Skip to content

Tag: SARS-CoV2

Published on Leave a comment on The Year in Review

It's fashionable for this time of year to give some reflections on the events of the last 12 months; seemingly every pundit/publication does it in some form or another. I won't buck the trend. What follows is a bit of a "highlight reel," plus the 3 things I'm watching closely for next year.

The Unexplained Explained

Recently we all had the opportunity to watch as a mystery outbreak unfolded in the Democratic Republic of Congo. Was it a novel pathogen set to launch a new pandemic or simply a localized outbreak of a known pathogen, complicated by poor health resources delaying accurate diagnosis and treatment? It took a little longer than I predicted to unravel everything, but we now have an answer from WHO as of December 27. That's still pretty quick, the original alert from the Panzi health zone in the Kwango province was November 29. I'm reassured that our global public health system is working well for outbreak detection.

The case definition used for investigation was fairly broad: "any person living in the Panzi health zone from September 2024 to date, presenting with fever, cough, body weakness, runny nose, with or without one of the following symptoms and signs: chills, headache, difficulty breathing, malnutrition, body aches." Here's an excerpt from the report:

"As of 16 December, laboratory results from a total of 430 samples indicated positive results for malaria, common respiratory viruses (Influenza A (H1N1, pdm09), rhinoviruses, SARS-COV-2, Human coronaviruses, parainfluenza viruses, and Human Adenovirus). While further laboratory tests are ongoing, together these findings suggest that a combination of common and seasonal viral respiratory infections and falciparum malaria, compounded by acute malnutrition led to an increase in severe infections and deaths, disproportionally affecting children under five years of age."

In other words, it was a combination of known pathogens already present in the area, layered on a background of falciparum malaria and malnutrition: a perfect storm. Let's hope the added health resources will dampen the outbreak in this very rural, isolated region of the DRC. Nutritional support is particularly needed.

WHO 2024

The WHO published its look back at 2024, including "highlights, breakthroughs and challenges." Many countries achieved milestones in either elimination or significant decreases of a number of diseases, including human African trypanosomiasis, leprosy, lymphatic filariasis, trachoma, malaria, measles, and mother-to-child transmission of HIV, syphilis, and hepatitis B. Their Expanded Programme on Immunization celebrated its 50th anniversary this year, with an estimated 154 million deaths prevented, most of them infants.

WRIS

CDC took a bit of a holiday break this week, so the level of detail in reports is less. However, Winter Respiratory Infection Season is officially High nationally.

The big 3 (covid, influenza, and RSV) all are increasing at this point. I'm hoping they don't peak at the same time and cause big logjams in healthcare settings.

What I'm Watching For

Mpox

In spite of the few cases in North America, Asia, and Europe, mpox is still primarily an African problem. As we know, however, no communicable disease in one area is just a problem limited to that area - international spread is always a few contacts away. In that regard, I found a recent review/opinion article enlightening.

Of interest, smallpox (vaccinia virus) vaccine protects against mpox infection. Our success in eliminating smallpox and subsequent cessation of smallpox vaccination led to a new population susceptible to mpox infection. A major hurdle to control the outbreaks will be vaccinia virus vaccine testing and distribution to high risk populations.

Avian Influenza

The influenza A H5N1 viruses now circulating in birds (both domestic poultry and wild birds) and dairy cows is the most likely source of a new pandemic, but fortunately the risk is still very remote especially if the public health system can keep on top of tracking infections and characterizing variants.

In the past week we learned that feeding your cat raw pet food derived from poultry is not a good idea, it resulted in 1 cat death in Oregon. I think most of us could have predicted that. One thing for cat owners to keep in mind is that the current avian flu, while still causing some respiratory symptoms in felines, is noteworthy for neurologic symptoms.

Also this week we learned about the mutation found in the hemagluttinin gene segment in the Louisiana human patient with severe avian flu illness. This is the H1 part of the virus which is important for attachment to respiratory epithelial cells. Mutations in this area can increase the effectiveness of spread in humans. However, it is completely expected that a human infected with the virus and experiencing severe disease would develop these types of viral mutations. What would be more concerning is if an isolate from a bird or cow developed such mutations, because of the potential for wider spread.

