Wave X

From wild type to Alpha (B.1.1.7), Delta (B.1.617.2), Omicron BA.1, BA.2, BA.5, BA.2.75, BQ.1, XBB, JN.1 and now XEC and LP.8.1, the virus keeps evolving, continuously demonstrating its ability to adapt and mutate. 

As we enter the tenth wave of COVID-19 in the U.S, the XEC variant has emerged as the dominant strain - in line with expectations. It could be "a weak leading variant"  but will it be a "very muted holiday wave relative to all prior years, due to weak evolution and large summer numbers"? 

Until recently in the US KP.3.1.1 was dominating wastewater samples and accounting for a considerable proportion of infections. Looking at the growth advantages of variants over the last year led to predictions of significantly lower impact than JN.1 that "XEC should only modestly bump what the winter wave would be without any new variant" by one of COVID forecasters. But other variants are also gaining traction. The offspring of now fading KP.3.1.1, MC.1 appeared on the CDC Variant Chart in the summer and more than tripled since. XEC.2, XEC.4 and XEC.5 are rising alongside XEC, though not yet on the CDC chart and only XEC.4 has a higher growth advantage. LP.8.1 has the highest growth advantage (and is already at 14% in travel samples and in 6.2% sequences in the US) followed by other potential contenders such as MC.10.1, MC.10.2, NB.1 and MV.1 - based on GISAID and nextclade (Nextstrain clades) lineages. MV.1 first appeared in Maharashtra, India in late June. It is descended from JN.1.49 by way of MB.1.1.1. That long evolutionary path has been most successful in samples from India, without any notable success elsewhere. For the circulating variants in the U.S., check the CDC's Variant Proportions Tracker and SARS-CoV-2 Lineage Competition dashboards.

Globally, XEC’s growth trends varied so far. Australia recently faced a severe COVID wave linked to the FLuQE KP.3.* variant, with deaths peaking in June. As of now, the dominant strain is XEC at 40% prevalence.  Similarly, this fall, XEC was reported across 27 countries, including the U.S., Canada, and Europe. Wastewater data indicated elevated viral activity in places like Canada’s Newfoundland and Labrador. This Fall, in Europe (excluding the UK), XEC sub lineages showed a 5% daily growth advantage over the DeFLuQE variants. This pace was thought to predict a crossover during October. Yet, in regions like India, where XEC was first reported, its rise has slowed, yielding to MV.1 and other variants. And in England it peaked in October but started rising again in December. In France, it seems to be outcompeted by MC.10 and a newcomer in the Omicron galaxy, MV.1 which comes from JN.1.49.1.  KP.3.1.1 and XEC remain the top variants. Interactive genomic sequencing tools, such as those by Mike Honey, cov-spectrum collections, SARS-COv2 lineage competition, Raj Rajnarayanan's COVID-19 Variant Dashboard, and forecasts by Jay Weiland and Mike Hoerger (Pandemic Mitigation Collaborative), provide valuable insights into these patterns.

The "X" in XEC's name comes from the fact that the strain looks to be a "recombinant" of two other closely related parent variants, both descendants of the JN.1 strain. It's a hybrid of KS.1.1 (BA.2.86.1.1.13.1.1.1) and KP.3.3 (BA.2.86.1.1.11.1.3.3, a descendant of the FLiRT variants). First discovered in Berlin in June 2024, that summer this lineage has spread to 27 countries, including the U.S., Canada, and several European nations. While its transmissibility is notable, XEC’s global trajectory suggests regional variations influenced by existing immunity and public health interventions.

Year over year comparison of US COVID-19 transmission, consistently shows two waves every year.  This year the expected midyear wave began in May, when the last winter's dominant subvariant, JN.1, gave way to a number of subvariants nicknamed FLiRT — a cheeky name based on the letters of two key mutations, F456L and R346T (Focus only on the letters and add an "i" as a connector, and you get FLiRT, which includes the officially named KP.2 subvariant.)

A successor subvariant, KP.3, had a different mutation — Q493E — and dropped R346T. It was nicknamed FLuQE, pronounced “fluke.” And an even more contagious subvariant — KP.3.1.1 — had a mutation that was deleted, giving it the unofficial moniker deFLuQE, or “de-fluke.” or the two-week period that began Aug. 18, KP.3.1.1 was estimated to make up 42.2% of coronavirus samples nationwide, up from 19.8% a month ago, according to the CDC. And then there were new variants beyond KP.3.1.1.

Meanwhile Flu activity is increasing in both clinical surveillance and wastewater maps. Louisiana joined 7 other states reporting human Bird Flu, with a patient hospitalized for severe H5N1– and California declares emergency. RSV, and Norovirus are also surging according to @Biobot , @WastewaterScan, Verily and NWSS and Canadian wastewater monitoring dashboard. UK HSA  and Australian boards show lower levels of COVID.


Expert forecasters, including Jay Weiland, estimate that 20% of the U.S. population was infected during the wave starting in June 2024. XEC’s impact could be milder than JN.1’s surge last year, but the story is still unfolding. While most attention remains on the XEC subvariant, LP.8.1 is now rapidly rising in the U.S. and could dominate in the coming weeks if its trajectory continues.

At the same time, Flu activity is climbing, evident in both clinical surveillance and wastewater data. Louisiana has joined seven other states reporting human Bird Flu, including a severe H5N1 hospitalization, while California has declared a state of emergency. Additionally, RSV and Norovirus are surging according to @Biobot , @WastewaterScan, Verily and NWSS and Canadian wastewater monitoring dashboards. In contrast, COVID levels in the UK  and Australia appear to be declining, as reflected in data from their health boards.

The interplay of multiple respiratory viruses underscores the complexities of this winter season. As these threats evolve, the season's trajectory will ultimately depend on the delicate balance between viral behavior, individual choices, and community dynamics.


REFERENCES

Tracking XEC (09/13/2024): https://x.com/RajlabN/status/1834633656289157194 (Transmission is higher in 2024 than during any prior September.)

XEC tracker -https://public.tableau.com/app/profile/raj.rajnarayanan/viz/TrackingSARSCoV2LineageXEC-Globally/XEC

https://public.tableau.com/app/profile/raj.rajnarayanan/vizzes

https://pmc19.com/data/

https://x.com/michael_hoerger

COVID-19 trends in Australia: https://github.com/Mike-Honey/covid-19-au-vaccinations#readme

 National Wastewater Surveillance System (NWSS) | National Wastewater Surveillance System | CDC

covSPECTRUM collections

https://cov-spectrum.org/collections/42

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