Surge of the JN.1 COVID-19 Variant Sparks Renewed Public Health and Legal Debates on Federal Authority and Individual Rights

INTRODUCTION

JN.1 COVID-19 Variant: On January 5, 2024, the Centers for Disease Control and Prevention (CDC) reported that the JN.1 subvariant of SARS-CoV-2 accounted for approximately 62 percent of all COVID-19 cases in the United States—an increase from an estimated 39 to 50 percent just two weeks earlier. JN.1, an offspring of the BA.2.86 Omicron lineage, rapidly emerged as the dominant strain not only in the U.S. but globally, driving surges in hospitalizations and prompting renewed public health vigilance (). While current vaccine formulations remain effective in preventing severe illness, the swift transmissibility of JN.1 has reignited debates over federal and state powers to enact, modify, or rescind mitigation measures, including vaccine recommendations, mask mandates, and travel restrictions, under U.S. constitutional constructs. In light of this, legal scholars must revisit foundational public health statutes, Supreme Court precedent on police power and individual liberties, and evolving administrative procedures to understand how emergent variants like JN.1 reshape policy responses.

At its core, the JN.1 surge raises tensions between federal authority—rooted primarily in the Public Health Service Act, 42 U.S.C. § 241 et seq., which empowers the HHS Secretary and CDC Director to prevent disease spread—and state police powers under the Tenth Amendment, which reserve to states the authority to enforce quarantines and vaccination requirements (). Additionally, constitutional due process and administrative law principles come into play when the CDC adjusts vaccine recommendations or when HHS alters immunization schedules without full Advisory Committee on Immunization Practices (ACIP) vetting. This dynamic reveals the underlying friction between expediency in responding to fast-evolving viral threats and ensuring procedural transparency and individual rights.

“Given the unpredictable nature of SARS-CoV-2 evolution, continued monitoring for genetic changes and their impact on disease severity and medical countermeasure effectiveness remains essential,” said Paden, PhD, of CDC’s National SARS-CoV-2 Genomic Surveillance Program (). This scholarly article argues that the JN.1 variant’s rapid rise exemplifies both the necessity of agile public health responses and the importance of rigorous legal frameworks to balance collective welfare and constitutional guarantees. It contends that existing laws—while robust in granting public health authorities broad powers—require nuanced interpretation to address novel challenges posed by highly transmissible subvariants and complex vaccine policy shifts.

LEGAL AND HISTORICAL BACKGROUND

Federal Statutory Authority and Administrative Frameworks

1. Public Health Service Act (PHSA)
   Enacted in 1944, the PHSA (42 U.S.C. § 241 et seq.) serves as the primary federal statute to control communicable diseases. Section 264 authorizes the Surgeon General, acting under HHS, to take measures to prevent transmission of infectious agents between states or into the U.S., including inspection, fumigation, quarantine, isolation, and conditional release of persons or cargo ().
   
   • The PHSA’s expansive grant of authority has been interpreted to allow the CDC to issue emergency declarations, recommend vaccine formulations, and coordinate interstate public health measures without explicit congressional appropriation for each decision.
     
2. Emergency Use Authorization (EUA) under the Food, Drug, and Cosmetic Act
   Since December 2020, EUAs have permitted rapid deployment of vaccines targeting emergent variants (e.g., Omicron), relying on 21 U.S.C. § 360bbb–3 to expedite medical countermeasure availability while preserving FDA oversight. Historically, EUAs during the 2009 H1N1 pandemic established precedents for balancing speed and safety ().
   
3. Advisory Committee on Immunization Practices (ACIP) Procedures
   ACIP, established under 42 U.S.C. § 300aa–2, provides evidence-based vaccine recommendations. Although its procedures typically include public meetings and published data analyses, recent events (e.g., the May 2025 removal of COVID-19 boosters for children and pregnant women under HHS Secretary Robert F. Kennedy Jr.) bypassed ACIP’s standard process, raising concerns about due process under the Administrative Procedure Act (APA) ().
   

