Gujarat Reports First Case of XE Variant of Coronavirus

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Ahmedabad: The XE variant of coronavirus, a more infectious but not more severe than the Omicron variety, has been found in Gujarat. An INSACOG laboratory in Gujarat, the Gujarat Biotechnology Research Centre (GBRC), has reportedly confirmed the variant. 

Additional Chief Secretary Manoj Aggarwal said that the variant was found in a 67-year-old man who had travelled to Vadodara from Mumbai. The man had tested positive for the coronavirus disease on March 12.

“Gujarat Biotechnology Research Centre detected the XE variant in the patient 12 days ago,” Aggarwal said. “The sample was sent for confirmation as per INSACOG [Indian SARS-CoV-2 Genomics Consortium] guidelines to a Kolkata laboratory. The confirmation report of the XE variant was received Friday night. We are getting more details and trying to trace his close contacts.”

INSACOG is a consortium of 10 laboratories that conducts genome sequencing of Covid-19 infections.

Vadodara Medical Officer Dr Devesh Patel told The Indian Express that the patient had developed symptoms including fever when he was staying with his wife at a hotel in the city.

Patel said that the couple had returned to Mumbai after their Covid-19 results came back positive and were under home quarantine there.

“He did not meet anyone in Vadodara,” the official added.

Last week, Mumbai civic officials reported a case of the XE variant from a sample isolated in February, but officials at the Indian Sarscov2 Genome Consortium (INSACOG), a network of labs that tracks sequences, and the Union Health Ministry, are yet to confirm if it is an XE variant.

While several variants of the coronavirus have emerged in the last two years because of mutations, recombination variants occur when, in extremely rare situations, two different lineages of the virus co-infect the same cell in the host and exchange fragments of their individual genomes. This generates a descendent variant having mutations that occurred in both the original lineages of the virus. The XE variant, for instance, is a recombinant of the BA.1 and BA.2 subtypes of the Omicron variant.

While the current XE variant has generated public concern because the World Health Organisation has signalled its potential for increased infectivity, there have been other recombinants of the Sarscov2 that have been identified by genome scientists. There are three hybrid or recombinant viruses in total that have been detected so far. These are XD, XE and XF, of which XD and XF are a combination of the Delta and Omicron variants.

So far, only 600 instances of the XE variant have been officially reported in the global repository GISAID and this is causing confusion among scientists on what relative proportion of genetic material from the BA.1 and BA.2 would qualify for a variant to be in the ‘XE’ category.

The Mumbai civic body that reported the possible case of the XE in Mumbai said that the person was double vaccinated, and had tested negative for COVID-19 on arrival in India. But on March 2, 2022, in routine testing conducted by Suburban Diagnostics, she was found to be positive and quarantined. The result of the test done the following day was negative.

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