COVID-19 Variant Surveillance: A Primer for Pharmacists Navigating Vaccine Questions

Since the emergence of COVID-19 in 2020, the SARS-CoV-2 virus has continuously evolved through genetic mutations that occur during replication. Although most mutations have a negligible impact, some produce variants with altered transmissibility, immune evasion, or vaccine responsiveness. Ongoing genomic surveillance enables scientists and public health agencies to monitor these changes, identify emerging variants, and inform vaccine composition and public health recommendations. As some of the most accessible and trusted health care professionals––approximately 90% of Americans live within 5 miles of a community pharmacy––pharmacists are frequently asked to interpret reports about new variants and decode the information for individual patients.^1. Questions such as “Does the vaccine still work?” require pharmacists to translate complex data into clear, evidence-based recommendations. This article reviews the fundamentals of SARS-CoV-2 variant surveillance and provides practical strategies for patient-centered counseling.

Key Definitions

Below are several key definitions to understand before diving into the world of variant surveillance²:

• Mutation: A single change in a virus’ genome. Although they occur frequently, most mutations do not meaningfully alter viral characteristics.
• Lineage: A group of closely related viruses with a common ancestor. All SARS-CoV-2 lineages cause COVID-19.
• Variant: A lineage carrying one or more mutations that may affect characteristics such as transmissibility, immune evasion, or disease severity, distinguishing it from other circulating lineages.
• Genomic sequencing: The process of decoding genetic material. Sequence comparison helps scientists track virus spread, monitor changes in characteristics, and update public health recommendations.
• Genomic surveillance: The systematic tracking of sequencing data to monitor circulating variants and detect emerging variants.

SARS-CoV-2 Virus Surveillance

The CDC established national genomic surveillance for SARS-CoV-2 in November 2020, using next-generation sequencing of positive specimens. The system evolved to incorporate wastewater surveillance, traveler-based surveillance, and public sequence databases to estimate the prevalence of circulating variants across the United States. The CDC COVID Data Tracker publishes weekly estimates of variant prevalence, enabling near-real-time tracking of circulating lineages. Globally, the World Health Organization (WHO) assesses emerging variants and classifies them according to public health risk. Table 1 provides an overview of CDC and WHO terms used to describe the severity of risk associated with different variants.^2,3 SARS-CoV-2 lineages are described using 3 primary nomenclature systems: Pango (Phylogenetic Assignment of Named Global Outbreak Lineages; eg, B.1.1.529), GISAID (eg, GR/484A), and Nextstrain (eg, 21K). The WHO assigns simplified Greek letter labels (eg, Omicron) to Variants of Concern (VOCs) to facilitate public communication.^3,4 As of 2023, the WHO reserves Greek letter designations exclusively for VOCs, whereas Variants of Interest are identified using their Pango or Nextstrain lineage names.

Variants and Vaccine Efficacy

Data from clinical studies have demonstrated that COVID-19 vaccines continue to provide strong protection against severe disease despite viral evolution. Two doses of an mRNA vaccination against the SARS-CoV-2 Alpha and Delta variants maintained a vaccine effectiveness (VE) rate against hospitalization of at least 85%, with booster doses increasing protection against the Delta variant to approximately 94%.^5,6 The emergence of Omicron and its sublineages led to substantial immune escape. Although VE against symptomatic infection with 2 vaccine doses dropped to as low as 8.8% beyond 25 weeks, booster doses restored short-term effectiveness to 62% to 70% at 2 to 4 weeks post vaccination.⁷ Importantly, VE against hospitalization remained above 95.5% across all variants among individuals who received 2 or 3 doses.⁵ This sustained protection is largely attributed to cellular immunity. Although neutralizing antibody levels decline over time, T-cell responses remain durable and protect against cross-variant infections.⁸ To account for ongoing antigenic drift, the WHO Technical Advisory Group on COVID-19 Vaccine Composition (TAG-CO-VAC) regularly reviews global surveillance data and recommends updated vaccine antigen compositions. Vaccines are updated to match circulating strains, analogous to the annual influenza vaccine update process.

Translating Surveillance Data for Patients

Pharmacists can use the ASPIRE (ask, share, provide, inform, recommend, empower) framework to communicate recommendations with patients (see Table 2).¹ Effective counseling and open dialogue begin with acknowledging uncertainty while avoiding unnecessary medical jargon. For example, instead of discussing “spike protein receptor-binding domain mutations,” pharmacists can explain that “the virus has changed over time, so vaccines are updated to better match circulating strains.” Clear, relatable explanations help patients understand evolving recommendations without undermining vaccine confidence.

Common Patient Questions

“Is the vaccine still effective?”
Yes. Updated COVID-19 vaccines are reformulated using global surveillance data reviewed by the WHO and regulatory agencies. Protection against severe disease remains the primary and most durable benefit.

“Why do I need another shot if the virus keeps changing?”
COVID-19 vaccination follows a strategy similar to that of seasonal influenza vaccination. Surveillance data are continually reviewed to identify strains most likely to circulate and update the vaccine for each season.

“I already had COVID-19—do I still need the vaccine?”
Yes. Hybrid immunity, the combination of prior infection and vaccination, provides the strongest and most durable protection. A systematic review found that hybrid immunity maintained 97.4% effectiveness against hospitalization at 12 months, compared with 74.6% following infection alone.⁹ Because infection-induced protection wanes, vaccination remains recommended regardless of prior infection history.

Resources for Pharmacists

Pharmacists can stay up to date by regularly reviewing trusted public health resources, including the WHO Tracking SARS-CoV-2 Variants, WHO TAG-CO-VAC vaccine composition statements, CDC COVID Data Tracker, Advisory Committee on Immunization Practices meeting summaries, Morbidity and Mortality Weekly Report, and the GISAID EpiCoV database for lineage tracking. Professional organizations such as the American Pharmacists Association and the American Society of Health-System Pharmacists also provide continuing education on emerging infectious diseases and vaccine recommendations.

Conclusion

Pharmacists are highly accessible, trusted, and embedded members of the health care community. By understanding how variants are identified, monitored, and incorporated into vaccine updates, pharmacists can confidently explain evolving recommendations for preventing severe illness. Bookmarking the WHO variant tracking page and CDC COVID Data Tracker for ease of access and regular review enables pharmacists to provide timely, evidence-based counseling that strengthens vaccine confidence and supports informed decision-making.

REFERENCES

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3. Parums D. Editorial: revised World Health Organization (WHO) terminology for variants of concern and variants of interest of SARS-CoV-2. Med Sci Monit. 2021;27:e933622. doi:10.12659/MSM.933622

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7. Andrews N, Stowe J, Kirsebom F, et al. COVID-19 vaccine effectiveness against the Omicron (B.1.1.529) variant. N Engl J Med. 2022;386(16):1532-1546. doi:10.1056/NEJMoa2119451

8. Tarke A, Coelho CH, Zhang Z, et al. SARS-CoV-2 vaccination induces immunological T cell memory able to cross-recognize variants from Alpha to Omicron. Cell. 2022;185(5):847-859.e11. doi:10.1016/j.cell.2022.01.015

9. Bobrovitz N, Ware H, Ma X, et al. Protective effectiveness of previous SARS-CoV-2 infection and hybrid immunity against the omicron variant and severe disease: a systematic review and meta-regression. Lancet Infect Dis. 2023;23(5):556-567. doi:10.1016/S1473-3099(22)00801-5