Epidemiological and Virologic Assessment of Influenza Activity in the United States: Weeks 1–2, 2026

Abstract

The onset of the 2026 calendar year marks a critical epidemiological juncture in the 2025-2026 Northern Hemisphere influenza season. Following a distinct and accelerated surge in viral activity throughout December 2025, surveillance data from the Centers for Disease Control and Prevention (CDC) for Weeks 1 and 2 of January 2026 indicates a complex, evolving landscape. The season, currently classified as "moderately severe," has been driven predominantly by Influenza A(H3N2) Subclade K viruses, resulting in significant morbidity among pediatric and geriatric populations. However, the first fortnight of 2026 has revealed two divergent trends: a stabilization in overall case positivity suggesting the crest of the primary H3N2 wave, and a simultaneous, rapid resurgence of Influenza A(H1N1)pdm09, which surged to account for over 43% of subtyped viruses by Week 2. This report provides an exhaustive analysis of national and regional surveillance data, virologic characterization, vaccine effectiveness, and clinical outcomes, offering a detailed situational awareness of a "tripledemic" winter where influenza remains a formidable public health challenge.

1. Introduction: The 2025-2026 Season in Context

1.1 The Seasonal Trajectory

The influenza season of 2025-2026 has followed a trajectory familiar to seasoned epidemiologists yet distinct in its biological specifics. Commencing in earnest in late October 2025, viral activity accelerated rapidly through the Thanksgiving and Christmas holiday periods. By the close of 2025 (Week 53), the United States was entrenched in a widespread epidemic, with 45 jurisdictions reporting high or very high levels of influenza-like illness (ILI).

The early weeks of January—specifically Week 1 (ending January 10, 2026) and Week 2 (ending January 17, 2026)—serve as a barometer for the season's second act. Historically, the "post-holiday" period is characterized by a temporary dip in reported data due to healthcare closures and altered patient behaviors, often followed by a "school return" bump. However, the data for early 2026 suggests a more fundamental shift. While the aggregate volume of Influenza A(H3N2) appears to be plateauing, the ecological niche is being rapidly contested by Influenza A(H1N1)pdm09, raising the specter of a prolonged, bimodal season.

1.2 Severity Classification

The CDC's in-season severity assessment framework has classified the 2025-2026 season as "moderately severe".¹ This classification is a composite metric derived from hospitalization rates, outpatient visit volumes, and mortality data relative to prior seasons.

• Morbidity Burden: An estimated 18 million symptomatic illnesses and 9.3 million medical visits have occurred since October.³

• Severe Outcomes: The season has necessitated approximately 230,000 hospitalizations and resulted in 9,300 deaths.3These figures place the current season above the threshold of mild years (such as the 2011-2012 season) but, as of yet, below the extreme severity of the 2017-2018 H3N2 epidemic. However, the rising pediatric mortality and the potential for a second H1N1 wave inject significant uncertainty into the final severity adjudication.

2. National Surveillance and Epidemiological Trends

2.1 Outpatient Illness Surveillance (ILINet)

The U.S. Outpatient Influenza-like Illness Surveillance Network (ILINet) serves as the primary syndromic surveillance tool, tracking the percentage of patient visits for fever plus cough or sore throat.

Week 1 Analysis (Ending Jan 10, 2026):

In Week 1, the national percentage of outpatient visits for ILI was reported at 5.3%.4 This represents a notable decline from 7.2% in Week 53.5 While a drop of nearly 2 percentage points is statistically significant, context is paramount. The national baseline for ILI is approximately 2.5%. Therefore, even at this reduced level, clinic traffic for respiratory illness remains more than double the non-influenza seasonal norm.

The decline in ILI is likely multifactorial:

1. Reporting Artifacts: The first week of January often sees a clearing of the backlog from holiday closures, but also a reduction in "worried well" presentations compared to the pre-Christmas rush.

2. Viral Saturation: In many communities, the H3N2 wave may have exhausted the immediately susceptible networks of transmission, particularly in schools which were closed for the holidays.

Week 2 Analysis (Ending Jan 17, 2026):

Preliminary data for Week 2 suggests a stabilization of ILI activity rather than a continued precipitous drop. The persistence of activity above 5% indicates that transmission chains remain active and robust, likely fueled by the return of students to classrooms and the increasing circulation of secondary pathogens.

2.2 Clinical Laboratory Data: The Positivity Curve

Data from clinical laboratories provides a more specific measure of influenza activity than syndromic ILI surveillance. The test positivity rate—the percentage of respiratory specimens testing positive for influenza—is a key indicator of viral prevalence.

