News Analysis India

Tag: covid variants

  • Five private labs join Covid-19 genome surveillance project

    Express News Service

    NEW DELHI:  In a boost to the Centre’s project that detects new and emerging Covid variants, at least five private laboratories have joined the network of 28 government laboratories involved in the task.Sujeet Kumar Singh, director with the National Centre for Disease Control which leads the consortium, told this newspaper that the private laboratories that fulfil the specifications listed by the Department of Biotechnology were approved to join the network.

    Beginning with 10 national research laboratories that came together in view of the B1617 variant of Covid, the INSACOG project went on to add 18 more regional laboratories over the past few months. While nearly 60,000 samples were subjected to whole genome sequencing till September, nearly 7,000 samples per month, the government plans to further enhance the capacity to 70,000 samples.

    “As of now, the turnaround time for samples undergoing WSG every month is nearly 10-15 days,” said a senior official. “We hope to bring it down to four-five days and adding private laboratories will be a big help in that direction.”

    Officials said that the works of these laboratories are crucial for the identification of variants of concern and interest so as to advise the policy makers for effective management of the Covid pandemic.The project, for instance, had first identified the Delta variant in February in Maharashtra. The variant later took the country by storm, triggering a massive second wave in India. Many experts feel that not enough attention was paid to the issue which led to the huge surge in Covid cases, shortage of hospital care and, eventually, deaths.

    Mahajan Imaging, Premas Life Sciences (Delhi), Strands Life Sciences, Genotypic Technology (Bengaluru), NMC Genetics India (Gurugram), and Mapmygenome India (Hyderabad) showed interest in joining the consortium.

    “After that certain specific criteria were laid down and the laboratories were asked to submit their expression of interest in a standardised format with details such as the type of sequencing platform that is operational, number of viral genome sequences that is being proposed to carry out per week or per month, number of trained laboratory personnel available,” an NCDC official said, adding that five laboratories so far have been approved to join the consortium. 

  • Mu and C.1.2 variants of SARS-CoV2 not found in India so far: INSAOCG

    The Indian SARS-CoV-2 Genomics Consortium (INSACOG) said Mu has mutations that indicate potential immune escape properties.

  • Two coronavirus variants of interest not found in India yet

    Express News Service

    NEW DELHI:  While there have been no cases of new Covid-19 variants — Mu, South African C.1.2 — in India so far, the national genomic surveillance consortium on Friday called for stronger implementation of existing recommendations on sequencing of positive samples from international travellers.

    The Indian SARS-CoV-2 Genomics Consortium (INSACOG) weekly bulletin shows that Delta and Delta sub-lineages continue to be the main VOC (variants of concern) in India and AY.4 is the most frequently seen sub-lineage in recent sequences from India, as well as globally. Of the 63,774 samples of VOC and Variants of Interest (VOI) sequenced by INSACOG, 42,833 were Delta.

    The WHO added B.1.621 (including B.1.621.1) to the list of VOI on August 30 and gave it the designation “Mu”. It has mutations that indicate potential immune escape properties. There appears to be a reduction in neutralization capacity of convalescent and vaccine sera, similar to what was seen for the Beta variant, but this needs to be confirmed.

    WHO has also added C.1.2 as a new VOI. C.1.2 is a sub-lineage of the C.1 variant seen in South Africa, which did not spread globally. The C.1.2 variant seems to have undergone many mutations in a short time, and contains mutations of all three types that have previously been found to be important for transmissibility and immune escape.

    The INSACOG data portal has started including sub-lineage labels up to AY.12 to enable better tracking. The latest update takes the classification to AY.25, with the following notification — “as previously outlined for AY.4-AY.12, each of the new AY.13-AY.25 lineages shows significant geographical clustering and these lineages have been designated to help researchers track the virus on a finer scale. However, their designation does not imply any functional biological difference from B.1.617.2 and, like B.1.617.2, they correspond to the WHO-defined Delta variant.”

  • Delta variant replicates 1k times more

    Express News Service
    BENGALURU: The Indian SARS-Cov2 Genomics Consortium (INSACOG) said on Thursday that genome sequencing of recent samples from across the country has shown that the Delta variant continues to be the dominant cause of the new Covid cases. They also said that evidence shows vaccines are offering high protection against the variant. 

    Meanwhile, a recent study published in the Lancet, stated that the Delta variant has been growing rapidly in people’s respiratory tracts, and has replicated over a thousand times more than the original strain of the virus. 

