Monday, April 23, 2018

San Diego: 6 Cases Of Wound Botulism Among Injection Drug Users

Credit CDC


According to the CDC, about 20 people each year (in the U.S.) contract wound botulism, mostly from subcutaneous injection of black tar heroin.

A pretty low number, which makes the following headline from San Diego's Office of Communications all the more remarkable.

Three More Wound Botulism Cases Reported in County

Three more cases of wound botulism in people who injected black tar heroin have been reported in San Diego County, bringing the total to six in the past month, the San Diego County Health and Human Services Agency announced today.

Five of the cases are men and have been confirmed with botulism by the California Department of Public Health. The latest case is a 25-year-old woman who is being tested for confirmation. Although all were hospitalized and treated with anti-toxin obtained from CDPH, one of the previously reported cases, a 67-year-old man, has died.

Two of the six cases are connected, but the others appear to be unrelated and the sources of the black tar heroin are unknown. Investigation is continuing and additional cases may occur.

“This is the largest group of wound botulism cases ever reported in San Diego County,” said Wilma Wooten, M.D., M.P.H., County public health officer. “Black tar heroin users can suffer from overdose, skin infections, endocarditis, botulism, and other serious illnesses that can be life-threatening. We urge anyone who uses this substance to seek treament.”

Symptoms of wound botulism occur within days or weeks of injecting contaminated drug and may be mistaken for drug overdose. Symptoms can include weak or drooping eyelids, blurred or double vision, dry mouth, sore throat, slurred speech, trouble swallowing, difficulty breathing, and a progressive symmetric paralysis that begins at the face and head and travels down the body.

If left untreated, symptoms may lead to paralysis of the respiratory muscles, arms, legs and trunk, and can cause death. Prompt diagnosis and treatment are critical to decreasing the severity and duration of illness.

(Continue . . . .)

Beyond the everyday hazards of overdosing, Hepatitis C, Hepatitis B, HIV, Staphylococcus aureus, and even tetanus, there are exotic risks including wound botulism and wound anthrax (see Eurosurveillance: Anthrax Encounters Of The 4th Kind).
Black tar heroin is cheap, and therefore popular, but it is crudely refined and can be cut (or more properly adulterated) with a variety of substances, including (reportedly) ground up paper, shoe polish, and whatever floor sweepings might be available.  
This creates a thick, sticky substance which is difficult to inject intravenously, making skin popping or muscle popping the preferred route, which can often lead to tissue necrosis and abscesses under the skin. 

According to the CDC's Wound Botulism page:
We don’t know how black tar heroin gets contaminated with the germ that causes botulism. Because the germ lives in soil, it might get into heroin when the drug is produced or transported, when it is cut or mixed with other substances, when it is prepared for use, or through some other way. Drug-use equipment (“works”) used to prepare or inject contaminated drugs might also spread the botulism germs to anyone who uses it.
Key facts:
  • You cannot see the germ that causes botulism. Contaminated drugs do not look different from non-contaminated drugs. Lab testing is the only way to tell if your drugs are contaminated with the germ that causes botulism.
  • Heating (“cooking”) heroin will not kill the botulism germ. It takes special conditions to kill this germ.
  • You cannot get botulism from another person. It is not contagious. But if you share contaminated heroin or equipment (“works”) with another person, both of you might get botulism.
Between the nation's mounting opioid epidemic, the recent outbreak of severe internal bleeding due to rat poison laced Spice/K2, and now this latest cluster of wound botulism in San Diego, the societal and personal costs of drug abuse continue to climb.


PAHO Epidemiological Update: Diphtheria In The Americas


According to the noted anthropologist and researcher George Armelagos (May 22, 1936 - May 15, 2014) of Emory University - in his work The Changing Disease-Scape in the Third Epidemiological Transition-  in the mid-1970s we entered the age of newly emerging infectious diseases, re-emerging diseases and a rise in antimicrobial resistant pathogens.