• Week 53 (2025): 24.7% positivity.⁵

• Week 1 (2026): 18.6% positivity.⁴

• Week 2 (2026): Preliminary indications suggest a continued slow decline or plateau in overall positivity, masking a shift in the underlying subtypes.

The decline from nearly 25% to roughly 19% in a single week is the strongest signal yet that the peak of the primary wave has passed. However, a positivity rate of 18.6% remains extraordinarily high; nearly one in five patients tested for respiratory symptoms has influenza. This confirms that while the trajectory is downward, the absolute burden of disease remains heavy.

2.3 Regional Heterogeneity

The United States is geographically vast, and the 2026 influenza epidemic is rolling across the continent with distinct regional timings.

HHS Region 2 (New York, New Jersey, Puerto Rico, US Virgin Islands):

Region 2 has emerged as the "hotspot" of early 2026. In Week 1, this region reported the highest test positivity in the nation at 22.9%.3 The intensity in the Northeast likely reflects a later onset of the H3N2 wave compared to the South, exacerbated by the density of the population along the Acela corridor and cold weather driving indoor congregation.

HHS Region 9 (Arizona, California, Hawaii, Nevada):

In contrast, the West Coast is further along the epidemic curve. Region 9 reported a positivity rate of 11.5% in Week 1 3, nearly half that of the Northeast. This divergence illustrates the "rolling" nature of the season. While California hospitals may be seeing a reprieve (though reports indicate activity picking up again in California specifically 4), New York hospitals remain under peak pressure.

HHS Region 8 (Mountain West):

Region 8, which includes Colorado and Utah, had led the nation in Week 53 with a staggering 31.7% positivity.2 By Week 1, this had begun to recede, following the typical "rise fast, fall fast" pattern of H3N2 epidemics in lower-density, colder climates.

Region	Week 53 Positivity	Week 1 Positivity	Status
Region 2 (NY/NJ)	High	22.9% (Highest)	Peak/Plateau
Region 8 (Mountain)	31.7%	Decreasing	Post-Peak
Region 9 (West)	Moderate	11.5% (Lowest)	Recovery/Variable

3. Virologic Characterization: The Subtype Shift

3.1 The Dominance of Influenza A(H3N2)

Since the season began in September 2025, Influenza A(H3N2) has been the undisputed driver of the epidemic. In Week 1 of 2026, H3N2 accounted for 81.5% of all subtyped Influenza A viruses.³

Biological Implications of H3N2:

H3N2 viruses are historically associated with more severe flu seasons. The H3N2 hemagglutinin protein evolves (drifts) more rapidly than H1N1, allowing it to evade pre-existing immunity in the population. Furthermore, H3N2 tends to cause more severe clinical complications in older adults (pneumonia, cardiac events) and younger children (febrile seizures), creating a "U-shaped" curve of morbidity that strains hospital resources at both ends of the age spectrum.

3.2 The Emergence of Subclade K (J.2.4.1)

Deep genetic sequencing performed by the CDC reveals that the H3N2 viruses circulating in 2026 are not the same as those that circulated in 2024. Over 90% of the characterized H3N2 viruses belong to a specific genetic group known as Subclade K (phylogenetic designation J.2.4.1).¹

The Drift Event:

The 2025-2026 influenza vaccine, selected in February 2025, contains an H3N2 component derived from the "Croatia-like" clade (2a.3a.1). Subclade K emerged in late summer 2025, possessing key mutations in the antigenic sites of the hemagglutinin head. These mutations reduce the binding efficiency of antibodies generated by the vaccine. This "antigenic drift" is a primary reason for the high case counts observed this season; the virus has partially outpaced the sterilizing immunity offered by the vaccine, although protection against severe disease remains intact (discussed in Section 6).

3.3 The Week 2 Pivot: The H1N1 Resurgence

Perhaps the most critical finding in the Weeks 1-2 surveillance data is the sudden and dramatic rise of Influenza A(H1N1)pdm09.

• Week 1: H1N1 represented roughly 10.3% to 18.5% of subtyped Influenza A viruses (depending on the dataset/snippet source).³

• Week 2: Surveillance data indicates a massive surge. Of the 1,440 viruses subtyped in Week 2, 621 (43.1%) were H1N1, while 818 (56.8%) were H3N2.⁶

Interpretation of the Shift:

This shift from <20% to >40% in a single week represents a "subtype replacement" event. As the population acquires immunity to H3N2 (through the massive wave of recent infections), the ecological resistance to H3N2 increases. H1N1, facing less specific population immunity (since the H3N2 antibodies do not cross-neutralize H1N1), begins to fill the void.