    The World Health Organisation (WHO) has been tracking the Delta variant on a day-to-day basis, and have found that in countries including India, the variant has shown increased transmissibility. Dr Maria Van Kerkhove, a scientist at WHO, said at a press conference, “We are tracking the variant’s behaviour. So far, increased transmissibility is being reported. We are working with a number of technical networks to really look at the incubation period. We are also looking at the time a person is exposed to the virus, how it is transmitted, whether it is transmitted in an indoor, closed setting or not,” she explained.

    The lineages of Delta variant- the AY1 and AY2- are also being tracked. It was also found that on an average, it takes about four days for the Delta variant to reach detectable levels in an infected person. The original strain could only be detected after 6 days of infection. Interestingly, the study found that the patient with Delta strain transmitted the virus in the initial days of the infection, underscoring the importance of immediate quarantine. 

    Agreeing to the severity of transmission and possibility that the third wave may also be predominantly driven by the delta variant, Dr Vishal Rao, Regional Director, Head Neck Surgical Oncology and Associate Dean, Centre of Academics and Research HCG Cancer Centre, who is also a member of the Covid-19 Genomic Surveillance Committee, GoK said, “Unless a new virulent mutation occurs again, the third wave will be predominantly driven by the Delta vaiant. We are also watching out for the Lambda variant, but so far, it has not been reported in the country.”

  • Three COVID strains detected among 75 patients in Mizoram

    By PTI
    AIZWAL: At least three different COVID strains have been detected among 75 patients from Mizoram whose samples were randomly selected and sent for whole genome sequencing, a health official said on Thursday.

    Seventy-three cases of India’s highly transmissible Delta variant (B.1.617.2), and one case each of United Kingdom’s Alpha (B.1.1.7) and Eta (B.1.525) strains were found among 100 samples, state nodal officer and official spokesperson on COVID-19, Dr Pachuau Lalmalsawma, said.

    The samples were sent for whole genome sequencing to the National Institute of Biomedical Genomics (NIBMG) in West Bengal’s Kalyani in June, he said.

    “The Mizoram government is making massive efforts to detect other variants in the state. People have to be very cautious and strictly follow the guidelines as different COVID variants may be already present in other parts of the state,” he said.

    Fifty-six of the 73 Delta variant cases were registered in Aizawl, nine in Lunglei, five in Kolasib and three in Serchhip, the official said, adding that both the Alpha and Eta variants were reported in Aizawl.

    Seventy samples from Aizawl, and 10 each from Lunglei, Kolasib and Serchhip districts were collected and sent to NIBMG for genome sequencing last month.

    The patients’ present conditions are yet to be ascertained, he said.

    On June 18, Mizoram had recorded four cases of Delta variants from among 217 samples sent for whole-genome sequencing in April.

    However, all four patients from Aizawl have fully recovered from the disease.

    Pachuau said that 69 samples were sent to NIBMG in March, 217 in April and 100 in June.

    Also, 150 more samples were sent on July 15, and results are awaited, he said.

    Quoting a study, Pachuau said that the Eta variant is more dangerous as 69 percent of the infected patients have been found to require treatment at the Intensive Care Unit (ICU).

    The mortality rate among patients infected with Delta variant is 0.1 percent, 2 percent for Alpha variant and 2.7 percent for Eta strain, he said.

  • Assam doctor infected with two different variants of COVID-19 virus simultaneously

    By PTI
    DIBRUGARH: A woman doctor in Assam may be the countrys first case of a COVID-19 patient infected with two different variants of the virus at the same time, Dr.B Borkakoty, senior scientist at the ICMRs Regional Medical Research Centre (RMRC) here, said.

    The doctor, despite being fully vaccinated, got infected with both Alpha and Delta variants of SARS-CoV-2, and the RMRC lab detected the double infection in the patient in May.

    There have been few such instances in the UK, Brazil and Portugal but such a case has not been reported from India so far, Dr Borkakoty said.

    A month after receiving the second dose, the woman and her husband, both doctors at a COVID Care Centre, tested COVID-19 positive and the latter was infected with the Alpha variant.

    “We collected their samples again and the second round of tests re-confirmed the double infection in her.

    We also did whole genome sequencing and it made us sure that it was a case of being infected by both variants at the same time,” Dr.Borkakoty said.

    The woman who had a mild sore throat, body ache and insomnia, recovered without hospitalisation, he added.

