What ails India’s coronavirus genome sequencing system

Synopsis: Sequencing and analysis of the novel coronavirus, a crucial step in infection containment strategy, declined sharply in India, even as cases of the resultant disease continued to rise.  

Introduction

India formed the Indian SARS-CoV-2 Consortium on Genomics (INSACOG), a consortium of 10 genome sequencing labs, in December 2020 to boost efforts for genome sequencing. The number of labs involved in coronavirus sequencing since then has gone up to 28. 

Despite government efforts, the number of coronavirus samples sequenced and analysed in the country went down by 76% in July.  

Whereas, the United Kingdom and the United States have sequenced and shared data for 866,000 and 755,000 samples already, according to GISAID, a global, open-access online repository of genomic data. India has sequenced only 82,000 samples, a meagre 0.2% of its cumulative cases.

More than 100 countries have sequenced a greater share of samples than India. 

How new guidelines hampered the process of sequencing and analysis of the novel coronavirus? 

Initial guidelines from the central government aimed to analyse 5% of all positive samples from each state. This method is known as ‘randomised surveillance’. 

However, four months later, the government decided to change the policy. Only 300 samples were decided to be sent from every state to genome sequencing labs every month. This is called ‘sentinel site surveillance’. 

The government justified the move, saying, as cases were rising exponentially at that time, a 5% sequencing would put a lot of load on the sequencing labs. Further, the revision was according to the World Health Organisation (WHO) standards for genome sequencing. 

What is the WHO’s recommendation in this regard? 

WHO never discouraged random surveillance and even said it is the more sensitive method. WHO has suggested Sentinel surveillance to be adopted by countries that have ‘minimal lab capacity’. Further, WHO had outrightly said that Sentinel surveillance might not be the best representation, contrary to what the government claimed. 

What issues and challenges are faced by India’s coronavirus genome sequencing system? 

Firstly, only two states (Maharashtra and Kerala) have genome sequencing facilities of their own. The rest of the country has to send samples to INSACOG labs run by the Centre. 

Secondly, it is difficult for a country as big as India to sequence a greater number of samples due to a high caseload. 

Thirdly, according to scientists working at an INSACOG lab, many labs, do not get an adequate number of quality samples either in time or with scientific parameters intact. 

Fourthly, India has a long turnaround time. The UK with 410,000 sequences had uploaded raw data within 16 days on an average. Whereas, India takes about 57 days.

Why the sequencing data needs to be in the public domain? 

The WHO has informed that the data of any sequencing done anywhere in the world should be submitted to open-access platforms like GISAID. This will allow a sequence done in one part of the world to be looked at by the global scientific community.  

If sequences are not shared in the public domain timely, it may defeat the purpose of sequencing because, by the time the sequence is uploaded, it would have undergone several mutations. 

Also, a scientist outside the government setup will not be able to see the nature or location of mutations in the genome sequence of the virus unless raw data is posted. 

Source: This post is based on the article “What ails India’s coronavirus genome sequencing system“ published in Down to Earth on 4th September 2021.