While emerging pathogens - like novel flu, hemorrhagic fevers, SARS and other exotic pathogens are a major concern -  antimicrobial resistance continues to rise to alarming levels around the world, and we are seeing the resurgence of old, nearly forgotten infectious diseases like measles, mumps, scarlet fever, and diphtheria. 
Pretty much as predicted 32 years ago by Dr. Armelagos.  For a more detailed review of his work, and the reasons behind his conclusions, you may wish to revisit my 2016 blog  The Third Epidemiological Transition.
A couple of weeks ago, in UK: `Exceptional' Scarlet Fever Season Continue, we looked at the (still) unexplained return of Scarlet fever around the world. 

A month ago, in ECDC RRA On Measles In EU & Harvard Study On Mumps Vaccine, we looked at two more infectious diseases - once nearly vanquished in Europe and the United States - which are on the rise again. 

And perhaps most surprisingly, we been following the come back of diphtheria around the globe.  A few recent blogs include:
WHO Update & Risk Assessment: Diphtheria At Cox's Bazar, Bangladesh
WHO: Diphtheria Spreading Rapidly In Cox’s Bazar, Bangladesh
Vietnam MOH Warns Of Diphtheria’s Spread From Laos
Over the past 50 years diphtheria has become so well controlled by vaccines in Western countries that many doctors can now go their entire career without ever seeing a case.  
But that success story may be in danger, as over the past few years we've seen more and more outbreaks around the globe. 
Last week PAHO (the Pan American Health Organization) released an epidemiological update on Diphtheria in the Americas, citing four countries (Brazil, Colombia, Haiti & Venezuela) that have reported cases in the past year.

Hardest hit, with more than 1600 confirmed or suspected cases since 2016, has been Venezuela (see last summer's Venezuela: Reports Of A Growing Diphtheria Outbreak).

Epidemiological Update
16 April 2018

Diphtheria in the Americas - Summary of the situation
In 2017, four countries in the Region of the Americas—Brazil, the Dominican Republic, Haiti, and the Bolivarian Republic of Venezuela—reported confirmed diphtheria cases. In 2018 as of epidemiological week (EW) 14 of 2018, four countries in the Region—Brazil, Colombia, Haiti, and Venezuela—have reported suspected and confirmed diphtheria cases.
The following is a summary of the situation in each country with reported suspected and confirmed cases in 2018.
In Brazil in 2017, there were 42 suspected cases reported in 14 states. Of the reported cases, 5 were confirmed in four states: Acre (1), Minas Gerais (2), Roraima (1 fatal case, imported from Venezuela), and São Paulo (1). The remaining 37 cases were ruled out. Three of the 5 confirmed cases (2 in Minas Gerais and 1 in São Paulo) had received the full vaccination scheme. The confirmed cases range from 4 to 66 years of age (median 19 years), and four are male and one is female. Additionally, in EW 14 of 2018, 6 suspected cases were reported in 6 states; one reported in the state of Roraima (imported from Venezuela) is currently under investigation. As of EW 14, none were confirmed.
In Colombia in EW 7 of 2018, a fatal confirmed case of diphtheria imported from Venezuela was reported in La Guajira Department. The case is a 3-year-old Venezuela national with an unknown vaccination history. Onset of symptoms was on 2 January 2018 and the case died on 8 January. The case was laboratory-confirmed based on clinical, epidemiological, and laboratory criteria (Gram-positive bacilli and RT-PCR positive for Corynebacterium diphtheriae with no identification of biotype or positive toxin).
In Haiti, since the beginning of the outbreak at the end of 2014 up to EW 6 of 2018, there have been 410 probable cases of diphtheria reported, including 75 deaths. 1 Reported case-fatality rates were 22.3% in 2015, 27% in 2016 and 10.7% in 2017 and 2018. During the first four epidemiological weeks of 2018, 2 to 5 probable cases per EW were reported similar to that observed during the last four weeks of 2017.
Females accounted for 57% of the total probable cases in 2015, 50% in 2016, 60% in 2017, and 47% in 2018 (up to EW 6). With respect to vaccination coverage, between 2015 and 2018 the unvaccinated cases accounted for 17% (2018) to 38% (2015) of the total cases. Children less than 10 years of age accounted for 64% of the probable cases reported between 2017 to EW 4 of 2018.
Per the Haiti Ministry of Public Health and Population, a probable case is defined as any person, of any age, that presents laryngitis, pharyngitis or tonsillitis with false adherent membranes in the tonsils, pharynx and / or nasal pits, associated with edema of the neck.
Since the beginning of the outbreak the departments reporting the highest number of probable cases are Artibonite, Centre, and Ouest.
In Venezuela, the diphtheria outbreak that began in July 2016 remains active (Figure 1). Since the start of the outbreak until EW 10 of 2018, a total of 1,602 suspected diphtheria cases were reported (324 cases in 2016, 1,040 in 2017, and 238 in 2018), of which 976 were confirmed by laboratory (314) or epidemiological-link (662), and 142 died (17 in 2016, 103 in 2017, and 22 in 2018). The cumulative case fatality rate is 14.5%
In 2016, cases were reported in five states (Anzoátegui, Bolívar, Delta Amacuro, Monagas, and Sucre), while in 2017, 22 states and the Capital District reported confirmed cases. In 2018, 9 federal entities have reported confirmed cases. Cases have been reported among all age groups; however, the majority of cases occurred among the 1-49 year age group while the highest incidence rate occurred among the 5-19 year age group.
Health authorities are intensifying epidemiological surveillance, investigations, medical care, and vaccinations. In addition, they are maintaining continuous training of healthcare workers (based on the updated manual of standards, guidelines, and procedures for the management of the disease) as well as health education.

