National Influenza Genomic Surveillance Report
Country: United States
Influenza season: 2026 Northern Hemisphere
Date of Report: 2026-05-20
Reporting period: 2026-01-01 – 2026-12-31
1. Executive Summary
This report summarizes influenza virus genomic surveillance conducted during the 2026 Northern Hemisphere influenza season in United States. Surveillance integrates routine virological testing with whole-genome sequencing to monitor circulating influenza strains, genetic diversity, antiviral resistance markers, and phylogenetic relationships.
Key findings:
|
Total Specimens
|
250
|
|
Influenza-positive specimens
|
241
|
|
Viruses sequenced
|
235
|
|
Dominant clades/subclades:
|
3C.2a1b.2a.2a.3a.1
|
2. Surveillance System and Sample Collection
|
Surviellance Systems
|
Sentinel outpatient influenza-like illness (ILI) surveillance
|
|
Specimen types
|
nasopharyngeal swab
|
|
Collection mediums
|
iral transport medium
|
|
Testing laboratories
|
Lab1, Lab2, Lab3, Lab4, Lab5
|
|
Age groups included
|
1 - 100
|
|
Geographic coverage
|
CA, GA, MI, NY, WA
|
3. Virological Screening Results
3.1 Total Specimens Tested
|
Metric
|
Count
|
|
Total specimens tested
|
250
|
|
Influenza-positive specimens
|
241
|
|
Influenza-negative specimens
|
9
|
3.2 Influenza Type and Subtype Distribution
|
Virus Type / Subtype
|
Count
|
Percentage (%)
|
|
Influenza A
|
192
|
96.0
|
|
└─ H3N2
|
113
|
56.5
|
|
└─ H9N2
|
43
|
21.5
|
|
└─ H1N1
|
24
|
12.0
|
|
└─ H5N1
|
12
|
6.0
|
|
Influenza B
|
8
|
4.0
|
|
└─ BVIC
|
8
|
4.0
|
|
Total influenza positive
|
200
|
100.0
|
4. Sequencing Overview
4.1 Sequencing Selection Criteria
Specimens were selected for sequencing based on:
|
Ct value range
|
10.0 - 25.0
|
|
Geographic coverage
|
CA, GA, MI, NY, WA
|
|
Temporal distribution across season
|
2025-01-01 - 2025-08-23
|
|
Age groups included
|
2 - 100
|
4.2 Sequencing Output and Quality
|
Metric
|
Count
|
Percentage (%)
|
|
Influenza-positive specimens eligible for sequencing
|
241
|
-
|
|
Specimens successfully sequenced
|
235
|
97.5
|
|
Specimen with complete genomes (all 8 segments pass QC)
|
211
|
89.8
|
|
Specimen with incomplete genomes (< 8 segments)
|
24
|
10.2
|
|
Specimen with complete HA segments
|
216
|
91.9
|
|
Specimen with complete NA segments
|
215
|
91.5
|
5. Clade and Subclade Distribution
5.1 Influenza BVIC
| V1A.3a.2 / C.5.6 |
8 |
100.0 |
| Total |
8 |
100.0 |
5.2 Influenza H1N1
| 5a.2a.1 / D.3 |
18 |
75.0 |
| 5a.2a / C.1.9 |
6 |
25.0 |
| Total |
24 |
100.0 |
5.3 Influenza H3N2
| 2a.3a.1 / J.2 |
113 |
100.0 |
| Total |
113 |
100.0 |
5.4 Influenza H5N1
| Undetermined / Undetermined |
12 |
100.0 |
| Total |
12 |
100.0 |
5.5 Influenza H9N2
| Undetermined / Undetermined |
39 |
100.0 |
| Total |
39 |
100.0 |
6. Antiviral Resistance Markers
6.1 Neuraminidase H275Y (A(H1N1)pdm09)
| A(H1N1)pdm09 genomes analyzed |
|
| Viruses with H275Y mutation |
|
| Percentage with H275Y |
|
Interpretation:
The H275Y substitution is associated with reduced susceptibility to oseltamivir.