    “A dual infection happens when two variants infect one person simultaneously or within a very short period. It occurs when someone gets infected with one variant and before immunity can develop, the person gets infected with another variant usually within two to three days of the first infection,” Dr. Borkakoty said.

    Quasi-species circulation of SARS-CoV-2 is not uncommon and has been reported during the initial phase of the pandemic in February 2020 too.

    However, infection by two “variants of concern” is rarely reported, he said.

    “Most cases of dual infection may be missed if genetic sequencing is solely based on next-generation sequencing where variant calling is by software and not by manual examination of the specific genetic sequence”, the scientist said.

    Such infection may even be common during the transition phase where replacement of one variant with a new variant takes place.

    During the initial phase of the second wave in Assam around February-March this year, most COVID-19 cases were due to the Alpha variant but from April, cases of Delta variant infections started to emerge.

    “Both the Alpha and Delta variants were circulating then and it is during this period when some people are most likely to have got infected with two different variants of the virus. When such infections are detected, it is called as a dual infection”, Dr. Borkakoty explained.

    It is very difficult to detect a dual infection as one variant will be circulating in a higher amount and be more dominant than the other, he said.

    Detection of double infection is done through genome sequencing but even that can give it a miss.

    “It has to be reconfirmed with another technology called Sanger sequencing, targeting the specific mutations and examining the chromatogram manually,” Dr. Borkakoty added.

  • Detection of multiple Covid variants puts Jharkhand on high alarm

    By PTI
    RANCHI: Alarmed by the detection of several variants of coronavirus in Jharkhand with 328 confirmed cases surfacing so far, the state government has directed the authorities to despatch samples within 48 hours of a patients death for conducting a genetic study to understand the mortality rate and evolve a strategy to contain the spread, a top official said Tuesday.

    Battling the deadly second wave of the COVID-19 that has claimed 5,100 lives in tribal-dominated Jharkhand, the state government is concerned as these variants like Delta, Alpha, and Kappa are said to be more transmissible.

    “As many as 328 of the 364 samples have tested positive for variants like Delta, Alfa, and Kappa in the state in course of whole genomic sequencing”, State Health Secretary, Arun Kumar Singh said.

    The state is committed to taking all necessary steps to stop the spread of the virus to protect its citizens by adopting evidence-based containment measures, the health secretary said.

    Whole genomic sequencing (WGS) is a laboratory process that is used to determine nearly all the approximately 3 billion nucleotides of an individuals complete DNA sequence, including non-coding sequence which is instrumental in characterising the mutations and tracking disease outbreaks.

    Of the 328 positive cases, 194 cases are of Delta variant B.1.617.2 which is a “variant of concern”, Singh said.

    A variant can be labelled as “of concern” if it is more contagious, more deadly, or more resistant to current vaccines and treatments, the World Health Organisation had said.

    “This variant is significantly more transmissible and somewhat resistant”, the official said.

    Twenty-nine cases were found to be of B.1.617.1 variant which has been named Kappa, the health secretary said In addition, 29 cases are of B.1.1.7 Alpha variant, he added.

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    The Alpha variant is also a strain “of concern” as it spreads more rapidly than the original strain.

    Apart from these, a few other variants of coronavirus have also been detected in the state, Singh said.

    A maximum of 145 cases has been detected from Jamshedpur followed by 56 from state capital Ranchi.

    Both the districts have been witnessing a high number of COVID-19 cases and fatalities.

    Dhanbad accounted for 49 cases of the variants, Hazaribag 48 and Palamu 30, he said.

    “For identifying the strains of the virus prevailing in the community, the state has sent 364 positive stored RT- PCR samples to Regional Genome Sequencing Laboratory (RGSL), Institute of Life Sciences (ILS) Bhubaneshwar for WGS,” State Chief Epidemiologist Dr.

    Praveen Kumar Karn said.

    The samples were sent from Ranchi Institute of Medical Sciences (RIMS), IRL, Itki Ranchi, District Palamu Medical College, and Mahatma Gandhi Memorial Medical College, Jamshedpur which have been identified as Sentinel Surveillance Sites.

    “This sequence will help in better planning for the future and alert f the Health Department to plan for better management of the patients”, Dr. Karn said.

    A total of 537 samples had been sent to ILS.

    Bhubneshwar between March and April 2021 for WGS out of which 364 were processed.

    In a letter to heads of the sentinel surveillance sites, the health secretary mentioned, “All labs are directed to get the SRF ID of the death cases from the District Administration and send the respective samples for WGS within 48 hrs.