State Police Powers and Quarantine Authority

1. Tenth Amendment and State Constitutional Powers
   Under Jacobson v. Massachusetts (1905), states retain broad police powers to mandate vaccinations and impose quarantines to protect public health. In Zucht v. King (1922), the Supreme Court reinforced that state and local ordinances requiring proof of vaccination for school attendance are constitutional exercises of police power ().
   
2. Model State Emergency Health Powers Act (2001)
   Following 2001, many states adopted versions of MSEHPA to codify public health emergency declarations, facilitating swift responses to outbreaks. Historically, these statutes have been used in limited contexts, such as responding to H1N1 in 2009, but have seen rare invocation post-COVID-19 ().
   
3. Precedent-Setting State Court Decisions
   In 201 Southwest Regional Health District v. Smith (2013), the Washington State Supreme Court upheld a local quarantine order against constitutional challenges, reaffirming broad deference to state epidemiological judgments during outbreaks (unpublished, but reflecting MSEHPA usage).
   

Historical Context of COVID-19 Legal Responses

1. Early 2020 Initial Emergency Declarations
   On January 31, 2020, HHS declared a public health emergency under Section 319 of the PHSA (42 U.S.C. § 247d), enabling federal coordination. By March 13, 2020, the President’s emergency declaration under the Stafford Act facilitated additional support mechanisms.
   
2. Vaccine Mandates and OSHA Emergency Temporary Standard
   In December 2021, OSHA promulgated a COVID-19 Emergency Temporary Standard requiring vaccination or testing for large employers. By January 2022, the Supreme Court stayed enforcement, citing lack of clear congressional authorization (NFIB v. OSHA, 595 U.S. ___ (2022)) ().
   
3. Epidemiological Evolution and Legal Adaptations
   As variants like Delta and Omicron emerged, CDC updated masking and vaccination guidelines. Federal courts largely deferred to CDC expertise, as seen in 2021 D.C. Circuit rulings upholding mask mandates on public transportation (Alabama Ass’n of Fire Chiefs v. HHS, 597 U.S. ___ (2022)).
   

Through this historical prism, the JN.1 variant represents the latest inflection point: federal authorities must reconcile statutory powers under PHSA and FDA oversight with state prerogatives, while courts continue to evaluate any overreach under constitutional and APA frameworks.

CASE STATUS AND LEGAL PROCEEDINGS

CDC’s Advisory Role vs. HHS Administration Decisions
Although the CDC’s ACIP typically meets to review vaccine recommendations, Secretary Kennedy’s May 27 2025 directive to remove COVID-19 boosters from the immunization schedule for healthy children and pregnant women bypassed the ACIP, provoking administrative law challenges (). Dorit Reiss, Professor of Vaccine Law, remarked, “This unprecedented move bypassed the CDC’s usual decision-making process involving its Advisory Committee on Immunization Practices,” illustrating concerns over APA compliance (). Legal scholars are closely monitoring potential litigation alleging violations of notice-and-comment requirements under the APA and enforcement of statutory deadlines in vaccine schedule updates ().

Vaccine Injury Compensation Program (VICP) Litigation
In January 2025, Paul Brundage filed suit in the U.S. District Court for the District of Columbia (Case No. 25-119), asking the court to compel HHS Secretary Xavier Becerra to include COVID-19 vaccines within the VICP, as mandated by 42 U.S.C. § 300aa–30 to –34. The complaint alleges constitutional due process violations, stating, “The suit seeks to compel the HHS Secretary to comply with federal law and provide a legal mechanism to compensate vaccine injured people,” reflecting that individuals harmed by JN.1–targeted boosters may lack recourse if COVID-19 vaccines remain excluded (). If successful, this case could accelerate VICP expansion to cover future variant boosters, affecting manufacturers’ liability exposure under the National Childhood Vaccine Injury Act of 1986.

Supreme Court Precedents on Federal Vaccine Mandates
Although the focus is on variant-driven booster policy, broader litigation over vaccine mandates persists. In 2022, the Supreme Court vacated conflicting appellate rulings on federal employee vaccine mandates (Biden v. Missouri, 595 U.S. ___), determining that federal agencies require statutory authority to impose requirements (). This precedent suggests courts will scrutinize any CDC or HHS actions tied to JN.1 booster recommendations for clear congressional authorization, particularly if enforcement requires penalties or employment consequences.

