Highly Pathogenic Avian Influenza H7N3 Phylogenetic Data from Mexico

Mexico experienced highly pathogenic avian influenza H7N3 outbreaks from June 2012 to August 2013, primarily in Jalisco and neighboring states. This dataset contains phylogenetic and phylogeographic analyses of full-length virus sequences from North America, modeling traits like location, subtype, host species, and pathogenicity. The research indicates the outbreak originated from the North American low pathogenicity virus pool through reassortment events involving wild birds from different migration flyways.

Use Cases

• Model location, subtype, and host species as discrete traits upon phylogenetic trees using continuous time Markov chains.
• Perform a joint hierarchical phylogenetic model analysis across virus segments to infer trait rates for location, subtype, and host species.
• Visualize the complete spatial diffusion process of the virus across North America using virtual globe software.
• Analyze the contribution of different North American flyways (central and western) to specific virus segments like HA, NA, NP, M, NS, PB2, PB1, and PA.

Strengths

• Analysis is based on full-length avian influenza virus sequences from North America.
• Models four discrete traits: location, subtype, avian host species, and pathogenicity.
• Employs a hierarchical phylogenetic model for joint inference across eight virus segments.
• Research provides a specific temporal context for outbreaks from June 2012 to August 2013.

Limitations

• The exact number of sequences, rows, or data points analyzed is not provided.
• Data is specific to the H7N3 subtype outbreak in Mexico, limiting generalizability to other influenza strains or regions.
• The analysis relies on available sequence data, which may have sampling gaps for certain locations or time periods.

Provenance

Source

Dryad, authored by Lu Lu.

Collection Method

Phylogenetic analysis of full-length AIV sequences using BEAST software for time-resolved trees and discrete trait modeling.

Time Range

Outbreaks analyzed from June/July 2012 to August 2013.

Freshness

Data was last updated in June 2020.

Geography

Focus on outbreaks in Jalisco and neighboring states, Mexico, with context from North American flyways.