The risk for widespread human A H5N1 infections is still extremely low. I'll be watching in 2025 for any evidence of human-to-human transmission as well as any significant changes in the virus circulating in the wild animal kingdom. Again, I'm reassured that surveillance is allowing for rapid sequencing of human isolates. I hope that resources continue to be available to track this virus in animal and human populations.

SARS-CoV-2

Covid remains a wild card. It has perhaps the highest mutation rate of any virus causing human disease, it has yet to develop a true seasonality like other coronaviruses making it difficult to plan vaccination recommendations, and infections are still relatively frequent plus underreported due to lack of resources for testing, public apathy, and misinformation/disinformation fueling political decision-making. In short, we're in big trouble if another new variant appears with significantly greater pathogenicity and infectivity.

WHO published another year in review on covid that included a big overview of what's happened since 2020. They do note that our tracking systems worldwide are diminished compared to earlier in the pandemic, so recent data are likely to be significant underestimates. In the post-pandemic phase, we all need to transition from the type of extensive pandemic case tracking into a more sustainable surveillance system similar to what we do for influenza.

I was surprised to see some areas blank for what's going on the US, perhaps due to delayed reporting, and I was also a bit overwhelmed trying to decide what graphs to display here; if you're interested I'd suggest perusing the document itself. First, I've copied a quick highlight summary:

  • While there are periodic waves of COVID-19 in some countries, SARS-CoV-2, the virus that causes COVID-19,
    largely circulates without clear seasonality and continues to infect, cause severe acute disease and post
    COVID-19 condition.
  • The impact of COVID-19 has varied by country depending on the circulating variants, national policies,
    capacities to respond and access to countermeasures.
  • WHO’s ability to monitor circulation, severity, virus evolution and impact is challenged by reduced
    surveillance, testing, sequencing, limited integration into longer term infectious disease prevention and
    control programs, and reporting, as Member States adapt from crisis management to longer term prevention
    and control of COVID-19.
  • Changes to COVID-19 surveillance over the past five years have been consistent and expected, adapting to
    the changing landscape of the pandemic. Many Member States are transitioning from comprehensive case
    reporting to integrating SARS-CoV-2 monitoring into existing respiratory disease and infectious diseases
    surveillance systems. This is an important step towards sustainable infectious disease surveillance,
    monitoring and risk assessment. At the present time, the integration of SARS-CoV-2 into existing influenza
    surveillance systems is variable across regionsranging from 41% in countries from the Western Pacific Region
    to 96% in countries in the European Region.

Here's a great overview of the past few years on a global level.

Even with more inaccuracies in tracking recently, it's nice to see how far we've come in lowering cases and deaths.

Here's a look at deaths by age group, but what isn't apparent in the graph is that mortality rates in infants are comparable to mortality in 20-45-year-olds. Another advertisement for vaccination of pregnant people, who themselves are in high risk group.

And here's the crazy lack of seasonality expressed as percentage of positive tests. I might be tempted to see a trend towards winter seasonality, but remember these data include the southern hemisphere and thus we should see a biphasic pattern if/when seasonality develops.

And lastly a look at how far our variants have drifted over time.

Auld Lang Syne

My apologies to Scotsman Robert Burns, but I must turn to Londoner (with Scottish heritage) Sir Rod Stewart for my favorite version of the song at Stirling Castle in Scotland, complete with bagpipes.

Wishing everyone a Safe and Happy New Year. See you next year.

Published on Leave a comment on Is It or Isn’t It?

The Democratic Republic of Congo has been back in the news, this time not for mpox but for a mystery illness in an isolated, rural region of the country. Varying numbers of fatalities have been noted, but solid facts are sorely lacking. I am reminded of how early outbreak news percolates and changes; odds are low but not zero that this is a serious, new pathogen. Meanwhile, we can discuss several new publications that are on more solid scientific footing.

Vaccine Effectiveness Updates

Two manuscripts accepted for publication provided new information on VE measurements, one concerning influenza and the other looking at covid vaccines in young children.

