Goa faces danger from novel triple mutant


Nandkumar M Kamat

At present the government has no idea about the different variants of SARS-COV-2 infecting the people. Due to movement of people from the locations such as West Bengal, Chhattisgarh, New Delhi and Maharashtra, having the presence of what is known as the new SARS-COV-2 strain, a ‘triple mutant’, Goa now faces another danger of ‘third wave’ anytime from middle of May to June, 2021.

At the time of writing this article on April 23, Goa had witnessed a disastrous week with total number of active cases crossing 10,000 and number of deaths reaching almost 1000. The test positivity rate (TPR) which gives an idea of extent and magnitude of the community transmission varied between 28 to 36 per cent.

On May 19 last year there were only 46 cases and no deaths but then we saw active cases rising to 166 on June 4, and 705 on June 19, when the first death was reported. The time series of morbidity and mortality shows that we had 1,576 cases and four deaths on July 3, 5,913 cases and 45 deaths on July 31. The caseload had reached 10,494 on August 13 last year with 91 deaths and once again Goa is pushed back to that situation.

If we see the progress of the pandemic month wise from August, 2020 then we get 11,748 total cases and 192 deaths on August 31, 33,418 cases and 428 deaths on September 30. On October 31, Goa had 43,626 cases and 604 deaths, on November 30, the total cases touched 47,963 and 688 deaths had occurred.

People thought that from November onwards the severity of the pandemic was diminishing. This was noticed in 51,066 total cases on December 31 and 739 deaths indicating an increase of only 3,103 new cases during December and 51 additional deaths. During the same period elsewhere in the country a ‘double mutant’ was evolving. Today we know it as B 1 L452R, E484Q because of the double mutations. It evades the immune system and the vaccines are not very effective against it.

As Goa entered the New Year, things were looking cheerful. On January 28, Goa met the WHO benchmark of below five TPR for 14 consecutive days. On January 31, the total cases stood at 53,409 with 768 deaths indicating addition of 2,343 new cases and 29 new deaths which pointed to Goa moving to attain a steady state which is a sign of end of the pandemic. On February 28, the total cases slowly increased to 54,986 and deaths touched 795. February 23 was the best day in the progress of the pandemic with the total number of active cases declining sharply to just 464.

It appears that certain variants entered Goa between February 15 to March 15, 2021 and now the state is taken over by these infectious novel variants. On March 31, the total cases reached 58,039 and deaths touched 830. Even then the increase was not very alarming.

But the real spikes began in April. The data in hand up to April 22 shows the infectivity of the novel variants circulating in the population. As compared to March 31, 2021, on April 22 total new cases increased by a phenomenal 14,185 and the number of deaths increased by 134. If this is the infectivity and lethality of the novel variants including the main culprit, the highly infectious double mutant. What will happen when the more potent ‘triple mutant’ enters Goa? The ‘triple mutant variant’ is formed when three mutations of a virus combine to form a new variant. In this new triple mutant, we have:

A deletion and two changes in spike protein.

Deletion of H146 and Y145.

Mutation in E484K and D614G in spike protein.

The ‘triple mutant variant’ is the second lineage of SARS-CoV-2 virus to be identified in India. It is being called B.1.618 and is mostly circulating in West Bengal. This is different from the ‘double mutant variant’ detected and named as B.1.617.

So far, we know about only four variants of COVID-19 as we haven’t heard about genomic sequencing of other samples. Just four out of 3611 samples to be sent and if 15 samples are already sent it’s just 0.14 per cent of genomic sequencing actually needed. The local variants circulating and detected in March 2021 are: B.1.1.7, B.1.36, B.1 L452R, E484Q and B.1.1.464.

A US government interagency group developed a Variant Classification scheme that defines three classes of SARS-CoV-2 variants: Variant of Interest (VOI), Variant of Concern (VOC) and Variant of High Consequence (VHC). Goa has so far two VOCs, two VOI and no VHCs.

It is possible to prevent entry of B.1.168 by genomic surveillance at border entry points. The following precautions are required:

Strict control of people entering Goa by road and railway, from states which have reported Bengal strain B.1.168, particularly any visitors from West Bengal, New Delhi, Chhattisgarh and Maharashtra.

If they enter with symptoms all such RT PCR Positive samples to be sent for genomic sequencing to check presence or absence of the B.1.618.

All travellers tested positive for B.1.618 to be quarantined and regularly monitored

Vaccine producers to be requested to conduct neutralisation tests in the lab to check if any existing vaccine is effective against B.1.618

If this produces good results, existing vaccines can be tweaked to stop B.1.618 and booster doses can be given once available.

We need to dread the ‘triple mutant’ entering Goa and possibly create a third wave in coming months. It should be prevented right now