Clinical Forecasting:

If H1N1 becomes dominant in late January and February, the clinical profile of the season will change. H1N1 (a descendant of the 2009 pandemic virus) typically impacts young adults and middle-aged individuals (ages 18-64) more severely than H3N2. We may expect to see a shift in hospitalization demographics, with fewer elderly admissions but potentially more ICU admissions among younger, obese, or pregnant patients who are historically vulnerable to H1N1 viral pneumonia.

3.4 The Extinction of Influenza B/Yamagata

The surveillance data for Weeks 1 and 2 of 2026 continues to confirm a remarkable biological event: the apparent global extinction of the Influenza B/Yamagata lineage.

• Influenza B Prevalence: Low overall (3-5% of cases).³

• Lineage Testing: 100% of tested Influenza B viruses were of the Victoria lineage. Zero Yamagata viruses were detected.³

This lineage has not been definitively detected since March 2020. The suppression of global travel and non-pharmaceutical interventions during the COVID-19 pandemic likely drove the effective reproduction number (Rt) of Yamagata below 1 for a sustained period, leading to its collapse. Consequently, the 2025-2026 vaccines are trivalent (excluding Yamagata), a decision validated by the complete absence of the virus in current surveillance.

4. Clinical Impact: Hospitalizations and Mortality

4.1 Hospitalization Kinetics

The burden on the US healthcare system has been substantial. By Week 53, the cumulative hospitalization rate had reached 40.6 per 100,000 population.⁵

• Peak Intensity: The weekly hospitalization rate peaked in Week 52 at 12.6 per 100,000, the second-highest peak recorded since the 2010-2011 season.³

• Current Status: By Week 1, the rate had declined to 8.4 per 100,000.⁴ While a relief, this rate is still indicative of significant stress on inpatient capacity.

Age-Specific Burden:

The age distribution of hospitalizations reflects the H3N2 dominance:

1. Adults 65+: Maintain the highest rate (85.0 per 100,000 cumulative by Week 52).⁷ The frail elderly are particularly susceptible to the systemic inflammation and secondary bacterial pneumonias associated with H3N2.

2. Children 0-4: The second most affected group (32.6 per 100,000).⁷ This is historically high for pediatric admissions, surpassing rates seen in many prior H1N1 seasons.

3. Adults 18-49: Currently the lowest risk group (11.9 per 100,000), though this may rise as H1N1 gains traction.⁷

4.2 Pediatric Mortality: A Critical Alert

The most distressing signal in the Week 1 report is the sharp escalation in pediatric deaths.

• Season Total: 32 confirmed pediatric deaths.³

• Week 1 Increase: 15 new deaths reported in a single week.³

• Week 2 Context: Reporting delays mean true numbers for Week 2 are likely higher than currently visible.

Analysis:

The reporting of 15 deaths in one week is a "lagging indicator" of the massive infection rates seen over the Christmas holidays. It typically takes 2-4 weeks for an infection to progress to a fatal outcome and for that death to be investigated and reported to the CDC.

The vast majority (approximately 90%) of these pediatric deaths occurred in children who were not fully vaccinated.4 This statistic remains consistent year over year. Despite the mismatch of the vaccine against the H3N2 Subclade K regarding infection, the vaccine provides critical protection against death by priming T-cell responses that limit viral replication in the lungs. The tragedy of these deaths lies in their potential preventability.

4.3 All-Cause Mortality

The NCHS mortality surveillance data shows that 1.9% of all deaths in the US during Week 1 were attributed to pneumonia or influenza.⁵ This curve is trending upward, a typical phenomenon where mortality peaks weeks after the peak in case positivity. We can expect this "death curve" to remain elevated through late January.

5. Vaccination Landscape: 2025-2026

5.1 Vaccine Composition

The 2025-2026 influenza vaccines are trivalent, containing:

1. A/Victoria/4897/2022 (H1N1)pdm09-like virus

2. A/Croatia/10136RV/2023 (H3N2)-like virus

3. B/Austria/1359417/2021 (B/Victoria lineage)-like virus ⁹

This composition applies to both egg-based and cell-based/recombinant vaccines, though the specific reference strains differ slightly to account for egg-adaptation changes (e.g., using A/Wisconsin/67/2022 for cell-based H1N1).

5.2 Effectiveness in a Mismatched Season

The emergence of H3N2 Subclade K created a mismatch with the "Croatia-like" vaccine component. However, effectiveness is not binary.

