News Scan for Aug 03, 2022

News brief

Canada's border closures may have stemmed COVID-19 variant imports

Dynamic restrictions on nonessential foreign travel into Canada helped slow COVID-19 variant introductions in early 2020 and 2021, allowing the government more time to scale up vaccination, testing, and contact tracing programs, according to a study published yesterday in eLife.

A team led by University of British Columbia researchers genetically sequenced SARS-CoV-2 samples in the first and second pandemic waves to estimate variants' geographic origins. They identified 2,263 introductions of SARS-CoV-2 variants into Canada, including 680 that went on to circulate within the country and 1,582 that didn't appear to circulate.

In the first wave, 49% of the sublineages originated in the United States and were introduced mainly into Quebec (39%) and Ontario (36%). While the United States was still the predominant source of variants in the second wave (43%), India and the United Kingdom made up 16% and 7% of introductions, respectively.

After Canada closed its borders to foreign travel on Apr 22, 2020, viral importations, which had peaked at 58.5 sublineages a week, fell 3.4-fold within 2 weeks and 10.3-fold within 4 weeks. New variants, however, continued to be introduced at a low rate until the second wave began in August 2020, possibly fueled by essential foreign workers supporting the supply chain.

In October 2020, after travel restrictions were eased slightly, SARS-CoV-2 introductions increased, and by the end of February 2021, an estimated 30 B.1.1.7 sublineages had been introduced.

Senior author Jeffrey Joy, PhD, of the University of British Columbia, said in an eLife news release that broad and long-term restrictions against nonessential international travel aren't necessarily advisable in light of their economic impacts.

"However, our analysis suggests that swift and stringent travel bans towards localities harbouring a high frequency of a new variant of concern, or an outbreak of an entirely new virus, not yet identified domestically, should be seriously considered to reduce the probability of seeding multiple, simultaneous outbreaks and overwhelming healthcare systems," he said.
Aug 2 eLife study and news release

Rhode Island reports Jamestown Canyon virus case

The Rhode Island Department of Health (RIDH) has reported a Jamestown Canyon virus case, which appears to be the first US case of the year. In a statement, it said the patient is a resident in his or her 50s who lives in Washington County in the southwest.

The individual had neurologic symptoms and is now recovering.

Jamestown Canyon virus is transmitted by mosquitoes, mostly between deer and mosquitoes, but it can also infect people. Illnesses can range from asymptomatic or mild to severe, resulting in meningitis or encephalitis.

Last year, Rhode Island reported its first Jamestown Virus case since 2013. According to the Centers for Disease Control and Prevention (CDC), infections typically occur from April through September. While the virus has been found throughout most of the United States, most infections have been reported in Minnesota and Wisconsin. The nation averages about 16 cases of the neuroinvasive form of the disease each year.
Aug 1 RIDH press release
CDC background on Jamestown Canyon virus
Dec 8, 2021, CIDRAP News scan on previous case

H5N1 avian flu infects more US wild birds, Russian poultry

The US Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) reported 114 more highly pathogenic H5N1 avian flu detections in wild birds, bringing the total since the middle of January to 2,004.

Most of the detections were from eastern states, including Florida, Maine, Massachusetts, New York, and Pennsylvania. Several seabirds were among the birds found dead with the virus from Maine and Massachusetts. Florida again reported several detections in black vultures.

In the west, Alaska, California, Oregon, Utah, and Washington reported detections in a variety of birds, including waterfowl, raptors, and a few ravens.

Sporadic detections and outbreaks in poultry have continued over the summer, both in the United States and Europe.

