Human Metapneumovirus Cases in Coastal Kenya with Genomic and Clinical Data

Individual case data for human metapneumovirus from surveillance in Kilifi, Coastal Kenya, covering the periods 2016-2017 and 2021-2024. It includes two linked datasets: one with demographic and clinical characteristics, and another with genomic characteristics such as variant and lineage.

Use Cases

• Analyze the distribution of genomic variants and nextclade lineages across different demographic groups like age and sex.
• Investigate correlations between clinical characteristics, such as symptom status or fever, and specific genomic variants of the virus.
• Study the temporal evolution of human metapneumovirus by examining variant data across the 2016-2024 surveillance periods in coastal Kenya.

Strengths

• Data spans two distinct surveillance periods (2016-2017 and 2021-2024), enabling temporal analysis.
• Integrates both demographic/clinical data and genomic characteristics like variant and lineage for each case.
• Data is part of ongoing surveillance within the Kilifi Health and Demographic Surveillance System (KHDSS).

Limitations

• The specific number of rows (cases) and columns (features) is unknown, limiting assessment of statistical power.
• Sample data and file formats are unavailable, making it difficult to preview data structure before access.
• The dataset's geographic scope is limited to the Kilifi area in coastal Kenya, which may limit generalizability.

Provenance

Source

Virus Epidemiology and Control (VEC) Dataverse, authored by Dorcas Okanda.

Collection Method

Data gathered through ongoing outpatient and community surveillance within the KHDSS, with genomic sequencing using Oxford Nanopore Technologies.

Time Range

2016-2017 and 2021-2024.

Freshness

The dataset was last updated on 2026-01-30, indicating recent maintenance.

Geography

Kilifi, Coastal Kenya.