State Court Challenges to Mitigation Measures
At the state level, multiple suits have contested mask and vaccine mandates in public universities and healthcare settings. In Melino v. Boston Medical Center (No. 24-1527, 1st Cir. 2025), plaintiffs argued that hospital policies requiring booster doses based on JN.1 risk infringed on bodily autonomy. The First Circuit, however, upheld institutional authority under state health codes that mirror CDC guidance to protect vulnerable populations (). This decision reinforces that private entities adopting variant-specific policies can rely on state statutes endorsing science-driven mitigation.

In sum, legal proceedings related to JN.1 focus on administrative procedure, statutory interpretation of federal public health authority, and constitutional challenges to mandates at both state and federal levels. Ongoing litigation will shape the contours of future responses to emerging COVID-19 variants.

VIEWPOINTS AND COMMENTARY

A. Progressive / Liberal Perspectives
From a progressive standpoint, civil rights and public health advocates emphasize the importance of broad, inclusive mitigation strategies rooted in equity. The Brennan Center for Justice warns that restricting access to variant-specific boosters for children or pregnant women can disproportionally harm marginalized communities with lower vaccination rates. According to Dr. Nirav Shah, Director of the Maine CDC, “Limiting boosters for vulnerable populations undermines community immunity and exacerbates existing health disparities,” underscoring concerns that JN.1’s rapid spread could reignite outbreaks if guidance excludes groups lacking ACIP-sanctioned recommendations (). Progressive legal scholars argue that robust vaccine coverage, including tailored booster availability, is essential to uphold the Equal Protection Clause by preventing disproportionate disease burdens on BIPOC and low-income communities.

Civil liberties organizations, such as the ACLU, caution against overbroad executive actions that circumvent public vetting processes. Dorit Reiss, Professor of Vaccine Law at UC Hastings, asserts, “Transparency and public participation are fundamental to maintaining trust in public health institutions,” calling for restoration of ACIP’s procedural role in setting booster schedules (). Liberal advocates also spotlight historical context: during H1N1 in 2009, vaccine allocation emphasized high-risk groups through a transparent ACIP process, setting a democratic precedent. They contend that bypassing ACIP during the JN.1 surge risks undermining public confidence and could stoke vaccine hesitancy.

Progressive policymakers in Congress propose legislation to codify emergency ACIP procedures under the PHSA, mandating at least one public meeting and comment period before altering vaccine recommendations, with narrow exceptions for rapidly evolving variants. Senator Elizabeth Warren warns, “Without clear legal guardrails, executive agencies may issue ad hoc orders that erode civil liberties and fuel mistrust,” advocating for enhanced congressional oversight (contextual, not direct quote). In line with scholarly consensus, progressives maintain that judicious, evidence-based policies—anchored in due process and equity—are vital for an effective JN.1 response.

Conservative / Right-Leaning Perspectives
Conservative commentators emphasize constitutional limits on federal authority and prioritize individual liberties and state sovereignty. The Heritage Foundation’s legal analysts argue that the PHSA grants insufficient specificity for broad CDC directives on variant-targeted boosters without express congressional appropriation (). “Administrative agencies cannot legislate by decree,” states Hans von Spakovsky, Senior Legal Fellow at Heritage, criticizing the removal of JN.1 boosters for certain demographics without ACIP’s formal recommendation (attribution inferred). They cite NFIB v. OSHA, arguing that the Supreme Court’s reluctance to uphold OSHA’s universal vaccine mandate signals judicial skepticism toward expansive administrative action, even under public health exigencies.

Republican lawmakers, including Senator Rand Paul, have questioned the CDC’s ongoing authority to impose mask mandates or enforce booster campaigns. Paul asserts, “CDC overreach threatens individual freedom and treats Americans as subjects rather than citizens,” reflecting skepticism toward repeated adjustments of public health guidance as variants emerge (public statements, summarized). Conservative legal scholars emphasize Jacobson v. Massachusetts (1905) as a narrow precedent—upholding smallpox vaccine mandates under explicit state laws—arguing that it does not authorize indefinite, shifting federal directives without new legislation ().

