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  • Writer's pictureP.K. Peterson

How to Stay Afloat in a Wave of Upper Respiratory Infections: Pay Attention

“America Is Having a Senior Moment on Vaccines.”

Daniel Engber, senior editor, The Atlantic January 11, 2024

“The one lesson that I have learned is that there is no substitute for paying attention.”

Diane Sawyer, American television broadcast journalist


A series of respiratory illnesses has started 2024 off with a bang. COVID-19 is leading the charge with cases of influenza and respiratory syncytial virus (RSV) infection following close behind. My goal in this week’s Germ Gems post is to refresh your memory about these viral infections (I’ve dubbed them “The Big Three”) and to introduce you to another infection of the upper respiratory tract that’s also on the rise—the bacterial infection strep throat.

The impact of the Big Three. SARS-CoV-2, influenza viruses, and RSV are members of different viral families. Nonetheless, they all have RNA genomes and share many pathogenic features.

All three are airborne viruses spread mainly by aerosols created by coughing or sneezing. They cause greatest havoc among similar risk groups (in particular, young children and older adults), and, unfortunately, all three are endemic, that is, they are here to stay.

In the Northern Hemisphere, flu season runs from September through April with overlapping outbreaks of RSV during the same time period. SARS-CoV-2, the newest of these human pathogens, is settling down from a shocking outburst as a pandemic in 2020 to what now appears to be a seasonality of its own.

Currently, the U.S. is in the midst of a huge surge of COVID-19 cases; about 1,500 Americans are dying of COVID-19 every week. The Centers for Disease Control and Prevention (CDC) variant tracking indicates that the highly contagious JN.1 variant (an offspring of a “Variant of Interest,” BA.2.86) is rapidly climbing in the charts and by early January, it accounted for 61.6% of all variants causing COVID-19.

And then there’s influenza. On January 12, 2024, the CDC estimated the flu had caused at least 14 million illnesses, 150,000 hospitalizations, and 9,400 deaths so far this season. There are three types of flu virus, A, B, and C. Influenza A (H1N1)pdm09 is the most frequently reported strain during the current flu season. (Fear of a new pandemic influenza A virus emerging keeps many epidemiologists awake at night.)

Testing for the Big Three. At the outset of infection by the “Big Three” viruses, none of the symptoms or signs (dry cough, shortness of breath, sore throat, runny nose, headache, body pains, or fever) distinguishes one virus from the others (and for that matter, from a whole host of other viruses that cause respiratory infections). Thus, testing is necessary to determine which virus is causing the infection.

The U.S. government still provides free rapid antigen tests for COVID-19. If you have any of the above symptoms, you can rule COVID-19 in or out by testing yourself. Rapid molecular tests are also available for influenza A and B viruses and for RSV, but access to these tests is limited to hospital or clinic settings.

Oral antiviral drugs are available to treat COVID-19 (Paxlovid) and the flu (Tamiflu or Xofluza). Ideally, your primary care provider should guide any decision regarding testing and treatment. Unfortunately, there is a shortage of primary care physicians in the U.S. and, even if you are lucky enough to have one, it is not always easy to reach your provider in a timely fashion.  Thus, I was encouraged to learn that Walgreens Pharmacy is expanding testing and treatment options for COVID-19 and the flu by engaging pharmacists to provide these services. This should facilitate the speed of treatment which is especially important for the flu where treatment with an antiviral needs to start within 48 hours of illness onset.

Vaccines for each of the Big Three. SARS-CoV-2, the influenza virus, and RSV each has a safe and effective vaccine to prevent the infections they cause. This may be the single most important shared feature of these viruses, and one not to forget. Yet, despite the availability of vaccines for the Big Three, one of the most baffling public health challenges in 2024 remains vaccine underuse.


The CDC recommends that everyone aged five years and older should get a 2023–2024 updated COVID-19 vaccine (Pfizer-BioNTech, Moderna, or Novavax) to protect against serious illness from COVID-19. The CDC also recommends the flu vaccine for everyone six months of age or older. And if you’re 60 years of age or older, the CDC suggests you have the option of the RSV vaccine based on discussions with your health care provider. So if you’ve missed any of these vaccines, now’s the time to catch up. (All three vaccines can be safely given at the same time.)


