Wednesday, December 06, 2023

France: MOA Raised H5N1 Risk To High - Orders 3rd Vaccine Dose For High Risk Ducks


Until relatively recently - with the notable exceptions of China, Indonesia, Egypt, Vietnam and Hong Kong - most of the world's nations have avoided the use of poultry avian influenza vaccination in favor of the long-standing OIE recommendation to `stamp out' HPAI infections by culling infected flocks.

That policy advised that vaccines should only be used as a temporary measure, stating that: `Any vaccination campaign must include an “exit strategy” i.e. a return to classic disease control measures.'

If properly designed and managed, however,  a well-matched, and continually updated poultry vaccine campaign should be both safe and effective. But far too often (see Egypt: A Paltry Poultry Vaccine and J. Virus Erad.: Ineffective Control Of LPAI H9N2 By Inactivated Poultry Vaccines - China), those standards are only loosely followed.

Even though the United States is conducting HPAI poultry vaccine trials of their own, and has  authorized the use of experimental H5 vaccines to protect endangered Condors, HPAI poultry vaccines are not currently approved for use in U.S. poultry.  

Last summer France announced their intention to begin vaccinating high risk poultry (ducks) against H5N1 this fall, after testing showed a two-dose regimen provided adequate protection. 

Yesterday the French MOA raised their avian flu risk level to `High' after four outbreaks were reported in the past week (see below), and this morning there are numerous media reports that the MOH - citing `New scientific evidence ' - has ordered a 3rd dose of the poultry vaccine for certain high risk poultry. 

Although I've not found the official document (I'll update this blog when I get a link), multiple media sources are quoting the MOH this morning as ordering:

"New scientific evidence has led us to adjust the vaccination protocol to guarantee the best possible protection of animals and avoid any epizootic outbreak.

For this, a three-dose protocol will be applied from (this week) until March 15, 2024 in areas identified at risk and targeting mulard ducks"

 This translated announcement from the French MOA.

Avian influenza: France placed at “high” risk level to protect poultry farms

Updated 06/12/2023

While a first outbreak in livestock farming was detected in Morbihan at the end of November, and the infection dynamic in Europe continues, the Ministry of Agriculture and Food Sovereignty took the decision to raise to its maximum the level of epizootic risk with regard to highly pathogenic avian influenza (HPAI). Preventive measures are being strengthened to protect poultry farms.

The continuing strong dynamic of HPAI virus infection recorded in Europe, while a first contamination of a farm had been detected a few days ago in France [1], has now led the public authorities to place all of the territory at high risk level with regard to HPAI. The decree was published this Tuesday, December 5 in the Official Journal .

This decision, one week after an initial increase in the level of risk, ensures better protection of farms in the face of the threat represented by the strong circulation of the virus in migratory wildlife.

The transition to “high” risk generalizes the following prevention measures throughout the territory :
  • Closure or protection by nets of birds kept in establishments with fewer than 50 poultry or captive birds (farmyards, zoos);
  • Shelter and protection of feeding and watering of birds in establishments keeping more than 50 poultry;
  • Mandatory equipment of vehicles intended for the transport of waterflies over three days old with tarpaulins or equivalent preventing any significant loss of feathers and down by a full or empty truck;
  • Prohibition of gatherings of poultry and captive birds;
  • Ban on racing pigeon competitions until 04/10;
  • Restrictions on the transport of calling birds and a ban on the release of game birds of the Anatidae family.
In areas at risk of diffusion (ZRD), i.e. with a high density of poultry farms, the following measures are made compulsory:
  • HPAI virological screening during movements of batches of palmipeds ready to fatten between two farms, thus complementing the surveillance already put in place as part of the Official HPAI Vaccination Plan.
  • Restriction of access, disinfection of vehicles.
  • All applicable measures are described in the ministerial decree of 09/25/2023 .
These prevention measures complement the compulsory vaccination campaign launched in France since October 1 for commercial farms keeping more than 250 ducks. Surveillance, biosecurity and vaccination are complementary pillars of HPAI prevention.

With H5N1 well-entrenched in wild and migratory birds, many countries are reluctantly considering the move to poultry vaccination.  The success or failure of this campaign in France has the potential to impact more than just the French poultry industry. 

Stay tuned. 

Tuesday, December 05, 2023

ECDC Risk Assessment On Transmission & Spread of Clade I Mpox From The DRC



Just over 10 days ago the WHO Reported the 1st Confirmed Cluster Of Sexually Transmitted MPXV Clade 1 in the DRC. Clade 1 Mpox is considered far more dangerous than clade IIb, which is currently spreading outside of Africa.

After presenting the evidence, the WHO warned that `The risk of mpox further spreading to neighbouring countries and worldwide appears to be significant.'  and that it poses `. . . an additional risk of mpox outbreaks with potentially more severe consequences than the one which has been affecting the world since 2022.'. 

