Highly contagious variant outpaces Omicron to become dominant strain
The rapid spread of a new Omicron sub-variant known as JN.1 has quickly made it the dominant COVID strain in the U.S. and many parts of the world, driving a record-setting surge of new infections. According to data from the CDC, JN.1 accounted for over 75% of new COVID cases in the U.S. last week, overtaking the previously dominant Omicron offshoots.
With even more mutations than Omicron, the new variant is concerning health experts with its ability to evade existing immunity. “This is certainly the most transmissible variant we have seen yet,” said CDC Director Dr. Rochelle Walensky in a press briefing Tuesday. “The sudden rise of JN.1 demonstrates that this virus continues to evolve unpredictably.”
JN.1 is believed to have first emerged in the U.S. sometime around mid-November last year. After spreading through Europe, the variant took off rapidly in America following the busy holiday travel season. Daily case counts have doubled nationwide in January amid JN.1’s proliferation.
Three most common JN.1 symptoms
The constellation of symptoms most frequently associated with JN.1 infections are:
- Sore throat
- Body aches and pains
Unlike earlier variants, cough, fever and shortness of breath are less common with JN.1. Anosmia —loss of smell— has also become less of a hallmark symptom.
“The symptoms really run the gamut and can vary quite a bit from person to person,” said Dr. Jeffrey Kopin of Northwestern Medicine. “We’re also seeing more instances of vertigo, nausea and vomiting reported.”
Up to a third of those infected experience no symptoms at all but can still transmit the virus, underscoring the need for continued vigilance.
Children returning to school drives case explosion
The timing of JN.1’s spread coincided with the return to school after winter holidays, leading to an exponential growth in infections among children.
Pediatric hospitalizations are now at their highest level of the entire pandemic as a result. Health officials widely expect case counts to continue rising as schools resume in-person instruction.
Table 1. Reported US COVID-19 cases among children
|Jan 16 (proj.)
“This virus continues to be extremely adept at infecting children in particular,” Walensky said Tuesday. “Parents and schools need to take this threat very seriously and uphold prevention measures.”
The heavier toll on kids is believed to be driven largely by JN.1’s mutations making it even more adept at binding to human cells. The variant also demonstrates a longer incubation time before symptoms emerge.
“JN.1’s genetics allow for stealthier spread among groups in close contact like students and classrooms,” said University of Minnesota epidemiologist Michael Osterholm in an interview with NPR Monday.
Long COVID risk climbs higher
Alongside astronomical case figures, experts warn JN.1 is likely to spawn a crushing new wave of long COVID cases in both adults and children. Up to 30% of those infected can experience symptoms like brain fog, headaches and fatigue lasting months after clearing the initial infection.
“Repeated re-infections only pile on more risk of developing lasting, debilitating symptoms,” said Osterholm.
He advises strict mask usage and distancing precautions for anyone exhibiting cold or flu-like symptoms to avoid infected others. “Assume its COVID and behave accordingly until proven otherwise,” he urges.
Research indicates each re-infection confers more damage to the body’s organs and vascular system. The crushing burden of disability from long COVID could last for decades.
“This is already a mass disabling event beyond anything we’ve seen since polio,” said cardiologist Eric Topol, founder of the Scripps Research Translational Institute. “We’re still grossly underestimating the footprint.”
JN.1’s rapid mutations evade immunity
The sudden replacement of preceding variants by JN.1 underlines how extensively and quickly SARS-CoV-2 continues to evolve. The virus accumulates around two new mutations per month – twice as fast as the flu.
JN.1 contains over 60 mutations from the original Wuhan strain. This includes 10 changes to the spike protein exploited for entry into cells, and another 15 on sites targeted by neutralizing antibodies.
Table 2. Spike protein mutations in major SARS-CoV-2 variants
|50% more transmissible than original
|Partially evades antibodies
|60% more transmissible than Alpha
|4x more transmissible than Delta
|Extremely high reinfection potential
This high degree of alteration renders antibodies from vaccination or prior illness less effective at blocking reinfection. In lab experiments, JN.1 demonstrates only 30% neutralization from 3 primary vaccine doses. 2 boosters raise that to around 55% protection.
Without better updated vaccines, experts fear waves of repeat breakthrough infections that chip away at immunity while spurring more disabling long COVID outcomes. The crushing burden could overwhelm healthcare systems anew.
“The virus continues to demonstrate its ability to revamp itself in ways that skirt population immunity,” said John Hopkins virologist Dr. Andrew Pekosz. “The scale of this ongoing shape-shifting cannot be overstated.”
New hybrid strains may emerge
The simultaneous circulation of JN.1, older Omicron offshoots like BQ.1/BQ1.1, and the Delta variant raises the prospect for recombinants that hybridize into even more problematic variants.
Delta’s severity combined with Omicron’s uncanny transmission already spawned XBB back in the fall. Now JN.1’s fusion potential worries scientists further.
“This period of peak infections and high reinfection risk coalescing multiple variant lineages can spawn more Frankenstein mutations we definitely want to avoid,” said Pekosz.
CDC sequencing surveillance is ramping up to monitor for such hybrids as the virus continues on its evolutionary path. Scientists urge genomic tracking efforts internationally to keep up with SARs-CoV-2’s mutable nature.
Vaccines vs Variants: The race continues
Pharmaceutical companies continue work updating vaccines to better match circulating variants beyond the original Wuhan strain. Efforts are underway targeting fall boosters to key mutations in JN.1 and other newest Omicron branches.
Experts consider this game of tag between vaccine designers and the virus’ evolution ongoing for years to come. They expect managing COVID to become endemic through some combination of repeated boosters alongside new oral antivirals and infection-fighting nasal sprays under development.
“This shapes up for a forever arms race against a highly adaptable virus already deeply embedded across much of the globe,” said Scripps’ Topol. “But with vigilance and science – and avoiding complacency – it can be tamed to manageable levels like other perennial respiratory pathogens.”
What’s Next? Continued volatility
Health officials caution that infection metrics have proven extremely variable week to week recently. Case counts could jump further as more returning vacationers get tested, then demonstrate steep declines from people testing less.
Experts urge examining trends over longer periods rather than reacting to daily fluctuations that may reflect changes in testing behavior.
“I expect reported cases will remain at elevated levels before peaking then gradually declining over next month or so,” said Osterholm.
CDC models indicate hospitalization rates topping last winter’s peak by early February. Afterwards a slow but erratic tail-off in COVID prevalence is projected heading into spring – until the next seasonal rebound or variant shift.
Vigilance and safety precautions like indoor masking are likely to remain recommended for years. But with gathering vaccination protection and continued innovation, public health leaders are hopeful COVID’s blows can steadily soften.
“This will continue requiring collective ongoing effort,” said Walensky. “But with responsible science plus community partnership, COVID’s trajectory can keep improving.”
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