Covid-19: XE variant enters India; here's all you need to know

While India last week lifted all Covid-19-related restrictions, the government authorities have indicated the presence of a new recombinant XE variant in Maharashtra. Even though national tally of Covid-19 cases is dipping, emerging variants of SARS CoV2 may disturb the flattened curve of the pandemic in India.

What do we know about XE variant?  

The WHO stated that the SARS-CoV-2 virus continues to evolve. Given the current high level of transmission worldwide, it is likely that further variants, including recombinants, will continue to emerge, it said. The apex global public health agency has explained that recombination is common among coronaviruses and is regarded as an expected mutational event.  

WHO is tracking recombinant variants, both recombinants of Delta (AY.4) and Omicron (BA.1) (e.g., XD Pango lineage), as well as recombinants of BA.1 and BA.2 (e.g., XE Pango lineage). The WHO said that the currently available evidence does not suggest that it is more transmissible than other circulating variants.  

The XE recombinant is being tracked as part of the Omicron variant. This recombinant was first detected in the United Kingdom on 19 January and approximately 600 sequences have been reported and confirmed as of 29 March 2022, as per WHO. Early estimates suggest that XE has a 10 per cent transmission advantage as compared to BA.2; however, this finding requires further confirmation, the WHO further said.
 
What is the situation in India?

 The Integrated Disease Surveillance Programme (IDSP) Public Health Department, Maharashtra in its bulletin issued on Wednesday said that new XE variant has been found in 50 year old female, a South African National. This lady came to India on February 10, 2022 from South Africa. She has been tested on February 27, 2022 for Covid-19 and was found positive. Her lab sample has been referred to Kasturba Hospital Central laboratory for WGS. It was found to be a new XE variant in initial sequencing. Though GISAID also confirmed it, INSACOG has decided to go for another round of genomic sequencing at National Laboratory for sure confirmation of XE variant. This lady is totally asymptomatic and was found to be RTPCR negative on repeat testing, the department said.

Indian SARS-CoV -2 Genomics Consortium (INSACOG) studies and monitors genome sequencing and virus variation of circulating strains of Covid-19 in India. The union health ministry, however, disagrees with the development related to XE.

"FastQ files 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 the genomic picture of 'XE' variant," Union health ministry said in a statement.

India's Covid-19 vaccination coverage is high. India's cumulative Covid-19 vaccination coverage has exceeded 185.20 crore on Thursday with over 2.04 crore vaccine doses administered for age group 12-14 years.  India's active caseload currently stands at 11,639 with 1,033 new cases reported in the last 24 hours. Recovery Rate currently stands at 98.76 per cent and weekly positivity rate is presently at 0.22 per cent.
 
Why should India worry?

According to a technical brief released by UK Security Agency on March 25, 2022 on SARS-CoV-2 variants of concern under investigation in England, three recombinant lineages are known - XD, XF and XE.  XD and XF are recombination of Delta variant and BA.1 lineage of Omicron. XD has been detected in France, Denmark and Belgium. XF have been detected in England, but in small numbers.  

XE is a recombinant of BA.1 and BA.2 and may have developed in a person infected with both BA.1 and BA.2.  In addition, it also has three mutations which are not present in BA.1 or BA.2 sequences. Significance of these mutations is being worked out, explains Lalit Kant, a scientist and former head of epidemiology and communicable diseases at the Indian Council of Medical Research (ICMR).  

He said that preliminary reports indicate a growth advantage (increased transmission) of nearly 10 per cent as compared to BA.2. Incidentally, BA.2 has 75 per cent greater relative growth rate as compared to BA.1. "But more data is needed to make a definite statement. It is also not known whether XE leads to higher hospitalisation or sever cases or is more lethal than BA.1 or BA.2," said Kant. "Given the early indications of advantage of higher transmissibility over the BA.2, XE has the potential to become the dominant lineage. It is too early to comment upon whether it would lead to more severe cases or higher number of deaths," he said.

Kant further warns that if XE starts to spread beyond England, given the traffic between India and England, it would reach India very soon on a massive scale.  "RT-PCR test picks up the XE, rapid tests are also likely to detect it. India should keep up the monitoring of genomic variation in SARS-CoV-2 isolated from India to detect it early.  Since BA.2 lineage is a substantial fraction in India, and as major part of XE comes from BA.2, immunity against BA.2 is likely to protect against XE also. Chances of breakthrough infections are possible," said Kant.

On whether XE has a potential to bring a fourth wave of infections, Kant said that as major portion of XE comes for BA.2 which was the primary cause of recent surge, people who got Omicron infection may have antibodies to protect against XE.  However, more data is required to make an informed statement, he said.
 
What are the recommended precautions?

Ranging from WHO to government departments and virologists, people should continue to follow a Covid appropriate behaviour. The WHO has recommended countries to carry on genomic surveillance. "The evolution rate and the risk of the emergence of new variants, including recombinants, is still very high. The implementation of continuous, comprehensive and representative community sampling and sequencing strategies, alongside timely sharing of data by Member States, remain critical for tracking and understanding the behaviour of SARS-CoV-2," the WHO's latest weekly epidemiological update said.

Public health experts have said that the new variants will continue to emerge but public need not to panic and follow covid appropriate behaviour. "There will be newer variants which appear, and we will need to watch out for those that are more virulent (cause more severe disease). We need to ensure that vulnerable individuals are protected with vaccinations, and boosted, when warranted. I do not think we should sensationalize newer variants and cause panic, unless they are indeed variants which are likely to cause more severe disease," Dr Lancelot Pinto, consultant pulmonologist and epidemiologist at PD Hinduja Hospital said.

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