7. Phylogenetic Analysis
7.1 Methods
- Alignment: [e.g., MAFFT]
- Phylogenetic inference: [e.g., IQ-TREE / FastTree]
- Reference strains: WHO vaccine reference strains for the [season] season
- Gene(s) analyzed: ☐ HA ☐ NA ☐ Whole genome
7.2 Phylogenetic Tree Summary
8. Data Sharing
|
Sample
|
GISAID Accession
|
GenBank Accession
|
|
3004125289_N8KIRZ8D_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125302_N8KIRZA6_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125307_N8KIRZAV_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125325_N8KIRZDD_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125328_N8KIRZDS_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125336_N8KIRZEW_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125339_N8KIRZFB_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125344_N8KIRZG0_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125405_N8KIRZOH_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125413_N8KIRZPL_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125414_N8KIRZPQ_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125420_N8KIRZQL_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125421_N8KIRZQQ_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125426_N8KIRZRE_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125441_N8KIRZTI_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125442_N8KIRZTN_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125448_N8KIRZUG_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125460_N8KIRZW4_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125478_N8KIRZYM_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125510_N8KIS032_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125532_N8KIS064_v1
|
EPI3004125
|
AF3004125.1
|
|
3004125588_N8KIS0DW_v1
|
EPI3004125
|
AF3004125.1
|
|
3004166252_N8KIWD9O_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166253_N8KIWD9T_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166254_N8KIWD9Y_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166255_N8KIWDA3_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166256_N8KIWDA8_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166257_N8KIWDAD_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166258_N8KIWDAI_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166259_N8KIWDAN_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166260_N8KIWDAS_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166261_N8KIWDAX_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166262_N8KIWDB2_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166263_N8KIWDB7_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166266_N8KIWDBM_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166268_N8KIWDBW_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166269_N8KIWDC1_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166273_N8KIWDCL_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166275_N8KIWDCV_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166277_N8KIWDD5_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166278_N8KIWDDA_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166280_N8KIWDDK_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166281_N8KIWDDP_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166283_N8KIWDDZ_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166286_N8KIWDEE_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166287_N8KIWDEJ_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166289_N8KIWDET_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166292_N8KIWDF8_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166293_N8KIWDFD_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166294_N8KIWDFI_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166295_N8KIWDFN_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166298_N8KIWDG2_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166299_N8KIWDG7_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166300_N8KIWDGC_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166301_N8KIWDGH_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166303_N8KIWDGR_v1
|
EPI3004166
|
AF3004166.1
|
|
3004166335_N8KIWDL7_v1
|
EPI3004166
|
AF3004166.1
|
|
3032470429_N90M7F9K_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470430_N90M7F9L_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470431_N90M7F9M_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470432_N90M7F9N_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470433_N90M7F9O_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470434_N90M7F9P_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470436_N90M7F9R_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470437_N90M7F9S_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470438_N90M7F9T_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470439_N90M7F9U_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470440_N90M7F9V_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470441_N90M7F9W_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470442_N90M7F9X_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470443_N90M7F9Y_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470444_N90M7F9Z_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470445_N90M7FA0_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470446_N90M7FA1_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470447_N90M7FA2_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470448_N90M7FA3_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470449_N90M7FA4_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470450_N90M7FA5_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470451_N90M7FA6_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470452_N90M7FA7_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470453_N90M7FA8_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470454_N90M7FA9_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470455_N90M7FAA_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470456_N90M7FAB_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470457_N90M7FAC_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470458_N90M7FAD_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470459_N90M7FAE_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470460_N90M7FAF_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470461_N90M7FAG_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470462_N90M7FAH_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470463_N90M7FAI_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470464_N90M7FAJ_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470465_N90M7FAK_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470466_N90M7FAL_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470467_N90M7FAM_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470468_N90M7FAN_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470469_N90M7FAO_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470470_N90M7FAP_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470471_N90M7FAQ_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470472_N90M7FAR_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470473_N90M7FAS_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470474_N90M7FAT_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470475_N90M7FAU_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470476_N90M7FAV_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470477_N90M7FAW_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470479_N90M7FAY_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470480_N90M7FAZ_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470481_N90M7FB0_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470483_N90M7FB2_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470484_N90M7FB3_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470485_N90M7FB4_v1
