On June 6, the government said revised strategy would detect new variants; on September 6, it said the first strategy had served the purpose
The Union Ministry of Health and Family Welfare issued a statement September 6, 2021, contradicting ‘media reports’ that genome sequencing and analysis had decreased in India. Down To Earth (DTE) had published a story In-depth: What ails India’s coronavirus genome sequencing system September 2.
It had pointed out that the number of samples sequenced and analysed in July gone down to 1,321 as compared to the month of June, when it stood at 5,542, according to data accessed August 31 from the Department of Biotechnology-Institute of Genomics and Integrative Biology (DBT-IGIB) portal.
The press statement issued September 6 said the number of samples sequenced in the month of July was 10,202. DTE, in its report, made it clear that the story talked about not just the number of samples sequenced but the number of samples sequenced plus analysed, last accessed August 31 was 1,321.
There is an important difference between just the number of samples sequenced and those sequenced plus analysed. The analysis of sequence, as explained in the story, would mean assigning lineage (what is the variant of the virus) after the sequencing is done.
The press statement also said the number of samples that had been sequenced and analysed, as indicated by the National Centre for Disease Control (NCDC), was 6,990 for the month of July.
Even today, when one accesses the data on the government portal for the month of July, it stands at 4,743, a difference of 2,247 as claimed in September 6’s press statement.
The government also said in the statement that the sequences reflected in the portal were according to the collection date of samples and did not depict the number of samples sequenced in a particular month.
However, the portal does not mention this on any of its pages. DTE, before filing the story, had tried to contact NCDC Director Sujeet Kumar Singh and DBT Secretary Renu Swarup. None of them had responded to requests.
Changes in guidelines: Shifting goalposts
The press statement stated that the objectives of sequencing five per cent of all positive samples had been met by January-end. This is called random sampling according to which a certain proportion of positive cases is sequenced.
The strategy of random surveillance was changed to sentinel surveillance in April according to which where 300 samples would be sent by every state from their 10 respective sites that had already been selected. This is called sentinel surveillance.
The press statement said:
For the detection of presence of VoC inside (the) country, five per cent of the positives (by RT-PCR) were targeted for sequencing. Both the objectives were achieved by the end of January, 2021.
In other words, the random surveillance was adopted to detect the presence of a variant of concern or VoC and the target of that was achieved. Hence, the shift to sentinel surveillance.
Contrary to this, the press statement issued June 15, 2021, said:
In line with global sequencing strategy and WHO guidance document, the sampling strategy has been revised (to sentinel surveillance) by INSACOG with the objective:
1. To detect emerging genomic variants / mutations by prospective sampling
2. To detect the VOCs / genomic variants in special / unusual events like large clusters, unusual clinical presentation, vaccine breakthrough, suspected reinfections, etc.
So, while the press statement issued September 6 said the strategy for random surveillance was changed to sentinel because the objective of detecting VoCs was met, the press release issued in June said the latter strategy was devised very much to detect VoC.
There is no clarity in the thought process of the government as to what would help detect VoCs — the earlier strategy or the revised one.
Where are the sequences?
The September 6 press statement said the government had sequenced 52,619 samples April through July. On March 24, 2021, the NCDC director had said in a press meet that 10,787 samples had been sequenced since then. This makes a total of 63,406 sequences till July.
However, there is no public platform where a scientist outside the government set-up can see these sequences. GISAID, an open-access global platform, where all countries are uploading their sequences, shows India has so far submitted 45,763 sequences, a difference of more than 17,000 sequences, a point that was highlighted in the DTE piece as well. The government release was silent on this.
The scientists quoted in the story had clearly said this difference in both the numbers was intriguing to them. They had added that the delay in uploading sequences on the open-access platform might reduce their significance as the sequence might have undergone a few more changes by the time it was uploaded.
To understand what exact mutation (or the change) has occurred in the virus, scientists need to read the sequences and not just the final analysis uploaded on the DBT-IGIB portal.
The press statement was also silent about the time lag difference pointed out in the story. The government had claimed in Parliament, as in press statements otherwise, that the turnaround time of samples to sequencing was two-three weeks, as opposed to a research paper (referenced in the story) that was published recently and highlighted that it was 57 days for India.
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