Has India Failed in Detecting the Double Mutant Covid Spread?

India is now the second worst hit nation after the US due to Covid crisis but it seems the country has failed in its efforts to find the new strains of coronavirus that are creating havocs across the globe, especially when the fourth deadlier strain of coronavirus or the double mutant coronavirus is a homegrown version. The other three deadlier mutants are UK variant, South African variant and Brazilian variant.

National Virology Centre, Pune, in genome sequencing analysis of 361 test samples from Maharashtra has found that the coronavirus double mutant was the main reason behind Covid-19 spread. 220 or 61% samples out of 361 samples confirmed presence of coronavirus double mutant or the coronavirus lineage now known as B.1.617.

NIV finding only corroborates what Maharashtra has been saying for long. Maharashtra’s health minister Rajesh Tope had recently said that his state suspected that a new strain or variant of coronavirus was spreading fast and took a shorter time to affect people. Maharashtra sent test samples to the National Centre for Disease Control to confirm this scientifically.

The new findings add to the previous data about coronavirus double mutant in Maharashtra, the state that is now recording over 50,000 cases daily in the second wave of Covid and carries around half of India’s active caseload burden. Between January and March, Maharashtra saw a growth of 15-20% of double mutant coronavirus samples. Two mutations found in the virus, E4840 and L452R, did not match with any VoCs previously catalogued.

‘Double mutant’ Covid variant means two mutations together in single virus, that if happened to a lethal virus part like spike protein, which the virus uses to infect a human cell, may make virus more infectious and deadlier. It changes the shape of the virus and help it escape the immune system as antibodies can’t recognize it. E484Q and L452 both are such escape mutations found in the double mutant’. Though less lethal, these mutations are more infectious and highly transmissible.

But India, so far, has not accepted that the recent surge in COVID cases in Maharashtra might be driven by the new coronavirus double mutant. The slow pace of genome sequencing analysis in the country might be the main reason behind it. While UK and the US have large scale investment and infrastructure behind coronavirus genome sequencing analysis and they started much before India, the country that is the leading producer and supplier of the Covid vaccine, is still a slow mover on this front.

The result, UK and the US contribute to around 65% of the coronavirus variant genome sequencing data while India’s contribution is negligible.

On December 30, India announced to establish the Indian SARS-CoV-2 Consortium on Genomics (INSACOG) to find new mutants or variants of concern (VoC) of coronavirus after mutant coronavirus strains were detected in many people coming to India from abroad. INSACOG is a network of 10 National Laboratories to analyze genomic sequence of the coronavirus to find out deadlier mutants or VoCs.

While launching INSACOG, Central Government assured to analyze 5% positive test sample from each state and 100% positive test samples from international travelers for genome sequencing to find out VoCs yet by March 30, the could analyze just 11,000 samples, or one-tenth of 5% target assured to the states.

On March 24, the Central Government announced detection of double mutant coronavirus but said the Maharashtra surge was not linked to it. The argument was, the number of such mutations were very small and so the new strain could not be behind the rapid surge in some states. Centre also said that more studies were needed.

The new strain was found in seven states but was mostly limited to the state of Maharashtra with 206 test samples showing its presence. Delhi was number two with nine positive samples for the double mutant. By March 24, 10,787 positive samples were analyzed which saw just a slight increase to 11064 samples on March 30 when the data was last released. Other mutant variants found in 18 states were 807 UK variants, 47 South African variants and one Brazilian variant.

Evolution of different genomic variants of viruses or mutants is a natural phenomenon. They evolve or mutate more rapidly when there is a greater and wider surge in inflections, something that is now the case in India where cases are increasing exponentially, and so the country need to act swiftly to the find out VoCs like the double mutant virus. India still sequences less than 1% of the coronavirus test samples in the country.

Coronavirus double mutant or B.1.617 has been detected in many Maharashtra districts – Akola, Thane, Aurangabad, Mumbai, Jalna, Palghar, Nanded, Amravati, Bhandara, Hingoli, Gondia, Chandrapur, Nagpur, Pune, Wardha and Yavatmal and Amaravati and Akola were the most hard hit districts. B.1.617 was found in 69% test samples of Amaravati and 85% test samples of Akola in the Vidarbha region of the district. Rapid surge in Amaravati saw a two-week lockdown in February-March and increased restrictions in Akola to break the virus chain of transmission. AIIMS Director Randeep Guleria in an interview corroborated that the new strain in Amaravati and Akola was highly transmissible and dangerous.

Many states and health officials are now demanding that more focus should be on identifying VoCs. They demand that genome sequencing analysis of more test samples should now be done on a bigger scale and results should be given as soon as possible, within three days as said by Dr Om Srivastava, member of the Maharashtra Covid Task Force. B.1.617 is the perfect example of this desperation. The strain was first detected on December 7, Centre confirmed it on March 24 but added that more time is needed to study the double mutant virus further.

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