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All Posts by

Alexa Sauvagere

Hello, my name is Alexa.

A One Health Investigation into H5N1 Avian Influenza Virus Epizootics on Two Dairy Farms

In early April 2024, we studied two Texas dairy farms which had suffered incursions of H5N1 highly pathogenic avian influenza virus (HPAIV) the previous month. We employed molecular assays, cell and egg culture, Sanger and next generation sequencing to isolate and characterize viruses from multiple farm specimens (cow nasal swab, milk specimens, fecal slurry, and a dead bird).

Machine learning-enhanced assessment of potential probiotics from healthy calves for the treatment of neonatal calf diarrhea

Neonatal calf diarrhea (NCD) remains a significant contributor to calf mortality within the first 3 weeks of life, prompting widespread antibiotic use with associated concerns about antimicrobial resistance and disruption of the calf gut microbiota. Recent research exploring NCD treatments targeting gut microbiota dysbiosis has highlighted probiotic supplementation as a promising and safe strategy for gut homeostasis.

A systematic review of using population-level human mobility data to understand SARS-CoV-2 transmission

The emergence of SARS-CoV-2 into a highly susceptible global population was primarily driven by human mobility-induced introduction events. Especially in the early stages, understanding mobility was vital to mitigating the pandemic prior to widespread vaccine availability. We conducted a systematic review of studies published from January 1, 2020, to May 9, 2021, that used population-level human mobility data to understand SARS-CoV-2 transmission.

Microsporidia and invertebrate hosts: genome-informed taxonomy surrounding a new lineage of crayfish-infecting Nosema spp. (Nosematida)

The Microsporidia, an often overlooked fungal lineage, exhibit increasing diversity and taxonomic understanding with the use of genomic techniques. They are obligate parasites infecting a diversity of hosts, including crustaceans. Crustacea are, in essence, ancient insects and their relationship with the Microsporidia is both diverse and convoluted.

Phylogenetic-informed graph deep learning to classify dynamic transmission clusters in infectious disease epidemics

Molecular epidemiology has become increasingly standard in pathogen outbreak surveillance and modeling of epidemic spread. Owing to short generation times and/or infidelity of pathogen replication machinery, the accumulation of mutations in viruses and bacteria is relatively rapid (compared to eukaryotes), occurring on a similar timescale as epidemiological processes.