    “Therefore samples of all those patients who have died on or after 1st April 2021 shall mandatorily be sent for WGS to ILS, Bhubneshwar.

    Hence, all identified Sentinel sites are directed to kindly comply with all activities for combating this large outbreak COVID-19”.

    Meanwhile, Chief Minister Hemant Soren said that even though the rate of recovery is more than 98 per cent in the state, the danger is not over.

    “According to experts, the third wave may trouble us in six to eight weeks and the state government has made preparations for it but it would not be possible without the help of people”, he added.

    The number of active coronavirus cases in Jharkhand has been recorded at 1,489 while the death toll has reached 5,100.

    New coronavirus cases were recorded at 122, which took the caseload to 3,44,665.

  • Samples sent for genome sequencing to identify new Covid-19 variant, says Maharashtra government

    By PTI
    PUNE: The Maharashtra government has sent a substantial number of samples from various districts for genome sequencing to verify if any new mutation of SARS-CoV-2 has taken place, with the aim being to identify new COVID-19 variant Delta Plus or AY.1, an official said here on Monday.

    The highly transmissible Delta variant of SARS-CoV-2 has mutated further to form the Delta Plus or AY.1 variant and it is said to be resistant to the monoclonal antibody cocktail treatment for COVID-19 recently authorized in India, he added.

    “We have sent substantial samples from various districts to investigate if there is any prevalence of Delta-plus ( or AY.1). The reports are expected to come by Tuesday,” said Dr.

    Pradip Awate, State Surveillance Officer.

    He said the state’s Directorate of Medical Education and Research (DMER) had signed an MOU with CSIR-Institute of Integrative and Genomic Biology (IGIB) under which BJ Medical here will be the nodal lab to perform genome sequencing of the samples.

    In its latest report on coronavirus variants, updated till last Friday, the health agency said Delta Plus was present in six genomes from India as of June 7.

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  • Pfizer, Moderna vaccines effective against COVID variants found in India: Study

    As of today, India registered 2,81,386 fresh infections were recorded in the last 24 hours, according to the Union Health Ministry #39;s data.

  • INTERVIEW | Pandemic will end up as an endemic, says immunologist Dr Dipyaman Ganguly

    Express News Service
    Senior immunologist Dr. Dipyaman Ganguly, principal scientist, CSIR-Indian Institute of Chemical Biology in Kolkata, has seen some encouraging signs. Few cases of reinfection and effectiveness of therapy using immunosuppressants are some of those. He prescribes a combination of personal commitments and policy-level commitments in addition to mass vaccination in order to reduce the pandemic to a manageable proportion. Excerpts…

    Q: So far, what have we understood about our immune response to the SARS CoV 2, and what remains to be understood?

    A: We could gather quite a bit of information from the earlier stints of the pandemic in 2020. But I must say the disease caused by the coronavirus is too enigmatic to be confident that we know everything about it by now. The most important lacunae are how the new variants will affect the course of the pandemic. It was clear from the very beginning that the virus is going to be a menace for humanity for a long time in the future. It is mostly clear that the pandemic will end up as an endemic disease.

    Q: We know that the immunity conferred by the natural infections, contributed by antibody-producing B cells and the T cells, is working well for one and half years. Even in this fast-evolving second wave of infection in India reports of reinfections are rare, which is a dependable testimony for this assuring conclusion.

    A: The evidence gathered from all over the world in support of a hyperactivated immune response in the patients succumbing to severe disease is also being supported in the second wave as well. Thus the medical therapy using immunosuppressants like corticosteroids is saving a lot of lives.

    The vaccines have been rolled out and most of the health care workers and a considerable fraction of the senior citizens in the country have received a complete regimen of the vaccines and anecdotal evidence suggests they are also not being documented to succumb to symptomatic disease in the second wave. These are all dependable positive information. Regarding the duration of immune protection conferred by the vaccines, we do not have enough data as the vaccines have been there for just six months or so. If vaccine-induced immunity also follows the pattern similar to natural infections, a lot of lives will be saved.

    Q: What does the current wave of Covid-19 infections, which is worse than the first national wave, indicate, and has it surprised you in any way?

    A: There are several non-mutually exclusive reasons for the much steeper and higher amplitude of the second wave. I believe a major reason has been an insidious complacency resulting from the gradual reduction in the number of cases, and more importantly too much stress upon the information that younger citizens are protected from disease severity. These had made the younger citizens too casual as the statutory lockdowns were over.