CDC, along with other investigators, published an analysis of influenza VE for the 2023-24 flu season. For that year, the vaccine strains were well-matched for what eventually circulated in the US. The most common strain circulating was A H5N1pdm2009. Looking just at the pediatric population, VE in preventing hospitalizations and urgent care/ED visits was very good in all age groups as shown below: 58% for both outcomes overall, though with a wider confidence interval for hospitalizations since these were less common events.

The covid vaccine article is quite complex, involving investigators at multiple sites and listing 35 identified authors! Sadly it doesn't have any nice tables/figures that allow a short summary. I see 2 categories of take-home messages from the data: 1) as always, VE depends on which outcome you're looking at; 2) covid vaccines aren't that effective at preventing infection, but do help significantly in preventing complications of infection.

This multi-center study is actually a grouping of 3 cohorts (total 614 subjects) of children who had longitudinally-collected data including weekly sampling during the period of omicron variant circulation, 9/19/22 - 4/30/23. Variants were verified by genetic sequencing of about half the strains. Antibody studies and history questionnaires at study entry were utilized to determine evidence of prior infection. Here are the numbers from the study:

  1. Children with prior infection had less chance of both infection and symptomatic infection than did those without prior infection: Hazard Ratio [HR]: 0.28 [95%CI: 0.16-0.49] and HR: 0.21 [95%CI: 0.08-0.54. This was true regardless of timing of prior infection.
  2. Children with prior infection AND vaccination also had lower hazard ratios: HR: 0.31 [95%CI: 0.13-0.77], compared to those who were unvaccinated with no prior infection.
  3. The one slightly unique finding in this study is as follows: "There was no difference in risk of infection or symptomatic COVID-19 by vaccination status alone, regardless of timing of vaccination or manufacturer type. However, naïve participants vaccinated with Pfizer-BioNTech were more likely to be infected and experience symptomatic COVID-19 compared to naïve and unvaccinated participants (HR: 2.59 [95%CI: 1.27-5.28]), whereas participants with evidence of prior infection and who were vaccinated with Pfizer-BioNTech were less likely to be infected (HR: 0.22 [95%CI: 0.05-0.95])." In other words, vaccination didn't do very well at preventing infection.

This study is very complex but also very rigorous; I can't do it justice in a small summary. The major limitation is the relatively low sample size, meaning that the investigators couldn't do much in the way of subgroup analysis to try to look at other variables. Relatively few children received the bivalent Pfizer vaccine, so it's very hard to interpret specific differences between Pfizer and Moderna vaccines. Also, the small sample size precluded any assessment of complication risks following natural infection, one of the big advantages for being vaccinated.

Does Nirsevimab Prevent Other Infections Besides RSV?

According to another new study, the answer is "sort of." Investigators looked at around 3000 infants randomized 2:1 to receive either nirsevimab or placebo and then followed with respiratory swab PCR testing. The pictorial bottom line:

Not mentioned in the pictorial summary is that the cumulative incidence of rhinovirus/enterovirus coinfections was lower in the nirsevimab group, leading to my "sort of" conclusion.

The important bottom line of the study, however, is that no replacement infections appeared. Replacement infections refer to the concern that once an infectious agent is greatly reduced by preventive measures, another pathogen will take its place, lessening the impact of the preventive measure. This was a concern for Hib vaccine early on, but no other meningitic pathogens arose. Later, the same concern arose for pneumococcal vaccination. There is evidence that replacement pneumococcal serotypes started to become more common, but the overall rates of pneumococcal infections still declined significantly. This is why we're still trying to add other pneumococcal serotypes to newer conjugate vaccines.

Parvovirus and Myocarditis

Last week I mentioned the reports about increase in parvovirus infections likely spurred by non-pharmaceutical measures to prevent respiratory pathogen spread during the pandemic. A spinoff of this kind of surge can be a surge in complications of these pathogens. I was intrigued by this report from Italy about parvoviral myocarditis, which is a slightly controversial topic. Etiology of viral myocarditis is difficult to determine without myocardial biopsy, and parvovirus myocarditis is particularly suspect because of older reports of parvoviral detection in cardiac tissue from individuals who never had concern for myocarditis. So, for an individual patient, it's hard to be certain of a parvoviral etiology for myocarditis even with a positive tissue biopsy. This post-pandemic surge may help clarify the situation.

