News Analysis India

Tag: Genome sequencing

  • COVID-19 is not over yet, prepared to manage any situation: Health minister Mandviya

    By Express News Service

    NEW DELHI: Amid a spike in Covid-19 cases globally, Union Health Minister Dr Mansukh Mandaviya on Wednesday held a high-level review meeting and stressed that Covid is not over yet and India is prepared to manage any situation.

    His remarks came after official sources said three cases of Omicron subvariant BF.7, which is driving the surge in China, have been detected in the country. 

    The ministry also announced stepping up random screening of passengers, especially those who are travelling from countries reporting a spike in cases, at Indian airports in the country, and urged people to wear masks in crowded places and to take booster doses.

    While reviewing the Covid-19 situation and the preparedness of the public health system for surveillance, containment and management gave rising Covid-19 cases worldwide; the minister directed all concerned to be on alert and strengthen surveillance. 

    “I also urge people to take Covid vaccination,” said the health minister as he advised states and union territories to send samples daily of all Covid-19 positive cases to INSACOG labs to facilitate tracking new variants.

    Underlining the challenge posed by the increasing number of Covid-19 cases in some countries across the world, such as China, Japan, South Korea, France and the US, Mandaviya noted the importance of being prepared and remaining alert against new and emerging strains, especially given the upcoming festive season

    He also urged people to follow Covid-Appropriate Behaviour.

    India has been witnessing a steady decline in cases, with average daily cases falling to 158 in the week ending December 19. However, a consistent rise in global daily average cases has been reported in the last six weeks, with 5.9 lakh average daily cases reported in the week ending December 19.

    The meeting comes a day after Union Health Secretary Rajesh Bhushan asked state governments and union territories to submit samples of positive cases on a priority basis to the genome sequencing laboratories.

    Official sources said two cases of BF.7 have been detected in the country. BF.7, a sub-lineage of the Omicron variant BA.5, is said to have the strongest infection ability since it is highly transmissible. It also has a shorter incubation period and a higher ability to cause reinfection. 

    It has already been detected in countries like the US, the UK and European Union, Belgium., Germany, France and Denmark, and also China, which is seeing a deadly surge.

    After the review meeting, NITI Aayog member (Health) Dr V K Paul said people should take the jab and wear masks in crowded places.

    “Only 27-28 per cent of people have taken booster doses. We appeal to others, especially senior citizens, to take it. Precaution dose is mandated and guided to everyone.” 

    He also urged people to use masks in crowded spaces, indoors or outdoors. “This is all the more important for people with comorbidities or higher age,” Paul added.

    Dr N K Arora, chairman of the Covid-19 working group National Technical Advisory Group on Immunization(NTAGI), said there is nothing to panic about as the country’s system is “vigilant”.

    Chaos has engulfed China after the government reversed its strict lockdown guidelines under its zero-Covid policy. According to reports, crematoriums in the country are overwhelmed by the large influx of bodies, though the government has denied the death tally reaching double digits.

    ALSO READ | Masks back up, booster shots: Centre’s advice amid Covid surge in China

    NEW DELHI: Amid a spike in Covid-19 cases globally, Union Health Minister Dr Mansukh Mandaviya on Wednesday held a high-level review meeting and stressed that Covid is not over yet and India is prepared to manage any situation.

    His remarks came after official sources said three cases of Omicron subvariant BF.7, which is driving the surge in China, have been detected in the country. 

    The ministry also announced stepping up random screening of passengers, especially those who are travelling from countries reporting a spike in cases, at Indian airports in the country, and urged people to wear masks in crowded places and to take booster doses.

    While reviewing the Covid-19 situation and the preparedness of the public health system for surveillance, containment and management gave rising Covid-19 cases worldwide; the minister directed all concerned to be on alert and strengthen surveillance. 

    “I also urge people to take Covid vaccination,” said the health minister as he advised states and union territories to send samples daily of all Covid-19 positive cases to INSACOG labs to facilitate tracking new variants.

    Underlining the challenge posed by the increasing number of Covid-19 cases in some countries across the world, such as China, Japan, South Korea, France and the US, Mandaviya noted the importance of being prepared and remaining alert against new and emerging strains, especially given the upcoming festive season

    He also urged people to follow Covid-Appropriate Behaviour.

    India has been witnessing a steady decline in cases, with average daily cases falling to 158 in the week ending December 19. However, a consistent rise in global daily average cases has been reported in the last six weeks, with 5.9 lakh average daily cases reported in the week ending December 19.

    The meeting comes a day after Union Health Secretary Rajesh Bhushan asked state governments and union territories to submit samples of positive cases on a priority basis to the genome sequencing laboratories.

    Official sources said two cases of BF.7 have been detected in the country. BF.7, a sub-lineage of the Omicron variant BA.5, is said to have the strongest infection ability since it is highly transmissible. It also has a shorter incubation period and a higher ability to cause reinfection. 

