27 June,2021 09:03 AM IST | Mumbai | Jane Borges
Additional BMC commissioner Suresh Kakani says Mumbai saw one Delta Plus case in the eastern suburbs in April. Sixteen close contacts of the female patient were traced. Pic/Suresh Karkera
It was nagging suspicion which compelled Mrunmai Joshi, district collector and magistrate, Palakkad, Kerala, to send a sample for genome testing last month. Somewhere around the end of April this year, the villages of Parali and Pirayiri, which fall under her jurisdiction, saw an "intense rise" in Coronavirus cases. After one person had contracted the virus, there seemed to be, what she describes a "chain reaction," with entire clusters getting infected. It was a cue for her team to begin work on war footing. "All the primary contacts of the infected individuals were traced, and isolated. Over time, everyone turned negative. But, these panchayats continued to be on our radar."
Last week, when the results of the genome surveillance came back, Joshi's hunch proved to be correct. Of the three reported cases of the new COVID-19 Delta Plus variant, two were from these villages.
While Pirayiri has a population of 42,000-plus, Parali is home to 35,000 residents. Both the villages have been sealed with immediate effect. "They are in complete lockdown," says Joshi, adding that the perimeters have also been secured. "We have cordoned off both these panchayats, and only essential movement is being allowed inside."
Joshi insists that there is no reason to panic, for now at least. "The test positivity rate (TPR) in these villages is more or less under control. We are taking these measures for precaution, so that people don't let their guard down."
The recently-identified Delta Plus is a mutant version of the COVID-19 Delta or the B.1.617.2 strain, which was the dominant strain identified in India starting October 2020, and responsible for the high case-load in the devastating second wave that hit India in April.
With cases of Delta Plus being identified in Maharashtra, Kerala, and Madhya Pradesh, last week, the Union Ministry of Health and Family Welfare (MoHFW) labelled Delta Plus as a "variant of concern," advising all three states to ramp up COVID-appropriate measures in the affected districts.
Of the 48 identified cases in India, Maharashtra has reported 21. Of these, nine were reported in Ratnagiri, seven in Jalgaon, and one case each in Mumbai, Navi Mumbai, Palghar, Thane and the Sindhudurg districts. An 80-year-old from Ratnagiri recently succumbed to the Delta Plus variant. The situation has forced the Maharashtra government to rethink its unlock plan, currently based on the availability of oxygenated beds and test positivity rate.
While the new orders came in last night with instructions that all restrictions will remain at a level not below 3, CM Uddhav Thackeray has already asked district collectors in the seven-odd districts, where the cases have been identified, to impose strict curbs keeping the risk factors of the new strain in mind. The health department too, is stepping up oxygen production to 3,000 MT a day, and working to increase the number of ICU beds across the state, in the likelihood of a sudden surge in cases.
Dr Subhash Salunkhe, advisor to the Maharashtra government on COVID-19 management, who described the Delta Plus mutation of the COVID-19 virus as "peculiar" in comparison to other viruses, says that these interventions are urgent and imminent, until experts are able to ascertain the transmissibility of Delta Plus. "Action needs to be taken at all levels, not just in the area where the mutant is presently seen. Contact tracing, finding the primary and secondary cases, is crucial. We also need to be prepared if the mutated virus has a virulent side," said Dr Salunkhe.
At this point in time, at least, the scientific community doesn't have sufficient data to determine how "virulent and transmissible" the Delta Plus strain is. Besides India, the variant, also known as AY.1, has been found in the US, UK, Portugal, Switzerland, Japan, Poland, Nepal, China and Russia. On the other hand, the
Delta variant, which was first identified in India, is now present in 80 countries.
Indian SARS-CoV-2 Genomic Consortia (INSACOG), the forum set up under the Ministry of Health and Family Welfare by the Government of India in December 2020, to study and monitor genome sequencing and virus variation of circulating strains of COVID-19 in India, warned that the variant had concerning characteristics. It's said to be more transmissible, binds more easily to lung cells and is potentially resistant to monoclonal antibody response, which means that therapy to enlist natural immune system to neutralise the virus, might not be effective enough.
A one-of-its-kind study on the SARS-CoV-2 Delta variant of concern (VOC) in Scotland, published in The Lancet on June 14, stated that the Delta variant doubled the risk of hospitalisation compared with Alpha, the previously dominant variant in Britain. "The risk of admission particularly increased in those with five or more relevant comorbidities," the study led by Aziz Sheikh, Jim McMenamin, Bob Taylor and Chris Robertson, on behalf of the Public Health Scotland and the EAVE II Collaborators, stated.
Professor Sheikh, Director of the Usher Institute, The University of Edinburgh, says that while his study focused on the Alpha VOC and Delta VOC, the latest Delta Plus, appears to be a mutation in the spike protein again. "And it's the spike protein, which is then responsible both for transmissibility of the virus, and virulence."
