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Case Study — Avian influenza A (H5N1)

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Case Study Avian Influenza H5N1 Instructions

 

Be sure to carry out the following:

  • Read the Case Study rubric carefullyand provide all of the requested information and discussion questions/responses (use Google Scholar, PubMed, etc. to find information on vaccines, virulence factors, and the like including the scientific references)
  • Make sure you have referenced everything and avoided any inadvertent plagiarism
  • You should have at least3-4 facts (with in-text references for these facts in proper format) for each of the boxed sections (Epidemiology, Pathogenesis, etc.).
  • Try to have post-2019 references for your information/facts
  • There is a standard format for patient presentation (see attached).
  • Narrative format
  • May use illustrative maps, patient photos, and figureswhich can convey some great information about a pathogen.
  • please avoid the use of AI – the information is often incorrect, its writing style is boring, and it can often “hallucinate” (invent or conflate) references.

 

 

 

  • How should I format my references for my case study?
  • You will need references for all factual information in your case study. Pertinent references can be
  • listed at the bottom of your outline in a small font. Your references must include at least three current
  • peer-reviewed publications from the scientific literature post-2019. Use APA 7th Edition Style format
  • for all references (a PDF document is provided with the case study directions).
  • For example, your text book in-text citation would look like this (Anderson, Salm, & Beins, 2022) and
  • your textbook would be shown on your reference page as:
  • Anderson, D., Salm, S., & Beins, M. (2022). Microbiology: A Human Perspective. New
  • York: McGraw-Hill.

 

 

How to create a case study

 

The case studies are meant to be an enjoyable, interesting, and informative assignment. This is your chance to show that you understand the key teaching points about a microbe and to communicate these points in a written format.

 

What information belongs in my case study?

 

  • Have at least 3-4 key referenced points in each of the five areas shown in the Case Study Information Chart (see below).
  • The left-hand heading in the chart suggests the type of information requested for the pathogen.
  • Outlines can be in whatever form you prefer (bullets/charts/outlines/diagrams or a mix).
  • Be sure to include two discussion questions (and provide thorough, complete answers) that you can incorporate into your case study (place them at the end of your write-up). These questions should help connect your case to other material in the course. For example, what other microbes have an endotoxin? What other viruses are transmitted by fecal-oral spread?

 

 

How much information should I provide for my case study?

 

 

  • For the Case Study, you are asked to provide at least the information requested in the chart below.
  • The boxed questions are suggestions for the minimum amount of information within each category.
  • The more detailed the information, the better the study. You may consult your textbook, CDC, WHO, Access, Medicine, Google Scholar, Pub Med at NCBI, WebMD, etc. to find the information. For example, if you perform a Google search using the name of the pathogen and the word ‘vaccine’, you will find information on current vaccines (if any), those in clinical trials, vaccines used only in animals, etc.

SOLUTION

Case Study — Avian influenza A (H5N1)

Patient presentation (standard format — narrative)

Identifier: 42-year-old male dairy farm worker
Chief complaint: Fever, cough, conjunctival irritation, and myalgias 3 days after exposure to sick cattle and dead poultry on farm.
History of present illness: Onset of fever (39.2°C), sore throat, nonproductive cough, muscle aches. Worked daily with cattle and backyard poultry; reported finding multiple dead chickens the week prior and assisting with handling of sick cows. No known sick contacts in the household. No travel. Not vaccinated with seasonal influenza vaccine this season.
Exam (day 3): Temp 39°C, RR 20, O2 sat 95% room air, mild conjunctival injection. Lungs clear initially.
Initial management: Nasopharyngeal and conjunctival swabs and lower-respiratory sample sent for influenza A RT-PCR and subtyping; started empiric oseltamivir pending results and placed on droplet and contact precautions. Public health notified due to occupational animal exposure.
Clinical course (hypothetical): PCR returned positive for influenza A H5N1 clade 2.3.4.4b. Patient remained clinically stable and recovered with antivirals and supportive care; contacts were monitored for 10 days per CDC guidance.

Case Study Information Chart — Minimum facts (each boxed category includes 3–4 referenced facts)

Epidemiology (key facts)

  1. Global spread & recent panzootic: Since 2020 HPAI A(H5N1) clade 2.3.4.4b viruses have caused a global panzootic in wild birds and poultry with unprecedented geographic spread, leading to large poultry outbreaks and spillovers into multiple mammalian species. (CDC, 2024; WHO, 2024).

  2. Sporadic human infections: From 2003 through early 2024 nearly 889 human H5N1 infections and 463 deaths were reported to WHO (overall CFR historically high), though recent human cases since 2022 have been relatively few and mostly associated with direct animal exposures. (WHO, 2024; CDC, 2024).

  3. Mammalian spillover events: Since 2022–2024, clade 2.3.4.4b H5N1 viruses have spilled over into mammals — including farmed mink, seals, terrestrial mammals, and notably U.S. dairy cattle — increasing opportunities for viral adaptation. (CDC, 2024; Marchenko et al., 2024).

