JN.1 makes up an estimated 61.6% of COVID cases, CDC data shows.
January 5, 2024, 3:49 PM ET
6 min read
A variant that has been circulating in the U.S. for the last couple of months currently makes up a majority of COVID-19 cases in the United States.
JN.1, a descendant of BA.2.86 -- which is itself an offshoot of the omicron variant -- now makes up an estimated 61.6% of cases in the country, according to data from the Centers for Disease Control and Prevention. This is up from the estimated 3.3% of cases the variant made up in mid-November, CDC data shows.
The Northeast is the region of the U.S. with the highest prevalence, making up an estimated 74.9% of COVID-19 cases, according to the CDC.
Last month, the World Health Organization listed JN.1 as a "variant of interest," meaning it contains changes that may result in increased spread or reduced efficacy of treatments or vaccine but is not as serious as a "variant of concern."
This comes as COVID-19 hospitalizations continue to increase across the U.S., rising for the eighth consecutive week to levels not seen since January 2023.
JN.1 has an additional mutation in its spike protein compared to its parent, BA.2.86, according to the CDC. The spike protein is what the virus uses to attach to and infect cells.
The CDC says this suggests that either the variant is more transmissible or better at evading the immune system than other variants that are circulating.
"It does seem to be more transmissible because it's rising up the charts, not only in terms of the majority of cases right now, but the rate of increase is really dizzying," Dr. Peter Chin-Hong, a professor of medicine and an infectious disease expert at the University of California, San Francisco, told ABC News.
He pointed that out that the U.S. being able to track JN.1 is sign that public health systems are successfully identifying new variants and following variant spread.
"To me, anyway, the U.S. lagged many countries early on in the pandemic, but right now, I think by tracking where JN.1 is going -- not only as a country but in regions -- really gives me confidence that, as we move along in the pandemic, we are able to hopefully identify new variants, the programs in airports, wastewater. They are all going to work together," he said.
Public health experts said there is no evidence JN.1 has different symptoms or causes more severe illness and that it's normal for the virus to mutate, causing new variants to emerge.
Additionally, existing tests, vaccines and treatments are still expected to work, experts say.
In an update on Friday, the CDC said that COVID test positivity levels in wastewater samples are higher than this time later year.
Chin-Hong said data from Singapore and from other countries, where JN.1 was predominant earlier, shows it does not seem to be causing a higher proportion of people to be hospitalized.
"But like with other variants that are more transmissible, the more people that get infected, even if a smaller percentage of them go to the hospital, it's going to numerically mean a lot," he said.
He explained that this is why it's important to get the updated vaccine. As of Friday, only 19.4% of adults ages 18 and older have received the updated vaccine, CDC data shows.
"We know that immunity wanes the fastest in those who are older and those who are immunocompromised," Chin-Hong said. "And for people who didn't get [COVID] in the summer, they might say, 'Well, look, I did all these things. I didn't get it.' It may not be true for JN.1. Enough time has elapsed since many [people] got a shot."
They come to my office every week, sometimes every day. One is a college professor trying to make tenure but cant teach because their heart rate jumps to 160 upon standing. Another is a nurse who is plagued by fatigue and cannot get through the grueling 12-hour shifts. A third has such profound fatigue they run their business from bed; they blur out the background on the zoom meetings and prop their head up with a hand.
These three, and many others, have been diagnosed with myalgic encephalitis, also known as chronic fatigue syndrome. The CDC recommends three criteria for diagnosis: a greatly lower ability to do activities that lasts six months or longer, worsening of symptoms after physical activity, and sleep issues that may include feeling weary after a full nights sleep. Other symptoms may include cognitive dysfunction (brain fog), chronic pain, and light-headedness or dizziness when standing.
There are between 1 and 2 million with this affliction in America today, and with the ongoing COVID crisis, the ranks of the afflicted threaten to grow by many more millions. The layers of their life often strip away like paint, and a first casualty is often their job and whatever worth they got from it. If they are lucky, they have the assistance of a family. If unlucky, they battle in solitude.