|
EPI3032470
|
AF3032470.1
|
|
3032470486_N90M7FB5_v1
|
EPI3032470
|
AF3032470.1
|
|
3032563002_N90M7FC8_v1
|
EPI3032563
|
AF3032563.1
|
|
3032563002_N90M7FCA_v1
|
EPI3032563
|
AF3032563.1
|
|
3032563002_N90M7FCC_v1
|
EPI3032563
|
AF3032563.1
|
|
3101505695_N90N7ACU_v1
|
EPI3101505
|
AF3101505.1
|
|
3101678967_N90NX5D4_v1
|
EPI3101678
|
AF3101678.1
|
|
3101678982_N90NX5HA_v1
|
EPI3101678
|
AF3101678.1
|
|
3101678985_N90NX5I4_v1
|
EPI3101678
|
AF3101678.1
|
|
3101678986_N90NX5IE_v1
|
EPI3101678
|
AF3101678.1
|
|
3101678987_N90NX5IO_v1
|
EPI3101678
|
AF3101678.1
|
|
3101678989_N90NX5J8_v1
|
EPI3101678
|
AF3101678.1
|
|
3101678991_N90NX5JS_v1
|
EPI3101678
|
AF3101678.1
|
|
3101678992_N90NX5K2_v1
|
EPI3101678
|
AF3101678.1
|
|
3101678994_N90NX5KM_v1
|
EPI3101678
|
AF3101678.1
|
|
3101678997_N90NX5LG_v1
|
EPI3101678
|
AF3101678.1
|
|
3101678999_N90NX5M0_v1
|
EPI3101678
|
AF3101678.1
|
|
3101679000_N90NX5MA_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679002_N90NX5MU_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679007_N90NX5O8_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679013_N90NX5PW_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679015_N90NX5QG_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679016_N90NX5QQ_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679017_N90NX5R0_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679018_N90NX5RA_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679020_N90NX5RU_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679022_N90NX5SE_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679024_N90NX5SY_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679025_N90NX5T8_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679027_N90NX5TS_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679028_N90NX5U2_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679029_N90NX5UC_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679031_N90NX5UW_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679036_N90NX5WA_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679041_N90NX5XO_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679042_N90NX5XY_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679044_N90NX5YI_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679048_N90NX5ZM_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679049_N90NX5ZW_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679054_N90NX61A_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679055_N90NX61K_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679058_N90NX62E_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679069_N90NX65G_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679070_N90NX65Q_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679071_N90NX660_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679073_N90NX66K_v1
|
EPI3101679
|
AF3101679.1
|
|
3101679076_N90NX67E_v1
|
EPI3101679
|
AF3101679.1
|
|
3104176725_N90OWZZK_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176732_N90OX00J_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176738_N90OX01D_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176739_N90OX01I_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176740_N90OX01N_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176748_N90OX02R_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176751_N90OX036_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176767_N90OX05E_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176805_N90OX0AO_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176807_N90OX0AY_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176819_N90OX0CM_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176829_N90OX0E0_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176834_N90OX0EP_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176849_N90OX0GS_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176882_N90OX0LD_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176894_N90OX0N1_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176903_N90OX0OA_v1
|
EPI3104176
|
AF3104176.1
|
|
3104176913_N90OX0PO_v1
|
EPI3104176
|
AF3104176.1
|
|
3104177046_N90OX185_v1
|
EPI3104177
|
AF3104177.1
|
|
3104177104_N90OX1G7_v1
|
EPI3104177
|
AF3104177.1
|
|
3104177274_N90OX23T_v1
|
EPI3104177
|
AF3104177.1
|
|
3104177349_N90OX2E8_v1
|
EPI3104177
|
AF3104177.1
|
|
3104177352_N90OX2EN_v1
|
EPI3104177
|
AF3104177.1
|
|
4001337248_N90O6VJD_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337252_N90O6VKH_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337258_N90O6VM5_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337260_N90O6VMP_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337263_N90O6VNJ_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337266_N90O6VOD_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337271_N90O6VPR_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337275_N90O6VQV_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337290_N90O6VV1_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337296_N90O6VWP_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337300_N90O6VXT_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337304_N90O6VYX_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337305_N90O6VZ7_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337311_N90O6W0V_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337314_N90O6W1P_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337321_N90O6W3N_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337322_N90O6W3X_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337327_N90O6W5B_v1
|
EPI4001337
|
AF4001337.1
|
|
4001337341_N90O6W97_v1
|
EPI4001337
|
AF4001337.1
|
|
4002020706_N90PF9PA_v1
|
EPI4002020
|
AF4002020.1
|
9. Limitations
- Sequencing coverage may not be fully representative of all regions.
- Selection bias due to Ct-based sequencing thresholds.
- Turnaround time varied during peak transmission periods.
10. Conclusions and Public Health Implications
**Update this in _quarto.yml!** Genomic surveillance during the 2026 influenza season demonstrated …., supporting national and global influenza risk assessment and vaccine strain selection processes.
11. Acknowledgements
We acknowledge sentinel sites, laboratories, clinicians, and data contributors supporting influenza surveillance in United States.