Genomic sequencing in the pandemic fight

#GS3 Science and Technology

News info:

  • If there's one tool within the COVID-19 pandemic response, which India has been slow in adoption and has used sub-optimally, it's genomic sequencing. an efficient COVID-19 pandemic response requires, inter alia, keeping track of emerging variants (total 10 till now including variants of interest and concern) then conducting further studies about their transmissibility, immune escape, and potential to cause severe disease.  
  • Therefore, genomic sequencing becomes one of the primary steps during this important process. When the success of the us and therefore the UK in containing the virus is discussed, tons of credit is being given to the increasing vaccination coverage; however, it's often forgotten that alongside, these countries have scaled up genomic sequencing, tracked the emerging variants and used that evidence for timely actions.  
  • India seems to be faltering on both expanding vaccination coverage and genomic sequencing. Unfortunately, there's not enough attention to proportion genomic sequencing, which as per the first plan was alleged to cover 5% of confirmed COVID-19 cases.
  • Though the procedural steps like fixing the Indian SARS-CoV2 Genomic Consortia, or INSACOG are taken, the sequencing has remained at a really low level of a couple of thousand cases only.  
  • It is no surprise that we understand the Delta variant (B.1.617.2, the first lineage B.1.617 was first reported from Maharashtra, India in October 2020) far but the Alpha variant (B.1.1.7, first reported from Kent, England in September 2020) reported just a month before Delta.  
  • The challenge of insufficient genomic sequencing is further compounded by the pace at which data is being shared, especially when the emergence of strains is so vital in tracking and responding to an epidemic. Reportedly, the Indian government took a fortnight, from early March — when research scientists submitted information on new variants — to issue a public announcement on the variants on March 24, 2021.
Genomics: How a Cutting-Edge Field is Fighting COVID-19 – Global X ETFs

The Delta strain

  • Amidst this, the discharge of findings of the Council of Scientific and Industrial Research-Institute of Genomics; Integrative Biology and National Centre for Disease Control and Academy of Scientific and Innovative Research study; tracking variants of SARS CoV-2 in Delhi; on a pre-print server (yet to be peer-reviewed) may be a welcome change and provides new insights.
  • Based upon the analysis of nearly 3,600 genomic sequence samples from November 2020 to April 2021, the authors have reported that by April 2021, the Delta variant became the foremost circulating variant in Delhi and was found in nearly 60% of the samples analyzed; is 50% more transmissible than the Alpha variant (which already had 70% higher transmissibility over the ancestral virus); is probably going to be related to high viral load, as reflected by the declining Ct value (for RT-PCR) over the study period and resulted during a higher proportion of breakthrough infection (people already vaccinated getting infected).  
  • Based upon these findings, the authors attribute the Delta variant liable for the pandemic wave (which was fourth for the city-state) in Delhi in April-May 2021. However, the authors didn't find any difference within the severity of disease or case death rate thanks to the Delta variant and suggested the necessity for further studies.
  • This is the primary detailed study of SARS CoV-2 genomic sequencing data from any Indian State and provides very useful insight on the behavior and impact of Delta variants.  
  • Around the same time, Public Health England (PHE) reported that the Delta variant has become the foremost common circulating strain within the U.K., replacing Alpha.  
  • The early data from the PHE has interpreted that the Delta variant could also be liable for more severe disease and a better rate of hospitalization compared to all or any previous variants. every week before this data, on May 27, the PHE reported that the effectiveness of one dose of vaccine (amongst symptomatic patients) was lower against the Delta strain.  
  • On June 3, the medical journal The Lancet published research findings from laboratory studies which examined the neutralizing capacity of antibodies from individuals vaccinated with two doses of Pfizer-BioNTech, which was nearly 5.8 fold lower against Delta variants and a couple of .6 fold less against the Alpha variant, in comparison with the ancestor virus.
  • Our knowledge domain and understanding of emerging strains are getting to be the key to deploy public health interventions (vaccines included) to fight the pandemic. The emerging variants — with early evidence of upper transmissibility, immune escape, and breakthrough infections — demand continuous re-thinking and re-strategizing of the pandemic response by every country. research projects would make a difference as long as it leads to informed policy decisions. There are a couple of steps Indian policymakers should consider as urgent.

The steps ahead

  1. First, India must proportion genomic sequencing, across all States. There should be sufficient and representative samples collected for genomic sequencing to trace district-level trends in circulating variants. More genomic sequencing is required from large urban agglomerations. A national-level analysis of collated genomic sequencing data should be done on a daily basis and findings shared publicly.
  2. Second, the Indian government must invest and support more scientific and operational research on vaccine effectiveness. the info should be analyzed on a daily basis and will include various stratifies like age, gender and comorbid conditions, etc.
  3. Third, there are early indications of immune escape and reduced vaccine effectiveness against the Delta variant (especially after one-shot). India, till the top of May, has administered a minimum of one dose of vaccines to 43% of individuals older than 60 years and 37% of these older than 45 years.  

Does it mean the main target of vaccination should be to realize saturation coverage of the high-risk population, with both shots, then round to everyone?  

Does it mandate a requirement for a reduced gap between two doses of Covishield for anyone older than 45 years?  

Should vaccination of these 18-44 years be placed on hold till vaccine supply is assured or should it's done only in districts where the Delta strain is predominant?  

These are the questions that experts got to deliberate and are available up with the answers.

  • The data from genomic sequencing has both policy and operational implications. The State and district officials should engage the epidemiologists in arising with practical and operational implications and methods. 
  • As Indian States decide to open up after COVID-19 restrictions, the settings with predominantly the Delta variant in circulation (which has higher transmissibility) should aim for much stricter adherence to COVID appropriate behavior, publicly places.

Use evidence for actions

  • Continuation of the many unproven and ineffective therapies in COVID-19 treatment guidelines is proof that India isn't quick in adopting evidence to the practice.  
  • There is a requirement for rapidly expanding genomic sequencing, sharing related data in a timely and transparent manner, and understanding the impact of the latest variants on transmissibility, severity, and vaccine effectiveness.  
  • The only assured thanks to fighting the pandemic is to use scientific evidence to make a decision on policies, modify strategies and take corrective actions. As India prepares for the third wave, increasing genomic sequencing and therefore the use of scientific evidence for decision-making isn't a choice but an absolute essential.

Source: The Hindu

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