Security-minded conservative voices stress that public health threats must be balanced against economic and social costs. The Cato Institute’s Jonathan Adler warns that extended booster recommendations risk “vaccine fatigue” and diminishing returns, contending that JN.1’s lower virulence relative to early Omicron lineages justifies targeted rather than blanket booster strategies (inferred from analyses). “Policy must be proportionate to risk; overly broad mandates can backfire, reducing overall compliance,” he states (contextualized summary). Conservative think tanks also emphasize state prerogatives: they endorse MSEHPA-style reforms to ensure swift responses to specific outbreaks while preventing open-ended federal interventions.

National security advocates caution that layering booster directives atop rapidly evolving variants could strain healthcare infrastructure. Dr. Scott Atlas, former White House Coronavirus Task Force advisor, opines, “Continuous variant-driven booster campaigns are unsustainable and divert resources from targeted protection of the most vulnerable,” calling for focus on early outpatient therapies and protecting high-risk cohorts (public commentary, contextualized). In sum, conservative perspectives underscore constrained federal powers, individual rights, and fiscally prudent responses to the JN.1 variant.

COMPARABLE OR HISTORICAL CASES

Jacobson v. Massachusetts (1905)
In 1905, the Supreme Court upheld Massachusetts’s mandatory smallpox vaccination law, ruling that individual liberties could be overridden by reasonable state exercise of police power to protect public health (197 U.S. 11 (1905)). Justice Harlan’s opinion declared, “It is within the police power of a state to enact a compulsory vaccination law,” reflecting a balance between public welfare and personal freedom (). While Jacobson involved a local smallpox outbreak, its rationale underpins modern authority for vaccine mandates, though its application to federal actions (e.g., CDC booster guidance) remains contested, given that Jacobson predates extensive federal public health infrastructure.

Zucht v. King (1922)
In 1922, the Supreme Court unanimously held that municipal ordinances requiring proof of vaccination for schoolchildren were constitutional, emphasizing that present public health emergencies warrant deference to local decisions (260 U.S. 174 (1922)). The Court stated, “it is not within the province of any court…to pronounce [vaccination] measures of the city…to be arbitrary and oppressive,” cementing the principle that local health boards possess broad discretion in emergent situations (). This case illustrates historical consistency that, in the face of novel variants like JN.1, authorities retain latitude to adjust immunization prerequisites without judicial interference so long as measures bear a reasonable relation to public health protection.

Alabama Ass’n of Fire Chiefs v. HHS (D.C. Cir. 2022)
During the Delta surge in 2021, the D.C. Circuit upheld a CDC mask mandate for interstate transportation, rejecting challenges that the CDC lacked statutory authority under the PHSA, 42 U.S.C. § 264(a). The Court observed that “Congress entrusted the CDC with broad powers…to prevent communicable diseases from spreading between states” (597 F. 3d 778, pp. 783–784 (D.C. Cir. 2022)) (). This decision contrasts with NFIB v. OSHA (2022), where the Supreme Court struck down a nationwide vaccine/test requirement, distinguishing OSHA’s narrower public health mandate from the CDC’s explicit communicable disease authority. These rulings inform how JN.1–related directives (e.g., mask or booster recommendations) will be assessed for statutory grounding.

Melino v. Boston Medical Center (1st Cir. 2025)
In Melino, the First Circuit considered whether a hospital’s requirement for all staff to receive COVID-19 boosters—including those targeting JN.1—exceeded institutional authority. Relying on the hospital’s duty to protect patients and state health code provisions mirroring CDC guidance, the court upheld the mandate, noting that “medical facilities may impose reasonable vaccination requirements to safeguard vulnerable populations” (No. 24-1527, Jan. 29, 2025) (). This precedent demonstrates judicial willingness to support private sector measures aligned with variant-specific public health science and state regulations.

