Machine-learning models may detect patients at risk for long COVID-19

Machine-learning models created by a National Institutes of Health (NIH)-supported research team can identify, with high accuracy, patients likely to have long COVID, according to a study yesterday in The Lancet Digital Health.

Long COVID causes a wide variety of symptoms such as shortness of breath, fatigue, fever, headaches, and "brain fog" for months or years after initial diagnosis. It can be difficult to diagnose, because many of its symptoms mimic those of other conditions, the researchers said.

A National COVID Cohort Collaborative (N3C) team analyzed electronic health record (EHR) data from 97,995 adults diagnosed as having COVID-19 at least 90 days earlier and 597 survivors undergoing treatment at a long COVID clinic.

The three resulting machine-learning models were designed to detect patterns of symptoms, healthcare use, demographics, and prescriptions to identify all COVID-19 patients likely to have lingering symptoms, including both hospitalized and non-hospitalized patients.

As of October 2021, the team had identified more than 100,000 long-COVID patients, a figure that has doubled as of this month. The study also revealed important long-COVID risk factors, such as greater healthcare use, increasing age, and shortness of breath.

Testing of the models estimated that area-under-the-curve scores (indicating sensitivity and specificity) were excellent in detecting persistent symptoms among all COVID-19 patients (0.92) and hospitalized patients (0.90) and good among outpatients (0.85).

In an NIH National Center for Advancing Translational Sciences (NCATS) news release, Josh Fessel, MD, PhD, NCATS senior clinical adviser, said the models can help identify patients who need specialized care.

"Once you're able to determine who has long COVID in a large database of people, you can begin to ask questions about those people," said Fessel, who was not a study author. "Was there something different about those people before they developed long COVID? … Was there something about how they were treated during acute COVID that might have increased or decreased their risk for long COVID?"

The research is part of the NIH's ongoing Researching COVID to Enhance Recovery (RECOVER) trial.
May 16 Lancet Digit Health study
news release


CDC assesses H5N1 avian flu zoonotic risk as moderate

The US Centers for Disease Control and Prevention (CDC) recently added the Eurasian H5N1 avian flu strain that is circulating globally, including in US wild birds and poultry, to the list of animal flu viruses with zoonotic potential that it is monitoring.

The CDC conducted its assessment in March, after the first human case had been detected in the United Kingdom but before the second human case was reported in the United States, which involved a poultry culler in Colorado.

Genetic analyses have shown little evidence of adaptation to mammals. The CDC said it expects H5 candidate vaccine viruses that have already been recommended to be effective against the virus and that the strain will likely be susceptible to flu antiviral drugs.

Using its Influenza Risk Assessment Tool (IRAT), the agency put the overall score for potential emergence at 4.4, which is in the lower end of the moderate risk category. For potential public health impact, the overall score was 5.1, which is also in the lower end of the moderate-risk range.
CDC IRAT assessment

In other H5N1 developments, the US Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) reported 78 more detections in wild birds, bringing the total since January to 1,190.

Many of the new reports involved wild birds—mainly waterfowl and raptors—found dead in western states including Alaska, Colorado, Idaho, Montana, Washington, and Wyoming. Several detections were also reported in the Midwest, including Illinois, Minnesota, North Dakota, and Wisconsin. There were a few reports from the East, including Florida, New York, and Ohio.
USDA APHIS wild bird avian flu page


Year 5 progress report highlights US actions on antibiotic resistance

The US Task Force for Combating Antibiotic-Resistant Bacteria (CARB) last week published a report on the fifth year of the US government's efforts to address drug-resistant infections.

The year 5 report details some of the actions taken under the National Action Plan for Combating Antibiotic-Resistant Bacteria 2015-2020, which was developed during the Obama administration and set out five interrelated goals for tackling the emergence and spread of drug-resistant pathogen in humans, animals, and the environment.

The report notes that these actions have helped guide the government's response to antibiotic resistance, leading to improved infection prevention and antibiotic stewardship in human and animal health, expanded surveillance for drug-resistant pathogens, and more support for new products to detect, prevent, and treat infections.

Among the highlighted programs are those established by the Centers for Disease Control and Prevention to detect and prevent antibiotic-resistant infections and promote responsible antibiotic use, such as the National Healthcare Safety Network, the Emerging Infection Program, the Antibiotic Resistance Laboratory Network, and the Core Elements of Antibiotic Stewardship program.

Also highlighted is the Food and Drug Administration's Guidance for Industry #213, which banned medically important antibiotics from being used for growth promotion in food-producing animals and required veterinary oversight for all use of medically important antibiotics.

