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Amid Maharashtra's worsening COVID-19 situation, virus variant with double mutation detected in state

The institutes working on a project under the NCDC have alerted the Union health ministry to label the variant with the double mutation as a likely variant of concern (VOC).

Published: 17th March 2021 02:21 AM  |   Last Updated: 17th March 2021 08:16 AM   |  A+A-

A health worker sanitizes the baggage of passengers as a precaution against COVID-19 at a long distance train station in Mumbai. (Photo | AP)

Express News Service

NEW DELHI:  Scientific institutes tasked with genome sequencing of the Covid-19 virus in the country have alerted the Centre on a virus variant with double mutation in Maharashtra, whose possible role in the surge in cases is being probed, this newspaper has gathered.

The institutes working on a project under the National Centre for Disease Control (NCDC) have alerted the Union health ministry to label the variant with the double mutation as a likely variant of concern (VOC).

VOCs have potential public health implications like the ones in the UK, Brazil and South Africa.

Sources working on the project said so far 7,000 virus samples have been sequenced, of which 200 were lifted from parts of Maharashtra, which has been hit the hardest with the fresh rise in cases.

“Of the samples from Maharashtra, about 20% have two mutations, E484Q and L452R,” said a source.

“While it is difficult to conclusively say that the variant is behind the surge, it has been established elsewhere that E484Q can escape antibody neutralisation and L452R is known to increase infectivity and has been linked to large pockets in the US.”

The Centre in December had formed a genomic surveillance consortium INSACOG of 10 institutes under the NCDC to work on genome sequencing of virus samples from various parts of the country amid concern over detection of the UK variant in India.

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A team sent by the health ministry to Maharashtra had also pointed to a possible role of the variant virus causing the second wave of infections in the state.

Officials said an epidemiological investigation being undertaken by the NCDC, will involve probing whether variants are causing the disease to spread in clusters and whether they are more infectious.

Epidemiologists will also examine whether there is significant digression in clinical outcomes in patients, found positive with the variant and whether people with previous history of infection are also being found re-infected with the mutant virus.

The government has earlier categorically denied the role of the virus with E484Q or any other mutation in the surge, but this mutation appearing with L452R in a region with a massive surge of infections has triggered fresh worries.

Maharashtra is in the beginning of second COVID-19 wave, a central team report has said, highlighting that there is very limited active effort to track, test, isolate cases and quarantine contacts, and there is no adherence to COVID appropriate behaviour among people in rural and urban areas.

Based on the central team report, Union Health Secretary Rajesh Bhushan has written a letter to the Maharashtra government, stating "measures such as night curfews, weekend lockdowns etc. have very limited impact on containing/suppressing the transmission" and urged the state to focus on strict containment strategies, strengthening surveillance and augmenting testing.

In a letter to Maharashtra Chief Secretary Sitaram Kunte, Bhushan said even though the health infrastructure is adequate as of now, the "state should plan for a worse-case scenario with sufficient lead time".

The central team which visited the state from March 7-11 inferred in its report that the administrative mechanism should be re-instated to the level witnessed in August-September 2020 to contain/supress COVID transmission.

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"ln all the districts visited by the central team, the test positivity rate was high, ranging from 51 per cent in Mumbai to 30 per cent in Aurangabad, implying that there are lot many cases that are not being tested and there is high transmission in the community," the report underlined.

ln view of limited contact tracing, a large pool of asymptomatic and pre-symptomatic people among contacts are not tracked and tested, the report said and stressed that testing must be considerably enhanced and protocol laid down by ICMR followed.

"The absence of rigorous tracing, testing and containment is leading to sustained community transmission," it said.

"The case-contact ratio is more than 1:20. Though it appears high, a deep dive into the methodology of contact tracing revealed that the main concept of contact tracing was not clearly understood by field level staff, who were mainly listing the immediate family and neighborhood contacts, for the sake of listing.

"The high-risk contacts in workplace settings, social settings and family settings were not investigated and listed," the report highlighted.

The report stated that the current case fatality was found to be very high among admitted cases in Government Medical College in Aurangabad and in Vasant Rao Pawar Medical College, Nashik which needs to be investigated in detail, including sending samples for whole genome sequencing, it said.