As doctors, we often tell them to fight, to struggle. Walk 10 minutes a day and next week you will be able to walk 20. Two-pound weight exercises will turn into five pounds. We will cheerlead you out of this illness. Often, though, this approach only makes things worse, and the standby of graded and increasing movement will improve function does not apply.
The patients I see in my lung clinic, though, afford us a rare opportunity. Prior to COVID, it was thought perhaps a viral illness triggered this cascade of decline and misery. The usual suspects are Epstein-Barr virus or its cousin cytomegalovirus. They are only suspects, though. Now with COVID-19 we believe we have detained an offender.
Former chief medical advisor to the president, Anthony Fauci is one doctor who sees the opportunity here. I spoke with him, and in his precise, careful fashion, he laid out a road map for how to approach ME/CFS.
First, stick with only post-COVID patients; do not dilute your sample with other post-viral conditions.
Second, make sure you have a very strict and agreed-upon definition of what long COVID constitutes: symptoms must be there for at least six months, and a level of significant disability must be documented.
Once you have your population, then cast a wide net into possible avenues of dysregulation. What blood markers were elevated at the start of their infection? What blood markers continue to be elevated after six months? Is there evidence of ongoing reaction to live or broken-down viral DNA? Who are the people who eventually get better? Who are the ones who continue to struggle?
Interesting data is being generated. One study in the journal Nature showed that patients who had died from COVID had clear evidence of viral substrate in tissues throughout the body, including the heart, intestine, and adrenal gland. Most damningly, the brain was frequently involved, with one patient having evidence of viral particles in their central nervous system a full 230 days after initial symptoms.
Another study from Yale shows that despite adequate heart and lung function, oxygen was not being utilized by muscles during exercise, pointing to mitochondrial dysfunction. A recent study out of the University of Pennsylvania implicated low levels of the neurotransmitter serotonin. No organ should be beyond analysis, beyond suspicion.
Large treatment trials have also begun, including interventions involving stem cells, exercise regimens, antibody infusions, and antidepressants like lithium and fluvoxamine. To date, however, there are no FDA approved medications for long COVID or ME/CFS. The mystery endures.
With COVID numbers recently rising, our sample size of people with long-term issues will continue to rise. The best protection against this is to avoid the disease if possible: hand washing, masks in high-risk situations, staying home if ill. Vaccines and boosters are very helpful, and recent studies have shown in both children and adults the vaccine significantly lowers the incidence of long COVID.
Suffering can be endured if there is the possibility of an end, if there is an expectation of convalescence, of the possibility of a return to a remembered life that was more productive, more engaged. We call this hope. With COVID-19 and the clinical trials going on, there is hope for the first time for the millions struggling under the crushing yoke of ME/CFS.
Michael J. Stephen M.D. is a Penn Medicine pulmonary physician and author of Breath Taking, A Biography of the Lungs.
India has recorded 756 new cases of Covid, while the number of active cases of the infection stood at 4,049, the Health Ministry said on Sunday.
Five deaths two each from Kerala and Maharashtra and one from Jammu and Kashmir have been reported in 24 hours, according to the Ministrys data updated at 8 a.m.
The number of daily cases had dropped to double-digits till December 5, 2023, but cases began to increase again after the emergence of a new variant and cold weather conditions.
After December 5, a maximum increase in single-day cases was reported on December 31, 2023, when 841 cases were reported, official sources said.
Of the total active cases, a large majority of these (around 92%) are recovering under home isolation.
The currently available data suggests that the JN.1 variant is neither leading to an exponential rise in the new cases nor a surge in hospitalisation and mortality, the sources stated.
India has witnessed three waves of COVID-19 in the past with the peak incidence of daily new cases and deaths being reported during the Delta wave in April-June 2021. At its peak, 4,14,188 new cases and 3,915 deaths were reported on May 7, 2021.
Since the pandemic began in early 2020, more than 4.5 crore people have been infected and over 5.3 lakh died.
