Genome sequencing by Indian SARS-CoV-2 Genomics Consortium progressively increased: Centre

New Delhi [India], September 6 : The Central government on Monday refuted the allegation that genome sequencing by the Indian SARS-CoV-2 Genomics Consortium (INSACOG) has declined sharply while adding that sample sequencing has progressively increased.
According to the Ministry of Health and Family Welfare, there have been some media reports alleging that genome sequencing and analysis of the COVID19 declined sharply in India even as cases of the disease continued to rise. The report further claimed that the country sequenced a very low number of samples till date.
"It is clarified that the number of sequences, as quoted in the report, seems to be taken from the Indian COVID19 Genome Surveillance portal. The sequences analysed in the IGIB SFTP are as per the collection date of samples and does not depict the number of samples sequenced in a particular month. The samples sequenced by labs of INSACOG consortium also depends on the samples sent by the respective states," the ministry clarified.
The number of samples sequenced in January was 2207, in February 1321, in March 7806, and in April it was 5713.
Additionally, in the month of May samples sequenced was 10488, in June it was 12257, in July 6990 and in August it was 6458.
Further, the Initial part sequencing of samples by INSACOG labs was aimed at detecting the Variants of Concern (VOC) among incoming international travellers and also to see whether any person with VOC has entered the country in past one month (double the incubation period of 28 days) from the date of establishment of INSACOG (26th Of December, 2020).
For the detection of the presence of VOC inside the country, 5 per cent of the positives (by RT-PCR) were targeted for sequencing. Both the objectives were achieved by end of January 2021, it said.
"Many states like Maharashtra, Punjab and Delhi started showing rising trends in the month of February and as a response, the sequencing was enhanced in four districts of Vidharbha, 10 districts of Maharashtra and around 10 districts of Punjab," the ministry added.
Moreover, the numbers have not been fixed to 300 samples per month or 10 sentinel sites per State. These are the indicative numbers and the states and UTs have been provided with the flexibility of identifying more sentinel sites ensuring geographic representation from all parts.
In addition to the sentinel sites, there is the option for the States of sending vaccine break-through, reinfection or other unusual presentation samples for sequencing to INSACOG Labs.
Furthermore, the strategy of sentinel surveillance made sure that samples from each State were geographically well represented as the 5 per cent of random sampling strategy resulted in samples from certain districts being over-represented, while some districts remained unrepresented from States.
With the decrease in positivity, the samples available from the sentinel sites catering to districts with zero or single-digit weekly new cases have also gone down. Currently, over 86 districts in the country are having zero weekly new cases.
For the past one month, the majority of the new cases are from only two states, namely Kerala and Maharashtra. At present, out of the total 45000 new cases, more than 32000 cases are from Kerala and more than 4000 cases from Maharashtra which means that 80 per ce cases are from 2 states and only 9000 cases, which is around 20 per cent, are from rest of the Indian states. This is also reflected in the samples sequenced from various states.
Since July onwards, for accurate sharing of sample particulars and timely communication of the WGS results, data for samples for WGS by the sentinel sites is being shared via the IHIP portal which ensures real-time sharing of sample particulars and WGS results, the ministry added.
Accordingly, 9066 samples were sent through sentinel sites in July and 6969 samples were shared in August.