دورية أكاديمية
أعرض في EDS

Improved detection of influenza A virus from blue-winged teals by sequencing directly from swab material.

التفاصيل البيبلوغرافية
العنوان: Improved detection of influenza A virus from blue-winged teals by sequencing directly from swab material.
المؤلفون: Ferreri LM; Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia., Ortiz L; Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia.; Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala., Geiger G; Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia., Barriga GP; Laboratory of Emerging Viruses, Virology Program Institute of Biomedical Sciences, Faculty of Medicine Universidad de Chile Santiago Chile., Poulson R; Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia., Gonzalez-Reiche AS; Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New York New York., Crum JA; Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia., Stallknecht D; Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia., Moran D; Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala., Cordon-Rosales C; Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala., Rajao D; Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia., Perez DR; Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia.
المصدر: Ecology and evolution [Ecol Evol] 2019 May 11; Vol. 9 (11), pp. 6534-6546. Date of Electronic Publication: 2019 May 11 (Print Publication: 2019).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Blackwell Pub. Ltd Country of Publication: England NLM ID: 101566408 Publication Model: eCollection Cited Medium: Print ISSN: 2045-7758 (Print) Linking ISSN: 20457758 NLM ISO Abbreviation: Ecol Evol Subsets: PubMed not MEDLINE
أسماء مطبوعة: Original Publication: [Oxford] : Blackwell Pub. Ltd.
مستخلص: Abstract: The greatest diversity of influenza A virus (IAV) is found in wild aquatic birds of the orders Anseriformes and Charadriiformes. In these birds, IAV replication occurs mostly in the intestinal tract. Fecal, cloacal, and/or tracheal swabs are typically collected and tested by real-time RT-PCR (rRT-PCR) and/or by virus isolation in embryonated chicken eggs in order to determine the presence of IAV. Virus isolation may impose bottlenecks that select variant populations that are different from those circulating in nature, and such bottlenecks may result in artifactual representation of subtype diversity and/or underrepresented mixed infections. The advent of next-generation sequencing (NGS) technologies provides an opportunity to explore to what extent IAV subtype diversity is affected by virus isolation in eggs. In the present work, we evaluated the advantage of sequencing by NGS directly from swab material of IAV rRT-PCR-positive swabs collected during the 2013-14 surveillance season in Guatemala and compared to results from NGS after virus isolation. The results highlight the benefit of sequencing IAV genomes directly from swabs to better understand subtype diversity and detection of alternative amino acid motifs that could otherwise escape detection using traditional methods of virus isolation. In addition, NGS sequencing data from swabs revealed reduced presence of defective interfering particles compared to virus isolates. We propose an alternative workflow in which original swab samples positive for IAV by rRT-PCR are first subjected to NGS before attempting viral isolation. This approach should speed the processing of samples and better capture natural IAV diversity.
Open Research Badges: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.3h2n106.
Competing Interests: None declared.
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معلومات مُعتمدة: HHSN272201400006C United States AI NIAID NIH HHS; HHSN272201400008C United States AI NIAID NIH HHS
فهرسة مساهمة: Keywords: Guatemala; Illumina; blue‐winged teal; influenza A virus; next‐generation sequencing; wild bird
سلسلة جزيئية: Dryad 10.5061/dryad.3h2n106
تواريخ الأحداث: Date Created: 20190626 Latest Revision: 20220408
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC6580304
DOI: 10.1002/ece3.5232
PMID: 31236242
قاعدة البيانات: MEDLINE
الوصف
تدمد:2045-7758
DOI:10.1002/ece3.5232