The number of people who have recuperated from the disease stands at over 4.4 crore with a national recovery rate of 98.81%, according to the Ministrys website.
According to the Ministry, 220.67 crore doses of Covid vaccines have so far been administered in the country.
India has recorded a single-day rise of 774 COVID-19 cases while the number of active cases stands at 4,187, the Union Health Ministry said on January 6.
Two deaths one each from Tamil Nadu and Gujarat were reported in a span of 24 hours, according to the Ministry's data updated at 8 a.m.
The number of daily cases was in double digits till December 5 but it began to rise again amid cold weather conditions and after the emergence of a new COVID-19 variant, JN.1 After December 5, the highest single-day rise of 841 cases was reported on December 31, 2023, which was 0.2% of the peak cases reported in May 2021, official sources said.
Of the 4,187 active cases, the majority (more than 92%) are recovering under home isolation.
An official source said, "The currently available data suggests that the JN.1 variant is neither leading to an exponential rise in the new cases nor a surge in the hospitalisation and mortality." India has witnessed three waves of COVID-19 in the past with the peak incidence of daily cases and deaths being reported during the Delta wave during April-June 2021. At its peak, 4,14,188 cases and 3,915 deaths were reported on May 7, 2021.
Since the pandemic began in early 2020, more than 4.5 crore people have been infected and more than 5.3 lakh have died across the country.
The number of people who have recuperated from the disease stands at more than 4.4 crore with a national recovery rate of 98.81%, according to the Ministry's website. According to the website, 220.67 crore doses of COVID-19 vaccines have been administered so far in the country.
The year is off to a rough start when it comes to respiratory illnesses. Though we may no longer be officially in the middle of a pandemic, COVID-19, which is still killing hundreds of people each day, and the usual suspects flu, RSV and other respiratory pathogens are sending thousands to the hospital. Heres what to to know and cover in the midst of this respiratory disease surge.
CDC wastewater data shows the current COVID-19 surge to be the largest increase since Omicron in December 2022, and wastewater detection of the virus continues to rise. As cardiologist and COVID commentator Eric Topol writes in the Los Angeles Times, an estimated 2 million infections a day are occurring in the U.S. The CDCs COVID Data Tracker shows that COVID test positivity appears to be stabilizing, emergency room visits (up 12.8%), hospitalizations (up 20.4%) and deaths (up 12.5%) are continuing to rise.
Frustratingly, the CDCs map of COVID test positivity, hospitalizations, deaths and hospital visits only provides data on geographic regions of the U.S. instead of individual states. But its clear that central Midwest states Kansas, Nebraska, Iowa and Missouri are faring the worst, followed by New England and Great Lakes states.
Its not just the U.S. experiencing a surge. Italys hospitals are overwhelmed with cases of COVID-19, flu, and other respiratory illnesses, and the KFF Global COVID-19 Tracker and WHO COVID-19 dashboard show substantial increases in other parts of Europe and Asia. Topols Substack documents an unprecedented jump in wastewater levels of COVID-19 from the latest COVID variant JN.1, which accounts for approximately 62% of COVID cases in the U.S. as of Jan. 5.
As epidemiologist Caitlin Rivers wrote in a recent post for her Substack, Force of Infection, were in the thick of it now. Doctor visits for influenza-like illnesses the catch-all phrase for flu and otherwise unidentified respiratory illnesses jumped more than a percentage point from the last week of 2023 to the first week of 2024. That means were nearly at last years peak of 7-8%. CDCs FluView shows that influenza test positivity, now at 17.5%, is rising, as are flu hospitalizations and deaths. CDC national data for RSV similarly shows a sharp rise in cases nearing or exceeding last years peak, depending on the metric, though the South shows a decline and infections may be tapering in the Northeast.
News stories began emerging in late November/early December about white lung syndrome or pneumonia, raising concerns about a new pathogen. But as I reported at Scientific American and as others reported elsewhere, white lung is not a real medical term. Its simply a scary lay description, not used by medical professionals, of what we see on a routine chest X-ray, says William Schaffner, M.D., a Vanderbilt professor of infectious disease and medical director of the National Foundation for Infectious Diseases.