 Last week, in CDC EID Journal: Clade I–Associated Mpox Cases Associated with Sexual Contact, the Democratic Republic of the Congo,  we looked at dispatch from the team in the DRC that discovered these clusters.  They wrote:

Population movement and previously unreported routes of transmission could exacerbate global distribution of MPXV, which could be compounded by the lack of routine diagnostic testing or inadequate access to rapid point-of-care testing. In view of this investigation, epidemiologic and genomic surveillance for MPXV, in both endemic and nonendemic regions, should be improved and strengthened. 

While obviously a concern, so far we've not seen any evidence of clade I transmission outside of the endemic regions of central Africa.  To be fair, however, clade IIb was probably circulating internationally long before surveillance first identified it in the UK in May of 2022. 

Today the ECDC has published a Risk Assessment for the EU on the spread of Clade I Mpox outside of Africa, where the currently set the overall risk for MSM with multiple sexual partners stemming from this outbreak in the DRC is low. The overall risk for the general population is also assessed as low.

First, the ECDC news release, followed by the Executive Summary and a link to the full risk assessment.

ECDC assesses risk associated with ongoing mpox epidemic in the Democratic Republic of the Congo
News story
5 Dec 2023

An outbreak of mpox is ongoing in the Democratic Republic of the Congo (DRC), with 12 569 cases reported between 1 January and 12 November 2023. The vast majority of infections are caused by Monkeypox virus (MPXV) clade I, which is generally considered to be more virulent than MPXV clade II, which has been driving the multi-country epidemic of mpox in 2022-23.

Currently, there is no evidence that MPXV clade I is circulating outside certain central African countries and available MPXV sequences do not suggest circulation in the EU/EEA. 

According to ECDC, the likelihood of infection for the general EU population from the ongoing epidemic of mpox due to MPXV clade I is very low, while the impact from such infection is assessed as low, resulting in an overall low risk.  

The likelihood of infection with clade I virus for the population of men who have sex with men (MSM) with multiple sexual partners in the EU/EEA is considered higher than that of the general population. However, it is still estimated as low, as immunity in this population due to prior infection with MPXV Clade II and/or vaccination in 2022-23 will probably decrease both the likelihood and the impact of such an infection. Therefore, the overall risk for MSM with multiple sexual partners stemming from this outbreak in the DRC is low. The overall risk for the general population is also assessed as low.

Public health authorities should continue efforts to increase awareness among clinicians about mpox. Contact tracing, testing and sequencing of samples from detected mpox cases should continue, along with sharing the detected sequences. In the event of mpox cases with increased severity and/or the detection of a MPXV clade I infection, the event should be promptly communicated at the EU level via EpiPulse - an online portal for European public health authorities and partner organisations to share disease and viral sequence data.

Implications for the EU/EEA of the outbreak of mpox caused by Monkeypox virus clade I in the Democratic Republic of the Congo
5 Dec 2023
An outbreak of mpox is ongoing in the Democratic Republic of the Congo (DRC), with 12 569 cases reported between 1 January and 12 November 2023.

Executive summary
  • The vast majority of infections are caused by Monkeypox virus (MPXV) clade I, which is generally considered to be more virulent than MPXV clade II.
  • A cluster of mpox cases from March 2023 was recently documented as the first detection of sexually transmitted MPXV clade I infections. The presumed index case of this cluster is a European traveller who reportedly developed mpox soon after his arrival in DRC.
  • Currently, there is no evidence that MPXV clade I is circulating outside certain central African countries and available MPXV sequences do not suggest circulation in the EU/EEA.
  • The likelihood of infection from the ongoing epidemic mpox due to MPXV clade I is assessed as very low for the general EU population and the impact from such an infection is assessed as low. The overall risk is assessed as low.
  • The overall risk for men who have sex with men (MSM) with multiple sexual partners in the EU/EEA from this outbreak in the DRC is low. Although the likelihood of infection with clade I virus for this population is considered higher than that of the general population, it is still estimated as low, as it is attenuated by the immunity in this population due to prior infection with MPXV clade II and/or vaccination in 2022-23. The impact from such infection is also estimated to be low, also influenced by increased immunity and availability of vaccines and therapeutics in the EU/EEA.
  • Public health authorities should continue efforts to increase awareness among clinicians about mpox.
  • Contact tracing, testing and sequencing of samples from detected mpox cases should continue, along with sharing the detected sequences. In the event of mpox case(s) with increased severity and/or the detection of a MPXV clade I infection, the event should be promptly communicated at the EU-level via EpiPulse.

Implications for the EU/EEA of the outbreak of mpox caused by Monkeypox virus clade I in the Democratic Republic of the Congo - EN - [PDF-383.79 KB]

While reassuring, in the summer of 2021 - roughly 1 year before clade IIb Mpox began its world tour - the ECDC issued a risk assessment following a family cluster of Monkeypox cases in the UK (index case imported from Nigeria). 

