Coronavirus and Avian Flu Tidbits #304, July 21, 2024

Summary from Stat:

• "CDC wastewater data indicates “high” viral activity in July, though nowhere near levels of this past January, or the peak of January 2022.
• This new outbreak may be due to the typical waning protective effects of booster shots people got in the fall, as well as quickly mutating Omicron subvariants.
• As always, immunocompromised patients are most at risk, though a new — if expensive — treatment is available to them, the monoclonal antibody pemivibart.
• Vulnerable populations should get a booster now, and then an updated one once it comes out in a few months."

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Test positivity, emergency department (ED) visits, and hospitalizations—the main markers the CDC uses to gauge virus activity—are all rising, especially in seniors and especially in western states.

Earlier this week, the New York City Department of Health and Mental Hygiene said on X that COVID-19 infections are increasing in the city, and it urged people—especially seniors and people with underlying medical conditions—to consider wearing masks in crowded indoor settings.

The percentage of ED visits for COVID, considered an early indicator, rose 23.5% last week compared to the week before.

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New from @CDCgov's biweekly SARS-CoV-2 variant projections KP.3 strains have grown to more than half of all COVID-19 cases of this summer's wave, when adding together KP.3 (32.9%) and KP.3.1.1 (17.7%) https://covid.cdc.gov/covid-data-tracker/#variant-proportions

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The red line shows the current (5th) year of the pandemic. Transmission is >3x higher than what is typical for this time of year (gray line).

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COVID-19 hits migrants, refugees especially hard

Migrants, refugees, and internally displaced people have an 84% higher COVID-19 infection rate and a 46% higher COVID death rate than the general population, a new systematic review and meta-analysis in EClinicalMedicine reveals.

migrants often live in crowded housing, work in essential and high-risk jobs, and lack support from the government. Also, social norms can increase the risk, such as expectations to attend community events.

https://www.cidrap.umn.edu/covid-19/covid-19-hits-migrants-refugees-especially-hard-review-shows

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Admission screening testing of patients and staff N95 masks are cost-effective in reducing COVID-19 hospital acquired infections

all scenarios were cost saving with health gains. Staff N95s + RAT admission screening of patients was the cheapest, saving A$78.4M and preventing 1,543 deaths state-wide per annum. Both interventions were individually beneficial: staff N95s in isolation saved A$54.7M and 854 deaths state-wide per annum, while RAT admission screening of patients in isolation saved A$57.6M and 1,176 deaths state-wide per annum.

https://www.sciencedirect.com/science/article/pii/S0195670124002366

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Study: COVID can trigger changes to the immune system

that may underlie persistent symptoms Over 90% of #COVID-19 survivors had no neutralizing antibody activity at 10 months, implying that they had lost protection from reinfection. https://cidrap.umn.edu/covid-19/study-covid-can-trigger-changes-immune-system-may-underlie-persistent-symptoms

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Tour de France:

"The Tour de France has reintroduced protective measures against COVID-19, with race organisation, media and guests now required to wear masks... following a number of COVID-19 cases in the peloton in recent days. Tom Pidcock, Juan Ayuso and Michael Mørkøv are among the riders to have abandoned the race after contracting the virus, while Geraint Thomas remains in the Tour despite testing positive for COVID-19." [Cycling News], via VioletBlue

"It's damning of the state of healthcare that they are reinstating mask mandates at cycle races before they reinstate them in hospitals." - Lucky Tran

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Cats get Covid

At least one clinical sign was identified in 16 cats seropositive to SARS-CoV-2 antibodies (16/38; 42%). While seropositivity to SARS-CoV-2 antibodies was not associated with the presence of one or more clinical signs, the prevalence of cats with at least one clinical sign was 2.12 times higher amongst cats with detectable viral RNA compared to those without.

Sneezing was the major symptom, followed by lethargy, vomiting, discharge, or cough. Tests are often negative.

https://bmcvetres.biomedcentral.com/articles/10.1186/s12917-024-04150-4

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With many people getting COVID from the summer surge, a reminder that the CDC's isolation guidelines are inadequate.

It's best to isolate until you test negative on multiple tests. If you can't stay home the whole time, wear an N95 mask to stop the virus spreading to others. pic.twitter.com/0cFRgmb59Q

— Dr. Lucky Tran (@luckytran) July 18, 2024

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Avian Flu:

Officials probe heat-wave factors in H5N1 spread to Colorado poultry cullers

As the investigation continues into recent avian flu infections in as many as five workers who culled Colorado poultry, officials today said that industrial fans in poultry barns where temperatures exceeded 104°F could have spread the virus through windblown feathers and through the air, potentially reducing the effectiveness of personal protective equipment (PPE).

Also, early genetic analysis suggests that the virus that infected the poultry and the workers is the same H5N1 genotype infecting dairy cattle, a useful clue for officials who are examining connections between the farms....

https://www.cidrap.umn.edu/avian-influenza-bird-flu/officials-probe-heat-wave-factors-h5n1-spread-colorado-poultry-cullers

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Bird flu invades the brain of mammals

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Remember that family in Oregon who suspected they got bird flu from their kid’s baseball game?

A CDC doctor told them it was “just seasonal flu plus pink eye” and the local health authority said they’ll only take action if the state lab says to.

They were unable to get tested. -- @mo_journeys

https://x.com/salamasinamusic/status/1812143704062234788/photo/1

and Rick Bright, 7/19:

I also hear from farm workers who believe they’ve been exposed & infected w/ #H5N1, very symptomatic. They’ve reached out to @CDCgov  for help, guidance, and mostly testing. They say, outreach has been ignored; no follow up, no call back, no investigation, no help getting tested.

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Other Infections:

New fungal infection discovered in China

Live Science  By Emily Cooke  July 16, 2024

Scientists in China uncovered a species of fungi that had never before been seen in humans. They say warmer temperatures could drive its evolution, for the worse.

The fungus, called Rhodosporidiobolus fluvialis, was found in clinical (blood) samples from two unconnected hospital patients. In experiments, the researchers found that the yeast was resistant to several first-line antifungal drugs at higher temperatures — around that of the human body. This temperature also gave rise to "hypervirulent mutants" capable of causing more-severe disease in lab mice.

The findings "support the idea that global warming can promote the evolution of new fungal pathogens," the researchers behind the discovery wrote in a report published June 19 in the journal Nature Microbiology.

The scientists made this discovery after examining fungi sampled from patients in 96 hospitals across China between 2009 and 2019. In all, 27,100 strains of fungi were collected and analyzed; of these, only R. fluvialis had never been seen in humans before.

https://www.livescience.com/health/viruses-infections-disease/new-fungal-infection-discovered-in-china

also https://www.thesun.co.uk/health/29286791/two-dead-never-seen-before-fungi-resistant-drugs/

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National shortage of Blood Culture Bottles!!!

I can't stress enough how serious this shortage is. One third of patients hospitalized with sepsis may die prior to discharge. Best practice recommends collecting at least 2 sets of blood cultures prior to antimicrobial therapy to help identify organisms....When a patient has a bloodstream infection it is absolutely critical to use the right antibiotic. Blood cultures give us this life saving information.

Without this, people are likely to remain on unnecessarily broad spectrum antibiotics and risk more side effects.