The miscommunication about white lung has been substantial enough that multiple hospitals have even published posts to dispel misinformation and anxiety about this term. (All these posts, like the stories linked above, contain excellent sources for respiratory disease articles.)
Still, Iveheard from a few people that their providers have warned them about the condition even though its not something new and distinct from existing pneumonia. Its therefore worth reminding people that white lung only refers to the white that appears in the lungs on an X-ray when someone has pneumonia, regardless of the underlying cause of the pneumonia.
Fall is traditionally when most journalism outlets post their seasonal flu vaccine stories, plus the addition of this years stories about the new COVID and RSV vaccines. But its worth continuing to report on vaccine availability into the new year. Its not too late to get these vaccines, and January and February usually see the highest rates of respiratory illnesses.
Katelyn Jetelina of Your Local Epidemiologist has an excellent graphic of the 2023-2024 respiratory virus vaccines, including what they are, who is eligible for them, how effective they are and when people should get them. Recent research shows that the current COVID-19 vaccine reduces risk of hospitalization and emergency room visits while previous COVID-19 vaccines no longer do so. Further, a recent systematic review found that COVID-19 vaccination in general reduces risk of long COVID, an area of conflicting evidence for several years.
The COVID-19 surge has also brought an upswing in mask requirements across the U.S. Reuters reports that California, Illinois, Massachusetts and New York have all instituted mask mandates at health care facilities. Its worth paying attention to local hospitals in your area to see if theyre requiring masking independent of city, county or state mandates.
Despite the politicization of masks during the pandemic and the CDCs repeated mask recommendation blunders, the data clearly show that masks reduce risk of COVID-19 and other respiratory infections, including for kids (see here, here, here, here and here for research on masking). Unfortunately, a misunderstanding about the limitations of randomized controlled trials and the underestimation of observational evidence has led to misinterpretations of studies and meta-analyses on masking effectiveness. But articles reminding audiences of the effectiveness of masks can help correct misinformation about their utility.
Eris and this winters other dominant SARS-CoV-2 variants
This fall, the dominant strains of SARS-CoV-2, the virus that causes COVID-19, are EG.5, unofficially named Eris, as well as FL 1.5.1 and HV.1, according to the Centers for Disease Control and Prevention (CDC), says Rebekah Sensenig, D.O., Infectious Disease Specialist for Riverside Health System.
As we head into the cooler months, illnesses caused by respiratory viruses, like COVID-19, increase. When its cold out, we all tend to spend more time inside, and viral particles spread between people faster indoors. So, its time to start thinking about protecting yourself and staying healthy through this season.
Since the world was first introduced to the SARS-CoV-2 coronavirus back in 2019 the virus has adapted and changed over time. The CDC tracks emerging strains of common viral illness so we can develop targeted vaccines to prevent infections.
According to the CDCs mid-October 2023 data, the strain EG.5, unofficially nicknamed Eris, makes up almost a quarter of all COVID-19 cases. Right behind Eris are HV.1, accounting for nearly 20% of cases and FL 1.5.1, responsible for 13.5% of cases.
Like all COVID-19 variants, this strand spreads through respiratory droplets. When a person with the infection breathes out droplets, the virus transmits into the air and onto surfaces where it can infect new people. So far, experts dont believe these new variants are more dangerous than other strains of COVID-19.
COVID-19 variants affect the upper respiratory tract the nasal passages, mouth, airways and lungs. Symptoms resemble the common cold and can last up to two weeks and range from mild to severe. Those with a higher risk of serious illness include infants, people over the age of 65 and anyone with a compromised immune system.
According to the World Health Organization (WHO), we will be dealing with COVID-19 for years to come. The good news is we have the tools to reduce the risk of infection and prevent serious illness.
One of the best ways to prevent COVID-19 is to get outside where respiratory illnesses are less likely to spread, says Dr. Sensenig.
You can take a few simple steps to protect yourself and others.