(Continue . . . )

Although the diphtheria vaccine is highly protective against the disease, vaccinated individuals can still can be asymptomatic carriers of toxigenic C. diphtheriae. 

And the vaccines' protection doesn't last forever, booster shots - even for adults - are required to maintain immunity (see WHO report below).
Diphtheria vaccine
Review of evidence on vaccine effectiveness and immunogenicity to assess the duration of protection ≥10 years after the last booster dose.
April 2017
So it doesn't take very long into the collapse of a nation's public health system before unvaccinated children and adults whose immunity has waned to start coming down with this highly contagious disease.
Diphtheria antitoxin (DAT) has been in short supply for several years, even in the EU (see ECDC RRA A case of diphtheria in Spain), complicating treatment.
A grim reminder of just how thin the veneer of modern civilization really is, and how easily an economic collapse, or some other major calamity (war, natural disaster, pandemic, etc.) can erode and disrupt those things we currently take for granted.

Sunday, April 22, 2018

Senate Committee Hearing: Are We Ready for the Next Hurricane Season?


Even though hurricane season doesn't start for another 5 weeks, I'm already starting to ramp up my preparedness in case - as I did last year - I'm forced to evacuate due to an approaching storm.
Compared to the folks in Texas, Puerto Rico, and South Florida I was very lucky, as my home was left standing, even though the power was out for 5 days. 
As a native Floridian, and a long time resident of both Florida's west coast and (briefly) the Keys, this wasn't my first brush with a natural disaster, but it did highlight some gaps in my preparedness (see A Post Irma Update).

On a much grander scale - cities, states, and numerous federal agencies, along with NGO relief agencies - found themselves severely challenged by last year's hurricane season, and are already gearing up for the upcoming season.
Earlier this month the U.S. Senate Committee On Commerce, Science & Transportation, held a 2.5 hour hearing on our nation's readiness to deal with the 2018 hurricane season.
The written testimonies and video are available below.  I'll return with a postscript when you return.

April 12, 2018
Are We Ready for the Next Hurricane Season? Status of Preparation and Response Capabilities for 2018

U.S. Sen. Roger Wicker (R-Miss.) will convene a hearing at 9:45 a.m. on Thursday, April 12, 2018, entitled “Are We Ready for the Next Hurricane Season? Status of Preparation and Response Capabilities for 2018.” The hearing will examine the status of local and federal agencies’ recovery from the 2017 Atlantic hurricane season, and ongoing preparation for the 2018 season.