    It has already been detected in countries like the US, the UK and European Union, Belgium., Germany, France and Denmark, and also China, which is seeing a deadly surge.

    After the review meeting, NITI Aayog member (Health) Dr V K Paul said people should take the jab and wear masks in crowded places.

    “Only 27-28 per cent of people have taken booster doses. We appeal to others, especially senior citizens, to take it. Precaution dose is mandated and guided to everyone.” 

    He also urged people to use masks in crowded spaces, indoors or outdoors. “This is all the more important for people with comorbidities or higher age,” Paul added.

    Dr N K Arora, chairman of the Covid-19 working group National Technical Advisory Group on Immunization(NTAGI), said there is nothing to panic about as the country’s system is “vigilant”.

    Chaos has engulfed China after the government reversed its strict lockdown guidelines under its zero-Covid policy. According to reports, crematoriums in the country are overwhelmed by the large influx of bodies, though the government has denied the death tally reaching double digits.

    ALSO READ | Masks back up, booster shots: Centre’s advice amid Covid surge in China

  • Step up genome sequencing to monitor mutants: PM Modi

    By Express News Service

    NEW DELHI:  Amid a continued surge of Covid-19 cases in Kerala and Maharashtra, Prime Minister Narendra Modi on Friday stressed the need to ensure adequate testing across the country and genome sequencing to monitor emergence of virus mutants. Reviewing the Covid situation in the country, Modi said the entire ecosystem to ensure increased oxygen availability, including oxygen concentrators, cylinders and PSA plants, need to be rapidly augmented.

    The states have been asked to maintain buffer stock of medicines in every district, an official statement from the Prime Minister’s Office said. Officials apprised the PM that around 58% of India’s adults have received the first dose and around 18% the second. 

    “It was discussed that across the world, there are countries where the number of active Covid cases continues to remain high. Figures from states like Maharashtra & Kerala indicate that there can be no room for complacency. However, the weekly positivity was at less than 3% for the 10th consecutive week,” the statement said.

    The prime minister was also briefed about the concentration of cases in a few geographies, districts with high test positivity as well as the week on week test positivity rate in the country. “The PM spoke about the need for constant genome sequencing to monitor emergence of mutants,” the statement said. Modi was informed that INSACOG,  a genome sequencing government consortium of laboratories, now consists of 28 labs across the country. This is also linked with a hospital network for clinical correlation. Sewage sampling is also done for genomic surveillance.

    “The prime minister was apprised that states have been requested to share SARS COV2 positive samples with INSACOG regularly,” it said. Modi also reviewed the status of augmentation of bed capacity for pediatric care and augmentation of facilities supported under ‘COVID Emergency Response Package II’.

    States asked to be on alertAccording to a statement from Prime Minister’s Office, states have been advised to redesign & orient primary care & block level health infrastructure in these areas to manage the situation.

  • Number of COVID-19 breakthrough infections in India within expected numbers: INSACOG

    It said that AY.12 that was first noted in Israel and currently driving infection in the country, which has inoculated 60 percent of its population, is not yet seen in India.

  • India was in dark on Delta variant: Dr Eric Feigl Ding

    Express News Service
    BENGALURU: The Delta variant of B 1.617.2 lineage has created havoc and is spreading fast even in the most-vaccinated countries. India, too, is still reeling under the effects of the deadly second wave due to this variant.

    Dr Eric Feigl-Ding, a US-based epidemiologist and Senior Fellow at the Federation of American Scientists, told The New Indian Express that India, where the Delta variant first emerged, was in the dark for a long time and with the evidence of the variant escaping vaccine efficacy, the country needs to now seriously ramp up genome sequencing and testing to mitigate the virus.

    “If a variant rises from your country, to stop it from spreading to the world and harming your own citizens, you need to invest in resources. Many variants may emerge and if there is a delay in identifying them, there might be many lockdowns in the future, not just in India, but across the world,” Dr Feigl-Ding said. 

    India has to speed up its genome sequencing, and invest in technology to ramp up not only whole genome sequencing, but also testing. Many variants may emerge, and if there is a delay in identifying them, there might be many lockdowns in future, not just in India but across the world, said Feigl Ding, epidemiologist, Senior Fellow at the Federation of American Scientists, in an exclusive interview with TNIE.

    India reeled under a deadly second wave of the coronavirus, caused mainly by the Delta variant of the Covid-19 virus. But now we are already talking about the third wave. Will India see another wave?It’s hard to say. I think India is still very vulnerable. We don’t know enough about Delta-Plus but it’s likely to be as transmissible as the Delta variant. Obviously, India doesn’t have enough vaccines rolled out, especially two doses. Delta is very evasive against one dose. Knowing that Delta-Plus has reinfection potential, I think it is worrisome.