If you are at high risk of serious illness, wearing a mask or respirator provides more protection from diseases transmitted by respiratory droplets like COVID-19.
When it comes to respiratory illnesses and COVID-19, our experts have you covered. From vaccines to treatment and everything in between, we are here to answer your questions and offer personalized recommendations. Make an appointment with one of our providers.
GENEVA (AP) The head of the U.N. health agency said Wednesday holiday gatherings and the spread of the most prominent variant globally led to increased transmission of COVID-19 last month.
Tedros Adhanom Ghebreyesus said nearly 10,000 deaths were reported in December, while hospital admissions during the month jumped 42% in nearly 50 countries mostly in Europe and the Americas that shared such trend information.
Although 10,000 deaths a month is far less than the peak of the pandemic, this level of preventable deaths is not acceptable, the World Health Organization director-general told reporters from its headquarters in Geneva.
He said it was certain that cases were on the rise in other places that havent been reporting, calling on governments to keep up surveillance and provide continued access to treatments and vaccines.
Tedros said the JN.1 variant was now the most prominent in the world. It is an omicron variant, so current vaccines should still provide some protection.
Maria Van Kerkhove, technical lead at WHO for COVID-19, cited an increase in respiratory diseases across the globe due to the coronavirus but also flu, rhinovirus and pneumonia.
We expect those trends to continue into January through the winter months in the northern hemisphere, she said, while noting increases in COVID-19 in the southern hemisphere where its now summer.
While bouts of coughs, sniffling, fever and fatigue in the winter are nothing new, Van Kerkhove said this year in particular, we are seeing co-circulation of many different types of pathogens.
WHO officials recommend that people get vaccinated when possible, wear masks, and make sure indoor areas are well ventilated.
The vaccines may not stop you being infected, but the vaccines are certainly reducing significantly your chance of being hospitalized or dying, said Dr. Michael Ryan, head of emergencies at WHO.
The Associated Press Health and Science Department receives support from the Howard Hughes Medical Institutes Science and Educational Media Group. The AP is solely responsible for all content.
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GENEVA
The head of the World Health Organization said Wednesday that holiday gatherings and the spread of the most prominent coronavirus variant globally led to increased transmission of COVID-19 last month.
Tedros Adhanom Ghebreyesus said nearly 10,000 deaths were reported in December, while hospital admissions during the month jumped 42% in nearly 50 countries mostly in Europe and the Americas that shared such trend information.
Although 10,000 deaths a month is far less than the peak of the pandemic, this level of preventable deaths is not acceptable, the WHO director-general told reporters from the agencys headquarters in Geneva.
He said it was certain that cases were on the rise in other places that havent been reporting, calling on governments to keep up surveillance and provide continued access to treatments and vaccines.
Tedros said the JN.1 variant was now predominant in the world. It is an Omicron variant, so current vaccines should still provide some protection.
Maria Van Kerkhove, technical lead at the WHO for COVID-19, cited an increase in respiratory diseases across the globe not just because of the coronavirus but also because of flu, rhinovirus and pneumonia.
We expect those trends to continue into January through the winter months in the Northern Hemisphere, she said, while noting increases in COVID-19 in the Southern Hemisphere, where its now summer.
Although bouts of coughs, sniffling, fever and fatigue in the winter are nothing new, Van Kerkhove said this year, in particular, we are seeing co-circulation of many different types of pathogens.
WHO officials recommend that people get vaccinated when possible, wear masks and make sure indoor areas are well-ventilated.
The vaccines may not stop you being infected, but the vaccines are certainly reducing significantly your chance of being hospitalized or dying, said Dr. Michael Ryan, head of emergencies at the WHO.
A study published in the journal Scientific Reports explains that pangolin's vulnerability to coronavirus infection might be due to their innate gene pseudogenization.
Study: An RNA-Seq analysis of coronavirus in the skin of the Pangolin. Image Credit:Makabas/ Shutterstock
Pangolins are 30 100 cm long anteaters found in Africa and Asia. Populations of all eight species of pangolin are decreasing in these two continents. Four pangolin species from Africa are now "endangered" or "vulnerable"; three species from East Asia are "critically endangered"; and one species from India is "endangered."
