XFG dominant strain, multiple Omicron subvariants spreading in Maharashtra, reveals genome study

Time of India

18-06-2025

Pune: Multiple emerging Covid-19 strains — all Omicron subvariants — were spreading across the state, Maharashtra's genome sequencing surveillance revealed.
The latest sequencing data from 184 samples across 10 districts showed XFG as the currently dominant variant with 84 cases.
It was followed by 38 unassigned variants, 34 LF.7.9 cases, 27 JN.1 cases and one NB.1.8.1 case detected in Pune.
Nine samples from Mumbai were detected with the XFG subvariant, while three others with LF. 7.9.
The NB.1.8.1, identified in a 29-year-old woman from Pune, showed high ACE2 affinity and immune evasion, hinting at the variant's potential to dominate future surges as per recent studies. ACE2 acts as a receptor for the spike protein of coronaviruses, allowing the virus to enter host cells.
XFG, dominating in Maharashtra, and LF.7.9 are noted for their strong immune escape because of specific mutations, though their lower receptor-binding efficiency may require further adaptations.
Dr Rajesh Karyakarte, Maharashtra's genome sequencing coordinator, BJ Medical College, told TOI, "After NB.1.8.1 was identified in Hong Kong as causing a surge in Covid cases, we at BJGMC, Pune, and NIV, Pune, parallelly started sequencing RT-PCR positive Covid-19 samples for the presence of this SARS-CoV-2 variant.
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CSIR-NCL, Pune's study also showed a spike in SARS-CoV-2 signals. Our findings after whole genome sequencing (WGS) revealed XFG to be the most dominant variant in the state, which wasn't a dominant global variant at that time around the world.
We also identified LF.7.9 as another major variant in tested samples."
Dr Karyakarte said, "The numbers confirm that XFG drove the current surge and not NB.1.8.1 (labelled Variant Under Monitoring [VUM] by WHO).
After studying the sequences uploaded on WHO recommended GISAID database, it is clear that NB.1.8.1 is more common in Southeast Asia, while XFG prevails in India, Pakistan and Bangladesh — possibly because of immunity factors. Recently, XFG has also been rising in the US."
Dr Ameet Dravid, infectious disease expert, Noble Hospital, said, "XFG is merely an Omicron sub-variant, similar to those in circulation during the third wave in 2022.
Thanks to immunity built from previous infections, we're seeing very few severe cases this time. XFG is highly transmissible because of mutations that allow it to spread easily from person to person, leading to many upper respiratory tract infections.
Its capacity to damage lungs or cause complications is minimal. So, patients with these symptoms are recovering well with outpatient treatment."
Dr Dravid said, "Only a tiny fraction requires admission for pneumonia or ARDS (Acute Respiratory Distress Syndrome), the complications we saw in the first three waves.
The damage has been limited despite low vaccination rates and waning vaccine-induced immunity over the last three years. We're relieved there hasn't been a significant surge in Covid admissions. While cases are increasing, most are mild, and improving with symptomatic care like nasal decongestants, cough suppressants and paracetamol for fever or body aches.
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Hospitals in the city reported a noticeable uptick in Covid cases this week compared to previous weeks.
Daily or alternate-day deaths, mostly among those with pre-existing conditions, have been recorded. The state health data indicated 31 fatalities since January this year — as many as 30 linked to comorbidities and one to another illness.
Infectious disease specialists said this trend mirrored past surges. Individuals with underlying health issues remain vulnerable as infections rise.
Dr Piyush Chaudhary, infectious disease specialist, Jehangir Hospital, said, "This variant (XFG) appears mild, but even mild strains can lead to some mortality, especially if the number of cases is high.
The elderly or those with comorbidities may experience severe outcomes. We also haven't seen worsening severity — patients in ICU were there because of other medical conditions, not Covid itself. We must determine if Covid contributed to deaths or if underlying comorbidities were the primary cause.
Currently, it seems, comorbidities, not Covid, are driving severe cases this season. Case numbers are definitely rising, though many with mild symptoms aren't testing. Among those tested, the positivity rate has increased proportionally."