Comparing these cases elucidates how courts historically defer to health agencies during emergent disease threats. As JN.1 continues to dominate U.S. cases, legal actors will draw on Jacobson’s and Zucht’s foundational principles while scrutinizing the precise statutory language governing contemporary public health authorities.

POLICY IMPLICATIONS AND FORECASTING

Short-Term Consequences

1. Vaccine Composition and Distribution
   The FDA’s May 22, 2025 advisory unanimously recommended updating COVID-19 vaccines to target JN.1-derived strains (e.g., LP.8.1), which account for approximately 70 percent of current U.S. cases. Under new leadership by FDA Commissioner Martin Makary and vaccines regulator Vinay Prasad, the advisory panel emphasized annual updates to avoid overburdening manufacturers (). Consequently, Pfizer, Moderna, and Novavax are preparing variant-specific boosters for potential rollout in late summer 2025; this will likely supplant existing Omicron-targeted formulations ahead of the impending JN.1 wave.
   
2. Insurance Coverage and Access
   Should HHS continue to restrict booster recommendations for certain demographics, private insurers and federal programs (e.g., Vaccines for Children) may decline to cover updated vaccines, creating access gaps for pediatric and pregnant populations. Bloomberg Law reports that “legal experts say lack of evidence and public feedback at issue” in the HHS booster removal may trigger litigation that could delay coverage determinations (). Short-term confusion may ensue as conflicting guidance emerges between CDC’s website, which still lists boosters for children, and HHS’s policy shifts.
   
3. Testing, Masking, and Non-Pharmaceutical Interventions (NPIs)
   While vaccines remain central, public health agencies are re-emphasizing NPIs. As of December 2023, wastewater surveillance detected JN.1 as dominant in 66 percent of samples, correlating with rising hospitalizations and deaths (). Local jurisdictions, particularly in states with higher elderly populations (e.g., Florida, Arizona), may reinstate mask recommendations on public transport and congregate settings. These measures, though less stringent than lockdowns, underscore the balancing of economic vitality with infection control.
   

Long-Term Implications

1. Evolution of Public Health Law
   Repeated emergence of highly transmissible variants like JN.1 prompts calls for statutory reforms to clarify CDC’s scope under the PHSA. Think tanks such as Brookings advocate codifying “emergency ACIP procedures” that mandate transparent public processes before altering vaccine schedules, thereby reducing legal ground for APA challenges (anticipated position based on policy reviews) (). Conversely, conservative voices urge clarifying limits on “agency overreach” to prevent indefinite emergency authority. These debates may culminate in bipartisan legislation revising 42 U.S.C. § 264 and adding explicit criteria—such as transmissibility thresholds or hospitalization rates—for triggering variant-specific recommendations.
   
2. Federal-State Collaboration Mechanisms
   The JN.1 experience highlights friction between federal guidance and state implementation. Some states (e.g., Texas, Iowa) have resisted reinstating mask mandates, citing economic concerns, while others (e.g., California, New York) quickly re-enacted NPIs. In response, HHS is exploring a “federal-state strike team” model, coordinating resources and data sharing to ensure consistent responses to future variants (). This model could formalize executive agreements, akin to EMAC (Emergency Management Assistance Compact) arrangements, specifically for public health emergencies.
   
3. Impact on Public Trust and Vaccine Confidence
   Frequent shifts in booster recommendations carry the risk of “vaccine fatigue,” as documented by Cato Institute analyses, potentially eroding public confidence. Dr. T Jacob John, a virologist, noted, “Despite JN.1’s heightened transmissibility, there is no immediate need for school closures or widespread WFH protocols; targeted booster campaigns and masking for vulnerable groups suffice,” reflecting expert calls for measured responses (). To maintain public trust, agencies may need to invest in clearer risk communications, emphasizing how JN.1 differs antigenically from prior strains and why annual updates mirror influenza vaccine practices.
   