The likelihood for further spread of the virus is very low due to the moderate transmissibility of the virus. However, infections among close contacts cannot be excluded, as demonstrated by the infections described above.

A perfectly reasonable assessment given the facts available at the time. But it does remind us that all risk assessments have a shelf life, and as the virus changes, so do the risks. 

Emerg. Microbes & Inf.: Characterization of HPAI A (H5N1) Viruses isolated from Cats in South Korea, 2023


Last July, while we were watching an outbreak of HPAI H5N1 in cats in Poland (see WHO Update WHO Update & Risk Assessment On H5N1 In Cats - Poland), word of a similar outbreak emerged from South Korea, where cats at two different shelters tested positive for the virus.

South Korea: MAFRA Press Release On H5N1 In Cats

Seoul: 3 (of 10 Cats Tested) Positive for H5 Antibodies At Animal Shelter in Gwanak-gu

Korean MAFRA/CDC: Implementation of Quarantine Measures Following the Confirmation of HPAI H5N1 in Cats in Gwanak-gu

Unlike from Poland, where information has been slow to emerge, South Korea quickly determined that the outbreak at the second shelter was due to contaminated cat food (see South Korea: MAFRA Statement On Detection Of H5 Contaminated Cat Feed).  

The first outbreak occurred at a private shelter, which has hampered the epidemiological investigation. Two samples (out of 40 cats), however, were delivered to the College of Veterinary Medicine, in Seoul, South Korea for analysis. 

As we've discussed often, the H5N1 threat isn't from a single viral entity, but rather from a diverse array of genetically similar viruses that continually evolve.  The H5N1 virus circulating in Egypt or Vietnam  today is genetically distinct from the H5N1 viruses circulating in Peru, Japan, or Canada. 

Influenza viruses are broadly categorized by their two surface glycoproteins - hemagglutinin (HA) and neuraminidase (NA) - hence we often talk about seasonal H1N1 or H3N2, or avian H5N1 or H9N2 viral  subtypes.

But each subtype is further divided into clades; broad categories based on the genetic makeup of the HA gene. Over time, dozens of clades can emerge for a given subtype, and while some are supplanted by more `biologically fit' strains, multiple clades can co-circulate. 

Clades can be further divided into sub-clades, and subclades (e.g. into genotypes (and variants within genotypes), producing a myriad of quasi-similar viruses - sometimes with differing characteristics (see Differences In Virulence Between Closely Related H5N1 Strains) - but still often referred to (outside of scientific journals) as a single subtype.

In 2020 a new clade H5N1 virus became dominant, and it - and its variants - have shown an enhanced ability to spill over into mammals around the globe (see here, here, here, and here). 

Today we've a letter to the editor, published in Emerging Microbes & Infections prior to final editing, from researchers in South Korea who analyzed the two samples gathered from the first H5N1 infected animal shelter. 

While their report doesn't fully answer how the virus made it into the shelter, it does classify this virus as a new genotype (South Korea genotype III) , and identifies a number of mammalian adaptions (see graphic below).

(B) Amino acid mutations in cat and avian isolates are color-coded: red text for mutations exclusively to SNU-01, blue text for mutations found in genetically close avian isolates with SNU-01, and green text for mutations common in most current Asian avian isolates. In other words, SNU-01 exhibits red, blue, and green mutations, closely related avian isolates with SNU-01 show blue and green mutations, and the majority of current Asian avian isolates display green mutations. CD, cytoplasmic domain; TD, transmembrane domain.

I've only posted some excerpts from the letter, so follow the link to read (or listen to) the report in its entirety.   I'll have a postscript after the break.  

Characterization of Highly Pathogenic Avian Influenza A (H5N1) Viruses isolated from Cats in South Korea, 2023

Kyungmoon LeeMinjoo YeomThi Thu Hang VuHai-Quynh DoWoonsung NaMikyung Lee, show all
Article: 2290835 | Accepted author version posted online: 04 Dec 2023


In June and July 2023, feline AIV infections, confirmed to be caused by H5N1, occurred at two different shelters in Seoul, South Korea, with no confirmed human cases involved [6]. The source of infection in the first case remains unclear; in the second case, the infection originated from infected poultry feed. This was the first case of mammalian infections caused by HPAI H5N1 in South Korea. This study covers the first case, whereas the second case is currently being analysed by the Ministry of Agriculture, Food and Rural Affairs. We describe the potential origin and genetic characteristics of HPAI H5N1 viruses from cats based on whole genome sequencing and phylogenetic analysis.