The greatest obstacle to pangolin conservation is the high susceptibility and frequent mortality of captive pangolins due to infections. The pseudogenization of immune system genes in the pangolin genome is believed to be the main contributing factor to high infection susceptibility. These pseudogenes are interferon Epsilon (IFNE), interferon-induced with helicase C domain 1, cyclic GMP-AMP synthase, stimulator of interferon genes, Toll-like receptor 5, and Toll-like receptor 11.
The scientists of the current study have previously analyzed brain and lung samples from a Malayan pangolin and detected a coronavirus infection that was closely related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pathogen of the most recent coronavirus disease 2019 (COVID-19) pandemic.
In the current study, scientists conducted RNA-Seq analysis of the pangolin skin tissue to understand the transcriptional antiviral response in pangolin skin, particularly in the context of interferon Epsilon(IFNE)-deficiency, which is a unique immune feature of pangolin.
They compared the expressions of differentially expressed genes (DEGs) between coronavirus-infected pangolin skin and healthy pangolin skin. They also compared these DEGs with those found in coronavirus-infected human lungs because a corresponding dataset for coronavirus-infected human skin was unavailable. As humans and pangolins are mammals, the scientists expected some similarities in immune responses between human lungs and pangolin skin.
Endogenous retrovirus genes are the remnants of once infectious exogenous retroviruses that became fixed in human or other animals' genomes. They can modulate the innate immune system and facilitate antiviral immune responses through various mechanisms. In this study, the scientists also evaluated how endogenous retrovirus gene expression in pangolin responds to coronavirus infection, particularly in the context of IFNE deficiency.
The scientists identified pangolin coronavirus RNA in the skin of Malayan pangolin. This virus is closely related to another pangolin coronavirus MP789, isolated from the Guangdong pangolin. Since both pangolins were kept at the Guangdong Wildlife Rescue Center, the scientists believe both coronaviruses originated from the same source.
The comparative analysis of DEGs between pangolin skin and human lung identified 2,835 pangolin skin-specific DEGs, 1,527 human lung-specific DEGs, and 366 shared DEGs. Three enriched pathways were identified in the pangolin skin-specific DEGS. These pathways were malaria andStaphylococcus aureusinfection pathways (upregulated) and arachidonic acid metabolism pathways (downregulated). The malaria pathway was also upregulated in the human lungs.
Previous studies have shown that malaria pathways are upregulated after SARS-CoV-2 infection and that anti-malarial drugs can suppress SARS-CoV-2 replication. Similarly, arachidonic acid pathways are known to have inhibitory effects on coronavirus replication. Thus, the findings of comparative analysis indicate that both the malaria pathway and arachidonic acid pathway can serve as potential targets to control coronavirus infection in pangolins.
Further pathway enrichment analysis revealed that the most significantly upregulated pathways in the pangolin skin were the COVID-19 pathway, immunity and inflammation (except IFN) pathways, cell proliferation pathways, and coagulation pathways. These findings are consistent with that observed in SARS-CoV-2-infected humans. In contrast, no enrichment in IFN-specific pathways was observed in the infected skin. It could be related to natural IFNE deficiency in pangolins.
High levels of expression of many endogenous retrovirus genes were observed in healthy pangolin skin samples. This could be beneficial for pangolins in terms of boosting innate immune responses in the absence of IFNE responses. However, in coronavirus-infected skin samples, a downregulation of these genes was observed. This suggests that pangolin coronavirus may suppress endogenous retrovirus gene expression to support viral replication.
The study detects replicating coronavirus in the skin of Malayan pangolin and provides transcriptomic landscapes of the host immune response to coronavirus infection. The study also finds that the pathways downstream of the lost immune system genes are not upregulated in response to the infection. This highlights that the pseudogenization of key immune system-related genes can significantly modulate pangolin's antiviral responses and make them susceptible to coronavirus infection.