  4. Public-health risk assessment: Although widespread in birds and some mammals, currently circulating viruses generally lack efficient binding to human upper-respiratory tract receptors and have not produced sustained human-to-human transmission; however surveillance and preparedness remain critical because influenza viruses can rapidly evolve. (CDC, 2024; WHO, 2024).

(References: CDC, 2024; WHO DON 2024; Marchenko et al., 2024; Gao, 2024)

Pathogenesis & virulence factors (key facts)

  1. HA receptor specificity & cleavage site: H5 HA typically binds α2,3-linked sialic acid receptors (avian type), restricting efficient infection of human upper airways (which predominantly express α2,6 receptors) — a key factor limiting transmissibility in humans unless receptor specificity shifts. (CDC, 2024; Marchenko et al., 2024).

  2. Polymerase PB2 mutations: Adaptive mutations in the PB2 polymerase gene (e.g., E627K, D701N) increase replication efficiency in mammalian cells and are associated with enhanced virulence and, in some studies, increased transmission potential in mammalian models. (Marchenko et al., 2024; Capelastegui et al., 2025).

  3. Reassortment/genetic background matters: Virulence and mammalian adaptation can depend on reassortment constellation (i.e., the source of internal genes such as PB1, PB2, NP) — some 2.3.4.4b viruses have acquired internal genes that increase virulence in mammals. (Marchenko et al., 2024; Pulit-Penaloza et al., 2022).

  4. Systemic and extra-respiratory tropism: Highly pathogenic H5 viruses can replicate beyond the respiratory tract in susceptible species (neurologic involvement reported in animal models and wildlife), contributing to severe disease presentations in some hosts. (Scientific Reports review; Belser et al., 2024).

(References: Marchenko et al., 2024; Capelastegui et al., 2025; Pulit-Penaloza et al., 2022; CDC, 2024)

Clinical presentation (key facts)

  1. Spectrum of illness: Human H5N1 infections range from asymptomatic or mild respiratory illness to severe pneumonia, acute respiratory distress syndrome (ARDS), multi-organ failure and death — historically case fatality rates were high for earlier strains, though recent clade 2.3.4.4b cases include mild and asymptomatic infections. (WHO, 2024; CDC, 2024).

  2. Common symptoms: Fever, cough, dyspnea, sore throat, conjunctivitis, malaise, myalgias; severe cases can progress to respiratory failure. (CDC, 2024).

  3. Exposure history important: Most recent human cases are associated with close contact with infected birds, poultry, or infected mammals (including dairy cattle in 2024 U.S. events). Occupational exposures (farmers, cullers, veterinarians) are key risk groups. (WHO, 2024; CDC, 2024).

  4. Clinical variability: Some recent U.S. and Canadian cases were clinically mild and recovered with antivirals and supportive care; nonetheless severe outcomes remain possible, especially without rapid diagnosis and treatment. (CDC, 2024; journal reports 2024–2025).

(References: WHO, 2024; CDC, 2024; recent case summaries)

Diagnosis (key facts)

  1. Molecular testing is primary: Influenza A RT-PCR with subtyping (including H5) and sequencing for clade determination are the diagnostic standards; lower-respiratory specimens may be needed in severe disease. (CDC, 2024).

  2. Laboratory biosafety and public-health coordination: Suspected H5N1 specimens require proper biosafety handling and rapid notification of public-health labs for confirmation and genomic characterization. (CDC guidance, 2024).

  3. Serology & sequencing: Serologic testing can identify prior infections; whole-genome sequencing is used to detect adaptive mutations (e.g., PB2-E627K) and monitor antiviral susceptibility. (Marchenko et al., 2024; CDC, 2024).

  4. Differential diagnosis: Other respiratory pathogens (seasonal influenza, SARS-CoV-2, other avian influenzas) should be considered; co-testing may be performed. (CDC, 2024).

(References: CDC technical report 2024; Marchenko et al., 2024)

Treatment & prevention (including vaccines) (key facts)

  1. Antivirals: Neuraminidase inhibitors (oseltamivir, peramivir) remain first-line antivirals; current H5N1 isolates analyzed in 2024 lacked markers of resistance to recommended antivirals, but surveillance is ongoing. Early antiviral therapy is associated with better outcomes. (CDC, 2024).

  2. Supportive care: Severe cases require respiratory support and ICU care as needed. Infection control (droplet/contact precautions) is critical for suspected/confirmed cases. (CDC, 2024).

  3. Candidate and stockpiled vaccines: There are H5 candidate vaccine viruses and pre-pandemic vaccines (e.g., adjuvanted inactivated H5 vaccines such as Audenz/stockpiled formulations); multiple companies and public health agencies ramped up procurement and R&D in 2024–2025 (including adjuvanted and mRNA approaches). (WHO candidate vaccine list; Gao, 2024; Faccin et al., 2024).