Three out of 40 cats housed in a non-profit private shelter in Seoul, South Korea between June 24 and 27, 2023 died of high fever and anorexia. Subsequent mortality persisted at 1–2-day intervals, and 38 of the 40 animals finally died; however, the exact cause of death was not revealed. The feline inhabitants of the shelter were originally stray cats and resided in separate rooms (four to five animals in each room) without being confined in individual cages. The closed structure of the shelter prevented cats from contact with the outside environment, including wild birds. Additionally, there were no poultry farms within a 10 km radius. Between July 4 and 6, two cats showing respiratory and neurological symptoms were transported to a veterinary hospital but died within two days. A private diagnostic centre detected influenza A virus in nasal swab samples collected from the dead cats. These two nasal swab samples were subsequently sent to our laboratory for further analysis.

The H5N1 subtype of AIVs was confirmed using real-time reverse transcription polymerase chain reaction after isolating them via inoculation into embryonated chicken eggs. Whole genome sequencing resulted in the designation of the two isolates as A/feline/South Korea/SNU-01/2023 (SNU-01) and A/feline/South Korea/SNU-02/2023. Their sequences were identical; therefore, subsequent analyses were conducted using only the SNU-01 isolate. The nucleotide sequences of these strains were deposited at GISAID ( (accession numbers EPI_ISL_1812700 and EPI_ISL_18102701).

Phylogenetic analysis of the HA gene confirmed that SNU-01 belonged to clade of H5N1 viruses (Figure S1). Further examination of the HA gene from SNU-01 revealed the presence of a polybasic amino acid sequence at the cleavage site, classifying them as HPAI (PLREKRRKR/G). Each of the eight gene segments in SNU-01 shared a high degree of sequence identities, ranging from 99.59% to 100%, with the HPAI H5N1 virus clade isolated from birds in Japan between November 2022 and April 2023, according to GISAID BLAST ( (Table S1).

Phylogenetic analysis of all eight gene fragments consistently placed SNU-01 within the same cluster as the Japanese avian isolates, reaffirming their close genetic relationship and high nucleotide identities observed earlier (Figure S1-S8). 

Notably, the HA, neuraminidase (NA), and matrix genes of SNU-01 originated from G10 genotype avian isolates previously identified in 2022 from China and South Korea [2, 7] (Figure 1A). In contrast, polymerase basic (PB) 2, PB1, polymerase acidic (PA), nucleoprotein, and non-structural protein genes had their origins in LPAIV of the Eurasian lineage that circulated in China, Russia, and South Korea between 2019 and 2022. The specific source of individual gene segments appeared different, although this reassortment pattern resembled that of the South Korean genotypes I and II reported in 2022 [3]. Therefore, we classified our cat isolates as South Korean genotype III.

SNU-01 has shown multiple mammalian adaptations in several gene segments that enhance the polymerase activity of AIVs in mammalian hosts [3, 5, 8-14] (Figure 1B). Interestingly, except for D701N, which significantly contributes to mammalian adaptation, the remaining mammalian adaptive mutations were not limited to SNU-01; they were also observed in avian isolates. These mutations were prevalent among most avian isolates currently circulating in Eurasia, and additional mutations were identified in bird isolates that share a common ancestry with SNU-01 within phylogenetic trees (Figure S1, S4-6). The D701N mutation has not been detected in avian isolates; however, its presence in wild birds cannot be ruled out, given recent cases in Chile [15]. Meanwhile, the function of the unique mutations in PA and NA gene segments, found exclusively in SNU-01 requires further study to understand their implications.

HPAI H5N1 cases in mammals continue to be reported globally [5], and our study described the first case of HPAI H5N1 in cats in South Korea. We discovered novel genotypes and identified the accumulation of diverse mammalian adaptations in avian and cat isolates. 

Our findings strongly indicated that the viruses responsible for infecting cats likely originated from migratory birds that travelled from Japan and South Korea during the previous winter. Additionally, an increase in genetic diversity of H5Nx clade was confirmed owing to reassortment among AIVs [1-5]. Several mammalian adaptive mutations already accumulated within avian populations, and these changes may play an important role in facilitating the interspecies spread of AIVs to mammals [3, 5, 8-14]. Ongoing monitoring is imperative to track the potential spread of these multiple mammalian adaptations within avian populations and across various regions. The shelters where feline influenza occurred lacked veterinary control, which restricted the scope of sampling and information gathering for epidemiological investigations. The scarcity of sequence data for South Korean avian isolates from the 2022–2023 winter season posed constraints on genetic analysis with domestic isolates.

The discovery of the HPAI H5N1 clade virus in cats and its potential origin from avian sources underscores the dynamic nature of cross-species transmission of AIVs. Active reassortment and the accumulation of numerous mammalian adaptations in currently circulating viruses may further facilitate interspecies transmission. The shelter environment where susceptible animal hosts live closely together increases the likelihood of infectious disease transmission compared to typical indoor settings. Therefore, it is crucial to enhance active surveillance in densely populated animal living areas and proactively identify and mitigate factors facilitating cross-species contact.

