News Scan for Nov 09, 2021

News brief

SARS-CoV-2–like coronavirus may be widespread in bats in Southeast Asia

A coronavirus sharing 92.6% of nucleotide identity with SARS-CoV-2 was detected in bats in Cambodia in 2010, according to a new study in Nature Communications, adding to the understanding of natural reservoirs for the virus causing the COVID-19 pandemic.

Before this study, the closest genomic relatives to SARS-CoV-2 were identified from horseshoe bats sampled in southern China's Yunnan province. This is the first study to suggest probable reservoirs outside of China, and the authors said the samples suggest that this viral lineage circulates in a much wider geographic area than previously reported.

"Our current understanding of the geographic distribution of the SARS-CoV and SARS-CoV-2 lineages possibly reflects a lack of sampling in Southeast Asia, or at least across the Greater Mekong Subregion, which encompasses Myanmar, Laos, Thailand, Cambodia and Vietnam, as well as the Yunnan and Guanxi provinces of China, linking the sampling area of the closest viruses to SARS-CoV-2 identified to date," the authors concluded.

In related news, National Public Radio (NPR) reports that a novel coronavirus, likely originating in dogs, is infecting people in Malaysia and Haiti. The virus is likely the eighth coronavirus known to cause disease in people.

The virus first sickened nurses and doctors working in Haiti in 2017, and later proved to be identical to a circulating coronavirus identified in children at a Malaysian hospital in 2017 and 2018.

The discovery suggests that the coronavirus was likely circulating in people, at low levels, around the world. Researchers believe a similar situation may have been happening with the coronavirus that causes COVID-19.
Nov 9 Nat Commun study
Nov 5 NPR story


World flu activity remains low, but plenty of sporadic detections

Flu activity across the world remained at lower than expected levels, though sporadic detections and respiratory syncytial virus (RSV) activity continue in many regions, according to an update from the World Health Organization (WHO) that covers the middle 2 weeks of October.

Levels are still classified as interseasonal in temperate regions of both hemispheres. In Southern Asia, the pace of flu activity is similar to past seasons, with both influenza A and B circulating. Flu levels in China are still low, with influenza B detections rising in the country's north while declining in the south.

The WHO included the caveats that flu circulation and detection are likely influenced by COVID-19 measures and testing priorities, and it urged caution in interpreting flu signals.

Globally, of respiratory samples that were positive for flu at national labs in mid-October, 60.2% were influenza B and 39.8% were influenza A, reflecting a small drop in influenza B dominance since the WHO's last update. Of subtyped influenza A viruses, 63.8% were H3N2. And of characterized influenza B viruses, all but one belonged to the Victoria lineage.
Nov 8 WHO global flu update


DRC notes earlier probable Ebola cases, but no new confirmed infections

No new Ebola virus cases have been confirmed over the past 9 days in the latest outbreak in the Democratic Republic of the Congo (DRC), but three probable cases have been added to the total as part of the investigations into deaths, the WHO African regional office and DRC office said in their latest updates.

The number of confirmed cases remains at 8, and the number of deaths holds steady at 6. The probable cases were all fatal, according to detailed investigations of cases that were reported on Oct 12, 16, and 22, the WHO said in its weekly outbreaks and health emergencies update.

The WHO's DRC office said today on Twitter that 505 people have been vaccinated.

The DRC is battling its 13th Ebola outbreak, which began in early October near Beni, one of the main hot spots in the country's large outbreak that occurred from 2018 to 2020. Initial sequencing suggested that the source of the current outbreak is linked to the earlier outbreak, possibly a survivor who may have harbored the virus in an immune-protected part of the body.
Nov 9 WHO African regional office weekly update
Nov 9 WHO DRC office tweet

Stewardship / Resistance Scan for Nov 09, 2021

News brief

UK report shows veterinary antibiotics have been cut in half since 2014

New data released today by the United Kingdom's Veterinary Medicines Directorate (VMD) show that the use of antibiotics in UK livestock continues to fall.

The 2020 UK Veterinary Antibiotic Resistance and Sales Surveillance Report (UK-VARSS) shows sales of antibiotics for use in food-producing animals fell by 1% from 2019 and have declined by 52% since 2014. In addition, sales of highest-priority critically important antibiotics (HP-CIAs) have declined by 79% since 2014.

HP-CIAs, which are considered the most vital antibiotics in human medicine, now only account for 0.5% of antibiotics sold for use in UK livestock. The report also shows that the amount of antibiotics prescribed in pigs, chickens, turkeys, and gamebirds declined in 2020.

Data collected on zoonotic and commensal bacteria from healthy animals at slaughter indicated that antibiotic resistance in Escherichia coli from broilers has declined since 2014, while resistance to HP-CIAs in broilers and turkeys remains very low. Since 2016, there's also been a decline in E coli from broilers and turkeys carrying resistance genes. The report suggests the reductions in veterinary antibiotic sales and use may be responsible for the declines in resistance.

"This year's VARSS report shows how the UK continues to make important reductions in antibiotic use in livestock across the board," Christine Middlemiss, the UK's Chief Veterinary Officer, said in a VMD press release. "It is encouraging to see farmers and vets continuing to work together to tackle antibiotic resistance through the responsible use of antibiotics, which in turn protects human health as well as reducing the burden of disease in animals."
Nov 9 UK-VARSS report
Nov 9 VMD
press release


UK livestock sector making progress toward 2024 antibiotic targets

In another UK report today, the Responsible Use of Medicines in Agriculture Alliance (RUMA) reported that the UK's livestock sector is making progress on its next set of targets for reducing antibiotic use, despite some setbacks during the pandemic.

The summary report, which covers 10 sectors across aquaculture, pigs, poultry, and ruminants, indicates many sectors are making progress toward hitting their 2024 targets on data collection, use of antibiotics, uptake of preventive measures such as vaccines and training, and development of industry initiatives. Some sectors, including the poultry, pig, and salmon industries, are ahead of schedule or have already achieved their goals.

But some sectors, like the beef and dairy industry, have not had enough time to collect accurate data on antibiotic use. And the pandemic delayed the launch of key initiatives in other sectors.

"Events of the past year have undoubtedly affected the industry in many ways, but producers, vets, and wider industry have continued to manage with the utmost professionalism and commitment to the responsible use of antibiotics through this challenging time," RUMA chair Cat McLaughlin said in a press release.

RUMA's 2017 targets for antibiotic use in UK livestock are widely credited for helping achieve the antibiotic sales and use reductions documented in the 2020 UK-VARSS report. The goals for 2021 through 2024, set last year by a RUMA task force, include a 30% reduction in antibiotic use in pigs, reductions of 15% in dairy herds and 25% in calf rearing units, and a 40% reduction in game birds.
Nov 9 RUMA report
Nov 9 RUMA
press release

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