Europe in general seemed to have an earlier surge in parvovirus infection than we did in the US, possibly because pandemic restrictions were lessened earlier there. Here is a breakdown of the Italian report by age and timing.

And a breakdown of how the diagnosis was made. Only 2 were with myocardial biopsy; blood PCR can persist positive for a long time after parvoviral infection. IgM serology always is suspect due to nonspecific factors. A matched control group without myocarditis to see rates of parvovirus IgM and blood PCR positivity would have been helpful.

Of course I'm hoping we don't see a surge of myocarditis cases soon. If cases do spike, it will be particularly tough to figure out if it happens during a covid surge.

Mycoplasma Complications Too?

Along similar lines, a study from Texas suggests that the Mycoplasma pneumoniae surge might be associated with a greater risk of complications. This is a retrospective review from a single institution documenting an increase in M. pneumoniae infections seen below the shaded section.

It's important to recognize, as the authors do, that this is a cohort skewed towards inpatients who had multiplex PCR testing. Also, mycoplasma PCR can persist positive for many weeks after infection (as do live organisms), so a positive PCR doesn't conclusively mean that the current illness is caused by mycoplasma. What was important and of some concern in the report is that 13 of the 41 children hospitalized with respiratory symptoms required ICU care. They also described 16 children with RIME (Reactive Infectious Mucocutaneous Eruption) with one of those children requiring ICU admission.

Avian Flu Updates

The news media (sometimes breathlessly) relayed new findings that a single mutation in influenza A H5N1 strains could increase adherence to human respiratory epithelium, increasing chances for greater infection rates in humans. I haven't yet bought into this panic.

Keep in mind that single mutations don't necessarily occur in isolation; often multiple mutations occur, some increasing virulence while others resulting in lower virulence. This in vitro study is an important contribution to our understanding of how avian flu might evolve and most importantly supports the need for close tracking of this agent in all animals, including humans.

Along those lines, I was please to hear that the US Department of Agriculture will implement mandatory milk testing nationwide for A H5N1. Previously this has been mostly a voluntary effort in the US. We still need much more monitoring for this agent in order to prepare for potential increase in human cases. Let's hope funding will be available to support these efforts.

WRIS

The winter respiratory infection season has begun, at least for RSV. We are now officially at moderate activity nationwide.

Influenza is increasing slowly with A H3N2 the most common subtype. COVID-19 projections are increasing, though not yet a big bump in clinical illness.

WHO to Help in the DRC

I figure I've been watching various feeds for outbreak alerts for about 30 years, starting with the ProMED service that still sends me at least a daily update. So, I've had early looks at these events, but also a slew of false alarms of new diseases that turned out to be mini-outbreaks of previously well-described illnesses. The latter are far more common than newly emerging infectious agents. So, I'm both watching closely but not overly concerned about the cluster of respiratory illnesses with significant mortality being reported from Kwango province (outlined in red) in rural southwestern DRC, bordering Angola.

Early reports suggest a predilection for children. The rural location with lack of medical facilities hinders any investigation. Also, this type of region, with close proximity of humans to many animal species, provides the potential for infectious agents to jump to other animal hosts. It appears the region now has appropriate support from WHO, and I would expect to hear more definitive information within the next several days, maybe in time for an update in my next post.

I guess the rural location is also a silver lining, with less risk for worldwide spread if this is in fact a new disease. I'll go out on a limb using past unknown outbreak experience and predict this won't be a new pathogen. Here's hoping.

Published on Leave a comment on Fall Back

Once again I find myself, an ostensibly tech-savvy individual,* faced with manually resetting the time on 11 clocks and appliances in my house. Only my phone, laptops, and tablet appear to have joined the 21st century by self-correcting to eastern standard time. Of course, if our country had truly joined the 21st century, we wouldn't be making this twice yearly switch in the first place.

My election anxiety is somewhat mollified by focusing on infectious diseases, so you can categorize the following as therapeutic in nature.