    Secondly, a major fraction of the infections in this second wave is due to the newly emerging variant strains. A number of them have documented higher transmission rates, e.g. the B.1.1.7 strain or UK strain. As a result of these different factors, we are actually seeing a high-amplitude second wave with a large number of younger citizens also being afflicted with symptomatic diseases.

    ALSO READ | Covaxin found to be effective against most Covid variants; expert says result “not surprising”

    Q: Do you think mutation might be having a big role to play in the ongoing wave of infections?

    a: As I already mentioned, the variant strains harbouring the concerning mutations are constituting a large fraction of the new infections, and some of them do have higher transmission rates, e.g. the N501Y mutation (now nicknamed Nelly) in the UK strain spike gene.

    As you must have noted from myriad media reports, a large number of these variants do have abilities to somewhat escape the immune protection conferred by the natural infection with the earlier strains or vaccines, e.g. the Eek (E484K) mutation in the South African B.1.351 and the Indian double mutant (B.1.617) strains. But personally, I am keenly following reports of reinfections in the second wave among individuals with a previous history of natural infection with the earlier strain or people who are fully vaccinated. Till now such reports are rare. That is sort of indicating that the immune escape of these mutant viruses registered in the laboratories may not be getting too dangerous in real-life scenarios. It may be that even the suboptimally efficient immune protection, against these so-called escape variants, is being able to prevent severe symptomatic diseases from occurring. We will have to be actively vigilant for such occurrences, by ramping up viral sequencing efforts all over the country as well as meticulously documenting the reinfections. If this trend remains as such it will be a great relief.

    I would also like to point out here that this also means that therapeutic approaches like convalescent plasma therapy should be explored in this wave too. The only antiviral therapy which is sought after leading to a temporary crisis regarding its supply is the repurposed drug Remdesivir. Interestingly, the importance that CPT was given in the first wave of the pandemic is absent in the second wave. The major reason for that has been contradicting results from different randomised control trials done in different parts of the world that explored its efficacy. Most meta-analyses failed to show a ‘universal’ efficacy of CPT in Covid-19. Of note here, the therapeutic benefit of Remdesivir was also not proven in clinical trials worldwide.

    In this regard, one should keep in mind that some of the well-documented trials, both from India and abroad, did show that CPT may confer a very significant survival benefit in the younger Covid-19 patients who were succumbing to severe disease. A smaller study done in Kolkata reported significant benefits in patients below 66 years of age. A much larger trial in the USA reported a similar efficacy in patients below 65 years of age. Given the larger number of younger citizens succumbing to severe symptoms in the second wave, these data should be paid heed to. After all precision medicine is the way forward in the medical sciences and thus depriving patients of a therapy that may be beneficial to them, even if not to all patients, is not prudent. At this phase of the epidemic, the potential convalescent donors are not in dearth. Just a well-coordinated awareness campaign, smooth running plasma banks, and a prudent protocol for selecting recipients who will benefit from it can save a lot of lives.

    Q: Some metropolitan cities like Delhi, Mumbai, and Pune which had seen quite a few peaks before are also seeing even a worse situation. Do you think serosurveys — showing quite high seropositivity rates in these cities- painted a misleading picture and lulled people and governments into some sort of complacence?

    A: I do not think that the seropositivity rates were misleading. The serosurveys never reported a level of seroprevalence that could even theoretically prevent pandemic progression. A large number of citizens were left susceptible and they are now getting infected. As I mentioned the second wave of the epidemic in India is yet to record a significant number of reinfections. One may consider the possibility that the seroprevalence data were wrongly read by the lay citizens, which perhaps led to their complacent behaviour of doing away with the physical distancing measures.

    Q: What level of Covid vaccinations should be achieved before we can see the pandemic ebbing?

    A: My understanding about the pandemic tells me that vaccination alone cannot end the pandemic. The so-called ‘Swiss cheese’ model of pandemic protection, which was originally proposed in 1990 by James Reason, a cognitive psychologist, to explain how to prevent accidents from occurring, is being frequently invoked by experts in the context of the present pandemic. This tells you that a single measure cannot be full-proof in preventing the pandemic from progressing. A combination of personal commitments to pandemic-related restrictions (like mask use and physical distancing) as well as policy level commitments to contact-tracing, ramped up testing and viral sequencing, easy accessibility to necessary healthcare, in addition to the mass vaccination measures, can reduce the pandemic to a manageable proportion and save a lot of lives.