After a long summer wave that peaked in August, COVID-19 activity continues to decline in most areas, with more downward trends seen in wastewater detections, test positivity, emergency department visits, and hospitalizations, the US Centers for Disease Control and Prevention (CDC) said in its latest respiratory virus updates today.

Deaths remain at low levels. According to CDC provisional data, 341 deaths were reported last week.

Wastewater detections remain at low levels nationally, but detections tracking a bit higher in the West and Midwest compared to other regions, according to CDC data. Similarly, WastewaterSCAN, a national wastewater monitoring system based at Stanford University in partnership with Emory University, said its monitoring has the nation at the medium level, with a downward trend over the past 3 weeks. It said the South and West are now in the low category.

XEC variant continues to rise

In updated variant proportion estimates today, the CDC said KP.3.1.1 is still dominant, making up 57% of viruses, similar to last week. However, levels of XEC—a recombinant of two JN.1 viruses—continue to rise steadily and are estimated to make up 17% of viruses, up from 10% 2 weeks ago. XEC has mutations that are thought to increase infectivity and evade immune response. The CDC said that, because the variant stems from JN.1 viruses, vaccines will likely provide protection because they include a JN.1 strain.

In its weekly respiratory virus overview, the CDC said it expects to see a winter COVID peak higher than the summer peak, similar to COVID trends over the past 4 years.

Flu activity, meanwhile, is minimal, the CDC said. And respiratory syncytial virus (RSV) activity remains low nationally, but there are signs of increased activity in the southeast, especially in young children.

A study by an international team of researchers suggests that widespread use of an antibiotic to prevent liver disease is causing cross-resistance to a last-resort antibiotic for treating vancomycin-resistant Enterococcus faecium (VRE). The findings were published this week in the journal Nature.

To understand the mechanisms behind increasing reports of daptomycin resistance in VRE, which is a multidrug-resistant pathogen and leading cause of hospital-related infections, a team led by researchers at the University of Melbourne conducted a combined genomic and phenotypic analysis of 998 VRE isolates collected in Australia from 2015 through 2018, 19.4% of which were daptomycin-resistant. 

The analysis revealed that daptomycin resistance in VRE is caused by an amino-acid substitution (rpoB) within the bacterial RNA of VRE that's associated with the use of rifaximin, an antibiotic predominantly prescribed to prevent recurrent hepatic encephalopathy in patients with liver cirrhosis, who are frequently colonized with VRE.

Implications for VRE treatment

Further analysis showed that the emergence of the rpoB mutations coincided with the first clinical use of rifaximin in 2006, that patients with recent exposure to rifaximin were more than eight times more likely to be colonized with VRE with rpoB mutations, and that VRE isolates with rpoB mutations have spread globally. In addition, animal experiments showed that administering rifaximin to VRE-colonized mice led to the emergence of daptomycin-resistant VRE strains within the gastrointestinal tract.

"We’ve shown that rifaximin makes VRE resistant to daptomycin in a way that has not been seen before," senior author Glen Carter, PhD, of the University of Melbourne, said in a university press release. "It is also of concern that these daptomycin-resistant VRE might be transmitted to other patients in the hospital; a hypothesis that we are presently investigating."

Carter and his colleagues say the findings are surprising, since rifaximin was previously thought to be a low risk for resistance. They suggest daptomycin should be avoided for empiric therapy of VRE in patients receiving or recently treated with rifaximin, due to the higher risk of daptomycin resistance, and that rifaximin should remain a second-line option for hepatic encephalopathy prophylaxis.

We’ve shown that rifaximin makes VRE resistant to daptomycin in a way that has not been seen before.

A white-tailed deer in Kalispell, Montana, has tested positive for chronic wasting disease (CWD), the first detection of the fatal disease in a wild herd in Hunting District (HD) 170 in the Flathead Valley, Montana Fish, Wildlife, and Parks (FWP) reported yesterday.

FWP said wildlife biologists euthanized a buck with CWD symptoms at the Flathead County Landfill after receiving reports on the animal. The deer tested positive for CWD, and a second follow-up test was sent for confirmation.

"FWP is working with Flathead County and will survey the landfill for any other potentially symptomatic deer on the property," the agency said in a news release. "Following the latest detection, all hunters in HD 170 are encouraged to get their harvested deer and elk tested for CWD."

An ongoing danger to cervids

CWD, a neurologic disease caused by misfolded infectious proteins called prions, was first identified in wild herds in Montana in 2017. The illness affects cervids such as deer, elk, moose, and reindeer. 

Following the latest detection, all hunters in HD 170 are encouraged to get their harvested deer and elk tested for CWD.

Prions are extremely resilient and can persist in the environment for years. CWD poses an ongoing threat to cervids, because it can spread from animal to animal and through environmental contamination. The disease isn't known to infect humans, but officials recommend not eating meat from a sick animal and using precautions when field-dressing or butchering cervids.

Pakistan reported seven wild poliovirus type 1 (WPV1) cases this week, and Afghanistan reported one, all part of an ongoing spike, the Global Polio Eradication Initiative (GPEI) said in an update yesterday. 

And three African countries—Chad, Niger, and Nigeria—reported three, one, and five circulating vaccine-derived poliovirus type 2 (cVDPV2) cases, respectively.

39 WPV1 cases in Pakistan, 23 in Afghanistan

The seven WPV1 cases in Pakistan, with paralysis onsets in August and September, are from Balochistan in the Quetta, Pishin Noshki and Chaman districts; two are from Sindh in the Sanghar and Mirpurkhas districts; and one is from Khyber Pakhtunkhwa in Lakkimarwat. The new cases bring this year's WPV1 total to 39.

The one WPV1 case in Afghanistan, from Hilmand province in the Masaqalah district, takes the country's total WPV1 cases to 23 this year.

In Chad, 3 new cVDPV2 cases in N'Djamena, Ouaddai, and Chari Baguirmi provinces in July and August boost the country's 2024 total to 11. Niger's 1 cVDPV2 case was reported in Zinder province in August, bringing the country's case tally to 10. With Nigeria's 5 new cVDPV2 cases—which were reported in August and September in Sokoto, Gombe, Jigawa, and Kaduna states—the country's case total is now 66.