What Do We Know About the New SARS-Cov-2 Variant PY.1 That is Suddenly Emerging and Becoming Predominant Fast!
Nikhil Prasad Fact checked by:Thailand Medical News Team Jun 16, 2025 3 weeks, 23 hours, 36 minutes ago
Thailand Medical News: As we had predicted…the world is going to see a prolonged COVID-19 surge globally this time round with not one but many different SARS-CoV-2 variants at play and they too will be very quickly displaced by newer variants with even more enhanced immune evasiveness and transmissibility. Do not be surprised that we even reach an anomalous state, when even previous infections and the vaccines offer not a single ounce of protection against the newer variants and their sub-lineages and people will be perpetually be reinfected with newer variants and sub-lineages!
What Do We Know About the New SARS-Cov-2 Variant PY.1 That is Suddenly Emerging and Becoming Predominant Fast!
While we are dealing with variants like NB.1.8.1, XFG, XFC, LP.8.1.1, XFG2, LF.7.9.1, XFJ, PQ2, NY.3, LF.7.7.2, NW.1, XFP etc and even the new BA.3.2 sublineages, a new variant called PY.1 has emerged on the scene and is becoming a concern to many variant hunters and researchers due to its rapid growth.
https://cov-spectrum.org/explore/World/AllSamples/Past2M/variants?aaMutations=S%3AA435S&nextcladePangoLineage=PY.1&
The SARS-CoV-2 variant PY.1 is a relatively new sub-lineage that emerged as part of the ongoing evolution of the virus.
Thailand Medical News is providing whatever information we have on the PY.1 variant so far:
-Origin and Lineage
Parent Lineage: PY.1 is a descendant of LF.7.9.1, which itself stems from JN.1.16.1, a subvariant of the Omicron lineage characterized by the Spike R346T mutation (part of the "FLiRT" group).
https://x.com/Mike_Honey_/status/1934150367832629684
https://x.com/Mike_Honey_/status/1934150361872535826
-First Detection: The earliest reported sample of PY.1 was identified in Ontario, Canada, in early March 2025. It subsequently spread to North America, Europe, and other regions globally, with notable success in India.
https://x.com/Mike_Honey_/status/1934150334043300048
-Characteristics
-Mutations: PY.1 is characterized primarily by nucleotide mutations rather than changes in the spike protein, which distinguishes it from other variants that often rely on spike protein alterations for immune evasion or transmissibility. This makes its rapid growth somewhat unique and challenging to explain without further study.
-Additional Mutations: Some samples of PY.1 have been noted to carry the A435S mutation alongside the 679R muta
tion, though the significance of these mutations is not yet fully understood.
https://x.com/JosetteSchoenma/status/1934529879212515618
-Prevalence and Spread
Global Prevalence: PY.1 initially remained below 1% of global SARS-CoV-2 sequences for several months but began to grow rapidly in mid-2025, reaching approximately 10% of global prevalence by June 2025.
https://x.com/xz_keg/status/1934467551574302845
-Regional Success: In India, particularly in Delhi, PY.1 has shown significant growth, reaching up to 40% frequency in recent sequences. However, its growth in India appears to be partly due to resumed sequencing efforts rather than an inherent growth advantage in all contexts.
https://x.com/Mike_Honey_/status/1934150350053019859
https://x.com/JosetteSchoenma/status/1934492924441407579
-Competition: PY.1 is competing with other variants such as NB.1.8.1 and XFG (and its sublineages like XFP and XFG*) for global dominance. Its success varies by region, with some sublineages potentially contributing to its rise, though it faces challenges from more dominant variants like XFG.
https://x.com/xz_keg/status/1934467551574302845
-Public Health Impact
Transmissibility and Severity: There is no definitive evidence yet that PY.1 is more transmissible or causes more severe disease compared to other circulating Omicron-derived variants. Its growth advantage may be due to factors like waning population immunity or slight immune evasion, but preliminary laboratory studies suggest it may have lower in vitro infectivity compared to variants like LP.8.1 and XEC.
-Current Status
Classification: PY.1 is not currently listed as a Variant of Interest (VOI) or Variant of Concern (VOC) by the World Health Organization (WHO) or the European Centre for Disease Prevention and Control (ECDC). It is likely being monitored as a Variant Under Monitoring (VUM) due to its recent growth.
-Surveillance: The WHO and regional health authorities continue to track PY.1 through genomic surveillance, emphasizing the importance of global sequencing efforts to monitor its spread and potential impact.
Limitations and Knowledge Gaps
-Data Limitations: The understanding of PY.1 is limited by gaps in global genomic surveillance, particularly in regions with low sequencing capacity. The lack of spike protein changes makes its growth mechanism unclear, requiring further research.
-Epidemiological Studies: There are no comprehensive studies yet on PY.1’s transmissibility, immune evasion, or clinical outcomes compared to other variants.
Conclusion
PY.1 is an emerging SARS-CoV-2 variant that has gained traction globally, particularly in India, since early 2025. While it has shown rapid growth in some regions, reaching around 10% of global sequences, it is not yet considered a significant public health threat compared to other Omicron subvariants like NB.1.8.1 or XFG. Ongoing surveillance is critical to understanding its impact. However, its success without notable spike protein changes suggests unique evolutionary dynamics that warrant further investigation.
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Read Also:
https://www.thailandmedical.news/news/what-we-know-so-far-about-the-sars-cov-2-variant-xfg-that-is-a-competitor-to-the-nb-1-8-1-variant
https://www.thailandmedical.news/news/covid-19-surge-in-india-is-driven-by-multiple-variants-including-xfg-xfp-and-nb-1-8-1-with-xfp-driving-disease-severity
https://www.thailandmedical.news/news/sars-cov-2-nb-1-8-1-s-new-spawns-pq-1-and-pq-2-acquire-sars1-mutations-raising-global-alarm
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