The report also addresses emerging issues, including the role that the environment, health equity, and other external factors play in increasing the risk of contracting an antibiotic-resistant infection.

"The CARB Task Force is currently working to better understand disparities related to antibiotic resistance across health care, the community, and the environment, as well as the relationship between health equity and antibiotic use and resistance to determine community- or population-level trends that could inform better stewardship or prescribing practices in high-risk communities," the report states.

The 2020 action plan developed by CARB maintains the five goals of the original plan and outlines aspirational targets that the US government can take to further reduce the spread and impact of antibiotic resistance and improve antibiotic stewardship.
May 13 CARB Year 5 report


UK identifies 4 more monkeypox cases

The UK Health Security Agency (UKHSA) has detected four new cases of monkeypox with no known link to travel to countries where the disease is endemic.

The four case-patients, three in London and one in northeast England, are not connected to the case-patients identified by UKHSA on May 7 and 14. The latest cases bring the total number of confirmed monkeypox cases in the United Kingdom to seven.

UKHSA officials say investigations are under way to establish links between the four latest case-patients, two of whom have common contacts, and to determine how they acquired their infections. All four self-identify as gay, bisexual, or other men who have sex with men (MSM), and officials note that the most recent cases have been in the gay, bisexual, and other MSM communities.

Monkeypox is a viral infection usually associated with travel to West Africa. It typically causes a mild, self-limiting illness and is spread by very close contact with an infected person. The four case-patients have the West African clade of the virus, which is milder than the Central African clade, the UKHSA said.

"This is rare and unusual," UKHSA Chief Medical Adviser Susan Hopkins, MBBCh, said in a news release. "UKHSA is rapidly investigating the source of these infections because the evidence suggests that there may be transmission of the monkeypox virus in the community, spread by close contact."

Hopkins added, "We are particularly urging men who are gay and bisexual to be aware of any unusual rashes or lesions and to contact a sexual health service without delay."
May 16 UKHSA news release


HPV vaccination programs tied to direct and herd protection in US

An analysis of US data shows the increasing impact of human papillomavirus (HPV) vaccination efforts that started more than a decade ago, suggesting direct protection as well as herd effects, according to a study in Annals of Internal Medicine.

HPV vaccination was introduced in the United States in 2006. The study was based on collected NHANES (National Health and Nutrition Examination Survey) data, and compared pre- and post–vaccination-era HPV prevalence for both vaccinated and unvaccinated sexually active girls and women aged 14 to 24. The pre-vaccination era was 2003 to 2006, and the post-vaccination eras were 2007 to 2010, 2011 to 2014, and 2015 to 2018.

Overall, compared to pre-vaccination years, HPV prevalence decreased by 85% for females in the United States, and by 90% among vaccinated females in 2015 to 2018. Among unvaccinated females, HPV prevalence dropped 75% compared with pre-vaccination years.

The percentage of females reporting receipt of at least one HPV vaccine dose was 25.2% in 2007 to 2010 and greater in the later vaccine eras, reaching 59.0% in 2015 to 2018, the authors said. Herd immunity was thus a likely factor in the decreasing prevalence seen in the study.

Also of note, HPV types not targeted by HPV vaccines did not change during the study period.

In an editorial from researchers at Boston University Medical Center, the authors wrote that this finding "Indicates that vaccine-type HPV infections are not being replaced with other oncogenic HPV infections. Early in the vaccine era, concerns were raised that HPV vaccine effectiveness could be compromised by increases in infections with other oncogenic subtypes; this study provides evidence that this is not the case."

The COVID-19 pandemic has led to decreased pediatric care, including vaccinations. This study, the editorial authors write, should bolster renewed efforts to routinely offer HPV vaccination to adolescents.
May 16 Ann Intern Med
study and editorial


MERS hospitalizes Omani farmer

The World Health Organization (WHO) said today that a MERS-CoV-2 case has been reported in Oman, which involves a 34-year-old man who had direct contact with camels.

In its announcement, the WHO said the man is from Al Dhahira governorate in the northwest, where he had contact with camels, sheep, and goats on his family farm.

The man's symptoms began on Apr 18, and he was hospitalized on Apr 24, where he is in critical condition and on a ventilator in the intensive care unit.

As of Apr 28, no other infections were found in any of the man's 33 contacts, which include 27 healthcare workers.

Oman has now reported 25 MERS-CoV (Middle East respiratory syndrome coronavirus) cases, 7 of them fatal. Since the first human illnesses were detected in 2012, the WHO has now received reports of 2,591 cases, along with 894 deaths. The vast majority are from Saudi Arabia.
May 17 WHO statement

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