    We are seeing Delta create havoc across the world. Do you think India identified the variant late?I think India doesn’t have genome sequencing capabilities like the UK does. Very few countries have the expertise. This data allows us to find out and know the variant in advance. Although we identified the variant months ago, we did not have the sequencing in order to know how much it was growing, how quickly, and to what percent it had spread in the population. Does the vaccine work against it? For this information, a lot of people have to be sequenced. Right now, we know that Delta is twice as contagious as the original strain, has about four times greater risk of hospitalisation, 2.5 times greater than Alpha, and four times more transmissible than the original variant. It is a very risky variant. But we learnt all this only because Delta has invaded the UK, and it is able to track down these numbers epidemiologically and genomically. But India was in the dark for a longer time.

    What should India do now?There should be a rule that India should do more testing. There are also shortcut tests like genotyping, instead of full genome sequencing. You need to develop genome typing shortcut tests, laboratory capabilities for genotyping, typing and do them fast. It requires infrastructure and investment from the government. Each country has different lessons to learn from each other. But if the variant rises from your country, then to stop it from spreading to the world and harming your own citizens, you need to invest in these resources. We need to wear masks, especially indoors. Ventilation is as critical as masks.

    Is it necessary that the next variant is more transmissible?It is not always worse. Mutations go in random directions until there is an evolutionary reason to direct into certain directions. We are reaching the point where we have more people who were infected and fewer people who have never been infected. The virus will now search to become more evasive — of immune system, vaccines etc. That’s the trend. Delta-Plus is not just another random mutation, it is Delta with a previously known tricky mutation that is known to be evasive.

    How important is vaccination?Vaccination is important but a country cannot rely only on this as a strategy, until vaccination is 80 per cent or more. Herd immunity by vaccination is a term used by many countries, but unvaccinated people have almost no protection, even if 40 per cent of the population is vaccinated. It happens only when almost 80 per cent vaccination is achieved. However, two vaccine doses definitely prevent hospitalisation.

  • Third Covid wave: India may not be doing adequate genome sequencing to identify threats quickly

    Express News Service
    NEW DELHI: India may still not be doing enough genome sequencing of SARS-CoV2 samples necessary to stay ahead of the virus and predict third Covid wave in time, feel experts.

    So far, genome sequencing of only about 15,000 samples across India has been carried out while experts say that considering India’s population, this number should have been at least 1 lakh if not more.

    It also grossly falls short of the target set up by the Centre in December-January to test 5 % of all positive samples in every state as part of its INSACOG initiative, which is a consortium of several institutions under the National Centre for Disease Control to carry out an extensive genomic surveillance  of Covid virus in India.

    This exercise, feel experts, is particularly necessary after it emerged that a new variant B.1.617, first detected in Maharashtra in India, which is highly transmissible had been driving the second wave of the pandemic apart from B117, a variant first identified in the UK.

    These two variants were different from the SARS-CoV2 strains prevalent in the first wave of the pandemic and have prompted many scientists to hypothesise that later waves of the infectious disease could be caused by new variants, which need to be identified quickly in order to make necessary public health interventions.

    “Considering India’s size, we ought to be sequencing more, around 1 lakh,” former ICMR director general NK Ganguly told The New Indian Express. “Currently we have sequenced 15,000 samples, which is very less. The more density of genome sequencing we can increase, the more information we can get, and we have to do this smartly.”

    ALSO READ | ‘In debt and skipping meals’: Survey finds Covid second wave has hit the poor hard

    He advised that India should make repository in which samples from various parts of the country can be genome sequenced

    Virander Singh Chauhan of the International Centre for Genetic Engineering and Biotechnology, who put together a report called ‘The Road Ahead for Smart Covid Testing and Tracing in India’, said  the country was able to identify new variants including the B.1.167 and its sub lineages and the spread of UK variant, but will need extensive sequencing for better surveillance and map the spread of mutant.

    Experts also feel that just identifying emerging variants may not be enough, unless there is a mechanism to translate data from sequencing into public health measures to effectively protect populations before it is too late.

    Manisha Bhinge, managing director, programs, health initiative at the Rockefeller Foundation stressed that an enabling culture of broad and diverse testing along with accelerated and methodical genomic sequencing and data integration will be essential to monitor variants of concern and assess effectiveness of countermeasure technologies.

    “This will take us a step closer to having early warning systems to pre-empt potential outbreaks,” she said.

    Many scientists associated with labs that are part of the INSACOG project however told this newspaper that fund crunch has been a major issue with the initiative, forcing the labs to manage the programme from their own scant resources, apart from little support from the department of biotechnology. 

  • 16 variants of Covid active in Uttarakhand, reveals genome sequencing

    Express News Service
    DEHRADUN: Genome sequencing of samples in Uttarakhand has revealed that there are at least 16 variants of the Covid-19 virus active in the hilly state. 