WRIS

Still not much going on, though I was intrigued that my state of residence is 1 of only 2 to show up with moderate respiratory illness activity last week.

I'm pretty impressed by how quiet the SARS-CoV-2 front is. However, it's still around, and we can expect to see a resurgence sometime.

The fact that influenza has not yet appeared might indicate we are returning to a more "normal" flu season. The graph below shows how different the prior 3 flu seasons were from pre-pandemic experiences, where last year had a very early peak and 2020-21 and 2021-22 had very low and atypical peaks. (Apologies for CDC's labelling here, but if you stare at it long enough you can pick out which line goes with which year.)

New Development in Bird Flu

The so-called highly pathogenic avian flu H5N1 cropping up in dairy and poultry farms and in wild bird populations has been in the news for many months now. It still seems to be a mild illness in humans, most of whom have direct exposure to these farms. Only 41 humans have confirmed infections in 2024 so far. What's a bit noteworthy this week is that the virus may now have shown up in pigs. USDA officials reported probable swine cases at a backyard farm in Oregon where poultry, cows, and pigs all mingle. The farm itself has no role in commercial production of any foods, so it isn't a risk to others. What is of slight concern is the fact that pigs are involved. Pigs have a special place in influenza science because they have both human and avian flu receptors in their respiratory tracts, making the chance for a recombination event to occur if they happen to be infected with human and avian viruses at the same time. Most of the time this doesn't cause creation of a new pandemic strain, and I wouldn't hit the panic button at all now. Actually I'm surprised it took this long for swine infection to be found. The affected animals were all euthanized and multiple studies are ongoing, so I'm sure we'll hear more about this.

Polio

The news isn't great as both wild and vaccine-variant polio cases continue to be reported. This Global Polio Eradication Initiative map is a good summary.

No new cases have been reported in Gaza, with just the 1 case confirmed so far. The interrupted vaccination campaign in northern Gaza restarted this week.

Dengue Still Going Strong

I was browsing the CDC dengue page this week; infections are still plentiful.

Puerto Rico has the greatest number by far, but note that we have had autochthonous (locally acquired without travel to endemic areas) dengue in the mainland US (California with 11 cases, Florida with 49).

*

Can I really claim to be tech-savvy? I think so. I have an advanced degree in educational technology with classes that included instruction in networks and the various hardware involved; the fact that my schooling ended in 2008 shouldn't disqualify me. Also, this past week I restored to full health our K-cup brewing machine that became confused and wouldn't deliver the appropriate coffee volumes or allow the correct menu choices in its buttons. I guess in the interest of full disclosure, when I couldn't find a satisfactory replacement brewer online, my astute intervention was reading the instruction manual, realizing that I hadn't ever de-scaled the device in the approximately 90 years I've owned it, and made it new again using only a low-tech tool (vinegar).

In spite of my skills with technology and vinegar, I'll be performing my semiannual time resets for the foreseeable future; I could never part with my grandfather's clock.

Published on Leave a comment on Joys of Summer Bites

The one or two regular readers of this blog know that I'm a favorite companion at outdoor summer activities, not because of my scintillating conversational repartee but rather due to my fabulous mosquto/gnat magnet properties. No one near me needs to worry about bug bites; all those bloodsuckers are feasting on me. One morning this week I gathered a couple dozen bites in a very short time and have been scratching ever since. I've been waiting for symptoms of West Nile virus infection, nothing so far. Meanwhile, another vector-borne disease may have worse consequences than previously known.

But first, ...

Covid Summer Surge

In spite of many breathless news reports, this is still nothing to get worked up about, other than for high-risk individuals to consider returning to masking in crowded indoor spaces and employing other mitigation strategies. Some of the lay reports seem to forget that wastewater levels are not the same as actual infections. Wastewater covid detections might be decreasing, especially in the West.

Percentage of emergency department visits due to Covid, one rough measure of clinical illness, is increasing though still at low levels.

Meanwhile, we have a little more clarity on one aspect of long covid. In one study, myalgic encephalitis/chronic fatigue syndrome in adults was no more common following covid than following an acute infection-like illness that was negative for covid. I've long been concerned that case definitions and studies haven't been focused on the heterogeneity of long covid. Fortunately, some studies are geared to looking at the ME/CFS cases separately from post-covid symptoms that might be related to end-organ damage persisting after severe pulmonary or other infection.

