TNM spoke to three experts to find out.

A man in PPE suit is sanitising a bus in Bengaluru which stands on the other side of a barricade
news Coronavirus Saturday, April 17, 2021 - 14:55

In a span of 11 weeks, Karnataka went from 5917 active COVID-19 cases on February 4 to 96,561 as of April 15. That’s a whopping 1531% rise in infections, as the test positivity rate went from 0.62% to 11.38%. The bulk of these coronavirus virus cases have come from Bengaluru, which went from recording 263 new COVID-19 cases on February 4 to an all-time daily high of 10,497 infections on April 15. Bengaluru’s test positivity rate has soared from 0.80% to 13.65% 

So, what explains this massive spike in infections in Karnataka and in particular Bengaluru? Are variants of the SARS-CoV-2 virus, which causes COVID-19, to blame for the surge, and if so which are the ones circulating in the city?  

A study by NIMHANS that was published in medRxiv, the pre-print server, in March found that out of 176 samples processed for genomic sequencing, 34 new lineages or sub-types of SARS-CoV 2 were circulating in Bengaluru between November 22, 2020 and January 31, 2021. The study had sequenced genomes from 73 international travellers arriving in Karnataka and from 103 local COVID-19 cases in Bengaluru. The B.1.1.7 variant, which was first identified in the UK, was the major lineage imported into the state, detected in 32.9% of samples processed, stated the paper. The study did not detect variants that were first reported from Brazil (P.1/B.1.1.28) and South Africa (B.1.351).

One of the key findings of the NIMHANS study was the detection of the B.1.36 variant, in  27.4% of the ‘imported’ samples processed. NIMHANS notes that the B.1.36 variant was first reported in Saudi Arabia in February 2020. Since then, it has been reported in several countries including Canada, UK and Denmark, besides India. 

Significantly, the same B.1.36 variant was also the dominant variant circulating in Bengaluru, detected in 43.7% local samples sequenced . “The lineage B.1.1.7 (a.k.a the UK variant) was the major lineage imported into the state (24/73, 32.9%), followed by B.1.36 (20/73, 27.4%) and B.1 (14/73, 19.2%). We identified B.1.36 (45/103; 43.7%), B.1 (26/103; 25.2%), B.1.1.74 (5/103; 4.9%) and B.1.468 (4/103; 3.9%) as the major variants circulating in Bengaluru city,” states the study.  

Researchers also found that a COVID-19 cluster in a Bengaluru college “was driven by related viruses belonging to the B.1.36 lineage”. 

B.1.36 variant and the Bengaluru surge 

Worldover much of the focus has been on the variants first identified in the UK, South Africa and Brazil, and more recently the double mutant variant (B.1.617) found in Maharashtra. Questions have been raised on their increased infectivity and whether these new strains are responsible for COVID-19 surges in many places. Similarly, could the B.1.36 variant be blamed for Bengaluru and Karnataka’s alarming spike in cases? TNM spokes to three experts to find out. 

Dr V Ravi, a virologist and the nodal officer for genomic confirmation of SARS-CoV-2 in Karnataka, who was also one of the authors of the NIMHANS study, says that it is very difficult to say based on one study if the present surge is on account of the B.1.36 variant. Noting that the B.1.36 variant is replacing the circulating strains not just in Bengaluru but in other districts as well, he points out that there are other variants also circulating in the city and in Karnataka. 

“Variants when they emerge, they will slowly take over. This B.1.36 is found in Andhra, Telangana, Kerala and other states. In Maharashtra, the double mutant strain is slowly taking over. That is because of super spreading events that have occurred in February. You have to trace back events to February,” Dr Ravi explains, adding, “What you have to understand is the increase in spread, mutants may be one of the ingredients. But the larger ingredients are crowds, rallies, elections, and closed spaces. It’s now not like the lockdown period where everything was controlled in a phased manner. It is true of the entire country, not just Karnataka.”  

“We human beings are very peculiar. We would like to find excuses for spreading the virus,” Dr Ravi notes.  

Gautam Menon, Professor of Physics and Biology at Ashoka University and Dr Giridhara Babu, an epidemiologist at the Public Health Foundation of India and a member of the Karnataka COVID-19 Technical Advisory Committee also say that the B.1.36 variant may only part explain the sharp rise in cases.  