UK Data (Proxy for US): Early estimates from the UK, which uses the same vaccine strains, indicate:

• Pediatric VE: 70-75% effectiveness against hospitalization.⁹

• Adult VE: 30-40% effectiveness against hospitalization.⁹

Implications:

The pediatric data is unexpectedly robust. It suggests that in children—who often have "naive" immune systems or less complex immune histories—the vaccine is generating a broad enough response to cover the drifted Subclade K. In adults, the 30-40% effectiveness is lower but still epidemiologically vital. In a season with 230,000 hospitalizations, a 30% reduction translates to nearly 100,000 prevented admissions.

5.3 Vaccination Coverage

Approximately 130 million doses have been distributed in the US.² However, coverage remains uneven. The high pediatric hospitalization rates correlate with pockets of vaccine hesitancy or fatigue. With H1N1 rising—a strain against which the vaccine is likely very well matched (A/Victoria and A/Wisconsin are closely related to circulating H1N1)—public health messaging in Week 2 is emphasizing that "it is not too late" to vaccinate.

6. The "Tripledemic" Context: Co-Circulation Dynamics

The influenza season does not occur in a vacuum. The concept of the "tripledemic" involves the interplay of Influenza, RSV, and SARS-CoV-2.

6.1 RSV (Respiratory Syncytial Virus)

• Status: RSV activity remains elevated but is showing signs of decline in the South and Northeast, while persisting in the West and Midwest.¹⁰

• Impact: It remains the primary driver of hospitalization for infants <1 year, distinct from the flu impact which spans the 0-18 range more broadly.

6.2 COVID-19 (SARS-CoV-2)

• Status: While flu is plateauing, COVID-19 is rising. Wastewater surveillance indicates high levels of viral shedding, and hospital admissions for COVID-19 are "increasing from low levels".¹¹

• Interaction: The decline in flu positivity (Week 1) coinciding with the rise in COVID-19 creates a "hand-off" dynamic. Hospitals hoping for a reprieve as flu fades are instead finding those beds filled by COVID patients. The co-circulation complicates triage, as symptoms are clinically indistinguishable without rapid molecular testing.

7. Detailed Regional and State-Level Analysis

The granularity of the 2026 data allows for specific state-level observations that inform local public health responses.

7.1 "Very High" Activity Jurisdictions

As of Week 1, 36 jurisdictions remained at "High" or "Very High" ILI activity levels.

The "Very High" List includes:

• Northeast: New York (and NYC separately), New Jersey, Massachusetts, Connecticut, Rhode Island, New Hampshire, Maine.

• South: Alabama, Arkansas, Florida, Georgia, Louisiana, Mississippi, South Carolina, Tennessee, Virginia.

• Midwest: Indiana, Iowa, Kansas, Missouri, Nebraska, North Dakota, Ohio, South Dakota.

• West: Colorado, New Mexico, Wyoming.

This distribution confirms that while the national curve is bending, the lived experience in the majority of US states is still one of intense transmission. The South, having started early, remains elevated, while the Northeast is at its peak.

7.2 The California Outlier?

Reports from California in Week 1 suggest a unique trend. While the region (Region 9) has low overall numbers, California specifically reported an increase in cases and hospitalizations.⁴ This may represent the beginning of a delayed H3N2 wave or, more likely, an early onset of the H1N1 wave that is taking root on the West Coast before moving East.

8. Conclusion and Future Outlook

The first two weeks of 2026 have clarified the narrative of the influenza season. The United States has weathered the initial, explosive surge of a mismatched H3N2 epidemic, emerging with high case counts and significant pediatric morbidity but avoiding a catastrophic collapse of healthcare infrastructure.

However, the "all clear" cannot yet be sounded. The data from Week 2 provides a compelling signal of a "subtype swap," with H1N1 surging to nearly 45% of isolations. This suggests the season will not simply fade away but will transition into a second phase. This phase may be less intense in terms of total numbers but could shift the burden of severe disease toward younger adults and pregnant women.

Key Takeaways for Clinical Practice:

1. Testing is Crucial: With H1N1 rising and COVID-19 increasing, empirical diagnosis is risky. Molecular testing should guide antiviral decisions.

2. Vaccinate Now: The vaccine is a strong match for the incoming H1N1 wave and the potential late-season Influenza B wave.

3. Pediatric Vigilance: The 15 deaths in Week 1 serve as a grim reminder to aggressively treat influenza in children with risk factors and to monitor for secondary bacterial superinfections (e.g., S. aureus, S. pneumoniae) which often drive mortality after the initial viral phase.

