ArticleJournal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc2022
Review of genome sequencing technologies in molecular characterization of influenza A viruses in swine.
Article in Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Isolation, identification, and whole genome sequencing analysis of influenza A virus clinical isolates from Shanghai, China, during 2022-2023.Virology journal · 2026Article
- Whole genome sequencing of hepatitis A virus: adapting Illumina protocols for foodborne investigation.NPJ science of food · 2025Article
- Whole-genome analysis of influenza A(H1N1)pdm09 viruses in Cameroon (2019-2024) using nanopore sequencing.BMC infectious diseases · 2025Article
- Custom barcoded primers for influenza A nanopore sequencing: enhanced performance with reduced preparation time.Frontiers in cellular and infection microbiology · 2025Article
- Complete molecular spectrum of β-globin gene mutations via direct sequencing identifies seven novel variants in β-thalassemia major.PloS one · 2025Article
- Article
- Influenza viruses and SARS-CoV-2 diagnosis via sensitive testing methods in clinical application.Heliyon · 2024Review
- Overview of Modern Commercial Kits for Laboratory Diagnosis of African Swine Fever and Swine Influenza A Viruses.Viruses · 2024Review
- The peculiar characteristics and advancement in diagnostic methodologies of influenza A virus.Frontiers in microbiology · 2024Review
- Descriptive Epidemiology and Phylodynamics of the "First Wave" of an Outbreak of Highly Pathogenic Avian Influenza (H5N1 Clade 2.3.4.4b) in British Columbia and the Yukon, Canada, April to September 2022.Transboundary and emerging diseases · 2024Article
- Improved influenza A whole-genome sequencing protocol.Frontiers in cellular and infection microbiology · 2024Article
- Overview of Diagnostic Methods, Disease Prevalence and Transmission of Mpox (Formerly Monkeypox) in Humans and Animal Reservoirs.Microorganisms · 2023Review
- Article
- Characterization of a Near Full-Length Hepatitis E Virus Genome of Subtype 3c Generated from Naturally Infected South African Backyard Pigs.Pathogens (Basel, Switzerland) · 2022Article
- Metagenomic Analysis of RNA Fraction Reveals the Diversity of Swine Oral Virome on South African Backyard Swine Farms in the uMgungundlovu District of KwaZulu-Natal Province.Pathogens (Basel, Switzerland) · 2022Article
- An overview of influenza A virus genes, protein functions, and replication cycle highlighting important updates.Virus genes · 2022Review
- A systematic review of influenza A virus prevalence and transmission dynamics in backyard swine populations globally.Porcine health management · 2022Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rapidly evolving antigenic diversity of influenza A virus (IAV) genomes in swine makes it imperative to detect emerging novel strains and track their circulation. We analyzed in our review the sequencing technologies used for subtyping and characterizing swine IAV genomes. Google Scholar, PubMed, and International Nucleotide Sequence Database Collaboration (INSDC) database searches identified 216 studies that have utilized Sanger, second-, and third-generation sequencing techniques to subtype and characterize swine IAV genomes up to 31 March 2021. Sanger dideoxy sequencing was by far the most widely used sequencing technique for generating either full-length (43.0%) or partial (31.0%) IAV genomes in swine globally; however, in the last decade, other sequencing platforms such as Illumina have emerged as serious competitors for the generation of whole-genome sequences of swine IAVs. Although partial HA and NA gene sequences were sufficient to determine swine IAV subtypes, whole-genome sequences were critical for determining reassortments and identifying unusual or less frequently occurring IAV subtypes. The combination of Sanger and second-generation sequencing technologies also greatly improved swine IAV characterization. In addition, the rapidly evolving third-generation sequencing platform, MinION, appears promising for on-site, real-time sequencing of complete swine IAV genomes. With a higher raw read accuracy, the use of the MinION could enhance the scalability of swine IAV testing in the field and strengthen the swine IAV disease outbreak response.
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