News Scan for Feb 28, 2022

News brief

New lineage of SARS-CoV-2 detected in Canadian deer

An investigation led by Canadian Food Inspection Agency scientists has identified a new and highly divergent lineage of SARS-CoV-2, the virus that causes COVID-19 in white-tailed deer (WTD) in that country. The findings, which are not peer-reviewed, are published as a preprint study on bioRxiv.

The divergent strain was seen in samples from Ontario deer that were collected from Nov 1 to Dec 31, 2021, during the annual hunting season. The researchers collected 213 nasal swabs and tissue from 294 retropharyngeal lymph nodes. Overall, the authors said, SARS-CoV-2 RNA was detected in 21 samples representing 6% (17/298) of hunter-harvested deer. All positive deer from were from southwestern Ontario.

Using nasal swab samples, the researchers produced 5 high-quality genomes and 3 partial genomes of the virus, and they identified a highly divergent strain that most closely resembled sequences seen in human and mink samples from Michigan collected in September and October 2020; southwestern Ontario borders Michigan.

"This high degree of divergence (and consequent long branch in the phylogenetic analyses) is indicative of a period of unsampled viral evolution leading to 49 mutations compared to the closest genomes," the authors said. "This is reminiscent of the long branch and viral evolution that led to the Omicron variant, which has recently been linked to a possible mouse reservoir."

The authors say there was no evidence of animal-to-human spillover with this strain but say it could be possible.

"At this time, there is no evidence of recurrent deer to human or sustained human to human transmission of the Ontario WTD SARS-CoV-2 clade," the authors wrote. "However, the emergence of Omicron and the end of deer hunting season has meant both human and WTD testing and genomic surveillance in this region has been limited since these samples were collected."

Interspecies spillover has been a growing concern among researchers around the world, and has been documented in mink and deer in North America.
Feb 25 bioRxiv study

Trial finds azithromycin does not reduce post-RSV wheezing in kids

A randomized trial conducted among infants with severe respiratory syncytial virus (RSV) bronchiolitis found that administration of azithromycin did not prevent future wheezing, researchers reported yesterday in The New England Journal of Medicine–Evidence.

For the double-blind, placebo-controlled trial, a team led by researchers from Washington University School of Medicine in St. Louis and Vanderbilt University enrolled 200 otherwise healthy 1- to 18-month-old children hospitalized with RSV bronchiolitis, which is a well-known risk factor for the development of childhood asthma. The infants were randomized 1:1 to receive either oral azithromycin—which the researchers hypothesized might attenuate airway inflammation during RSV bronchiolitis—or placebo for 14 days. The primary outcome was the occurrence of recurrent wheeze over the following 2 to 4 years.

A total of 188 infants (96 in the azithromycin group and 92 in the placebo group) had at least one follow-up visit. While children who received azithromycin had lower levels of interleukin 8 (a marker of airway inflammation) compared with those who received placebo, azithromycin did not reduce the risk of post-RSV recurrent wheeze. Forty-five percent of children in the azithromycin group developed recurrent wheeze, compared with 37% in the placebo group (adjusted hazard ratio, 1.45; 95% confidence interval [CI], 0.92 to 2.29; P = 0.11).

Azithromycin also did not reduce the risk of recurrent wheeze among infants already receiving other antibiotic treatment at the time of enrollment (44.8% in the azithromycin group vs 46.2% in the placebo group; hazard ratio, 0.94; 95% CI, 0.43 to 2.07). In contrast, among antibiotic-naïve participants (133), azithromycin therapy resulted in a risk of subsequent recurrent wheeze compared with placebo (47.8% vs 31.8%; hazard ratio, 1.79; 95% CI, 1.03 to 3.10).

"In conclusion, azithromycin therapy during early-life acute severe RSV bronchiolitis did not reduce recurrent wheeze occurrence over the following 2 to 4 years," the study authors wrote. "Our findings are consistent with national bronchiolitis guidelines, which recommend against the use of antibiotics during acute bronchiolitis because of a lack of effect on the acute illness, and they extend this recommendation by demonstrating the lack of a salutary effect on recurrent wheeze."
Feb 27 N Engl J Med Evidence study

Avian Flu Scan for Feb 28, 2022

News brief

Waterfowl testing finds high-path H5 avian flu in 3 more states

Federal health officials have announced 45 more high-pathogenic H5 avian flu detections in waterfowl, including the first involving wild birds in Alabama, Maine, and New Jersey in the recent spread of the virus. Also, officials reported two more outbreaks involving other types of birds in New York.

The new waterfowl detections lift the number reported in the United States to 297, according to the US Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS). Of the 45 new detections, 21 were from testing of live birds from Cape May County in New Jersey, located on the southern tip of the state on the Atlantic shore. The new reports also include the first from Alabama, which involved a hunter-harvested bird from Limestone County, which borders Tennessee and is on the Tennessee River.

Maine, which has already reported the virus in Knox County poultry, reported its first detections in waterfowl, which involved live testing in birds from Washington County, located in the east on the Atlantic shore.

Meanwhile, earlier affected states reported more detections in waterfowl, including Kentucky (Henderson and Meade counties) and Connecticut (New Haven County).

In related developments, APHIS reported two more detections in other bird settings, both in New York. One involved backyard birds of mixed species in Dutchess County, which is in the southeastern part of the state near the Connecticut border. The other involved captive wild birds in neighboring Ulster County.

The outbreaks in waterfowl and other birds are part of ongoing Eurasian H5N1 activity under way, mainly across the Atlantic seaboard. However, the virus has already turned up at poultry farms in inland states, including Indiana, Kentucky, and Michigan. Federal and state officials have ramped up testing, which includes all migratory bird flyways.
USDA APHIS wild bird avian flu page
USDA APHIS poultry and other bird settings page

H5N6 avian flu infects 4 more people in China, 1 fatally

China has reported four more H5N6 avian flu infections in humans, one of them fatal and all in people who had exposure to poultry or had visited a live-bird market, Hong Kong's Centre for Health Protection (CHP) said today.

The patients are from four different provinces, with illness-onset dates from Jan 20 to 28. They include a 46-year-old man from Fujian province who died on Feb 10. Two others are also adults, one of them a 48-year-old man from Sichuan province and a 35-year-old man from Guangxi province. Both are were hospitalized within a few days of symptom onset and are listed in critical condition.

The fourth patient is a 6-year-old girl from Jiangsu province who was hospitalized on Jan 25 and is in critical condition. Most of the country's earlier H5N6 infections, known to be severe or fatal, were in adults.

China has now reported 71 H5N6 infections since 2014. Last year, the country reported a dramatic uptick in cases. This year, officials already have recorded 9 such cases.
Feb 28 Hong Kong CHP statement