Describing the virulence or harmfulness of the Delta VOC, he says, in April this year, Scotland had virtually no cases of the variant, which was first found in India. "But within three weeks, it became the dominant form. So by May 19, more than half of the cases [in Scotland] were of Delta VOC, and now, [the variant is responsible for] most of the cases in Scotland and England. Delta can take hold very rapidly," says Sheikh.
According to Dr Om Shrivastav, infectious diseases expert and a member of the Maharashtra COVID-19 task force, when investigating symptoms of the COVID-19 Delta VOC, some novel findings had emerged. Apart from being highly transmissible, the classical symptoms of the Delta variant were also different from those associated with COVID-19. "Both doctors and people need to be aware of it," says Dr Shrivastav.
Where cough, shortness of breath, body pain, headache, sore throat, and loss of taste or smell are common COVID-19 symptoms, pain in the abdomen, nausea, vomiting and diarrhoea were seen among those with the Delta infection. While it's too early in the day to predict the representation of the Delta Plus variant, experts feel that it won't be too far removed from what they've seen with the Delta infection till now.
Earlier this week, leading virologist Dr Gagandeep Kang in an interview to the BBC had maintained that "there is no data yet to support the variant of concern claim," being made by the Indian health ministry.
Epidemiologist Giridara Gopal Parameswaran, who is also the lead at the India COVID Apex Research Team (iCART), a volunteer research and development group, which comprises professionals and students from multiple fields, agrees. He says that "robust surveillance" would be required to determine if Delta Plus is a variant of concern.
"Since COVID-19 is an RNA virus, its natural property is to mutate and change with time. So, the concern here is not as much about it mutating rapidly, but whether the mutation is making the virus more virulent or dangerous," says Parameswaran, adding that this can only be possible, if there's specific testing of individuals who are infected with these variants. "We don't have this kind of granular data available at the moment."
Putting it down in numbers, he says, that though Delta was identified as a dominant strain in India, this was determined on the basis of the very "few samples, which were fortunate enough to go in for genomic surveillance". "As of now, around 25,000 to 30,000 samples have been tested for genomic surveillance. When you compare that with the 2 crore-odd infections we have had [in India], it's roughly 0.1 per cent of the total cases. This [sample size] is definitely not sufficient to predict whether a variant is increasing or is of concern," adds Parameswaran.
What we need right now is real-time genomic testing, says Dr Khusrav Bhajan, intensivist at PD Hinduja Hospital and member of the State Task Force. "We need more genomic and clinical studies to know Delta Plus's infectivity, virulence, its effect on vaccine escape and antibody cocktail therapy."
Genomic testing is what helped the UK understand the Delta VOC better, says Sheikh. "We are in a very fortunate position here, because there's a lot of sequencing going on. The more we can do this, the more we can understand, which variant is driving, taking hold, or not so involved [in the spread of the virus]. That requires developing infrastructure abilities, on priority. And, I think everyone needs to really try and develop their sequencing capacity." The challenge, feels Sheikh, with a country like India, is its population size. "Eventually, this is about numbers, and we should be able to generate the answer within weeks. The longer the delays, the more difficult it is going to be to catch-up with the variants."
Nearly 400 km from Mumbai, in Jalgaon district in northern Maharashtra, work is already underway to trace, test and isolate suspected patients. Jalgaon, along with Ratnagiri, reported most number of the Delta Plus cases in Maharashtra.
"All the cases were reported from one single village in the rural block of Jalgaon in May," says Abhijit Raut, collector of Jalgaon, adding that as per protocol, he wouldn't be able to disclose the name of the place.
The seven people who tested positive for the Delta Plus variant were related to each other, and had not taken a single dose of the vaccine when they contracted the infection. Raut learnt that they had the variant only two weeks ago. "We usually send a set of 100 random samples each month for genomic testing. As far as I know, the Delta Plus variant was seen in 21 of the 7,500 samples from the state," he adds in a telephonic interview.
"By then, all the seven people had recovered, and tested negative for COVID-19. Even when they had the infection, all seven were either asymptomatic or mildly symptomatic, and did not require any hospitalisation," he adds.
Though the results have come a month too late, the entire local machinery is working overtime to test and collect more samples from the village. "We have already conducted a mass screening of the village to find out if there is something different from the rest of the district. But, the TPR was matching that of the district's, which is 1.2 per cent. We also investigated the village's history to understand how badly it had been hit by the second wave, and realised that the wave had not massively impacted the village. There was no abnormally high mortality, neither were a majority of them hospitalised," says Raut, adding that at least the empirical data available right now, doesn't suggest anything concern-worthy.