Panel 1 (testimony only):
Mr. Chuck Lindsey, City Manager, Marathon, Florida
Mr. Jamie Miller, Deputy Director for Governmental Affairs and Chief Innovation Officer, Mississippi Development Authority
Ms. Jennifer Pipa, Regional Chief Executive Officer, American Red Cross of Central Florida

Panel 2 (testimony followed by questions):
Rear Admiral Tim Gallaudet, Ph.D., USN Ret., Assistant Secretary of Commerce for Oceans and Atmosphere and Acting Under Secretary of Commerce for Oceans and Atmosphere, National Oceanic and Atmospheric Administration
Rear Admiral Linda Fagan, Deputy Commandant for Operations, Policy, and Capabilities, U.S. Coast Guard
T. Bella Dinh-Zarr, Ph.D., Member, National Transportation Safety Board

*Witness lists subject to change.

Hearing Details:

Thursday, April 12, 2018
9:45 a.m.
Full Committee

This hearing will take place in Russell Senate Office Building, Room 253. Witness testimony, opening statements, and a live video of the hearing will be available on 

Governments and NGOs can only do so much, and they are often focused on the `bigger picture'; getting roads cleared, the power back on, hospitals running, and the delivery of emergency supplies to distribution points.
On an individual level, those caught up in a major disaster may find themselves needing to fend for themselves for 72 hours or longer.
As I've written often (see #NatlPrep: Disaster Buddies) people who live alone - nearly 1 person in 10 in the United States - are particularly vulnerable during a disaster.
For some of them, having a place to go when staying put would endanger their safety, and a way to get there, can literally mean the difference between life and death.
If a disaster struck your region today without warning, and the power went out, stores closed their doors, and water stopped flowing from your kitchen tap for the next 7 to 10 days  . . .  do you have:
  • A battery operated NWS Emergency Radio to find out what was going on, and to get vital instructions from emergency officials?
  • A decent first-aid kit, so that you can treat injuries?
  • Enough non-perishable food and water on hand to feed and hydrate your family (including pets) for the duration?
  • A way to provide light (and in cold climates, heat) for your family without electricity?   And a way to cook?  And to do this safely?
  • A small supply of cash to use in case credit/debit machines are not working?
  • An emergency plan, including meeting places, emergency out-of-state contact numbers, a disaster buddy,  and in case you must evacuate, a bug-out bag?
  • Spare supply of essential prescription medicines that you or your family may need?
If your answer is `no’, you have some work to do.  A good place to get started is by visiting  

Mexico: SENASICA Announces Two More Outbreaks Of HPAI H7N3


Mexico has a long history of sporadic outbreaks of both LPAI (low pathogenic) and HPAI (Highly PathogenicH5 & H7 outbreaks, going back more than two decades. Large outbreaks have been fairly rare the past few years, but in 2012-2013 (see OIE: Mexico Reports HPAI H7N3 In Two States), H7N3 forced the culling of more than 22 million birds.
Roughly 6 weeks ago, in Mexico: SENASICA Announces Two Outbreaks Of HPAI H7N3 - their first avian flu report since notifying the OIE of the detection of subclinical H7N3 at a single farm in Jalisco State in April of 2017.
Yesterday (h/t Tetano & Pathfinder on FluTrackers), Mexico's SENASICA (National Health Service, Food Safety and Food Quality) announced two new outbreaks of HPAI H7N3 discovered at small non-commercial poultry holdings in Guanajuato and Querétaro.

First the (translated) statement, and then I'll return with a bit more.

SENASICA reported to the OIE, and immediate closure of two outbreaks of avian influenza AH7N3
After confirming in their laboratories presenc ia the virus, he ordered the depopulation of two farms in the states of Guanajuato and Queretaro.

Author: National Health Service, Food Safety and Quality
Publication date : April 21, 2018

The National Service of Health, Food Safety and Quality (SENASICA) reported to the World Organization for Animal Health (OIE by its French acronym) the finding of avian influenza AH7N3 highly pathogenic in two properties, one located in the municipality of Irapuato, Guanajuato and one in Pedro Escobedo, Queretaro.

The agency reported that none of the two cases was identified on commercial farms, so they do not pose a risk in domestic poultry production, which has an inventory of more than 200 million laying hens and 300 million broilers to cycle.