Long chains of infections - such as you'd see in an animal shelter (or on a fur farm) - provide avian viruses with additional opportunities to adapt to a mammalian host, as demonstrated by the classic serial passage experiment shown below.
While we don't know exactly what combination of changes are needed to turn HPAI H5N1 from primarily an avian threat to a well-adapted mammalian virus - or even if that combination is even possible - the genetic dice are being tossed millions of times each day in birds and mammals around the globe. 

While there may be some as-yet unknown species barrier that protects us, given the stakes, it really isn't something we should be counting on.

Monday, December 04, 2023

J.I.D.: Influenza Vaccine Effectiveness (VE) Against Flu-Related Emergency Department, Urgent Care, and Hospitalization Encounters Among U.S. adults, 2022-2023


CDC's New Wild to Mild Flu Campaign


Quantifying how well the flu vaccine works every year is no easy task, since millions of people get mild-to-moderate`influenza-like illnesses' (ILIs) but never seek medical attention, and are therefore never tested or counted. 

Their illnesses could be due to flu, or to a long list of `other' respiratory pathogens (see ILI’s Aren’t Always The Flu). Even in October 2009, at the height of the H1N1 pandemic (see chart below) non-influenza illnesses (e.g RSV, Adenoviruses, Rhinoviruses, etc) outnumbered influenza by more than 3 to 1. 


Many who get the flu shot, only to get sick with the `flu', are infected with a non-influenza virus against which the vaccine has no effect. But to them, it is a sign that the vaccine didn't work.  

Up until about a dozen years ago, the CDC and other public health agencies tended to overestimate the effectiveness of the flu vaccine, often stating: ". . . for healthy adults under the age of 65, in years when the vaccine is a good match to circulating strains, effectiveness ranges from 70%-90%."

In 2011 the CDC lowered those estimates somewhat, to 50-70%. But over the past decade we've seen flu shots struggle to even reach that 50% vaccine effectiveness (VE) mark, particularly when H3N2 influenza was the dominant subtype.  The CDC now states:

How effective are flu vaccines?

CDC conducts studies each year to determine how well influenza (flu) vaccines protect against flu. While vaccine effectiveness (VE) can vary, recent studies show that flu vaccination reduces the risk of flu illness by between 40% and 60% among the overall population during seasons when most circulating flu viruses are well-matched to those used to make flu vaccines. In general, current flu vaccines tend to work better against influenza B and influenza A(H1N1) viruses and offer less protection against influenza A(H3N2) viruses.

Given how difficult it is to parse out influenza infections from other respiratory illnesses in the general population, a more reasonable metric is how well flu vaccines prevent ER & Urgent Care visits, and Hospitalizations, from lab-confirmed influenza infections. 

We've seen a shift towards this sort of targeted VE analysis (see last months C.I.D. VE Report on Pediatric Medical encounters for Influenza), and last September the CDC unveiled a new strategy, hoping to `reset' public expectations this fall as to what benefits they can realistically expect from the flu vaccine, emphasizing a reduction in severity over simply preventing infection. 

This week, researchers at the Influenza Division, Centers for Disease Control and Prevention, have published an analysis of the effectiveness of last year's flu shot in Adults in the Journal of Infectious Diseases, which finds a moderate VE (44%) against flu-related medical encounters.

I've only posted the Abstract, so follow the link to read it in its entirety.  I'll have a postscript after the break. 
Influenza vaccine effectiveness against influenza-A-associated emergency department, urgent care, and hospitalization encounters among U.S. adults, 2022-2023
Mark W Tenforde, MD, PhD, Zachary A Weber, PhD, MS, Duck-Hye Yang, PhD, Malini B DeSilva, MD, MPH, Kristin Dascomb, MD, PhD, Stephanie A Irving, MHS, Allison L Naleway, PhD, Manjusha Gaglani, MBBS, Bruce Fireman, Ned Lewis, MPH
The Journal of Infectious Diseases, jiad542,
Published: 02 December 2023 Article history




The 2022-2023 United States influenza season had unusually early influenza activity with high hospitalization rates. Vaccine-matched A(H3N2) viruses predominated, with lower levels of A(H1N1)pdm09 activity also observed.

Using the test-negative design, we evaluated influenza vaccine effectiveness (VE) during the 2022-2023 season against influenza-A-associated emergency department/urgent care (ED/UC) visits and hospitalizations from October 2022-March 2023 among adults (age ≥18 years) with acute respiratory illness (ARI). VE was estimated by comparing odds of seasonal influenza vaccination among case-patients (influenza A test-positive by molecular assay) and controls (influenza test-negative), applying inverse-propensity-to-be-vaccinated weights.

The analysis included 85,389 ED/UC ARI encounters (17.0% influenza-A-positive; 37.8% vaccinated overall) and 19,751 hospitalizations (9.5% influenza-A-positive; 52.8% vaccinated overall). VE against influenza-A-associated ED/UC encounters was 44% (95% confidence interval [95%CI]: 40-47%) overall and 45% and 41% among adults aged 18-64 and ≥65 years, respectively.
VE against influenza-A-associated hospitalizations was 35% (95%CI: 27-43%) overall and 23% and 41% among adults aged 18-64 and ≥65 years, respectively.