Avian Flu

Similarly, the highly pathogenic avian flu A H5N1 continues to crop up in dairy and poultry workers but doesn't seem to represent a broad risk to others, with no known human-to-human transmission. I neglected to mention last week some preliminary results from the seroprevalence study in Michigan dairy workers: none of 35 tested workers had antibody to the virus, suggesting that asymptomatic infections aren't common. However, we need a sample size larger than 35 to get a better handle on this.

Last week's MMWR contained a report supporting the impression that this particular avian flu strain in humans is a very mild disease.

Wash Your Parsley

Did you know that the FDA performs regular microbiologic surveillance sampling of foods? Last week they reported results from sampling of basil, parsley, and cilantro, 3 of my favorite herbs. Below are numbers for the prevalence of various pathogens in different herbs; 95% CI are in parentheses.

HerbCyclospora
cayatenensis		Salmonella
spp		Escherichia
coli
Cilantro9.2% (4.4-16.5)2.8% (1.1-5.7)0% (0-1.5)
Parsley1.3% (0.5-2.6)0.9 (0.4-1.8)0.1% (0.4-1.8)
Basil0% (0-2.6)0.7 (0.1-2.7)0.7% (0-1.4)

For comparison, grocery store Salmonella spp. contamination rates for chicken vary from about 8 to 24%, depending on the study.

Want Some Listeria With Your Liverwurst?

CDC has been investigating a Listeria outbreak linked to deli counter sliced foods, and now one brand of liverwurst tested positive for Listeria. It's possible that a single product could have contaminated slicing devices, causing Listeria to end up in other deli foods. I hope your favorite deli counter practices good cleansing practices for their slicing machines. If not, you might get a side of Listeria with other deli products too.

Ever Heard of Oropouche?

Probably not, unless you are an infectious disease nerd or familiar with the island of Trinidad or the Amazon basin. Oropouche virus (OROV) is still known by the old practice of using a geographic term to name it Now we have new attention focused on this virus, previously thought to cause a relatively harmless though uncomfortable febrile illness. It was first discovered on Trinidad in 1955, in a forest worker from Vega de Oropouche, Trinidad. OROV is endemic to the Amazon basin, and Brazil is seeing a big upsurge in Oropouche fever this year.

With that have come some troubling new reports. OROV is an arbovirus related to dengue, and it mostly causes an acute febrile illness with sometimes very painful myalgias, similar to dengue, zika, chikungunya, malaria, and similar infections. It is transmitted primarily by Culicoides paraensis, a biting midge, but also can be transmitted by other biting insects including Culex mosquitoes.

Last week the Brazilian health ministry confirmed 2 deaths from Oropouche fever, both in healthy young women. The clinical descriptions resemble dengue hemorrhagic fever. Also, the Pan American Health Organization is investigating possible vertical transmission of the virus from 2 infected mothers. One pregnancy resulted in miscarriage, the other with intrauterine fetal death. PAHO has issued guidelines for evaluating possible vertical transmission of OROV. These studies should help us understand if OROV is similar to Zika virus's ability to cause fetal malformations and other severe outcomes. [Note that you may need to activate Google Translate to read these links.]

Meanwhile, I haven't seen any C. paraensis around my house.even though they do range into the northern US, including Maryland. They are pretty tiny, can be less than a millimeter, so good chance I would miss them. I'm somewhat curious to know if I'm also a midge magnet, but really I'd rather not find out.

Published on Leave a comment on Belated Eloquence of the Inarticulate

The title above is one of several great turns of phrase in the book I just finished reading, Edith Wharton's Age of Innocence. It refers to an episode where the protagonist was at a loss for words during a poignant encounter and presumably only later thought of something better to have said. I've been there.