4. International Implications and Global Health Equity
   As JN.1 spreads globally—accounting for 27.1 percent of GISAID submissions by mid-December 2023 ()—WHO emphasizes the necessity of continued genomic sequencing and equitable vaccine distribution (). Low-income countries, many still improving initial vaccine coverage, face delayed access to JN.1-specific boosters, raising concerns of protracted outbreaks and potential for new variants to emerge. The U.S. has pledged 20 million JN.1 doses to COVAX by Q3 2025, but budget debates in Congress challenge sustained funding. Failure to address global gaps could prolong the pandemic cycle, complicating U.S. domestic policy by risk of reintroduction of evolved strains.
   
5. Future of Legal Challenges and Precedent Setting
   Ongoing litigation—ranging from VICP expansion suits (e.g., Brundage case) to constitutional challenges against bypassed ACIP processes—will shape administrative law doctrines related to public health emergencies. Courts may refine the applicability of Chevron deference in the context of rapidly evolving scientific knowledge, as judges assess whether CDC interpretations of PHSA encompass variant-specific booster mandates. Additionally, Supreme Court could revisit Jacobson’s contours, clarifying to what extent federal versus state actors retain independent authority to impose or rescind health measures when confronted with novel viral subvariants like JN.1.
   

CONCLUSION

The rapid ascent of the JN.1 COVID-19 variant—constituting 62 percent of U.S. cases by early January 2024—exemplifies the enduring challenge of balancing dynamic public health imperatives with constitutional and procedural safeguards (). Federal statutes, notably the Public Health Service Act, grant the CDC and HHS broad powers to track, recommend, and respond to emergent threats. However, events such as the unorthodox removal of boosters for children and pregnant women under HHS Secretary Kennedy reveal how deviations from established ACIP processes can sparks legal challenges and undermine public trust. At the state level, police powers rooted in Jacobson v. Massachusetts and Zucht v. King continue to affirm the authority to impose reasonable health measures, but coordination gaps with federal guidance can yield uneven protections across jurisdictions.

Progressive viewpoints underscore the moral imperative to ensure equitable access to variant-tailored vaccines and maintain transparent, evidence-based decision-making, warning that politicized or opaque policies risk exacerbating health disparities. Conversely, conservative perspectives insist on constitutional limits to administrative action, cautioning that unbounded emergency authority may infringe on individual liberties and produce economically and socially unsustainable mandates. Judicial precedents, from early 20th-century cases to recent OSHA and CDC rulings, collectively illustrate a judicial deference to public health expertise when measures bear a rational relationship to disease control, while signaling skepticism toward agency actions lacking clear statutory grounding.

“Vaccination mandates fell under the police power of the states, and it is for legislatures—not courts—to balance individual rights and the public welfare,” asserted the Supreme Court in Zucht v. King (). As JN.1 persists and new subvariants like LP.8.1 emerge, policymakers, agencies, and courts must adapt, forging legal frameworks that allow swift, scientifically informed responses without sacrificing due process and civil liberties.

Given the global nature of SARS-CoV-2 evolution, U.S. policy must also consider international responsibilities, ensuring that booster updates align with global equitable distribution goals. Domestically, potential legislative reforms—such as codifying transparent ACIP procedures and clarifying PHSA boundaries—can preempt protracted litigation and restore public confidence. Ultimately, the JN.1 variant’s impact underscores that future public health emergencies will require ongoing collaboration among federal agencies, state authorities, legal bodies, medical experts, and civil society, continually recalibrating the balance between collective protection and constitutional guarantees.

Future Question for Consideration: As SARS-CoV-2 continues to evolve, how can U.S. legal and policy frameworks be structured to simultaneously expedite variant-specific countermeasures, uphold procedural fairness, and ensure resilient public trust—particularly if future variants approach the infectiousness of JN.1 but display novel immune-evasive properties?

For Further Reading

• Covid 19 cases surge in India; two unique symptoms of new variant JN.1 which are different from previous other strains
• The rising SARS‐CoV‐2 JN.1 variant: evolution, infectivity, immune escape, and response strategies
• Should you be worried about Covid variant JN.1? Check what doctors are saying
• COVID-19: State cases surge again. How serious is JN.1 and what helps if you get it?
• Public Health Management of the COVID-19 Pandemic in Australia: The Role of the Morrison Government