VE was moderate during the 2022-2023 influenza season, a season characterized with increased burden of influenza and co-circulation with other respiratory viruses. Vaccination is likely to substantially reduce morbidity, mortality, and strain on healthcare resources.

Even in seasons with moderate VE like the 2022-2023 season, however, vaccination is likely to have a substantial public health impact by preventing millions of medical visits, tens of thousands of hospitalizations, and thousands of deaths [20-22]. This reduction in medically attended illness and associated morbidity and mortality is especially critical to reduce burden on health care resources should influenza, SARS-CoV-2, RSV, and other respiratory viruses continue to co-circulate in high numbers.

          (Continue . . . )

Although flu vaccines have improved greatly over the past 15 years (e.g. cell culture-propagated vaccines , adjuvanted and high dose vaccines, quadrivalent formulas, etc.), most years they still only provide moderate protection against influenza infection, and are pretty much `strain-specific'.

Work continues on developing a `Universal Flu Vaccine' (see NIH: Clinical Trial of Universal Hexavalent Flu Vaccine Candidate Begins), but even then, the immediate goals are fairly modest.

The good news is that - even if the current flu vaccine doesn't always prevent infection, it can often reduce the severity of one's illness - and that can have both immediate and long term benefits

Something we've looked at repeatedly over the years (see here, here, and here) has been the flu vaccine's apparent impact on reducing heart attacks, strokes, and possibly even dementia later in life.

  • `. . . compelling evidence that influenza vaccination is associated with a decreased risk of major cardiovascular events'.
  • Specifically, the authors found that ". . . patients who received the influenza vaccine experienced a remarkable risk reduction of over 20% in cardiovascular death". This particular analysis focused on patients with an existing diagnosis of CVDs (Cardiovascular diseases).

While a VE of less than 50% is disappointing, a fifty percent reduction in severe flu is still significant -  and when you add in the reduced risk of cardiovascular events - the flu shot undoubtedly saves a lot of lives every year. 

Which is why I get the flu shot every year, and urge others to do the same. 

Sunday, December 03, 2023

CDC NCIRD: Pediatric Pneumonia Update


Over the past few months we've seen an unusual uptick in pediatric pneumonia cases in Northern China (see FluTrackers threads here, here, and here), which have been repeatedly attributed to normal seasonal illnesses (like flu, RSV, COVID, and mycoplasma pneumoniae) by local health authorities.  

While the WHO has asked China for more detailed information, thus far we've seen nothing to suggest anything `novel' is behind this surge. 

We've also seen upticks in pediatric pneumonia outside of China (see Denmark SSI Declares A Mycoplasma Pneumonia Epidemic), with the ECDC reporting at least 6 EU/EEA countries seeing increased M. pneumoniae activity.

But once again, the ECDC reported `There are currently no reports of atypical strains or evidence of resistance to first-line macrolide antibiotics.'

To this list we can add the CDC's National Center for Immunization and Respiratory Diseases (NCIRD), which released an update very late on Friday evening (see below), which finds only expected seasonal levels of pediatric pneumonia in the United States. 

First the update, after which I'll have a brief postscript.

Pediatric Pneumonia Update

 December 1, 2023, 8:30 PM EDT

CDC is posting updates on respiratory viruses every week; for the latest information, please visit CDC Respiratory Virus Updates.

Key Information
  • CDC is monitoring reports of increased respiratory illness around the world.
  • Diagnosis of pneumonia in children, along with other respiratory illnesses, increases every year in the fall and winter months.
  • In the United States, CDC monitors increases in respiratory illness, including pneumonia, through multiple data sources.
  • The weekly percent of emergency department visits with diagnosed pneumonia is largely consistent with previous years for children aged 0 to 4 years, with slight increases above typical levels for children aged 5 to 17 years, but still consistent with pre-pandemic years.
  • These increases are likely caused by viruses and bacteria we expect to see during the respiratory illness season.
  • There are many ways to protect yourself from serious illness this fall and winter, including effective immunizations that protect against viral and bacterial diseases that can lead to pneumonia.
Pediatric Pneumonia Update

CDC has been monitoring increases in respiratory illness reported recently around the world, including in China and several European countries. CDC is working closely with international, state, and local public health partners to maintain strong situational awareness. In the United States, CDC uses multiple data sources to monitor for increases in respiratory illness, including pneumonia, which can be caused by many pathogens. One data source is the National Syndromic Surveillance Program (NSSP), which monitors anonymized daily visit data from around 78% of emergency departments in the United States.

