACOG in the past three months?

A knowledge-based approach would have demanded the Goa government to identify, select and send five per cent or about 2500- 3000 samples from about 59 thousand positive cases to INSACOG. But we are told that not even 50 Covid positive swab samples have been sent and reports are yet to be received. The precise information the citizens need to ask the government before rushing to get the vaccine is –please tell us what we are likely to be infected with, because none of the fast-tracked vaccines is effective against all the variants. But some of the vaccines can create some immunogenicity for some time and are never lifelong. Booster doses would be required every year.

The government and the medical community just cannot dismiss the importance of precise molecular identification of local Covid-19 genotypes and serotypes in association INSACOG. Is it correct to rush and push the educated people of Goa to get vaccinated to meet a numerical target without having in hand precise knowledge of antigenic drift of Covid-19 in
the state?

All the advanced countries opting for mass adult immunization have the knowledge of Covid-19 variants infecting their citizens. The so-called “herd immunity” against fast mutating Covid-19 is a wonderful illusion. Human civilization can never dream to build “herd immunity” against all the strains of mutating RNA viruses. This pandemic is forcing all the governments to continue to buy time so that health facilities do not collapse. The adult mass vaccination is part of the WHO driven global normal pandemic exit strategy. A novel more infectious variant, possibly adapted to local temperature, humidity and host biotypes may be the real cause of the spurt in infections in Goa after 23 February 2021. It is not just a “second wave” but it may be the beginning of the first of the many subsequent waves to be produced by a novel Covid-19 variant each time. But the government in absence of a local virology research centre and full-fledged modern Biosafety level IV virological laboratory (despite clinical history of 200 different types of viruses infecting humans and animals locally) is taking the people and even the scientific and teaching community for a long ride.

Government may buy two more expensive RT PCR machines by spending nearly Rs 6-10 crores. This is good and proves that there is no shortage of funds. As per the national policy Goa government needs to send five percent of Covid19 positive swab samples for genomic sequencing and molecular identification of the strain. But the Goa government has procrastinated for more than a year to create a fully knowledge based informed strategy requiring precise molecular identification of the strains which have infected nearly 59 thousand people so far. Even from Goa University when microbiological cultures are sent to central government laboratories or private service providers, we get the precise molecular identification in maximum 15 days. And each identification costs less than Rs 5000. No doubt NGS or (Next Generation sequencing) of Covid-19 variants is expensive but with just one time investment of Rs. 4-5 crores Goa government by now could have got more than 2500 samples identified. Such a molecular knowledge database would have made a huge difference immunologically, epidemiologically, and clinically. RNA viruses do not need RNA to infect us. They attack the specific receptors on host cell surfaces they invade. The Spike protein encoded by the S gene of Covid-19 has a receptor-binding domain specifically evolved to bind to the human angiotensin-converting enzyme-2 (ACE2) receptor found on the surface of many human cells, including those of the nasal cavity, lungs, kidneys, intestines, brain, heart, and blood vessels. RT PCR tests are not based on detection of any such coat proteins. Precise viral proteomics studies are needed to even detect the changes in coat proteins. These RT PCR probes used by GMC and other labs are based on the evolutionarily the most conserved region of the novel Coronavirus. RT PCR tests for Covid-19 only tell you whether you have a viral RNA in your sample which has a region identical to the reference strain of Covid-19. RT PCR tests are blind to novel variants.

There were no Covid-19 positive patients in Goa till March 24, 2020. On February 23 this year, Goa had just 464 Covid19 positive cases and now active cases have touched almost 2000. Instead of thinking in a standard “business as usual” linear fashion, the top health authorities of the state need to immediately work on the possibility that each sustained spike in new positive cases lasting over several weeks could be due to a locally adapted but more infectious novel variant of Covid-19. Government must not play with data by selectively disclosing sequencing information on old 2020 samples. We need sequencing of RNA from Covid-19 positive samples specifically from March 2021 positive cases to verify if current spikes are due to a “summer variant of Covid-19”. Only such rational, objective, knowledge based, and transparent scientific approaches would lead to a sound pandemic exit strategy.