Next Round for Covid Vaccine

The FDA's Vaccine and Related Biological Products Advisory Committee finally had their meeting last week; it had been postponed to give a little more time to see which way the new SARS-CoV-2 variants were headed. I was able to listen in on most of the meeting and have reviewed all the documents. The vote was unanimous to choose a monovalent JN.1-based vaccine for the next iteration, no surprise and in agreement with the recent WHO decision I discussed recently. (For those interested, there is quite a bit of international collaboration on these types of decisions. See the ICMRA posting about covid vaccines.) Still, there were some interesting updates on covid in general. I'll try to distill this down into the main takeaways.

The Latest on Epidemiology (from Thornburg FDA presentation)

Current circulation of SARS-CoV-2 is relatively low. Although our reporting is not as reliable these days, looking just at percentage of positive covid tests in orange you can see we are in a lull now, though perhaps with a hint of an uptick. This is pretty similar to last summer when we saw a bit of a surge in summer into fall and winter. SARS-CoV-2 still has not come around to a winter seasonality seen with other coronaviruses of with influenza, making predictions for surges and vaccine composition very tough.

JN.1 lineages replaced XBB.1.5 lineages during winter 2023-2024. I like the depiction below because it's looking at normalized numbers of positive tests rather than a percentage of positive tests due to different variants. This gives a better appreciation of numbers of cases and shows that we are still talking about relatively low numbers compared to 2022.

Here's a closeup of the most recent part of the above slide showing that KP.2-like, KP.3, and other JN.1 derivatives are starting to take over, though still all at very low numbers.

The recent subvariants have very few differences from other JN.1-derived strains and antigenically are very similar. This has important meaning for vaccine choice - should it be the original JN.1 variant or one of these newer KP.2 or KP.3 type subvariants, currently at extremely low numbers? Look at the last 2 rows in the table below, showing that these newer subvariants have very few mutation differences from the earlier JN.1-like variants.

In a totally new and as yet unpublished CDC analysis, severity of JN.1 infections does not appear to be worse than earlier lineages. The trend was towards milder illness, though not statistically significantly different. Note these numbers are just for adults.

Vaccine Effectiveness in Children (from Link-Gelles FDA presentation)

This it tough to estimate because children generally have milder disease, plus so few children are vaccinated. Adult data is pretty favorable for VE; SGT failure is a faster method of testing and correlates will with JN.1 lineage strains. 2023-2024 VE drops a little with these strains compared to effectiveness against XBB lineage strains.

On the pediatric side, it's important to remember that the vast majority of US children have been infected with SARS-CoV-2 at some time in their lives - this has been apparent since late 2022.

So, it's important to determine any VE now in light of prior infection and vaccination. We can't rely on older estimates. Here's the best and latest estimates for VE in children who received vaccine in the past year. Confidence intervals are relatively wide, reflecting the small numbers able to be studied, but do show benefit in prevention of ED or urgent care use. VE wanes with time after vaccination as it does with all age groups, but there is clear benefit for covid vaccination of children.

David Wentworth, representing WHO, delivered a wonderful explanation of the complexities in choosing among current subvariants for vaccine inclusion. He had this great quote: "... antigenic evolution just speeds up waning immunity." The variant evolution we're seeing now is parallel, i.e. lots of different subvariants evolving on their own, in parallel, rather than one subvariant evolving into another, and then into another, etc. Parallel evolution is what XBB lineages did previously, and we're seeing it now in the JN.1 groups. The slide below demonstrates this process with a timeline on the X axis.

The dilemma in choosing composition of the next vaccine is that no one knows which way the very new subvariants will evolve in terms of antigenic similarity to earlier JN.1 strains. Currently, KP.2, KP.3, and JN.1.23 are within what is thought to be close proximity to JN.1 in terms of antigenic similarity and therefore a vaccine based on any of those likely will have cross-reactivity with one another, enough to provide protection. However, as illustrated by the arrows, it just isn't known how the offspring of the newer subvariants will evolve - will it be farther away from JN.1 and each other, or will it remain relatively stable?

No one can predict what next fall's or winter's subvariants will look like. Once they appear, new lab testing would need to be done, ideally using human serum containing antibody to the newer strains, which Wentworth stated would take about a month to produce. So, it's not something that can be turned around quickly.

