# National Influenza Genomic Surveillance Report

**Country:** \
**Influenza season:** \
**Date of report:** \
**Reporting period:** –

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## 1. Executive Summary

This report summarizes influenza virus genomic surveillance conducted during the
**[season]** influenza season in **[country]**. Surveillance integrates routine
virological testing with whole-genome sequencing to monitor circulating
influenza strains, genetic diversity, antiviral resistance markers, and
phylogenetic relationships.

### Key Findings

- Dominant (sub)type: **[e.g., A(H3N2)]**
- Dominant clade/subclade: **[e.g., 3C.2a1b.2a.2a.3a.1]**
- Notable resistance markers: **[e.g., none / H275Y in X%]**

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## 2. Surveillance System and Sample Collection

| Metric                          | Value |
|---------------------------------|-------|
| Sentinel sites                  |       |
| Specimens received              |       |
| Date range of collection        |       |

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## 3. Virological Screening Results

### 3.1 Total Specimens Tested

| Metric              | Count |
|---------------------|------:|
| Specimens tested    |       |
| Influenza positive  |       |
| Percent positivity  |       |

### 3.2 Influenza Type and Subtype Distribution

| Type / Subtype      | Count | Percent |
|---------------------|------:|--------:|
| A(H1N1)pdm09        |       |         |
| A(H3N2)             |       |         |
| B/Victoria          |       |         |
| Unsubtyped          |       |         |

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## 4. Sequencing Overview

### 4.1 Sequencing Selection Criteria

- Ct value threshold: **[e.g., ≤ 30]**
- Geographic representation across sentinel sites
- Temporal spread across the reporting period

### 4.2 Sequencing Output and Quality

| Metric                      | Value |
|-----------------------------|------:|
| Samples sequenced           |       |
| Genomes passing QC          |       |
| Mean genome coverage (%)    |       |

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## 5. Clade and Subclade Distribution

| Subtype        | Clade / Subclade | Count |
|----------------|------------------|------:|
|                |                  |       |

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## 6. Antiviral Resistance Markers

### 6.1 Neuraminidase H275Y (A(H1N1)pdm09)

| Metric                             | Count |
|------------------------------------|------:|
| A(H1N1)pdm09 genomes analyzed      |       |
| Viruses with H275Y mutation        |       |
| Percentage with H275Y              |       |

**Interpretation:**
The H275Y substitution is associated with reduced susceptibility to oseltamivir.

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## 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

![Phylogenetic tree of circulating influenza A(H3N2) viruses.](media/tree.png)

- Circulating viruses clustered primarily with **[reference clade/strain]**.
- Genetic diversity was **[low / moderate / high]**.

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## 8. Data Sharing

| Repository | Segment | Sequences submitted |
|------------|---------|--------------------:|
| GISAID     | HA      |                     |
| GISAID     | NA      |                     |

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## 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.

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## 10. Conclusions and Public Health Implications

_Summarize implications for vaccine strain selection, clinical management, and
public health response._

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## 11. Acknowledgements

We acknowledge sentinel sites, laboratories, clinicians, and data contributors
supporting influenza surveillance in **[country]**.

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## 12. Contact Information

**Institution:** \
**Email:** \
**Phone:**