Infectious Disease Roundup: 2/2/2025

Second Largest US Egg producer hit with H5N1, Probable Human H5N1 case in Delaware, Clade Ib MPOX spreading in DRC and a new case in the UK, Polio Detected in wastewater of several EU countries...

This human T cell (blue) is under attack by HIV (yellow), the virus that causes AIDS. The virus specifically targets T cells, which play a critical role in the body’s immune response against invaders like bacteria and viruses. I chose this image as a reminder that eliminating global support for reduction of HIV spread, and control of HIV/AID through the distribution of low-cost small molecule drugs will rapidly increase global spread and deaths from HIV. This will likely begin to impact the United States directly within the next 6 months.

Image Credit: Seth Pincus, Elizabeth Fischer and Austin Athman / National Institutes of Health

Egg Prices Higher For The Foreseeable Future?

The United States is getting slammed with highly pathogenic avian influenza (H5N1) outbreaks. Massachusetts health officials have declared bird flu (H5N1) ‘widespread’ (Press release: here), the second largest laying hen operation in the United States, Rose Acre Farms of Indiana has confirmed an outbreak of H5N1 potentially impacting up to 2.8 million birds.

Per the USDA the majority of states in the US have had an outbreak in a commercial flock impacting over 19 million birds in the last 30 days, with a total of about 150 million birds impacted since 2022.

According to FRED (Federal Reserve Economic Data) egg prices for the month of December 2024 were nearly as high as they were at the peak in 2022, and are expected to continue to trend higher.

Business Insider (BI) recently wrote about why “Eggs May Be Expensive Forever”. It doesn’t only have to do with H5N1, but farmers interviewed by BI indicated that there doesn’t seem to be a coordinated plan to address the massive outbreaks. If you choose to start a backyard flock at this time, please review ways that you can keep yourself and your new birds as safe as possible.

Vaccines against avian influenza have been approved in the past (four vaccines are licensed for avian influenza - HA subtype, H5N1, H5N3, and H5N9) but none of these are approved for the highly pathogenic H5N1 clade 2.3.4.4b which is causing the current outbreak. The USDA announced in 2023 that they were starting vaccine trials against highly pathogenic H5N1, however I was unable to find an update or information on the progress of these trials, however previously developed vaccines have been highly efficacious in poultry (Master Question List for Highly Pathogenic Avian Influenza, August 8th, 2024 p. 19).

Probable Human Case of H5N1 in Delaware

Per CIDRAP a probable case of H5N1 was detected as part of the state’s routine surveillance. After testing the sample multiple times the CDC was unable to confirm the case but stated that the infection met the criteria for probable H5N1 infection. There was no identified source of exposure with this patient. This brings the total number of cases with unknown exposure source to two (2), in total there have been 66 cases with known exposure to cattle or poultry.

It is my personal opinion (stated online in ~November 2024) that we will see person to person transmission of highly pathogenic H5N1 some time in the next two years. We have some pre-existing immunity to H5N1 because the N1 portion is similar enough to H1N1 per some research studies that there may be cross-protective immunity in those vaccinated for influenza (the vaccine contains H1N1) and/or infected with Influenza A H5N1 (this would be more difficult to know since there are other Influenza A types in circulation). To read more about H5N1, here is a comprehensive write up.

Clade Ib MPOX Outbreak Expands

Clade Ib MPOX has a significantly higher case fatality rate (3.3%, NEJM study) and is more transmissible than the Clade II MPOX that drove the United States outbreak in 2022-2023 (< 0.1% case fatality). Currently sustained transmission of Clade Ib MPOX has also been reported in two neighboring countries (Uganda and Burundi), and 9 countries, including the United States have reported one or more cases. Between October 30th, 2024 and January 31st, 2025 the UK has confirmed 8 cases of Clade Ib MPOX, the most recent case was reported January 31st, 2025, and all were linked to recent travel or household exposure.