Also, it bears mentioning that virtually all of the immunity studies involve neutralizing antibody. Antibody does correlate well with VE, but T-cell immunity also is important. We don't see as much data about this arm of the immune system because the studies are more difficult.

All 3 US vaccine manufacturers, Moderna, Pfizer, and Novavax, presented their new data at the meeting. They are developing and testing new vaccines "at risk," meaning the companies are making vaccines without funding currently, risking their own research and development dollars, hoping whatever they are working on will be recommended for the next covid vaccine rounds and allow them to recoup their investment. Moderna and Pfizer have both developed JN.1- and KP.2-based mRNA vaccines. Novavax, the adjuvanted protein-based vaccine, only developed a JN.1-based vaccine. The protein vaccine takes much longer to construct than do mRNA vaccines, about 6 months to get good data in all. So, if a KP.2 or other vaccine were recommended, Novavax would need to start over and wouldn't be ready until about December.

I don't usually like to use pharma slides to illustrate points, but this one from Pfizer isn't biased in favor of their product and I think nicely shows the current situation, including how closely related the newer subvariants are to JN.1.

In the discussion after the vote to have a monovalent JN.1-based vaccine, which could mean one based on KP.2, the majority of the group felt that using the JN.1 variant rather than KP.2 or another subvariant was the best route, both to allow Novavax to be ready this fall but also not to take a chance that fall and winter predominant subvariants might be more antigenically removed from KP.2 antigenically. All in all I felt this was the right choice, though I probably wouldn't have let Novavax's problems affect the decision; very few US residents have received Novavax in the past, though it is nice to have an alternative to mRNA vaccines available.

On June 7 the FDA formally recommended sticking with the JN.1 strain for this next vaccine round. Next step with be the CDC's Advisory Council on Immunization Practices meeting the end of this month, where the official seal of approval will be issued. I'm sure Moderna, Pfizer, and Novavax already are ramping up production.

NASEM Long Covid Report Available

Long covid remains a quagmire, lots of different symptoms, many of which are vague, and still no definite light shed on diagnosis and treatment of what is likely a heterogenous group of conditions requiring different approaches. The National Academies of Science, Engineering, and Medicine published their full report, available free online. I haven't gotten through all of it, it's pretty long, but it is of interest to those practitioners who see these patients. Most of the evidence is from adults, but it appears that pediatric patients tend to have a better prognosis, especially if improvements are occurring in the first year after onset. Note that a positive covid test is not required for diagnosis testing may not have been done at the time of the triggering infection and antigen or PCR tests will have reverted to negative by the time a long covid diagnosis is considered.

Doxycycline for Post-Exposure Prophylaxis of STIs

The official guidelines appeared this past week, although the gist of the recommendations had been floated previously. Particularly high risk groups are gay, bisexual, and other men who have sex with men and transgender women. The summary is very helpful for practitioners who may want to print out and post Box 1 and Box 2 in their workspaces. Note that the recommendations apply just to those high risk groups.

Summer Bugs!

Bugs in the sense of both insects and microbes. We now have more details about a new rickettsial agent, termed species C6269, that caused a Rocky Mountain Spotted Fever-like illness in 2 individuals in northern California last summer. Both had severe disease, were hospitalized and treated with doxycycline, and survived. As always, keep RMSF and other tick-borne diseases in mind during our warm months.

Speaking of bugs, our dog came down with a skin abscess, expertly debrided by her veterinarian. She is now enjoying chewable amoxicillin/clavulanate but is less thrilled with her "cone of shame." The vet had another bug concern, however. She didn't want the dog to spend much time outside - apparently it is also maggot season, and they love open dog wounds. The vet doesn't know I'm an ID doctor, and I was trying to come up with some clever comment on maggots but failed at that moment - belated eloquence of the inarticulate!

Courtesy of Wikipedia. Hope you aren't eating as you read this.

Unless otherwise indicated, the content and opinions expressed on this web site are those of the author(s). They are not endorsed by and do not necessarily reflect the views of the George Washington University.
Viewing Message: 1 of 1.
 Notice

This site uses cookies to offer you a better browsing experience. Visit GW’s Website Privacy Notice to learn more about how GW uses cookies.