In related news, Russia reported H5N1 in poultry for the first time in Magadan oblast in the eastern part of the country, according to a notification from the World Organization for Animal Health (WOAH). Most of Russia's earlier H5N1 outbreaks in poultry have occurred in the west. The latest outbreak began on Jul 22 and killed 6,443 of 7,775 chickens at a commercial farm.
USDA APHIS update on avian flu in wild birds
Aug 2 WOAH report on H5N1 in Russia

Stewardship / Resistance Scan for Aug 03, 2022

News brief

Meta-analysis finds antibiotic use common in COVID-19 patients

In findings that are consistent with previous studies, a systematic review and analysis of 22 studies revealed a high rate of antibiotic use among COVID-19 patients during the first year and a half of the pandemic, despite a low prevalence of bacterial coinfection, researchers reported this week in PLOS One.

To determine the prevalence of bacterial coinfection and antibiotic use among patients with laboratory-confirmed COVID-19, a team of researchers in Scotland reviewed English-language studies published from January 2020 through June 2021. Of the 1,058 studies screened, 22 hospital-based studies were eligible, comprising 76,167 patients. Most of the studies included in the review were conducted in the United States (10), United Kingdom (4), and China (3), with 1 study each in France, Germany, Indonesia, the Netherlands, and Spain. The mean age of patients was 61 years, and 54% of subjects were male.

Random-effects meta-analysis of all combined studies estimated that the prevalence of bacterial coinfection and antibiotic use in COVID-19 patients was 5.62% (95% confidence interval [CI], 2.26% to 10.31%) and 61.77% (95% CI, 50.95% to 70.90%), respectively. Sub-group analysis showed that bacterial coinfection (7.89%; 95% CI, 3.30% to 14.18%) and antibiotic use (68.84%; 95% CI, 62.27% to 75.05%) was highest in North America.

"The results from this review demonstrates that there is insufficient evidence supporting considerable empiric antibiotic prescribing in patients with COVID-19 due to a low prevalence of bacterial coinfection," the study authors wrote. "Nonetheless, antibiotics use was high, mirroring the findings in other reviews. As the pandemic evolves, and new COVID-19 specific therapeutics come into clinical practice, it will be important to assess their impact on antibiotic use."
Aug 1 PLOS One study

VA study shows high antibiotic use during end-of-life care

A nationwide study of Veterans Affairs (VA) patients found high levels of antibiotic exposure during end-of-life (EOL) care, researchers reported yesterday in Clinical Microbiology and Infection.

The retrospective cohort study, conducted by researchers with the Iowa City VA Health Care System and the University of Iowa Carver College of Medicine, analyzed a cohort of VA patients who died from January 2014 through December 2019 and had been hospitalized within 6 months prior to death.

The researchers looked at demographics, comorbid conditions, duration of inpatient antibiotics administered, and outpatient antibiotics dispensed. They then compared antibiotic use in hospitalized VA patients placed into palliative care or hospice versus hospitalized patients who did not receive palliative or hospice care.

Of the 101,208 patients who died during the study period, 9,808 were in hospice care and 40,796 received a palliative care consult, and they were matched to 50,604 patients without palliative or hospice care.

Within 14 days of placement or consultation, 41% (4,040/9,808) of hospice patients and 48% (19,735/40,796) of palliative care patients received at least one antibiotic, while 25% (2,420/9,808) of matched non-hospice and 27% (10,991/40,796) of matched non-palliative care patients received antibiotics. Entry into hospice was independently associated with a 12% absolute increase in antibiotic prescribing (as measured by days of therapy) and entry into palliative care was associated with a 17% absolute increase during the 14 days post-entry versus pre-entry period.

The study authors note that while patients at the EOL are more susceptible to infection, the decision of whether or not to prescribe an antibiotic poses a unique challenge, since it will not likely change the ultimate outcome.

"Rather than focusing on cure, palliative and hospice goals of care typically include minimizing suffering and maximizing quality of life," they wrote. "However, how these goals apply to antibiotic use at the EOL remains unclear."

The authors go on to say that future studies are needed to identify optimal targets during EOL for collaboration between antibiotic stewardship programs and hospice or palliative care teams.
Aug 2 Clin Microbiol Infect abstract