After confirming the presence of the virus in official laboratories, SENASICA ordered the immediate depopulation of both properties, one located in Guanajuato, which had a population of 60 birds of combat, of which 35 died from the disease and rest was eliminated.

Moreover, the site located in Queretaro maintained a population of two thousand 604 birds of organic stance, of which 563 thousand were killed and the rest were killed.

In accordance with established procedures for such findings, official personnel conducting the monitoring of farms and properties located on the periphery of 10 kilometers and so far no health problems have been detected elsewhere.

Outbreaks of avian influenza were found thanks to the work of epidemiological surveillance carried out by the body, in order to timely detect the virus and prevent its spread to commercial poultry.

While most notorious for their ability to cause great damage in poultry flocks, avian H7 viruses have shown some propensity to infect humans as well. Beyond the obvious example of H7N9 in China:
With the exception of H7N9, which emerged in China in 2013, human H7 infections have generally been mild. Once regarded as a low public health risk, H7N9's recent over-achievements have put H7 viruses in a new light.
The CDC's IRAT (Influenza Risk Assessment Tool) currently tracks 14 novel viruses viewed as having at least some `pandemic potential', and of those, 4 are avian H7 viruses (2 strains of H7N9, H7N7, and H7N8).  
For now H7N3's main threat is as a poultry epizootic - and with the spring migration well underway - poultry interests along the northbound flyways in Mexico, the United States, and Canada should pay special attention to their biosecurity over the next few weeks.

Saturday, April 21, 2018

CDC Update: Candida Auris - April 2018


In June of 2016 the CDC issued a Clinical Alert to U.S. Health care facilities about the Global Emergence of Invasive Infections Caused by the Multidrug-Resistant Yeast Candida auris.
C. auris is an emerging fungal pathogen that was first isolated in Japan in 2009. It was initially found in the discharge from a patient's external ear (hence the name `auris').  Retrospective analysis has traced this fungal infection back over 20 years.
Since then the CDC and public health entities have been monitoring an increasing number of cases (and hospital clusters) in the United States and abroad, generally involving bloodstream infections, wound infections or otitis.
Adding to the concern:
  1. C. auris infections have a high fatality rate
  2. The strain appears to be resistant to multiple classes of anti-fungals  
  3. This strain is unusually persistent on fomites in healthcare environments.
  4. And it can be difficult for labs to differentiate it from other Candida strains
The CDC has updated their C. Auris surveillance page, where they show - as of March 31th - 247 confirmed cases and 30 probable cases, across 11 states.

Additionally, based on targeted screening in four states reporting clinical cases, the CDC reports an additional 475 patients have been discovered to be asymptomatically colonized with C. auris.

As mentioned, this isn't just a problem in the United States (see map above), and this week the CDC's MMWR carries a `Notes from the field' report on C. Auris in Colombia that illustrates how easily this fungal infection can fly under the surveillance radar. 
Something that is probably happening in many other places around the world.
I've only included some excerpts, so follow the link to read the report in its entirety.

Notes from the Field: Surveillance for Candida auris — Colombia, September 2016–May 2017
Weekly / April 20, 2018 / 67(15);459–460

Patricia Escandón1*; Diego H. Cáceres2,3*; Andres Espinosa-Bode4; Sandra Rivera1; Paige Armstrong2; Snigdha Vallabhaneni2; Elizabeth L. Berkow2; Shawn R. Lockhart2; Tom Chiller2; Brendan R. Jackson2; Carolina Duarte1

After a 2016 CDC alert describing infections caused by the multidrug-resistant fungus Candida auris (1), the Colombian Instituto Nacional de Salud (INS) queried the country’s WHONET† database of invasive Candida isolates to detect previous C. auris infections.
No C. auris isolates were identified during 2012–2016. However, C. auris is often misidentified as Candida haemulonii (2), a yeast that rarely causes invasive infections, and 75 C. haemulonii isolates were reported during May 2013–August 2016.

These isolates came primarily from patients in intensive care units in the country’s north region, approximately 350–600 km (220–375 miles) from Maracaibo, Venezuela, where C. auris cases were first identified in 2012 (3). Of the 75 reported Colombian C. haemulonii isolates in WHONET, INS obtained 45 isolates from six medical institutions dating from February 2015 through August 2016, all of which were confirmed to be C. auris by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry.