The ongoing outbreak of Clade Ib MPOX is continuing to expand in the Democratic Republic of Congo. A recent report (NEJM, linked below) detailing the outbreak between 2022-2024 recorded 45,652 cases and 1,492 deaths, a 3.3% case fatality rate across 12 African countries. To put this into perspective, for adults 18-49 years old in the United States the case fatality rate of influenza infection was 0.1% in 2021-22. Two recent studies that detail the the outbreak and spread of the disease can be found here: Ndembi, N. M.P.H., Ph.D., et al. NEJM. Jan 29th, 2025 and Brosius, I. MD, et al. Lancet, Jan 29th, 2025. Their findings are reviewed below.

Unlike the more mild Clade II MPOX virus co-morbidity (also infection with) HIV was not a feature of these outbreaks and higher rates of adults (97%) had active skin lesions. The distribution of infection was roughly equal between the sexes (48% of patients were female). Per the Lancet study 14% of the cases were in preschoolers where the rash pattern indicated the virus was contracted through non-sexual contact with a caregiver. Two deaths have occurred in infants (0.4% case fatality rate). In pregnant women with detailed hospital follow-up, four (67%) of six had adverse pregnancy outcomes.

Although the JYNNEOS vaccine given in the United States is expected to be protective against Clade Ib MPOX, recent a recent study, pre-print Collier, A.Y. et al. 2024 showed that protection from MPOX infection wanes significantly. Additionally the JYNNEOS vaccine does not offer complete protection and boosting as soon as two years post initial vaccination may be important depending upon exposure risk (for a PDF of the CDC reference search for: “Interim Clinical Considerations For Use Of Vaccine For MPOX Prevention In The United States MPOX CDC” in this post).

In the US the less transmissible Clade II MPOX virus grew out of control (2022-23) until the vaccine was split 1:5 to immediately increase the amount of available vaccine, bringing the spread under control. Clade Ib MPOX spreading in the US could be disastrous. The WHO is working in the areas affected to attempt to bring these outbreaks under control. Currently, there are no reports of CladeIb MPOX spreading in the United States.

First Detection of (vaccine derived) Polio in Wastewater of Several European Countries

In a January 30th, 2025 report from the European Centre for Disease Prevention and Control vaccine derived Polio has been detected in the waste water of several counties:

“Between September and December 2024, four countries in the EU/EEA (Finland, Germany, Poland, Spain) and the United Kingdom reported detections of circulating vaccine-derived poliovirus type 2 (cVDPV2) in sewage samples. This is the first time cVDPV2 has been detected in EU/EEA countries from environmental surveillance.

To date, no human polio cases have been reported and the EU/EEA continues to be polio-free, but such findings call for increased vigilance.”

cVDPV2 outbreaks are linked to areas with low population immunity to poliovirus and despite a reasonably high vaccination rate across the EU/EEA region coverage is highly heterogenous with only 39% of reporting districts reaching 90% vaccination coverage. Due to intermittent SARS-CoV-2 lockdowns about 600,000 children aged 12–23 months may not have received a full primary polio vaccination course in 2022 and 2023. These recent detections, especially in winter months when Polio typically spreads in warmer summer months, indicates a need to continue Polio vaccination campaigns. For more information about cVDPV2 and strategies to control the spread the Circulating Vaccine-Derived Polioviruses Global Update from the Global Polio Eradication Initiative can be found here.

Personal Note

Thank you all for reading and sharing this Substack newsletter and helping to keep good Science alive. Science and scientific research in the United States is currently in a state of upheaval. I’ve seen new PhD students concerned they will have to drop out soon, later-stage PhDs trying to figure out if they have enough research completed to graduate and so many in between that simply may drop out or perhaps be awarded a token masters degree after years of research. The funding disruption through the many agencies of the HHS impact student trainees, University research labs, small business grants meant to bring scientific discoveries to the public, clinical trials, publications, data tracking and analysis, and so much more. Unfortunately, there is still no update as to the reason for the grant funding review freeze or any communication as to how we will go forward. In my 26 year research and science career a shut down of this magnitude, without communication is unprecedented.

I know there is a lot going on out there at the moment, please be sure to take good care of yourself and I will keep the updates coming.