“We need to know how cases associated with this variant have increased in time, displacing the original strain as well as other variants. There is some evidence that this variant  is present in a good fraction  of samples, but perhaps insufficient to say whether this variant is driving the spike in cases,” says Gautam Menon. 

Dr Babu says more genome sequencing will have to be carried out to prove if the B.1.36 variant is driving the spike. “In that only a part of the surge can be explained by that. Now if you were to do more cluster investigations. For example, there are 100 clusters, and you have investigated five of them. And in those five you have done genome sequencing, and then you have done genome sequencing for the contacts of the primary cases and then we would have done some in vitro testing to find out how infectious these are. We are reduced to guessing that there might be more variants but neither can it be proved nor can it be disproved,” he observes. 

But what explains the regional differences in variants? More than 60% of genome samples in Maharashtra belonged to the ‘double mutant’ variant, while in Punjab the variant first identified in the UK was found in 80% of COVID-19 cases

Gautam Menon says, “Mutations occur at random, so there is no particular surprise in that some variants are dominant in some places while others are in other places. However, with time, since people travel, one would expect to see a broader spread of these variants. We would also expect the more transmissible variants to replace the less transmissible ones. Only careful genetic epidemiology will yield the answers to these questions.”

The emergence of new variants depends on the proportion of susceptible people, explains Dr Babu. Once an infection is introduced in the population as a result of the variants, it spreads like fire, he says, and as consequence each region may have a different variant. “The second reason is more the circulation, more the viral replication and more the viral replication, more will be the errors in the genetic makeup (of the virus).Some of these mutations will lead to change in proteins and some of these will become new variants of concern,” the epidemiologist says, adding the only way to prevent the emergence of newer variants is by immediately curbing the high transmission.    

Observing that it is in the nature of the virus to mutate and spread, Dr Ravi emphasises the importance of COVID-appropriate behaviour among people. “Today it is B.1.36, tomorrow it will be something else, day after tomorrow it will be something else. Unless we change our behaviour, we can’t outsmart the virus without masks and crowding. Till a large proportion of the country is immunised, only then you will prevent infections,” he says. 

But are vaccines effective against newer variants? 

Dr Babu says vaccines should be tested against these variants to know how effective they are. “Then we should be developing the next generation vaccines built on these isolates,” he says. 

“We don't know, for any of the Indian variants. There have been some suggestions that the efficacy of some vaccines is reduced against the Brazil variant. This is an argument for having a larger basket of vaccines, so that at least some will continue to work as variants emerge,” explains Gautam Menon. 

Dr Ravi, who is also a member of the scientific advisory board for the Sputnik V vaccine, however, says, “All vaccines are effective against variants with varying degrees of proportion. But all vaccines guarantee protection against severe disease and death. No vaccine guarantees prevention. We don’t have a vaccine anywhere in the world that can stop transmission.” 

The way forward 

And given some variants are associated with increased infectivity, should governments be changing their strategy when it comes to the fight against COVID-19 and its variants?  

“The strategy is the same. Mutant or no mutant. We know masking, social distancing everything works. So it is important from a research and scientific perspective to see mutants are emerging. But that does not in any way alter the precautions people have to take - whether it is the Wuhan virus, or UK variant or whether it is B.1.36. It is the same,” says Dr Ravi. 

Dr Giridhara Babu also reiterates that the strategy remains unchanged as far as public action goes. But says that genome sequencing, as mandated by the Government of India in December, will help understand and limit the spread of newer variants. Gautam Menon adds, “One important thing to do would be to understand the clinical implications of being infected by specific variants. For example, does being infected with B.1.36 or the Maharashtra variant lead to more severe disease or, perhaps, less. To do this, genomic and clinical data must be correlated.”

Genome sequencing in India, however, is inadequate. Dr Ravi says, “INSACOG (Indian SARS-CoV-2Genomic Consortia) has sequenced more than close to 14,000 samples. Sequencing is an enormously resource intensive exercise. It is not PCR. Sequencing is a highly intensive job. And it takes five to seven days to sequence one sample or 96 samples. It takes that much time. After that one has to match it with a parent. Bioinformatics takes time. That’s why INSACOG has set a turnaround time of 10-14 days for a sample. By that time, a lot of spread would have occurred. My only  appeal is that variants are important but they do not explain the current surge. We need to understand that unless people are careful, this will continue.” 

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