Covid XE variant in India? Centre denies reports confirming first case

Confusion reigned supreme on Wednesday on what reportedly was India’s first case of XE variant of SARS-CoV-2 with the Centre rejecting the Maharashtra government and BrihanMumbai Municipal Corporation’s claims of detecting such a variant in the western metropolis.

The patient is a 50-year-old lady costume designer who works in the Hindi film industry and has a travel history to South Africa. The patient’s identity has been kept confidential.

The state authorities and BMC confirmed the detection of the new variant. “The lab sample has been referred to Kasturba Hospital central laboratory for whole-genome sequencing. It has been found to be an XE variant in initial sequencing,” Maharashtra Public Health Department said in a statement.

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The Union government, however, denied it. "FastQ files (raw genome data) in respect of the sample, which is being said to be XE variant, were analysed in detail by genomic experts of INSACOG who have inferred that the genomic constitution of this variant does not correlate with a genomic picture of XE variant. The present evidence does not suggest it as an XE variant,” official sources said in Delhi.

Sources at INSACOG told DH that such confusion was created due to “inadvertent errors in the automatic system” to identify the variants.

“The automated software for variant annotation presently misclassifies any Omicron with specific Delta variants as XE. This could be a sequencing or analysis artefact (errors) or a real case. The only way to verify is manually checking from raw data,” sources said.

Also Read | India's first XE Covid-19 variant case reported in Mumbai

The INSACOG was conducting a genomic analysis of the case, official sources said in Delhi. Officials from the Integrated Disease Surveillance Programme of Maharashtra too said a reconfirmation was being done.

“There is no need to panic. The patient recovered in two days last month. But we have to be vigilant,” Mumbai’s municipal commissioner Iqbal Singh Chahal said.

According to the BMC, the patient arrived in Mumbai on February 10 and initially was found Covid negative. But during the second round of testing, she tested positive on March 2.

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“The patient has a foreign travel history. We put this sample for genome sequencing along with 229 samples. “Out of the 230 samples, 228 are Omicron BA.2, one Kappa and one XE. The XE patient has recovered in 2/3 days and all high-risk contacts are negative. There is nothing to worry about,” it said.

Earlier in the day, the World Health Organisation said the XE recombinant (BA.1-BA.2) - detected first in the United Kingdom on January 19 - was being tracked as part of the Omicron variant.

“Early estimates based on limited preliminary data suggest that XE has a community growth rate advantage of about 10% as compared to BA.2. However, this finding requires further confirmation. Some media have misreported the potential growth advantage of 10% as 10 times. This is incorrect. If the 10% increase in growth is confirmed, this variant would be 1.1 times more transmissible, not 10 times,” the UN health body said.

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