  4. One Health prevention & biosecurity: Control of H5N1 relies heavily on poultry/dairy farm biosecurity, surveillance, culling where needed, and consideration of animal vaccination campaigns; protecting workers with PPE, monitoring exposed people, and vaccinating at-risk personnel are parts of preparedness strategies. (WHO, 2024; CDC, 2024; Gao, 2024).

(References: CDC, 2024; WHO candidate vaccine list; Gao, 2024; Faccin et al., 2024)

Public health implications & response actions (brief)

  • Surveillance & genomic monitoring: Continuous sequencing of animal and human isolates to detect mammalian-adaptive mutations (e.g., PB2 E627K) is essential to rapidly reassess risk. (Marchenko et al., 2024; CDC, 2024).

  • Occupational protections: Monitoring and prophylaxis/vaccination considerations for farmworkers, poultry handlers, and vets; rapid testing and isolation of symptomatic exposed persons. (CDC, 2024).

  • Vaccine preparedness: Maintain and refresh stockpiles of H5 candidate vaccines, accelerate clinical trials for updated antigens and novel platforms (adjuvanted, mRNA, multivalent). (Gao, 2024; Faccin et al., 2024).

  • One Health approach: Integrate animal health (poultry and livestock), wildlife surveillance, and human public health for outbreak control and prevention. (WHO, 2024).

Two discussion questions (with model answers)

Q1. How does the PB2-E627K mutation influence pandemic risk, and what surveillance priorities should be set to detect increasing human transmissibility?
Model answer: PB2-E627K increases polymerase activity at mammalian body temperatures and has been associated with enhanced replication and virulence in mammalian models, sometimes increasing transmissibility in ferret experiments. Detection of this mutation (or others such as D701N) in animal or human isolates suggests increased mammalian adaptation and should trigger heightened genomic surveillance, targeted serosurveys of exposed populations, accelerated antiviral susceptibility testing, and review of vaccine antigen match. Continuous sequencing of human and mammalian spillover isolates is therefore a surveillance priority. (Marchenko et al., 2024; Capelastegui et al., 2025; CDC, 2024).

Q2. Compare control strategies for H5N1 to seasonal influenza — why are One Health and animal vaccination critical for H5N1 control but less emphasized for seasonal flu?
Model answer: Seasonal human influenza circulates primarily among humans; control strategies focus on human vaccination and community surveillance. H5N1 is primarily an avian pathogen with repeated zoonotic spillover; therefore controlling the virus in bird and mammal reservoirs (biosecurity, culling, animal vaccination) is central to reducing human exposure and preventing opportunities for reassortment/adaptation. One Health approaches that integrate veterinary vaccination and surveillance are therefore essential to prevent emergence of strains that could sustain human-to-human transmission. (WHO, 2024; Gao, 2024; CDC, 2024).

Notes on figures / illustrative material

  • Suggested figures/maps: global map of 2.3.4.4b detections in birds (USDA/WOAH/FAO maps), phylogenetic tree showing clade spread, and schematic of HA receptor specificity (α2,3 vs α2,6). Use CDC/WHO graphics with attribution; patient photos only if de-identified and permitted by local IRB/ethics.

References (APA 7 — selected, includes ≥3 peer-reviewed items post-2019)

Centers for Disease Control and Prevention. (2024, June 5). Technical report: Highly pathogenic avian influenza A(H5N1) viruses — June 2024. U.S. Department of Health and Human Services. https://www.cdc.gov/bird-flu/php/technical-report/h5n1-06052024.html

World Health Organization. (2024, April 9). Avian influenza A(H5N1) — United States of America (Disease outbreak news). https://www.who.int/emergencies/disease-outbreak-news/item/2024-DON512

Marchenko, V. Y., Panova, A. S., Kolosova, N. P., et al. (2024). Characterization of H5N1 avian influenza virus isolated from bird in Russia with the E627K mutation in the PB2 protein. Scientific Reports, 14, Article 26490. https://doi.org/10.1038/s41598-024-78175-y

Gao, F., Wang, Q., Qiu, C., Luo, J., & Li, X. (2024). Pandemic preparedness of effective vaccines for the outbreak of newly H5N1 highly pathogenic avian influenza virus. Virologica Sinica, 39(6), 981–985. https://doi.org/10.1016/j.virs.2024.11.005

Faccin, F. C., et al. (2024). Pandemic preparedness through vaccine development for avian influenza viruses. Human Vaccines & Immunotherapeutics. (Open access review) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11141480/

Capelastegui, F., et al. (2025). H5N1 2.3.4.4b: a review of mammalian adaptations and implications for human health. [Journal]. https://doi.org/10.XXXX/XXXXX (Note: use this or similar 2024–2025 review as available in your library; replace doi as appropriate.)

Pulit-Penaloza, J. A., et al. (2022). Pathogenesis and transmissibility of North American highly pathogenic avian influenza A(H5N1) virus in ferrets. Emerging Infectious Diseases, 28(9), 1913–1915. https://doi.org/10.3201/eid2809.220879

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