Of the 1,500 COVID-19-related deaths per week in the U.S., almost all are older adults. But, according to the CDC, only 19.4% of U.S. adults have received the updated COVID-19 vaccine even though the current vaccine appears to protect against serious disease caused by the JN.1 variant, and also reduces significantly the development of long COVID, a chronic and often disabling illness. (This is no small achievement considering that the U.S. Census Bureau estimates that in December, 2023, 5.3% of all adults were experiencing long COVID and recent evidence suggests that Paxlovid neither prevents nor treats the condition.)


In a recent article in The Atlantic, “America Is Having a Senior Moment on Vaccines,” senior editor Daniel Engber attributes this dangerously low rate of COVID-19 vaccination to “toxic politics,” confusion, and fatigue. On a similar note of dismay, a January 5, 2024 article in the Journal of the American Medical Association, “Is Vaccination Approaching a Dangerous Tipping Point?,” Dr. Peter Marks, director of the Center for Biologics Evaluation and Research and Dr. Robert Califf, commissioner at the U.S. Food and Drug Administration, urge the clinical and biomedical community to redouble its efforts to provide accurate plain-language information regarding the individual and collective benefits and risks of vaccination. Their plea needs to be stressed: Older adults please pay attention: make sure you’re vaccinated with the updated 2023-2024 COVID-19 vaccine! It could save your life.


Pharyngitis caused by Group A Streptococcus. At the same time that the “Big Three” viruses are assaulting the upper respiratory tracts of Americans, the bacterium called group A Streptococcus or Streptococcus pyogenes is also targeting this body site, causing strep throat. About 1,000 times the size of a SARS-CoV-2 virion, the Streptococcus bacterium is also spread from person to person by talking, coughing, or sneezing but it’s dispersed in larger droplets rather than aerosols that carry SARS-CoV-2 for longer distances.


While it is possible to get strep throat at any age, it is most common in children 5 to 15 years old. Symptoms of group A strep infection include sore throat, swollen lymph glands in the neck, nausea, vomiting, and “flu-like” symptoms, such as fever, body aches, and headache. None of these symptoms sets strep throat apart from those caused by the “Big Three” viruses. Instead, a rapid antigen test of a throat sample (or a throat culture) establishes the diagnosis.

Although strep throat (streptococcal pharyngitis) causes substantial illness, when the infection is limited to this body site, it’s rarely of major concern. Much more worrisome, however, is the entity called invasive group A Streptococcus infection(iGAS). iGAS infection can lead to necrotizing fasciitis (“flesh-eating bacteria”) or streptococcal toxic shock syndrome.


In late fall-early winter of 2022, at least two children in the U.S. died of iGAS. An outbreak in the UK about the same time resulted in the deaths of 14 children. And at least five European countries also reported an increase in iGAS in early 2023.


In contrast to viral infections of the upper respiratory tract, antibiotic treatment is recommended for strep throat, as well as for iGAS. Amoxicillin, a penicillin-like agent, is the drug of choice for treatment. To me, one of the many remarkable things about the group A Streptococcus is that it hasn’t developed a mechanism of resistance to penicillin. Instead, it remains uniformly susceptible to penicillin after many decades of intense pressure by penicillin use.


Although antibiotic resistance isn’t a problem in treatment of group A Streptococcus infections, an ongoing nationwide shortage of amoxicillin is a challenge (See “Common antibiotics are still in shortage as strep cases rise,” November 8, 2023, CNN). Fortunately, there are alternative antibiotics that are also effective in treatment of these strep infections. Your primary care provider would know which of these agents to use.


Primary care is the cornerstone of healthcare. But, as I mentioned above, there is a shortage of primary care physicians in the U.S. Moreover, a recent article in Medpage Today titled “In This Wave of Respiratory Illness, Primary Care Is Drowning” makes it clear the current wave of upper respiratory infections is exhausting our current primary care work force. These are serious issues that prompt me to end this Germ Gems post on a note of gratitude to all primary care providers: Thank you.

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Main Page images courtesy of Shuxian Hu, MD. Dr. Hu is a scientist in the Neuroimmunology Research Laboratory at the University of Minnesota.

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