    Health department officials said that reports of 531 samples are still pending to decide which variant is dominating the scene. “The genome sequencing has revealed that 16 variants are active as we speak. However, a majority of samples are still pending to determine which dominant variant is prevailing,” an official said on the condition of anonymity.

    Officials from the state health department said that total 851 simples were sent to a Delhi lab out of which reports of 285 samples have arrived. 

    Out of these 285 samples, reports of 208 samples were detected with Sara Cov 2 variant (original variant) while UK variant B117 was detected in 32 samples, one sample has B16171 variant, two have B16172 variant and 42 were detected with various other kind of variants of the virus. 

    Other strains include UK variant B16171, UK variant B16172, P681R, P681H, P681RQ1071H, Q677H, N440K, N501Y, L452R, E484K, L452RP681R, N501YP681H, DN50N and E484QLRP681RQ1071H. 

    Last month with the National Centre for Disease Control (NCDC) confirming detection of a total of six cases of various strains, according to doctors in Dehradun’s Viral Research and Diagnostic Laboratory (VRDL), it was  confirmed that highly contagious double mutant strain of SARS-CoV-2 had registered its presence before the Mahakumbh 2021 started on April 1. 

    The experts confirmed that three of the six are of the double mutant strain, two are of the UK strain and one is yet to be identified. 

    The samples which confirmed the double mutant strain was sent to the NCDC in March end.

    The mega religious event was attended by millions of people from across the country with 35 lakh on April 12 Shahi Snan and 13.51 lakh on April 14 Shahi Snan.

    At present Uttarakhand has 78802 active cases of Covid 19. The number of active cases came down from 80,000 in comparison with Friday as 5034 people recovered from Covid 19 on Sunday while 4496 new cases were added. 

    Sunday also marked lowest number of new cases surfacing in one day since last 21 days. The number of recoveries were also higher than new cases. 

     Last time this happened on March 30 with 147 recoveries and 128 new cases in one day. 

  • Twenty more people in India test positive for UK strain of COVID-19, tally at 58

    By PTI
    NEW DELHI: Twenty more people have tested positive for the new UK variant of SARS-CoV-2, taking the total number of such cases in the country to 58.

    The new cases have been identified at the National Institute of Virology (NIV) Pune.

    “The total number of cases infected with the new strain of the novel coronavirus first reported in the UK now stands at 58,” the Union Health Ministry said.

    All these persons have been kept in single room isolation in designated Health Care facilities by respective state governments.

    Their close contacts have also been put under quarantine. Comprehensive contact tracing has been initiated for co-travellers, family contacts and others. Genome sequencing on other specimens is going on, the ministry said.

    The situation is under careful watch and regular advice is being provided to the States for enhanced surveillance, containment, testing and dispatch of samples to INSACOG labs.

    Of the 58, the mutated UK strain was detected in eight samples at National Centre for Disease Control (NCDC), New Delhi, 11 in the Institute of Genomics and Integrative Biology (IGIB), Delhi, in one in  National Institute of Biomedical Genomics (NIBMG), Kalyani (near Kolkata), 25 in the National Institute of Virology in Pune, three in Centre for Cellular and Molecular Biology (CCMB) in Hyderabad and ten was sequenced in National Institute of Mental Health and Neuro Sciences Hospital (NIMHANS)Bengaluru.

    The INSACOG labs at NCBS InSTEM, Bengaluru, CDFD Hyderabad, ILS Bhubaneswar, and NCCS Pune have so far found no mutant virus.

    The new UK variant has already been reported by several countries including Denmark, the Netherlands, Australia, Italy, Sweden, France, Spain, Switzerland, Germany, Canada, Japan, Lebanon and Singapore.

    The Government of India took cognizance of the reports of virus reported from the UK and put in place a proactive and preventive strategy to detect and contain the mutant variant, it said.

    This strategy includes temporary suspension of all flights coming from  the UK with effect from the midnight of December 23 till January 7 and mandatory testing of all UK-returned air passengers through RT-PCR test.

    The samples of all UK returnees found positive in RT-PCR test will be genome sequenced by a consortium of 10 government labs i.e. INSACOG.

    Further, all the international passengers who have arrived in India between December 9 and 22, if symptomatic and tested positive for COVID-19 will be subjected to genome sequencing as part of the Centre’s strategy to detect the mutated UK variant in them.

    Others will be followed up by the respective state and district surveillance officers and will be tested as per the ICMR guidelines (even if asymptomatic) between 5th and 10th day, according to the Union Health Ministry’s guidance document on genomic sequencing.

    Further, epidemiological surveillance of the passengers, who have arrived in India since November 23 will be conducted in the community through active follow up.

    Besides, standard operating protocol for states and UTs to tackle the mutant variant of SARS-CoV-2 was issued on December 22.