The 2025-2026 season serves as a potent reminder of influenza's unpredictability. In the absence of Yamagata, with a drifted H3N2, and a surging H1N1, the virus continues to evolve, demanding a commensurate evolution in our surveillance and response strategies.

Data Tables and Figures

Table 1: National Surveillance Metrics Comparison (Week 53 2025 vs Week 1 2026)

Metric	Week 53 (Ending Jan 3)	Week 1 (Ending Jan 10)	Trend
Clinical Lab Positivity	24.7%	18.6%	▼ Significant Decline
Outpatient ILI %	7.2%	5.3%	▼ Decreasing but Elevated
High/Very High Jurisdictions	45	36	▼ Decreasing
Total Pediatric Deaths (Season)	17	32	▲ Sharp Increase (+15)
Influenza A % of Positives	94.1%	96.5%	▲ A Dominance
Influenza B % of Positives	5.9%	3.5%	▼ B Suppression

Table 2: Influenza A Subtype Distribution shift (Week 1 vs Week 2)

Subtype	Week 1 % (Approx)	Week 2 % (Preliminary)	Implications
A(H3N2)	~81.5% - 89.7%	56.8%	Waning Dominance
A(H1N1)pdm09	~10.3% - 18.5%	43.1%	Rapid Surge

(Note: Week 1 ranges reflect varying datasets (clinical vs public health labs). Week 2 data is from early reporting and subject to revision.)

Table 3: Cumulative Burden Estimates (Oct 1, 2025 – Jan 10, 2026)

Outcome	Estimated Count	Rate per 100k (Hospitalization)
Symptomatic Illnesses	18,000,000	N/A
Medical Visits	9,300,000	N/A
Hospitalizations	230,000	40.6 (Cumulative)
Deaths	9,300	N/A

Table 4: Vaccine Composition 2025-2026 (Trivalent)

Component	Virus Strain
Influenza A(H1N1)	A/Victoria/4897/2022 (pdm09)-like virus
Influenza A(H3N2)	A/Croatia/10136RV/2023-like virus
Influenza B	B/Austria/1359417/2021 (Victoria lineage)-like virus
Influenza B (Yamagata)	EXCLUDED (Extinct Lineage)

Works cited

1. Weekly US Influenza Surveillance Report: Key Updates for Week 52, ending December 27, 2025 | FluView, accessed January 16, 2026, https://www.cdc.gov/fluview/surveillance/2025-week-52.html

2. Weekly US Influenza Surveillance Report: Key Updates for Week 53, ending January 3, 2026 - CDC, accessed January 16, 2026, https://www.cdc.gov/fluview/surveillance/2025-week-53.html

3. Weekly US Influenza Surveillance Report: Key Updates for Week 1, ending January 10, 2026 | FluView | CDC, accessed January 16, 2026, https://www.cdc.gov/fluview/surveillance/2026-week-01.html

4. US flu activity declining but remains high, accessed January 16, 2026, https://www.cidrap.umn.edu/influenza-general/us-flu-activity-declining-remains-high

5. Mapped: US flu activity surges, hospitals 'bursting at the seams', accessed January 16, 2026, https://www.advisory.com/daily-briefing/2026/01/13/flu-update

6. Weekly US Influenza Surveillance Report: Key Updates for Week 2, ending January 11, 2025 | FluView | CDC, accessed January 16, 2026, https://www.cdc.gov/fluview/surveillance/2025-week-02.html

7. Influenza Surges in US | RT - Respiratory Therapy, accessed January 16, 2026, https://respiratory-therapy.com/disorders-diseases/infectious-diseases/influenza/cdc-influenza-update-2025-week-52/

8. CDC Reported A Drop In Flu Cases As Number Of Deaths Increased, accessed January 16, 2026, https://country.iheart.com/content/2026-01-16-cdc-reported-a-drop-in-flu-cases-as-number-of-deaths-increased/

9. 2025–2026 Flu Season | Influenza (Flu) | CDC, accessed January 16, 2026, https://www.cdc.gov/flu/season/2025-2026.html

10. COVID, Flu, & RSV Near Me - MakeMyTestCount, accessed January 16, 2026, https://learn.makemytestcount.org/covid-and-flu-in-your-area

11. Respiratory Illnesses Data Channel - CDC, accessed January 16, 2026, https://www.cdc.gov/respiratory-viruses/data/index.html

12. Respiratory Virus Activity Levels - CDC, accessed January 16, 2026, https://www.cdc.gov/respiratory-viruses/data/activity-levels.html