The diagnosis of pneumonia in children, along with other respiratory illnesses, increases every year during the fall and winter months in the United States. As of November 25, 2023, NSSP data indicated that the weekly percent of emergency department visits with diagnosed pneumonia was
  • 1.7% for children aged 0–1 years,
  • 2.4% for children aged 2–4 years, and
  • 1.5% for children aged 5–17 years.
These rates are roughly in line with previous years for patients aged 0–1 years and 2–4 years nationally (Figure 1).

The percent of emergency department visits diagnosed with pneumonia among patients aged 5–17 years is similar to pre-pandemic years, and it remains lower than that seen among younger children. CDC will continue to work with state and local health departments to monitor these rates closely.

Based on laboratory findings, these increases in pediatric pneumonia do not appear to be caused by a new virus or other pathogen. Instead, these increases are likely caused by viruses and bacteria we expect to see during the respiratory illness season. CDC will continue to work with state and local officials to monitor the situation.
Additional information about the current state of viral respiratory illness can be found at: Weekly Viral Respiratory Illness Snapshot (
As we progress into respiratory season, we can do more than ever to help prevent people from becoming severely ill from respiratory illness. This includes:
  • Safe and effective immunizations – For the first time ever, immunizations are available for three major fall and winter viral respiratory diseases – flu, COVID-19, and respiratory syncytial virus (RSV) — which can cause pneumonia. Pneumococcal vaccines are also available to prevent the most common type of bacterial pneumonia. Pertussis (whooping cough) vaccines are available to prevent another common bacterial respiratory infection that can lead to pneumonia.
  • Widely available, effective treatments – Antiviral treatments are available for flu and COVID-19, and antibiotics are used to treat respiratory diseases caused by bacteria such as Mycoplasma pneumoniae infection, pneumococcal disease, and whooping cough. These treatments can reduce risk of severe illness, hospitalization, and death.
  • Testing – Tests, some of which can be used at home, can quickly detect COVID-19 and flu. There are also tests for illnesses caused by bacteria, but a healthcare provider needs to perform these tests. Getting tested quickly is important, so there is no delay in treatment and other actions that can protect family, friends, and coworkers.
  • Other ways to protect yourself – Other actions like masking, physical distancing, washing hands, and improving ventilation in the places where people live and work can provide additional layers of protection.
Last Reviewed: December 1, 2023
Source: National Center for Immunization and Respiratory Diseases

There are always caveats to reports like this.  M. pneumoniae is not a `reportable' disease in the United States - or most of the world - meaning a lot of cases go unreported.  According to the CDC:
M. pneumoniae infections are common, but the true number of people affected is unknown. An estimated 2 million cases of M. pneumoniae infections occur each year in the United States.

And - particularly over the holidays -  reporting of data often lags, sometimes by several weeks.

Surveillance is like looking in the rear view mirror as you barrel down the highway; it can tell you where you've been, but provides little information about where you are, and even less on where you are going.  

While nothing we've seen thus far suggests we are dealing with a `novel' pathogen, we will continue to keep a close eye on these reports as the winter respiratory season continues. 

Saturday, December 02, 2023

ECDC On Increased Mycoplasma Pneumonia Reported In EU/EEA Countries

Credit CDC


While tabloid, social, and even some mainstream media outlets seem determined to present the recent uptick in respiratory illnesses in China - and around the world - as scary precursors to the next pandemic, so far we've seen no indication of anything `novel' at work, or any direct link between China's outbreaks and those being reported in Europe or the United States. 

Admittedly, global surveillance, testing, and data sharing are limited - and new information could change that assessment - but right now we appear to be dealing with an uptick in known, seasonal respiratory illnesses. 

The `Mystery Pneumonia' which has been identified in China and many other countries is by all accounts Mycoplasma pneumoniae, which sparks minor epidemics every few years.  Exact numbers are hard to come by, since this in not a `reportable' disease in most countries, but the CDC estimates:

Estimated incidence

M. pneumoniae infections are common, but the true number of people affected is unknown. An estimated 2 million cases of M. pneumoniae infections occur each year in the United States.

Trends over time

The number of M. pneumoniae infections varies over time, with peaks of disease every 3 to 7 years. This illness can happen any time during the year but may be more common in summer and early fall.


Outbreaks occur mostly in crowded environments like college residence halls and nursing homes. Outbreaks can be prolonged due to the long incubation period of M. pneumoniae.

It is always possible for a new strain to emerge, or one that has increased antibiotic resistance, but so far we haven't seen any reports suggesting either in the EU/EEA or the United States.  

Yesterday the ECDC published their weekly Communicable Disease Threats Report, where they reported on upticks in M. pneumoniae in the EU/EEA in recent months.  

Increase in respiratory infections due to Mycoplasma pneumoniae in the EU/EEA during the season 2023/2024


Epidemics of M. pneumoniae occur periodically, typically every one to three years [1]. Transmission requires close contact with an infected individual, with slow-onset and often atypical respiratory symptoms once infected. Infections typically present with mild, self-remitting upper respiratory tract symptoms; however, patients presenting with prolonged or atypical, severe lower respiratory tract symptoms require antibiotic treatment. 

