States prep for Delta+ as mutation cases rise

NEW DELHI : India has begun setting up a sentinel surveillance system specifically for SarsCov-2 variants, with five hospitals and labs in each state sending samples for whole genome sequencing on a regular basis, people familiar with the matter said on Wednesday, adding that 40 cases of the Delta Plus variant have been detected in India so far.

Delta Plus refers to a variant scientifically known as the AY.1, which belongs to the same lineage as the Delta variant that is now established to be significantly more transmissible and possibly resistant to vaccines. AY.1 was classified as a “variant of concern” (VOC) by India on Tuesday. A new genome surveillance system will allow a better understanding of how the virus is mutating and could potentially help catch variants of concern before they take hold.

“In addition to what was earlier being practised, hospitalbased sentinel sites in all states for sample collection are being operationalised. As many as 18 more labs have been recently added to the list of 10 labs in the national Insacog network to scale up genome sequencing. Also, states have to regularly provide 5% positive samples from community to Insacog labs,” said a senior official in the Union ministry of health, on condition of anonymity.

Insacog refers to the Indian Sars-Cov-2 genomic sequencing consortia, which was set up in December after the Alpha variant arose. The network had raised an alarm about the Delta variant but authorities were subsequently accused of delaying timely action which could have mitigated the severity of the second wave that began in March. For instance, not enough viral genomes were sequenced in the run-up to the second wave. The establishment of the sentinel sites should address that gap.

The Union health ministry in a statement on Wednesday added that there are approximately 40 confirmed infections with the Delta Plus variant, an increase from 22 announced by the Union health ministry on Tuesday. These cases have been found in six districts – two each in Maharashtra, Madhya Pradesh and Kerala.

The Union government asked officials in these states to redou

ble containment and testing efforts, and carry out surge vaccinations, it said on Tuesday.

In Kerala, three villages have been shut, officials said, and residents are being mandatorily tested for Covid-19. The cases were among three people, a fouryear-old boy and two women in their 50s, all of whom have now recovered, said an official.

In Maharashtra, state health minister Rajesh Tope announced that 100 samples from each district will immediately be sent for genome sequencing.

Officials in Karnataka on Wednesday said genome sequencing found Delta Plus variant cases in three people, and that they had stepped up efforts to sequence more samples.

According to the Union health ministry statement, states have identified five laboratories and five tertiary care hospitals as sentinel sites, and each is expected to send 15 samples routinely to designated regional genome Sequencing Laboratories (RGSLs).

According to the health ministry, in addition to the sentinel surveillance, there will be additional event-based surveillance for special or unusual clusters – where cases have either grown unexpectedly, there is a change in symptoms or hospitalisation, or that show high breakthrough infections (those that happen despite vaccination).

The details of the epidemiological investigations, study methodology, number of samples to be collected for genome sequencing would depend on the situation or event, the person added.

One expert said more needs to be done, especially since Insacog has sequenced only 45,000 viral genomes since its inception. “We need baseline plus targeting; 5% or 3% of all positive samples plus all deaths, vaccine breakthroughs, unusual presentations, children with hospitalisations, etc, [must be done]. 5% of the 20 million cases we have had since Insacog was established is 1 million. So, we have done onetwentieth of what was proposed,” said Dr Gagandeep Kang, physician-scientist, Christian Medical College, Vellore, Tamil Nadu.

Another said resource limitations must be kept in mind for successful genome surveillance efforts. “When the case load is higher than what you can handle, the best thing to do is to go for smart sequencing, and do more sequencing in areas that look problematic such as areas from where such cases are being reported more, clusters or reporting of other conspicuous events,” said Shahid Jameel, senior virologist, and director, Trivedi School of Biosciences, Ashoka University. Jameel headed an advisory group to Insacog before he resigned from the position in mid-May.

“What is interesting is that for the Delta Plus variant you don’t need to do whole genome sequencing which is expensive and time consuming. One can go for genotyping assays that are cheaper and faster to do and can provide results in even 48 hours. It’s no rocket science as you already know the mutation, so you design probes to detect those changes. Public Health England is already doing this and for a country like ours, smart sequencing and genotyping assays will give us good results,” he added.

“The actual Iinsacog work started around mid February when caseload was around 10-12,000 new cases per day but the country didn’t have the capacity to handle 5% of 200,000-400,000 cases that were getting reported in a day at one point. All 10 labs put together had the capacity to perform about 30,000 sequences per month and that is when they put on hold all other work and focus only on Covid-19. The grouping has done well in finding out what’s circulating, and alerted in March about B.1.617 variant that is now being called the Delta variant, and later on also about the Delta Plus variant,” he added.

The Union health ministry also said that all sub-lineages of the Delta variant , including AY.1 and AY.2, are now considered VOCs. “All Delta sub-lineages are treated as a variant of concern, although properties of AY.1 are still being investigated. Currently, the variant frequency of AY.1 is low in India. Cases with AY.1 have been mostly reported from nine countries of Europe, Asia and America,” it said in a statement.

The inclusion of AY.1 (Delta Plus) and AY.2 in VOC’s list was first made by Public Health England in its most recent technical briefing on June 11.

With inputs from HT Correspondents isn Mumbai, Bengaluru and Thiruvananthapuram