Respiratory virus levels climb as JN.1 dominates COVID detections

Respiratory illness activity is elevated or increasing across most of the United States, and JN.1 is now the dominant SARS-CoV-2 variant, the Centers for Disease Control and Prevention (CDC) said in its latest updates just before Christmas.

In its tracking of three main viruses that drive visits to health providers for symptoms such as fever and sore throat, the CDC said respiratory syncytial virus (RSV) activity remains elevated, especially for young children. Meanwhile, COVID-19 activity is increasing in many parts of the country, as is seasonal flu, though hospital bed occupancy and intensive care unit (ICU) capacity for all patients remains stable.

ED visits for COVID highest in infants and seniors

The CDC’s two main severity markers rose compared to the previous week, with hospitalizations up 10.4% and deaths up 3.4%. States in the Midwest and Northeast have numerous counties at the medium level for COVID hospital admissions, with some counties in those regions listed at the high level.

Nationally, only 3% of deaths were due to COVID during the reporting period, with higher levels reported by a few states: Kentucky, Missouri, Iowa, Minnesota, Maryland, and Massachusetts. The CDC characterized the COVID death trend as stable.

The CDC’s early indicators also reflected rises, with emergency department (ED) visits up 6.6% compared to the previous week and test positivity showing a slight rise. The marker rose to the substantial level in Iowa, and Illinois, Michigan, and Indiana were at the moderate level.

ED visits for COVID were highest in infants and older adults but were also elevated in young children, the CDC said in its latest respiratory virus snapshot.

Nationally, test positivity was 11.7% and was highest in the lower Midwest, followed by the rest of the Midwest, the Northeast, and the Southwest.

JN.1 vaults to top lineage

The proportion of JN.1 viruses over the past 2 weeks was up sharply, rising from 21.3% to 44.2%, the CDC said in its latest estimates, putting it far above the next most common variant, HV.1. In a separate update on JN.1, the CDC said it is also seeing an increasing share of infections caused by JN.1 in travelers, wastewater, and most world regions.

“JN.1’s continued growth suggests that the variant is either more transmissible or better at evading our immune systems than other circulating variants. It is too early to know whether or to what extent JN.1 will cause an increase in infections or hospitalizations,” the CDC said, adding that existing vaccines, tests, and treatments still work against JN.1.

JN.1, under the BA.2.86 umbrella, has the L455S mutation in the spike protein, which is thought to increase its immune-evasion capabilities. Last week, the World Health Organization (WHO) designated JN.1 as its own variant of interest, following a rapid increase in proportions at the global level.

Both the WHO and CDC have said JN.1 doesn’t seem to pose a bigger public health risk than other variants, though it could trigger fresh COVID surges at a time when other respiratory viruses are circulating.

Flu markers climb higher

Meanwhile, flu activity continues to rise in all regions of the United States, the CDC said in its latest update. The highest levels have been in the southern tier of states, with Louisiana and South Carolina now listed at the top of the CDC’s “very high” category, which stands out as blue among varying shades of red in the high and very high categories.

The 2009 H1N1 virus is still the predominant strain, but the CDC said it has also received reports of H3N2 and influenza B viruses.

ED visits for flu are on the rise, especially in school-age children, and test positivity for the virus also continues to increase, at 12.8% at clinical labs. Hospitalizations for flu continue an upward trend, affecting all age-groups, with the highest rates in seniors.

No new pediatric flu deaths were reported last week, keeping the season’s total at 14.

Global COVID picture

In its monthly profile of COVID activity, the WHO said cases have risen 52% over the last 28 days, while deaths declined by 8%. However, the WHO emphasized that few countries are testing and reporting cases and that trends aren’t likely to accurately reflect the global picture.

At the regional level, four areas reported rises in new COVID cases, most dramatically in South East Asia, followed by Africa, the Western Pacific, and Europe. Deaths were up in South East Asia, as well as—to a lesser degree—Europe.

Of the few countries that regularly report hospital data, the data suggest hospitalizations were up 23% and a 51% rise in new ICU admissions for COVID.