Six EU/EEA countries have reported recent increases in M. pneumoniae infections at the national level or in specific hospitals. Increases have been reported in all age groups but are predominantly observed in children and adolescents. Additionally, one country observed an increase in severe cases admitted to the intensive care unit.

There are currently no reports of atypical strains or evidence of resistance to first-line macrolide antibiotics.

ECDC assessment:

M. pneumoniae is not notifiable in most EU/EEA countries, leading to limited available information regarding diagnosed cases, proportion of detections amongst respiratory laboratory samples, or historical detection data. As a result, making country-level comparisons should be done with caution. M. pneumoniae epidemics occur cyclically in Europe every one to three years [1]. 

Various factors contribute to this cyclical pattern, such as the decline of population immunity over time or the introduction of new strains into the population. The reported increases are observed following a three-year period of very limited transmission and detection of M. pneumoniae in the EU/EEA, following widespread implementation of non-pharmaceutical measures during the COVID-19 pandemic,resulting in reduced population immunity, particularly amongst those with little or no pre-existing exposures to M. pneumoniae.

There are currently no reports of atypical M. pneumoniae strains or resistance to first-line macrolide antibiotics from reporting countries. However, it remains important for countries to monitor and report the occurrence of atypical and/or severe forms of disease, evidence of resistance to antibiotics, and strains on the healthcare system related to M. pneumoniae cases as winter progresses and the combined burden of respiratory pathogens increase.


ECDC continues to monitor the situation. Countries are encouraged to continue reporting to EpiPulse with additional information: 2023-IRV-00008. In particular, countries with laboratory systems that routinely screen respiratory samples for M. pneumoniae are encouraged to report current and historic trend data for detections, as well as strain characterisation and antibiotic susceptibility data, if available

Not surprisingly, we are also seeing reports of sporadic outbreaks here in the United States (see Warren Ohio Health Dept. Press Release), and additional outbreaks are to be expected. While there doesn't appear to be anything `novel' about these outbreaks, that doesn't make them benign. 

The CDC advises:

People at Risk 

Mycoplasma pneumoniae infections are most common in young adults and school-aged children, but can affect anyone. People living and working in crowded settings are at increased risk. These settings include:
  • Schools
  • College residence halls
  • Military training facilities
  • Long-term care facilities
  • Hospitals
Other people at increased risk for serious infections include those:
  • Recovering from a respiratory illness
  • With a weakened immune system

Help protect yourself and others from Mycoplasma pneumoniae infection by practicing good hand hygiene.

People can get infected with Mycoplasma pneumoniae more than once. While there is no vaccine to prevent M. pneumoniae infections, there are things people can do to protect themselves and others.

Good hygiene

Like many respiratory germs, Mycoplasma pneumoniae most commonly spread by coughing and sneezing. Some tips to prevent the spread of M. pneumoniae include:
Cover your mouth and nose with a tissue when you cough or sneeze.
  • Put your used tissue in a waste basket.
  • If you don’t have a tissue, cough or sneeze into your upper sleeve or elbow, not your hands.
  • Wash your hands often with soap and water for at least 20 seconds.
  • If soap and water are not available, use an alcohol-based hand rub.
Preventive antibiotics

Doctors generally do not prescribe antibiotics to help prevent someone else from getting sick (for example, a close contact of an infected person).

Mycoplasma pnuemoniae infections are generally mild, but some people may need care in a hospital.

Most people will recover from an infection caused by Mycoplasma pneumoniae without antibiotics. Ask your doctor or pharmacist about over-the-counter medicines that can help you feel better while you are recovering.

However, if someone develops pneumonia (lung infection) caused by M. pneumoniae, doctors usually prescribe antibiotics. There are several types of antibiotics available to treat pneumonia caused by M. pneumoniae. Antibiotics can help patients recover from the infection faster if started early on.

Some M. pneumoniae are resistant to some antibiotics used for treatment. Learn more about the potential danger of antibiotic resistance, and how to prevent it at CDC’s Be Antibiotics Aware website.


While M. pneumoniae usually cause mild infections, severe complications can occur that require care in a hospital. M. pneumoniae infections can cause or worsen the following complications:
  • Serious pneumonia
  • Asthma attacks or new asthma symptoms
  • Encephalitis (swelling of the brain)
  • Hemolytic anemia (too few red blood cells, which means fewer cells to deliver oxygen in the body)
  • Renal dysfunction (kidney problems)
  • Skin disorders like Stevens-Johnson syndrome, erythema multiforme, toxic epidermal necrolysis

We are entering what is likely to be a messy winter respiratory season, with a mixture of influenza viruses, COVID, RSV, adenoviruses, rhinoviruses, and bacterial pneumonia. 

Some can be reduced by vaccines, while others are susceptible to non-pharmaceutical measures like hand hygiene and face masks. 

As always . . .