Based on these findings, INS issued a national alert and mandated reporting of suspected isolates on August 30, 2016§ (3,4). In September 2016, a team from INS, CDC, and medical staff members from hospitals with documented C. auris cases investigated the 45 MALDI-TOF–confirmed C. auris cases identified before the INS alert. This investigation involved two hospitals in the north region and two in the central region. Cases were clustered within specific hospital units, and surveillance sampling demonstrated transmission in health care settings (INS and CDC, unpublished data, 2018).

Infections caused by C. auris are occurring in Colombia; the pathogen has been present in Columbia since at least 2015, and case counts are increasing. The number of reported cases likely does not reflect the true number of infected and colonized persons because of underreporting and underdiagnosis, as well as misdiagnosis as other yeast species (6).

To contain the spread of C. auris in Colombia, INS updated the C. auris national clinical alert in July 2017 specifying which yeast isolates must be sent to INS for confirmation and mandating that medical facilities implement enhanced infection control practices, including using contact precautions and single rooms for patients with C. auris infections, minimizing the number of health care personnel in contact with infected patients, and daily and terminal cleaning of patient rooms and medical equipment with a disinfectant effective against Clostridium difficile spores** (2).

Clinical laboratories should be aware that automated laboratory systems might incorrectly identify C. auris, particularly as C. haemulonii, although the species reported depends on the system (2).
        (Continue . . . )

For more on this emerging fungal pathogen, you may wish peruse the CDC's dedicated web page:

And for some older blogs on the topic, you may wish to revisit:

Friday, April 20, 2018

C.I.D.: Predicting Influenza H3N2 Vaccine Efficacy from Evolution of the Dominant Epitope


After this past winter's severe H3N2 flu season, which was aided and abetted by a seriously disappointing H3N2 component to the seasonal flu vaccine, the last thing anyone wants to see are the headlines from yesterday forecasting another poor vaccine performance this fall.
Rice University study suggests 2018 flu vaccine will have 20 percent success rate -
Rice University study suggests 2018 flu vaccine will have 20 percent success rate - CW39
Fall 2018 flu vaccine will be 20 percent effective, study predicts -UPI
April 19 (UPI) -- This fall's flu vaccine will be 20 percent effective for the dominant circulating strain of influenza A, the same as shots given the past two years, a new study predicts.
        (Continue . . . )

Admittedly, not exactly the message that public health officials want to see splashed all over the media during the run up to next fall's vaccination campaign (or for the Southern Hemisphere's campaign right now).
While the performance of next fall's H3N2 vaccine component - which suffers from mutations generated during its passage through eggs (see PLoS Path.: A Structural Explanation For The Low VE Of Recent H3N2 Vaccines) - seems likely fall short again next fall, that is (thankfully) not the whole story.  
We've had two H3N2 dominant flu seasons in a row.  While it is certainly possible we'll be unlucky enough to see a third, right now H1N1 appears to be picking up steam around the globe, and we may see it become the dominant strain next fall (see WHO Update below)

62.7% of Influenza A  H1N1 / 37.3% H3N2

Although H1N1 cases were few and far between this past winter, the CDC's Interim Vaccine Effectiveness numbers (released in Feb) estimated a 67% (CI = 54%–76%) VE against A(H1N1)pdm09 viruses.
Even assuming that proves optimistic due to the small sample size, the VE against H1N1 has generally run over 50%.
Which means - depending upon the mix of influenza A & B viruses next fall - the vaccine may not prove to be as much of a dud as these headlines would suggest.  Only time will tell.

All of this dire reportage stems from what I'm sure is a fascinating study, published this week in Clinical Infectious Diseases, that is (alas) almost entirely behind a pay wall.  There is not much I can do but provide a link.
Predicting Influenza H3N2 Vaccine Efficacy from Evolution of the Dominant Epitope
Melia E Bonomo Michael W Deem
Clinical Infectious Diseases, ciy323,
Published: 17 April 2018


We predict vaccine efficacy with a measure of antigenic distance between influenza A(H3N2) and candidate vaccine viruses based on amino acid substitutions in the dominant epitopes. In 2016-2017, our model predicts 19% efficacy compared to 20% observed. This tool assists candidate vaccine selection by predicting human protection against circulating strains.
        (Continue . . . .)

