All samples in last 2 weeks were of new Covid variant JN.1: Genome lab amid spike in cases

On Tuesday, the WHO designated JN.1 as a “variant of interest”, but underlined that the additional global public health risk posed by the new variant “is currently evaluated as low” – implying that the existing therapies and vaccine will continue to provide protection against severe Covid-19 infection.

Union Health Minister Mansukh Mandaviya on Wednesday urged the states and UTs to ramp up testing and refer a large number of samples of Covid positive cases and pneumonia-like illness to INSACOG on a daily basis for sequencing. The reiteration came at a review meeting with the states, where Mandaviya also suggested that mock drill at hospitals be conducted every three months to ensure they are prepared in case of a surge.

The states have been continuously asked to undertake genome sequencing as it is an important tool for surveillance, which ensures an early warning for any increase in cases. It also helps keep track of the variants in circulation, and whether the variant in circulation leads to any changes in symptoms, hospitalisation patterns, or failure of testing kits and therapies.

The past two weeks’ INSACOG data indicates the new JN.1 variant could likely become the dominant one in circulation in the coming weeks in India, as seen in countries such as the USA and Singapore. According to the official data, 21 cases of JN.1 have been detected here so far — 19 from Goa, one from Kerala and one from an area near the Goa-Maharashtra border. There has been no clustering of cases, said the Health Ministry.

Despite the importance of genome sequencing, INSACOG laboratories from states such as Andhra Pradesh, Jharkhand, Madhya Pradesh, Uttar Pradesh, Chhattisgarh, Assam and Meghalaya stopped sending in samples in June and July, according to data analysed by The Indian Express and officials in the know.

The single laboratories in Punjab and Chennai stopped sending samples in April and March, respectively. The laboratory in Bihar stopped sending samples last October. Not all states have a laboratory and some of the bigger laboratories also process samples from neighbouring states.

From states where the JN.1 variant was detected, the samples were submitted in the past two months. The last batch of sequences from the Goa laboratory came on December 17 and from one of laboratories in Maharashtra on November 5.

Even in Kerala, which is known for its public health measures, surveillance of Covid-19 has not been up to the mark. “Most of the tests in Kerala were using rapid antigen kits, while they can give a general idea on the trends; they are not as accurate as RT-PCR. More importantly, the samples taken for rapid antigen tests cannot be sequenced,” an official said.

The last batch of samples from the only INSACOG lab in Kerala came on December 4 after a gap of five months. The previous batch was submitted on July 14. Official data also shows that there have been 16 deaths related to Covid-19 across the country over the past two weeks. Across the country, the number of active cases increased from 115 on December 6 to 614 by December 20. Kerala recorded at least 516 cases and 3 deaths in the past 24 hours, said the Union Health Ministry.