bioRxiv (Cold Spring Harbor Laboratory) · 2024 · 113 citations · 61 references
Life SciencesInfectious DiseasesMolecular BiologyEmerging Infectious DiseasesMolecular VirologyVirologyAnimal Infectious DiseasesAnimal VirusesDisease Transmission PathwaysEvolutionary EpidemiologyGenomic EpidemiologyLivestock Infectious DiseasesAvian Influenza InfectionAvian Influenza VirusAvian Influenza VirusesBarriers To Cross-species TransmissionCross-species Transmission BarriersGenomic Diversity AnalysisGenomic Dna AnalysisWild Bird Transmission
Abstract Highly pathogenic avian influenza (HPAI) viruses cross species barriers and have the potential to cause pandemics. In North America, HPAI A(H5N1) viruses related to the goose/Guangdong 2.3.4.4b hemagglutinin phylogenetic clade have infected wild birds, poultry, and mammals. Our genomic analysis and epidemiological investigation showed that a reassortment event in wild bird populations preceded a single wild bird-to-cattle transmission episode. The movement of asymptomatic cattle has likely played a role in the spread of HPAI within the United States dairy herd. Some molecular markers in virus populations were detected at low frequency that may lead to changes in transmission efficiency and phenotype after evolution in dairy cattle. Continued transmission of H5N1 HPAI within dairy cattle increases the risk for infection and subsequent spread of the virus to human populations.
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Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li, Richard Durbin · Bioinformatics · 2009 · 62.8K citations · Full text
fastp: an ultra-fast all-in-one FASTQ preprocessor
Shifu Chen, Yanqing Zhou, Yaru Chen et al. · Bioinformatics · 2018 · 29.7K citations · Full text