What we do have is a press release (below) from Rice University, which provides some pretty good background on the study.  It too, glosses over the possibility that next year could be an H1N1 dominant year, which undoubtedly explains the media's slant.
Study predicts 2018 flu vaccine will have 20 percent efficacy
Jade Boyd – April 19, 2018 David Ruth


Jade Boyd

Study predicts 2018 flu vaccine will have 20 percent efficacy
Rice U. study finds egg adaptations will limit efficacy of new flu vaccine

HOUSTON — (April 19, 2018) — A Rice University study predicts that this fall’s flu vaccine — a new H3N2 formulation for the first time since 2015 — will likely have the same reduced efficacy against the dominant circulating strain of influenza A as the vaccine given in 2016 and 2017 due to viral mutations related to vaccine production in eggs.

The Rice method, known as pEpitope (pronounced PEE-epih-tope), was invented more than 10 years ago as a fast, inexpensive way of gauging the effectiveness of proposed flu vaccine formulations. The latest pEpitope study, which is available online this week in Clinical Infectious Diseases, suggests pEpitope is a more accurate predictor of vaccine efficacy than long-relied-upon ferret tests, particularly for data gathered in the past decade. The pEpitope method accounts for 77 percent of what impacts efficacy of the vaccine in humans.

pEpitope is a computational method that measures critical differences in the genetic sequences of flu strains. In the new study, the method accurately predicted vaccine efficacy rates for more than 40 years of flu records. These included the past two flu seasons in which vaccines offered only limited protection against the most widely circulating strain of influenza A.

“The vaccine has been changed for 2018-19, but unfortunately it still contains two critical mutations that arise from the egg-based vaccine production process,” said Michael Deem, Rice’s John W. Cox Professor in Biochemical and Genetic Engineering and professor of physics and astronomy. “Our study found that these same mutations halved the efficacy of flu vaccines in the past two seasons, and we expect they will lower the efficacy of the next vaccine in a similar manner.”

(Continue . . . )

As I said, this appears to be a fascinating project, and I look forward to seeing more on it.  And until we change the way flu vaccines are produced, it is very likely - particularly with H3N2 - that these VE problems will continue.

By the middle of last summer it was becoming apparent that the 2017-18 H3N2 vaccine component was likely to be `suboptimal' once again (see The Enigmatic, Problematic H3N2 Influenza Virus) and the prospects of a another H3N2 dominated North America flu season were looking pretty good.  
Despite those warning signs, I got the flu vaccine last September and urged others to do so as well, figuring that some protection beats no protection at all.   
While this year's flu vaccine was far less effective than we'd like, the CDC's mid-season estimate of the overall U.S. VE (Vaccine Effectiveness) against both A & B subtypes was 36%. Some age groups however - notably adolescents (9-17), and adults 50 and older - showed no statistically significant protection from the vaccine.
One bright spot is that kids aged 6 months through 8 years saw as much as 59% protection from this year's vaccine.  And in a year where we've seen more than 150 flu-related pediatric deaths, without the vaccine, that number would undoubtedly have been higher.
Although I think the benefits of the flu vaccine are sometimes oversold, it does have genuine value, even in years when its VE is sub-par. A few recent studies showing this include:
CMAJ Research: Repeated Flu Vaccinations Reduce Severity of Illness In Elderly
CID Journal: Flu Vaccine Reduces Severe Outcomes in Hospitalized Patients
More Evidence Flu Shots May Improve Outcomes In Critical Patients
Study: Flu Vaccine May Reduce Heart Attack Risk
Despite being far from perfect, the flu vaccine – along with practicing good flu hygiene (washing hands, covering coughs, & staying home if sick) – still remains your best strategy for avoiding the flu and staying healthy this winter.

Regardless of what the headlines say.