Referring to the findings of the team, Bhushan said that containment strategy needs to be re-introduced, containment zones must be better defined based on contact listing, digital mapping of cases and contacts and should be much larger to include the area of influence of cases/ contacts.

"The buffer zones need to be delineated. The perimeter control needs to be strictly enforced. For each containment zone, the Rapid Response Teams should develop an operational plan," he said.

Bhushan also stressed on augmenting testing to bring the test positivity rate to less than 5 per cent and strengthening surveillance by active house to house search for active cases/contacts in containment zones (as per the containment plan).

 Further, passive surveillance for ILI and SARI must be enhanced through health institutions,and involvement of  private practitioners.

"The Incident Command under the leadership of district collector and municipal commissioner should be actively re-instated with whole of government approach to contain/ suppress the transmission. This should be monitored at the highest level," Bhushan said.

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For every positive case, at least 20 to 30 close contacts (including family contacts, social contacts' workplace contacts and other casual contacts) need to be promptly traced and tracked and the practice of isolating 80-85 pre cent of active cases kept in home isolation needs to be reviewed, he said in the letter.

"Vaccine hesitancy among frontline workers needs to be addressed as their services would be required if the trajectory follows the upward swing as is being witnessed now. The state should also expedite vaccinating those with co-morbidities and elderly,"  Bhushan stated.

The pandemic situation in Maharashtra became grimmer on Tuesday as the state recorded 17,864 new cases -- highest one-day rise this year -- and 87 deaths, a health official said.

The caseload in the state rose to 23,47,328 and death toll reached 52,996.

As many as 9,510 patients were discharged from hospitals during the day, taking the total of recoveries to 21,54,253.

There are 1,38,813 active cases in the state now.

Earlier, the state had recorded 17,000-plus cases in a day more than once in September 2020.

On Tuesday, Pune city recorded the highest 1,954 new cases followed by 1,951 in Nagpur and 1,922 in Mumbai city.

Pune division comprising civic bodies of Pune, Pimpri Chinchwad as well as districts of Pune, Solapur and Satara reported 3,994 new cases, highest among the divisions.

The number of cases in the Pune division stood at 5,66,518 and death toll at 11,884.

Mumbai's COVID-19 tally increased to 3,47,597 and four deaths took the fatality count to 11,543.

Mumbai division reported 3,671 new cases and six deaths, taking the cumulative caseload to 7,66,578 and death toll to 19,974.

Nashik division's case tally stood at 3,23,173 and the death toll at 5,387.

Kolhapur division has reported 1,21,415 cases and 4,091 deaths till now, while Aurangabad division's case tally stands at 93,452 and death count at 2,115.

Latur division has reported 94,418 cases until now and 2,570 fatalities.

Akola division has reported 1,20,995 cases while 1,935 people have succumbed to the disease until now.

Nagpur division has reported 2,60,633 infections and 4,949 fatalities so far.

With 1,06,274 tests carried out on Tuesday, the state has so far tested 1,77,15,522 samples for coronavirus.

For the first time the state carried out over one lakh tests in a day in this calendar year.

There are 6,52,531 people in home quarantine while 6,067 are in institutional quarantine.

Out of 87 deaths, 36 occurred in the last 48 hours and 31 in the last week.

Rest were from the period before that.

Maharashtra's COVID-19 figures are as follows: Positive cases: 23,47,328, New cases: 17,864, Death toll: 52,996, Discharged: 21,54,253, Active cases: 1,38,813, people tested so far: 1,77,15,522.

(With PTI Inputs)

Trends and the big picture

  • MP government to impose night curfew in Bhopal and Indore from Wednesday (10 pm to 6 am). Also, shops ordered to close at 10 pm in eight other cities.

  • Gujarat to increase night curfew timings by two hours in Ahmedabad, Surat, Vadodara and Rajkot from 10 pm to 6 am.

  • India recorded 24,492 new COVID-19 cases, going past  20,000 for the sixth day in a row. Total cases in the country stood at 1,14,09,831.

  • 5.86 crore doses of Made in India Covid vaccines provided to 71 countries both as grant as well as commercial sales as of Monday.

  • Amid concern over adverse  effects of AstraZeneca’s vaccine, the European regulator said there was no indication the shot was responsible for blood clots, adding benefits outweigh risks.

  • China makes it mandatory for people from India and 19 other nations to get Chinese-made vaccines if they want to visit the country.



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