MinION sequencing to genotype US strains of infectious laryngotracheitis virus.

In this study, the genotyping system was simplified to six genotypes by amplicon sequencing and examining discriminating single nucleotide polymorphisms (SNPs) within these open reading frames. Using phylogenomic analysis of 27 full genomes of ILTV, a single allele (ORFA/ORFB) was identified containing SNPs that could differentiate ILTVs into genotypes congruent with the phylogenetic partitioning. The allelic variations allowed for the cataloging of the 27 strains into 5 genotypes: vaccinal TCO, vaccinal CEO, virulent CEO-like, virulent US and virulent US backyard flocks from 1980 to 1990, correlating with the PCR-RFLP genotypes I/ II/ III- (TCO), IV - (CEO), V - (virulent CEO-like), VI - (virulent US) and VII/VIII/IX - (virulent US backyard flock isolates). With the unique capabilities of third generation sequencing, we investigated the application of Oxford Nanopore MinION technology for rapid sequencing of the amplicons generated in the single allele assay. This technology was an improvement over Sanger-based sequencing of the single allele amplicons due to a booster amplification step in the MinION sequencing protocol. Overall, there was a 90% correlation between the genotyping results of the single allele assay and the multi-allele assay. Surveillance of emerging ILTV strains could greatly benefit from real time amplicon sequencing using the single-allele assay and MinION sequencing. Research Highlights Multi-allelic assay has identified 9 ILTV genotypes circulating in t...
Source: Avian Pathology - Category: Pathology Authors: Tags: Avian Pathol Source Type: research

Related Links:

Publication date: Available online 10 October 2019Source: Comparative Immunology, Microbiology and Infectious DiseasesAuthor(s): Marc. K. Kouam, Herman M.F Biekop, Bridget Katte, Alexis TeguiaAbstractSalmonella infections in poultry farms are overlooked in many African countries; yet these infections are mostly zoonotic with impact on both poultry industry and public health. Considering the impact of Salmonella in laying hens, and the role of laying hens as a source of Salmonella outbreak in human, knowledge of the status of Salmonella on laying hen farms as well as the factors influencing the presence of Salmonella is imp...
Source: Comparative Immunology, Microbiology and Infectious Diseases - Category: Infectious Diseases Source Type: research
Publication date: Available online 8 October 2019Source: Microbial PathogenesisAuthor(s): Momena Habib, Tahir Yaqub, Aziz-ul-Rahman, Tayyebah Sohail, Muhammad Shahbaz, Wasim Shehzad, Muhammad Munir, Muhammad Zubair ShabbirAbstractNewcastle disease (ND), caused by Avian orthoavulavirus 1 (AOAV-1), affects multiple avian species around the globe. Frequent disease outbreaks are not uncommon even in vaccinates despite routine vaccination and, in this regards, viruses of diverse genotypes originating from natural reservoirs (migratory waterfowls) play an important role in a disease endemic setting. Though genomic characterizati...
Source: Microbial Pathogenesis - Category: Infectious Diseases Source Type: research
Publication date: December 2019Source: Molecular Phylogenetics and Evolution, Volume 141Author(s): Serafeim C. Chaintoutis, Anna Papa, Danai Pervanidou, Chrysostomos I. DovasAbstractWest Nile virus (WNV) is an arbovirus causing neuroinvasive disease to humans and equines. Since 2004, lineage 2 WNV strains have been identified in Europe and have been implicated in severe outbreaks, with that of 2018 exceeding the total number from the previous seven years. The aim of this study was to explore the evolutionary process that shapes the genetic diversity of lineage 2 WNV strains (belonging to the Central European/Hungarian subc...
Source: Molecular Phylogenetics and Evolution - Category: Molecular Biology Source Type: research
NLM Informatics and Data Science Lecture Series Genomics-informed surveillance is now recognized as an important extension to the monitoring of rapidly evolving pathogens. Next generation sequencing has the ability to produce large amounts of data for tracking viruses of public health importance. Biomedical informatics approaches are able to facilitate the translation of these data into information for public health surveillance. Thus, epidemiologists can identify new outbreaks or monitor the course of a known epidemic by leveraging pathogen sequences (and corresponding metadata) generated from the clinical specimens of si...
Source: Videocast - All Events - Category: General Medicine Tags: Upcoming Events Source Type: video
This report describes an outbreak of erysipelas in a colony of captive Humboldt penguins (Spheniscus humboldti). The only previously reported case in a related species was of an individual little blue penguin (Eudyptula minor). Five Humboldt penguins in a mixed colony displayed non-specific signs of illness, including lethargy, inappetence and regurgitation after movement for exhibit upgrading. There was no improvement after 5 days of treatment with oral enrofloxacin (10 mg/kg q24h). Four Humboldt penguins, including two that were not part of the original five displaying signs of illness, died during this outbreak and...
Source: Journal of Comparative Pathology - Category: Pathology Source Type: research
Armando Isibasi Constantino López-Macías The clinical effects and immunological response to the influenza vaccine in women who later become pregnant remain to be thoroughly studied. Here, we report the medical outcomes of 40 women volunteers who became pregnant after vaccination with an experimental virus-like particle (VLP) vaccine against pandemic influenza A(H1N1)2009 (influenza A(H1N1)pdm09) and their infants. When included in the VLP vaccine trial, none of the women were pregnant and were randomly assigned to one of the following groups: (1) placebo, (2) 15 μg dose of VLP vaccine, or (3) ...
Source: Viruses - Category: Virology Authors: Tags: Article Source Type: research
Publication date: Available online 12 September 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Serafeim C. Chaintoutis, Anna Papa, Danai Pervanidou, Chrysostomos I. DovasAbstractWest Nile virus (WNV) is an arbovirus causing neuroinvasive disease to humans and equines. Since 2004, lineage 2 WNV strains have been identified in Europe and have been implicated in severe outbreaks, with that of 2018 exceeding the total number from the previous seven years. The aim of this study was to explore the evolutionary process that shapes the genetic diversity of lineage 2 WNV strains (belonging to the Central European/Hunga...
Source: Molecular Phylogenetics and Evolution - Category: Molecular Biology Source Type: research
This study emphasizes the unforeseen consequences of ecological disturbance for species interactions and highlights the importance of considering ecology in urban planning. PMID: 31480937 [PubMed - in process]
Source: Biology Letters - Category: Biology Authors: Tags: Biol Lett Source Type: research
In March 2013, the first human case of zoonotic H7N9 avian influenza virus (AIV) infection was reported in China. This virus has been circulating in domestic poultry in China while mutating to highly pathogenic AIV (HPAIV) since 2017, which caused human infections and poultry outbreaks. In 2019, a novel reassortant H7N2 HPAIV, A/chicken/China/SJZ1/2019(SJZ1), was isolated from H7 –Re2-vaccinated layers. We analyzed the genetic, pathogenic, and antigenic characteristics of SJZ1. Analysis of the entire SJZ1 genomic sequence revealed that it comprised at least two different sources; the PB2, PB1, PA, HA (H7), M, and NS ...
Source: Journal of Infection - Category: Infectious Diseases Authors: Tags: Letter to the Editor Source Type: research
Abstract Highly pathogenic avian influenza H5N8 clade 2.3.4.4 virus caused outbreaks in poultry and unusually high mortality in wild birds in 2016-2017. The pathobiology of one of these viruses was examined in mallards and chickens. High mortality and transmission to direct contacts were observed in mallards inoculated with medium and high doses of the virus. However, in chickens, high mortality occurred only when birds are given the high virus dose and no transmission was observed, indicating that the virus was better adapted to mallards. In comparison with the virus inoculum, viral sequences obtained from the ch...
Source: Virology - Category: Virology Authors: Tags: Virology Source Type: research
More News: Bird Flu | Nanotechnology | Outbreaks | Pathology | Study