He, however, states that Delta Plus could become dangerous, if it replaces the current dominant Delta variant. "To ensure that this doesn't happen, we are tracking all the contacts of the people who contracted the variant - this is not just the primary and secondary contacts, but also tertiary, which means also from neighbouring villages, where they have likely visited in the last two months."
A more stringent method has been employed in Joshi's jurisdiction in Palakkad, Kerala, where unlike Maharashtra, which has been following a level-wise unlock plan for the last two weeks, restrictions continue to be tighter. The villages of Parali and Pirayiri will remain sealed until the surveillance is complete. "We are currently following a three-pronged strategy in these villages," says Joshi.
The first includes extensive testing in the panchayat and the neighbouring areas, in order to identify if there are a "high number of cases anywhere else in the vicinity of these panchayats". They are also cautioning neighbouring districts, where people from here may have travelled, as villages in Kerala are well connected. Additionally, they are also carrying out extensive surveillance to identify cases, where people have influenza-like symptoms. "Now that the monsoon has begun, many people are coming in with influenza-like symptoms. We are making both Antigen and RT-PCR compulsory for them." The next measure involves the effort of the Rapid Response Teams, to confirm, if people are following quarantine rules, and adhering to social distancing. "If they cannot isolate at home, we are sending them to our domiciliary care centres." The third, and most important, is intensifying vaccination drive in these areas. "We are particularly, prioritising the second doses," she says.
Vaccination has proved to be most crucial in tackling the Delta variant. While evidence from the Scottish study suggested that protection from vaccines against the Delta variant, might be lower than the effectiveness against the Alpha variant, both the Oxford-AstraZeneca and Pfizer-BioNTech COVID-19 vaccines were shown to be "effective in reducing the risk of SARS-CoV-2 infection and COVID-19 hospitalisation in people with the Delta". Sheikh, who was part of this study, asserts that vaccination is our best chance. "Both the Oxford-AstraZeneca and Pfizer-BioNTech vaccines are still very effective. They are performing very well, and much better than, say, the flu vaccine. What we need to ensure is maximum coverage of populations as rapidly as possible, particularly [of] second doses, because this would mean maximising protection." This, he says, will eventually reduce community transmission and pressure on health systems.
The World Health Organisation recently said that two-vaccine doses are needed for full-level protection against the Delta variant, intensifying the call within the scientific community to reduce the gap between the two Covishield doses in India, which is currently between 12 and 16 weeks.
"I think this is a question of supplies," says Sheikh. "If supplies allow, the gap [between the doses] should be brought down to the manufacturer recommended dose intervals. But, in the absence of sufficient supplies, this becomes a complex public health issue. The public health agencies will have to consider where the balance lies, in terms of offering at least some protection to as many people as possible through a first vaccine dose versus giving maximum protection through second doses. It's difficult to advise India as an outsider on where this balance lies."
Mumbai, meanwhile, is not taking any chances, especially with the third wave looming.
According to Suresh Kakani, additional commissioner, BMC, the city reported one case in the eastern suburbs. Sixteen close contacts of the woman, who had contracted the virus, were traced, when she was diagnosed in the month of April. "The patient recovered within eight days, and except for her son, the other 15 suspects, who had followed 14-day quarantine, were not infected," he says.
The BMC currently sends its samples to the National Institute of Biologicals (NIB) and National Centre for Disease Control (NCDC) for genome sequencing. "I don't blame them for the delays. Their work load is really high, as they get swab samples from across India."
In order to ensure that they receive data in real time, the BMC has now decided to set up its own lab. "The decision was taken a long time ago, when we started getting information about these variants," he adds. The lab will be operational within the next two weeks. "We are waiting to procure a machine, which has cost us Rs 6.5 crore. It has already been shipped from the US, and should reach us soon. Once it arrives, we will conduct a test-run and then, start operations immediately. We are also tying up with experts to help us analyse these samples." This lab, he says, will reduce the turnaround time from a month to four days. "It will help us zero-in on individuals, who have different variants, and not just Delta."
For now, the municipal body is keeping all its jumbo centres and COVID-dedicated hospitals functional. "We are introducing four more jumbo facilities. Also, 70 per cent of our upcoming beds will have oxygen supply system." Following, COVID-appropriate behaviour, feels Kakani, is also key to tackling the third wave, and
delay its onset.
Epidemiologist Parameswaran says that a new virulent variant cannot alone be responsible for a third wave. "There is what we call the epidemiology triad, wherein three factors, and their interaction with each other, determine whether a wave is going to happen or not. The first is the virus - whether it is more virulent, or if it's developing more mutations. The next is the people - are they taking precautions, following social distancing, or are they vaccinated. And lastly, the environment - has the government relaxed norms, is it testing enough, is more contact tracing happening,? The next wave will be influenced by all these factors. Right now, we cannot be negligent."
7,500
No of samples sent for genomic surveillance by state in May
